Total parameters: 3,199
| idea_id | cell_type_code | parameter | description |
|---|---|---|---|
| 009mzd0abh1c | M | mean_macrophage_nucleus_circularity | This parameter measures the average circularity of macrophage nuclei within the tumor (epithelial) compartment. Circularity is determined by a shape descriptor calculated using the area and perimeter of each nucleus, ensuring that it is a normalized metric. The average of these values provides a robust summary that is independent of the absolute number of cells and can be compared across different patient cases. |
| 063wycbdlwb5 | Tc,B | median_distance_vessel_adjacent | Median_distance_vessel_adjacent represents the median Euclidean distance measured from cytotoxic T cells that are considered vessel-adjacent (i.e., cells with a distance to the nearest vessel less than 50 pixels) to their nearest B cell in the stromal compartment. This parameter provides a normalized central measure of proximity that enables comparison across different patient patches. |
| 063wycbdlwb5 | Tc,B | median_distance_non_adjacent | Median_distance_non_adjacent is the median distance from cytotoxic T cells that are not adjacent to vessels (with a vessel distance of 50 pixels or more) to their closest B cell in the stroma, offering a normalized measure of spatial relationship in regions less influenced by vessels. |
| 063wycbdlwb5 | Tc,B | median_distance_all | Median_distance_all captures the median distance from all cytotoxic T cells found in the stromal compartment to their nearest B cell, regardless of vessel proximity, thus serving as an overall normalized metric of cell-cell proximity. |
| 063wycbdlwb5 | Tc,B | mean_distance_vessel_adjacent | Mean_distance_vessel_adjacent is the arithmetic average of the distances from vessel-adjacent cytotoxic T cells to their closest B cell in the stroma, providing a normalized value that reflects the typical proximity in vessel-influenced regions. |
| 063wycbdlwb5 | Tc,B | mean_distance_non_adjacent | Mean_distance_non_adjacent is the mean distance computed from non-vessel-adjacent cytotoxic T cells to the nearest B cell, reflecting the average spatial separation in stromal areas not closely associated with vessels in a normalized manner. |
| 063wycbdlwb5 | Tc,B | mean_distance_all | Mean_distance_all represents the overall arithmetic average of distances from all cytotoxic T cells to their nearest B cell in the stroma, offering a general, normalized measure of cellular proximity across patches. |
| 063wycbdlwb5 | Tc,B | std_distance_vessel_adjacent | Std_distance_vessel_adjacent is the standard deviation of the distances from vessel-adjacent cytotoxic T cells to their nearest B cell, indicating variability in spatial proximity within vessel-adjacent regions while being normalized for cross-case comparison. |
| 063wycbdlwb5 | Tc,B | std_distance_non_adjacent | Std_distance_non_adjacent computes the standard deviation of distances for non-vessel-adjacent cytotoxic T cells to their nearest B cells, reflecting the variability in proximity metrics in regions away from vessels in a normalized context. |
| 063wycbdlwb5 | Tc,B | std_distance_all | Std_distance_all is the overall standard deviation for all cytotoxic T cells’ distances to their nearest B cell, capturing the dispersion of spatial relationships across the entire stromal compartment in a normalized form. |
| 0at0ykis942f | B | mean_distance_to_tumor | mean_distance_to_tumor measures the average Euclidean distance, measured in micrometers, between the centroids of B cells located in the stromal compartment and the nearest point on the tumor boundary. It provides a numeric indicator that allows for comparing spatial distribution patterns across different patient cases or patches. |
| 0at0ykis942f | B | median_distance_to_tumor | median_distance_to_tumor captures the middle value of the Euclidean distances from B cell centroids in the stroma to the tumor boundary, offering a robust measure of the typical spatial proximity despite potential outliers. This parameter facilitates inter-case comparisons as it is normalized over the patch-level observations. |
| 0at0ykis942f | B | min_distance_to_tumor | min_distance_to_tumor records the smallest Euclidean distance from any B cell in the stromal compartment to the tumor boundary in a given image patch. It indicates the closest observed immune-tumor proximity and serves as a numeric measure that can be compared across different patient samples. |
| 0at0ykis942f | B | max_distance_to_tumor | max_distance_to_tumor documents the largest Euclidean distance from any B cell in the stroma to the tumor boundary. Being a numeric value measured in micrometers, it provides insight into the range of spatial dispersion and can be used for comparisons across patches and patient cases. |
| 0at0ykis942f | B | std_distance_to_tumor | std_distance_to_tumor quantifies the variability or dispersion of the distances from B cell centroids in the stroma to the tumor boundary. This numeric parameter, expressed in micrometers, helps in understanding the consistency of spatial relationships, making it useful for cross-case comparisons. |
| 0bra4wu8pzwc | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | All_Cell_Type_AspectRatio_CV | All_Cell_Type_AspectRatio_CV represents the coefficient of variation of the nuclear aspect ratios across all valid cell types in a tissue patch. It is calculated by dividing the standard deviation of the aspect ratios by their mean (with a small epsilon to avoid division by zero), resulting in a dimensionless measure of variability that allows for normalized comparisons across different patient cases. |
| 0bra4wu8pzwc | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | All_Cell_Type_AspectRatio_Mean | All_Cell_Type_AspectRatio_Mean denotes the average aspect ratio of the nucleus bounding boxes calculated from all considered cells. The aspect ratio for each cell is determined as the ratio of the longer to the shorter edge of its minimum rotated rectangle, producing a pure numerical, dimensionless value suitable for cross-case comparisons. |
| 0bra4wu8pzwc | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | All_Cell_Type_AspectRatio_Std | All_Cell_Type_AspectRatio_Std reflects the standard deviation of the aspect ratios of the cell nuclei. This numeric measure quantifies the dispersion in nuclear shapes across the tissue patch, providing insight into the variability of nuclear morphology in a normalized manner. |
| 0bra4wu8pzwc | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | All_Cell_Type_AspectRatio_Min | All_Cell_Type_AspectRatio_Min indicates the minimum aspect ratio observed among the computed values across all included cells. This metric defines the lower bound of the spread of aspect ratios and is inherently normalized since it derives from a ratio of length measures. |
| 0bra4wu8pzwc | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | All_Cell_Type_AspectRatio_Max | All_Cell_Type_AspectRatio_Max indicates the maximum observed aspect ratio among the computed values. Like the minimum, this maximum value is dimensionless and represents the upper bound of nuclear aspect ratio variation, making it useful for standardized comparisons across patient cases. |
| 0ejb3tqm7k9u | Ff,F,MFp,MF,Tc | mean_fsp1_pos_fibroblast_chain_length | This parameter represents the average number of cells in chains formed exclusively by FSP1-positive fibroblasts. It is computed by identifying contiguous groups of FSP1+ fibroblasts based on a fixed spatial proximity threshold, calculating each chain's length as the number of cells, and then averaging these lengths to provide a typical chain size for this cell subtype in a tissue patch. |
| 0ejb3tqm7k9u | Ff,F,MFp,MF,Tc | max_fsp1_pos_fibroblast_chain_length | This parameter denotes the maximum chain length observed among the FSP1-positive fibroblast chains, reflecting the largest contiguous grouping of these cells detected in a given tissue patch. |
| 0ejb3tqm7k9u | Ff,F,MFp,MF,Tc | mean_fsp1_neg_fibroblast_chain_length | This parameter captures the average chain length for FSP1-negative fibroblasts. It is derived by grouping adjacent FSP1- fibroblasts into chains and then averaging the cell counts of these chains, thereby providing an insight into the typical chain size for this population. |
| 0ejb3tqm7k9u | Ff,F,MFp,MF,Tc | max_fsp1_neg_fibroblast_chain_length | This parameter reflects the maximum number of cells found in any chain composed of FSP1-negative fibroblasts, indicating the largest connected group of these cells in the analyzed region. |
| 0ejb3tqm7k9u | Ff,F,MFp,MF,Tc | mean_pdpn_pos_myofibroblast_chain_length | This parameter represents the average chain length for PDPN-positive myofibroblasts. It is calculated by identifying clusters of adjacent PDPN+ myofibroblasts and averaging the number of cells in each chain, providing a measure of typical connectivity for this subtype. |
| 0ejb3tqm7k9u | Ff,F,MFp,MF,Tc | max_pdpn_pos_myofibroblast_chain_length | This parameter indicates the maximum chain length among PDPN-positive myofibroblast chains, showing the size of the largest contiguous group of these cells within the tissue patch. |
| 0ejb3tqm7k9u | Ff,F,MFp,MF,Tc | mean_pdpn_neg_myofibroblast_chain_length | This parameter measures the average number of cells in chains formed by PDPN-negative myofibroblasts, computed by averaging the chain lengths of contiguous PDPN- myofibroblast groups, thus summarizing the typical chain size of this cell category. |
| 0ejb3tqm7k9u | Ff,F,MFp,MF,Tc | max_pdpn_neg_myofibroblast_chain_length | This parameter represents the maximum chain length observed in chains of PDPN-negative myofibroblasts, highlighting the largest grouping of these cells within the patch. |
| 0ejb3tqm7k9u | Ff,F,MFp,MF,Tc | mean_all_fibroblast_chain_length | This parameter provides the overall average chain length calculated across all fibroblast and myofibroblast types combined. It summarizes the typical connectivity by averaging the number of cells per chain over all fibroblast-derived chains in the tissue region. |
| 0ejb3tqm7k9u | Ff,F,MFp,MF,Tc | max_all_fibroblast_chain_length | This parameter denotes the highest chain length observed among all fibroblast and myofibroblast chains combined, identifying the largest contiguous group of these cells present in the analyzed area. |
| 0ejb3tqm7k9u | Ff,F,MFp,MF,Tc | mean_tcell_distance_to_fsp1_pos_fibroblast_chain | This parameter measures the average minimum spatial distance, in micrometers, from cytotoxic T cells to the nearest FSP1-positive fibroblast chain. It quantifies how far, on average, T cells are located from these chains, thus providing insight into spatial relationships between immune cells and the FSP1+ fibroblast structures. |
| 0ejb3tqm7k9u | Ff,F,MFp,MF,Tc | pct_tcells_near_fsp1_pos_fibroblast_chain | This parameter represents the percentage of cytotoxic T cells that are situated within a predefined proximity threshold of FSP1-positive fibroblast chains. It indicates the proportion of T cells that are in close spatial contact with these chains, reflecting potential immune-tumor interactions. |
| 0ejb3tqm7k9u | Ff,F,MFp,MF,Tc | mean_tcell_distance_to_fsp1_neg_fibroblast_chain | This parameter calculates the average minimum distance from cytotoxic T cells to the nearest chain formed by FSP1-negative fibroblasts. It serves as an indicator of the spatial separation between T cells and FSP1- fibroblast clusters in the tissue patch. |
| 0ejb3tqm7k9u | Ff,F,MFp,MF,Tc | pct_tcells_near_fsp1_neg_fibroblast_chain | This parameter indicates the percentage of cytotoxic T cells that are found within the defined proximity threshold of FSP1-negative fibroblast chains, thereby reflecting the relative closeness of T cells to these cell groups. |
| 0ejb3tqm7k9u | Ff,F,MFp,MF,Tc | mean_tcell_distance_to_pdpn_pos_myofibroblast_chain | This parameter provides the average minimum distance, in micrometers, from T cells to the nearest chain formed by PDPN-positive myofibroblasts. It quantifies the typical spatial gap between immune cells and these myofibroblast chains. |
| 0ejb3tqm7k9u | Ff,F,MFp,MF,Tc | pct_tcells_near_pdpn_pos_myofibroblast_chain | This parameter represents the percentage of T cells that are located within a set proximity threshold of PDPN-positive myofibroblast chains, highlighting the proportion of T cells in close vicinity to these structures. |
| 0ejb3tqm7k9u | Ff,F,MFp,MF,Tc | mean_tcell_distance_to_pdpn_neg_myofibroblast_chain | This parameter measures the average minimum distance from cytotoxic T cells to the closest chain of PDPN-negative myofibroblasts, thereby quantifying the spatial separation between T cells and these chains. |
| 0ejb3tqm7k9u | Ff,F,MFp,MF,Tc | pct_tcells_near_pdpn_neg_myofibroblast_chain | This parameter denotes the percentage of cytotoxic T cells that reside within the specified distance threshold relative to PDPN-negative myofibroblast chains, thus reflecting the closeness of T cells to these cell assemblies. |
| 0ejb3tqm7k9u | Ff,F,MFp,MF,Tc | mean_tcell_distance_to_all_fibroblast_chain | This parameter calculates the average minimum distance from T cells to the nearest chain among all fibroblast types combined. It offers a general measure of how far T cells typically lie from any fibroblast chain in the tissue patch. |
| 0ejb3tqm7k9u | Ff,F,MFp,MF,Tc | pct_tcells_near_all_fibroblast_chain | This parameter represents the percentage of T cells that are found within the established proximity threshold of any fibroblast chain, combining all subtypes. It reflects the overall extent of close spatial association between T cells and fibroblast structures across the analyzed region. |
| 0fe71ygdthxs | Th,Treg,M | stromal_t_helper_density | stromal_t_helper_density represents the density of T helper cells (CD4+ cells) in the stromal compartment of a tissue section. It is normalized by dividing the number of T helper cells by the stromal area (in mm²), allowing for comparisons across different patient cases. |
| 0fe71ygdthxs | Th,Treg,M | stromal_t_reg_density | stromal_t_reg_density represents the density of regulatory T cells in the stromal region. The measurement is normalized by calculating the number of regulatory T cells per mm² of stroma, ensuring consistency across samples. |
| 0fe71ygdthxs | Th,Treg,M | stromal_macrophage_density | stromal_macrophage_density measures the density of macrophages within the stromal compartment. This value is normalized by dividing the macrophage count by the area of the stroma (in mm²), making it suitable for comparisons across different samples. |
| 0fe71ygdthxs | Th,Treg,M | stromal_combined_t_cell_density | stromal_combined_t_cell_density quantifies the combined density of T helper and regulatory T cells in the stromal compartment. It is obtained by summing the counts of the two T cell subtypes and then normalizing by the stromal area (mm²), providing a unified measure of T cell infiltration. |
| 0fe71ygdthxs | Th,Treg,M | stromal_th_treg_to_macrophage_ratio | stromal_th_treg_to_macrophage_ratio is a ratio that compares the combined density of T helper and regulatory T cells to the density of macrophages in the stroma. This normalized metric accounts for differences in cell densities and helps assess the balance between immune effector cells and macrophages, which could reflect the state of immune regulation within the tumor microenvironment. |
| 0j2i2tx1a66f | M | MEDIAN_NUCLEAR_ORIENTATION | MEDIAN_NUCLEAR_ORIENTATION represents the median angle (measured in degrees from 0 to 180) of the orientations of macrophage nuclei located in the stromal compartment. This parameter reflects the central tendency of nuclear orientation and is computed by applying principal component analysis on each nucleus's boundary coordinates. |
| 0j2i2tx1a66f | M | MEAN_NUCLEAR_ORIENTATION | MEAN_NUCLEAR_ORIENTATION provides the arithmetic average angle of the nuclear orientations of stromal macrophages. It gives an alternative measure of central tendency to assess the typical orientation state in a given tissue patch. |
| 0j2i2tx1a66f | M | STD_NUCLEAR_ORIENTATION | STD_NUCLEAR_ORIENTATION is the standard deviation of the nuclear orientation angles of macrophages in the stroma. It offers insight into the variability or dispersion of nuclear orientations across the analyzed cells. |
| 0j2i2tx1a66f | M | MIN_NUCLEAR_ORIENTATION | MIN_NUCLEAR_ORIENTATION indicates the smallest recorded nuclear orientation angle among stromal macrophages, offering a boundary reference for the range of measured orientations. |
| 0j2i2tx1a66f | M | MAX_NUCLEAR_ORIENTATION | MAX_NUCLEAR_ORIENTATION indicates the largest recorded nuclear orientation angle among stromal macrophages, providing the upper boundary for the range of measured orientations. |
| 0k039xed4c6a | TU,Tc,Th,Treg,B,P,M,G | co_clustering_index | The co-clustering index represents a normalized metric that quantifies the average number of immune cells within a defined proximity (50 µm) of each tumor cell. It is calculated by dividing the total number of immune cell neighbors by the number of tumor cells in a given tumor region patch, thereby standardizing the measure across different patient cases. |
| 0lcmfdtir34p | Tc,Treg,B | T_to_B_ratio | T_to_B_ratio is a normalized numeric indicator measuring the balance between T cells and B cells within the stromal compartment of breast cancer tissue. It is computed as the ratio of the sum of cytotoxic and regulatory T cell counts to the B cell count, providing a comparative measure that allows for patient case comparisons by mitigating the effect of absolute cell count differences. |
| 0p1lez357jh6 | TU,Ff,F,M,G,Th,Treg | MIN_DIST_TUMOR_TO_FSP1_FIBROBLAST | MIN_DIST_TUMOR_TO_FSP1_FIBROBLAST measures the smallest distance, in micrometers, from any tumor cell to the infiltration front created by FSP1+ fibroblasts. This distance is computed by first outlining the boundary where these fibroblast cell polygons converge and then determining the nearest proximity from tumor cell polygons to this boundary. It provides a normalized metric that allows for the comparison of tumor-stroma interaction across different patient cases or image patches. |
| 0p1lez357jh6 | TU,Ff,F,M,G,Th,Treg | MIN_DIST_TUMOR_TO_GRANULOCYTE | MIN_DIST_TUMOR_TO_GRANULOCYTE measures the smallest distance, in micrometers, from any tumor cell to the infiltration front created by granulocytes. The front is defined by combining the individual regions of granulocytes found in the stroma to form a continuous boundary, and then the minimal distance from tumor cell boundaries to this convex hull is computed. This numeric value is normalized to facilitate comparative analysis across different samples. |
| 0p1lez357jh6 | TU,Ff,F,M,G,Th,Treg | AVG_MIN_DIST_TUMOR_TO_INFILTRATION_FRONT | AVG_MIN_DIST_TUMOR_TO_INFILTRATION_FRONT represents the average of the minimum distances from tumor cells to the infiltration fronts of various stromal and immune cell types, including fibroblasts (both FSP1+ and FSP1-), macrophages, granulocytes, helper T cells, and Tregs. This aggregated metric summarizes the overall spatial proximity between tumor cells and multiple infiltration fronts, ensuring a balanced and normalized measure for comparisons across patient cases. |
| 0q97rpnxk35t | TU,M,Ff | combined_density_ratio | The combined_density_ratio parameter is a normalized metric that quantifies the relative abundance of macrophages and FSP1+ fibroblasts in the stromal region compared to the tumor cells in the tumor region. This ratio is calculated by summing the counts of macrophages and FSP1+ fibroblasts and dividing by the number of epithelial tumor cells, ensuring that the metric is comparable across different patient cases. A higher value indicates a greater presence of these supportive stromal cells relative to tumor cells, which may reflect a favorable microenvironment for tumor progression. |
| 0x8dda7aow8a | MFp | PDPN_MF_Nucleus_Perimeter_CV | PDPN_MF_Nucleus_Perimeter_CV measures the relative variability of PDPN+ myofibroblast nucleus perimeters by calculating the ratio of the standard deviation to the mean. This normalized metric enables comparison across different patient cases and tumor patches. |
| 0x8dda7aow8a | MFp | PDPN_MF_Nucleus_Perimeter_Mean | PDPN_MF_Nucleus_Perimeter_Mean represents the average perimeter of PDPN+ myofibroblast nuclei within a stromal compartment patch, providing a central tendency measure that is comparable across different patients given consistent measurement scales. |
| 0x8dda7aow8a | MFp | PDPN_MF_Nucleus_Perimeter_StdDev | PDPN_MF_Nucleus_Perimeter_StdDev quantifies the spread of PDPN+ myofibroblast nucleus perimeter values around their mean within a patch, offering insight into the variability of nuclear sizes and ensuring numeric comparability across different samples. |
| 0x8dda7aow8a | MFp | PDPN_MF_Nucleus_Perimeter_Min | PDPN_MF_Nucleus_Perimeter_Min indicates the smallest PDPN+ myofibroblast nucleus perimeter recorded in a tumor patch, serving as an absolute measurement which can be used comparatively if the imaging parameters remain consistent. |
| 0x8dda7aow8a | MFp | PDPN_MF_Nucleus_Perimeter_Max | PDPN_MF_Nucleus_Perimeter_Max reflects the largest PDPN+ myofibroblast nucleus perimeter found in the analyzed patch, capturing extreme values and allowing standardized comparisons across patient cases. |
| 0x8dda7aow8a | MFp | PDPN_MF_Nucleus_Perimeter_Median | PDPN_MF_Nucleus_Perimeter_Median provides the middle value of the PDPN+ myofibroblast nucleus perimeter distribution within a patch, offering a robust statistic for central tendency that is less affected by outliers and is suitable for cross-patient analysis. |
| 0zwpgfl63btr | Tc,F | mean_distance_cytotoxic_t_cells_um | mean_distance_cytotoxic_t_cells_um: This parameter measures the average distance in micrometers from cytotoxic T cells located in the epithelial (tumor) region to the nearest blood vessel. It is derived by calculating the minimum distance from each cell to any vessel and then computing the mean of these distances, providing a normalized metric for comparative analysis across patient cases. |
| 0zwpgfl63btr | Tc,F | mean_distance_fsp1neg_fibroblasts_um | mean_distance_fsp1neg_fibroblasts_um: This parameter calculates the average distance in micrometers from FSP1-negative fibroblasts in the epithelial region to the closest vessel. It is determined by measuring the minimal distance from each fibroblast to the vessels and averaging these measurements, allowing for normalized comparison across different patient patches. |
| 0zwpgfl63btr | Tc,F | difference_in_mean_distances_um | difference_in_mean_distances_um: This parameter represents the difference between the mean distance of cytotoxic T cells and that of FSP1-negative fibroblasts to the nearest blood vessel (computed as cytotoxic T cell mean distance minus fibroblast mean distance). It provides a normalized comparative assessment of the spatial infiltration patterns of the two cell types. |
| 11ubbp8lqjqr | Tc,Th,Treg,B,P,M,G,MFp,E | interplay_score | Interplay score is a composite metric that integrates normalized densities of immune cells, PDPN+ myofibroblasts, and endothelial cells with the fraction of immune cells that are spatially co-localized with both PDPN+ myofibroblasts and endothelial cells. It provides an overall measure of the immune-fibrovascular interaction in the stroma, making it comparable across different patient cases. |
| 11ubbp8lqjqr | Tc,Th,Treg,B,P,M,G,MFp,E | co_localization_fraction | Co-localization fraction represents the proportion of immune cells in the stromal region that are in close proximity (within a fixed threshold of 20 pixels) to both PDPN+ myofibroblasts and endothelial cells. This fraction is a normalized value between 0 and 1 and reflects the degree of spatial interaction between these cell types. |
| 11ubbp8lqjqr | Tc,Th,Treg,B,P,M,G,MFp,E | immune_density_mm2 | Immune density per mm² is the normalized density of immune cells in the stromal region. It is derived by dividing the immune cell count by the effective stromal area and then scaling to a per square millimeter basis, allowing for comparisons across different tumor patches. |
| 11ubbp8lqjqr | Tc,Th,Treg,B,P,M,G,MFp,E | myofibroblast_density_mm2 | Myofibroblast density per mm² measures the number of PDPN+ myofibroblasts per square millimeter in the stroma. This normalization by the effective stromal area ensures that the value is comparable across diverse patient samples. |
| 11ubbp8lqjqr | Tc,Th,Treg,B,P,M,G,MFp,E | endothelial_density_mm2 | Endothelial density per mm² represents the density of endothelial cells in the stromal region, normalized to a square millimeter. This measure facilitates direct comparisons across different tissues by accounting for variations in the stromal area. |
| 13efspei7hnf | P | PLASMA_CELL_NUCLEUS_CIRCULARITY_MEAN | PLASMA_CELL_NUCLEUS_CIRCULARITY_MEAN represents the average circularity of plasma cell nuclei within a tumor patch. The value is obtained by computing the circularity for each plasma cell nucleus using the geometric property derived from the nuclear polygon and averaging these values, thus providing a normalized metric usable for comparisons across patient cases. |
| 13efspei7hnf | P | PLASMA_CELL_NUCLEUS_CIRCULARITY_STD | PLASMA_CELL_NUCLEUS_CIRCULARITY_STD is the standard deviation of the circularity values calculated for all plasma cell nuclei within the analyzed patch. This parameter quantifies the variability or dispersion in nuclear circularity among plasma cells, offering insight into the heterogeneity of nuclear shapes. |
| 13efspei7hnf | P | PLASMA_CELL_NUCLEUS_CIRCULARITY_MIN | PLASMA_CELL_NUCLEUS_CIRCULARITY_MIN denotes the minimum circularity value observed among plasma cell nuclei in the tumor patch. This metric highlights the lowest degree of nuclear circularity detected, serving as a normalized measure reflective of extreme cellular morphologies. |
| 13efspei7hnf | P | PLASMA_CELL_NUCLEUS_CIRCULARITY_MAX | PLASMA_CELL_NUCLEUS_CIRCULARITY_MAX indicates the maximum circularity value recorded among plasma cell nuclei in the tissue region. It captures the highest extent of nuclear circularity found, providing a normalized metric for comparing the upper bounds of cellular morphology across cases. |
| 144ijpego00z | TU,G,E,Ff | nn_dist_tumor-granulocyte | nn_dist_tumor-granulocyte: This parameter measures the average Euclidean distance between each tumor cell and its nearest granulocyte within the angiogenic area. It quantifies the spatial separation by looping through tumor cells and identifying the closest granulocyte, then averaging these minimum distances. |
| 144ijpego00z | TU,G,E,Ff | nn_dist_tumor-endothelial | nn_dist_tumor-endothelial: This parameter represents the average nearest neighbor distance from tumor cells to endothelial cells in the buffered angiogenic area. It captures how far, on average, tumor cells are located from vessel-lining endothelial cells in the region of interest. |
| 144ijpego00z | TU,G,E,Ff | nn_dist_tumor-fsp1_fibroblast | nn_dist_tumor-fsp1_fibroblast: This parameter calculates the average nearest neighbor distance from tumor cells to FSP1+ fibroblasts. It indicates the degree of spatial proximity between tumor cells and these fibroblasts, using the minimum Euclidean distance for each tumor cell. |
| 144ijpego00z | TU,G,E,Ff | nn_dist_granulocyte-endothelial | nn_dist_granulocyte-endothelial: This parameter computes the average minimal distance between granulocytes and endothelial cells. It reflects the spatial interaction between these two cell groups within the defined angiogenic area. |
| 144ijpego00z | TU,G,E,Ff | nn_dist_granulocyte-fsp1_fibroblast | nn_dist_granulocyte-fsp1_fibroblast: This parameter measures the average distance from granulocytes to FSP1+ fibroblasts based on their nearest neighbor distances. It is used to evaluate the spatial relationship between these cell types in the region. |
| 144ijpego00z | TU,G,E,Ff | nn_dist_endothelial-fsp1_fibroblast | nn_dist_endothelial-fsp1_fibroblast: This parameter represents the average nearest neighbor distance between endothelial cells and FSP1+ fibroblasts. It is calculated by finding the nearest fibroblast for each endothelial cell and averaging the distances. |
| 144ijpego00z | TU,G,E,Ff | reciprocal_tumor-granulocyte | reciprocal_tumor-granulocyte: Derived as the reciprocal of the average nearest neighbor distance between tumor cells and granulocytes, this parameter scales the interaction intensity such that smaller distances yield higher reciprocal values, facilitating better cross-case comparisons. |
| 144ijpego00z | TU,G,E,Ff | reciprocal_tumor-endothelial | reciprocal_tumor-endothelial: This parameter is the reciprocal of the average distance from tumor cells to endothelial cells. By converting the distance into an interaction index through inversion, it allows for a normalized comparison of spatial proximity. |
| 144ijpego00z | TU,G,E,Ff | reciprocal_tumor-fsp1_fibroblast | reciprocal_tumor-fsp1_fibroblast: This parameter is the inverse of the average nearest neighbor distance between tumor cells and FSP1+ fibroblasts. It serves as a normalized indicator of the closeness of interaction between these cell types. |
| 144ijpego00z | TU,G,E,Ff | reciprocal_granulocyte-endothelial | reciprocal_granulocyte-endothelial: Calculated as the reciprocal of the average nearest neighbor distance between granulocytes and endothelial cells, this parameter translates the measured distance into an index where higher values indicate closer interactions. |
| 144ijpego00z | TU,G,E,Ff | reciprocal_granulocyte-fsp1_fibroblast | reciprocal_granulocyte-fsp1_fibroblast: This parameter is the reciprocal of the average distance between granulocytes and FSP1+ fibroblasts, offering an interaction metric that increases as the cell types are in closer proximity. |
| 144ijpego00z | TU,G,E,Ff | reciprocal_endothelial-fsp1_fibroblast | reciprocal_endothelial-fsp1_fibroblast: This parameter represents the inverse of the average nearest neighbor distance between endothelial cells and FSP1+ fibroblasts, providing a normalized measurement of their spatial interaction. |
| 144ijpego00z | TU,G,E,Ff | overall_interaction_score | overall_interaction_score: This parameter is computed as the mean of all valid reciprocal indices for the six cell-type pairs. It provides a composite measure of overall spatial interaction intensity among tumor cells, granulocytes, endothelial cells, and FSP1+ fibroblasts in the angiogenic area. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | B_mean_distance | B_mean_distance: The average geodesic distance in micrometers from vessels for B cells determined by calculating each cell’s minimal distance from vessel boundaries and then averaging these values over all B cells within a patch. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | B_median_distance | B_median_distance: The median geodesic distance from vessels for B cells, which represents the midpoint of the distance distribution for these cells. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | B_min_distance | B_min_distance: The smallest geodesic distance from vessels found among B cells, indicating the closest B cell to a vessel in the patch. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | B_max_distance | B_max_distance: The largest observed geodesic distance from vessels for B cells, representing the farthest distance among them. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | B_std_distance | B_std_distance: The standard deviation of the geodesic distances for B cells, reflecting the variability of their distances from the vessels. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | Plasma_mean_distance | Plasma_mean_distance: The average geodesic distance in micrometers from vessels for Plasma cells calculated over all Plasma cells in a given region. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | Plasma_median_distance | Plasma_median_distance: The median of geodesic distances from vessels for Plasma cells, indicating the center value in the distribution of distances. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | Plasma_min_distance | Plasma_min_distance: The minimum geodesic distance from vessels recorded among Plasma cells in the patch. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | Plasma_max_distance | Plasma_max_distance: The maximum geodesic distance from vessels for Plasma cells, showing the greatest separation from a vessel. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | Plasma_std_distance | Plasma_std_distance: The standard deviation of the geodesic distances of Plasma cells, which quantifies the spread of the distance measurements. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | Treg_mean_distance | Treg_mean_distance: The average geodesic distance from vessels for regulatory T cells (Treg), computed by averaging each cell’s minimal distance to a vessel. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | Treg_median_distance | Treg_median_distance: The median geodesic distance for Treg cells, representing the middle value in the ordered list of distances. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | Treg_min_distance | Treg_min_distance: The smallest geodesic distance from vessels among Treg cells, identifying the Treg cell closest to the vessel network. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | Treg_max_distance | Treg_max_distance: The largest geodesic distance from vessels for Treg cells, indicating the maximum separation within their population. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | Treg_std_distance | Treg_std_distance: The standard deviation of the geodesic distances for Treg cells, measuring the variability of their distances. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | Helper T_mean_distance | Helper T_mean_distance: The average geodesic distance in micrometers from vessels for Helper T cells, reflecting the typical distance of these cells from vessels. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | Helper T_median_distance | Helper T_median_distance: The median geodesic distance for Helper T cells, serving as the central value of their distance distribution. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | Helper T_min_distance | Helper T_min_distance: The minimum geodesic distance to vessels among Helper T cells, showing the closest proximity of any Helper T cell to a vessel. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | Helper T_max_distance | Helper T_max_distance: The maximum geodesic distance from vessels observed among Helper T cells, indicating the farthest cell in this category. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | Helper T_std_distance | Helper T_std_distance: The standard deviation of the distances for Helper T cells, providing a measure of the dispersion in their proximity to vessels. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | PDPN+ Myofibroblasts_mean_distance | PDPN+ Myofibroblasts_mean_distance: The average geodesic distance from vessels for PDPN+ Myofibroblasts calculated over all such cells in the patch. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | PDPN+ Myofibroblasts_median_distance | PDPN+ Myofibroblasts_median_distance: The median geodesic distance for PDPN+ Myofibroblasts, representing the middle value of the distribution. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | PDPN+ Myofibroblasts_min_distance | PDPN+ Myofibroblasts_min_distance: The smallest geodesic distance from vessels among PDPN+ Myofibroblasts, indicating the cell closest to a vessel. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | PDPN+ Myofibroblasts_max_distance | PDPN+ Myofibroblasts_max_distance: The highest geodesic distance from vessels recorded for PDPN+ Myofibroblasts, marking the maximum separation in this cell type. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | PDPN+ Myofibroblasts_std_distance | PDPN+ Myofibroblasts_std_distance: The standard deviation of the geodesic distances for PDPN+ Myofibroblasts to vessels, showing the variability of distances. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | Tumor_mean_distance | Tumor_mean_distance: The average geodesic distance from vessels for tumor cells, providing a normalized measure of how far tumor cells lie from vessel structures. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | Tumor_median_distance | Tumor_median_distance: The median distance from vessels for tumor cells, representing the center of their distance distribution. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | Tumor_max_distance | Tumor_max_distance: The maximum observed geodesic distance from vessels among tumor cells, demonstrating the farthest measured distance. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | Tumor_std_distance | Tumor_std_distance: The standard deviation of the geodesic distances for tumor cells, quantifying the variability of their distances from vessels. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | overall_mean_distance | overall_mean_distance: The average geodesic distance calculated across all analyzed cell types in the patch, offering a composite measure of vessel proximity. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | overall_median_distance | overall_median_distance: The median geodesic distance from vessels across all cell types, providing a central tendency measure for the entire cell population. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | overall_std_distance | overall_std_distance: The standard deviation of the geodesic distances for all cells, reflecting the overall variability in distance measurements within the patch. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | B_vs_Tumor_mean_distance_diff | B_vs_Tumor_mean_distance_diff: The difference between the average geodesic distance of B cells and that of tumor cells. A positive value indicates that B cells are, on average, further from vessels than tumor cells, whereas a negative value implies the opposite. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | Treg_vs_Tumor_mean_distance_diff | Treg_vs_Tumor_mean_distance_diff: The difference in mean geodesic distance between Treg cells and tumor cells, used to compare their relative proximities to vessels. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | HelperT_vs_Tumor_mean_distance_diff | HelperT_vs_Tumor_mean_distance_diff: The difference between the average geodesic distances of Helper T cells and tumor cells, highlighting relative differences in vessel proximity. |
| 158dimv31hk3 | B,P,Treg,Th,MFp,TU | PDPN_Myo_vs_Tumor_mean_distance_diff | PDPN_Myo_vs_Tumor_mean_distance_diff: The difference in mean geodesic distance between PDPN+ Myofibroblasts and tumor cells, indicating whether these myofibroblasts are generally closer to or farther from vessels compared to tumor cells. |
| 1cfd0h6sv4l4 | M,G,MFp | COMBINED_INFILTRATION_RATIO | COMBINED_INFILTRATION_RATIO is a normalized parameter that represents the ratio of the combined count of macrophages and granulocytes (immune cells) in the stroma to the count of PDPN+ myofibroblasts also in the stroma. This ratio provides a relative measure of immune cell infiltration compared to the presence of PDPN+ myofibroblasts and is useful for inter-patient comparisons as it adjusts for variations in absolute cell counts. |
| 1fdso8035e4z | A | AVG_APC_NUCLEUS_AREA | AVG_APC_NUCLEUS_AREA represents the average area of antigen presenting cell nuclei measured in square micrometers. This normalized metric facilitates cross-patient and cross-sample comparisons by providing a mean value of the nucleus size within each patch of tissue analyzed. |
| 1fdso8035e4z | A | STD_APC_NUCLEUS_AREA | STD_APC_NUCLEUS_AREA indicates the standard deviation of antigen presenting cell nucleus areas, reflecting the variability in nuclear sizes across the analyzed sample. Its normalized nature supports robust comparisons between different patient cases. |
| 1fdso8035e4z | A | MIN_APC_NUCLEUS_AREA | MIN_APC_NUCLEUS_AREA is the smallest measured nucleus area among antigen presenting cells within the sample. As a normalized measurement, it provides insight into the lower bound of APC nucleus sizes across different tissue patches. |
| 1fdso8035e4z | A | MAX_APC_NUCLEUS_AREA | MAX_APC_NUCLEUS_AREA is the largest detected nucleus area among antigen presenting cells in the sample. This normalized value helps in assessing the upper range of nuclear sizes and is comparable across patient cases. |
| 1fdso8035e4z | A | MEDIAN_APC_NUCLEUS_AREA | MEDIAN_APC_NUCLEUS_AREA represents the median area of APC nuclei, offering a robust measure of central tendency that minimizes the influence of extreme values. This metric is normalized, making it suitable for comparative analysis across different patient samples. |
| 1hkda6c727jq | TU,Th,Treg,B,P,M,MFp,MF,F,E | STROMAL_ANISOTROPY_INDEX | STROMAL_ANISOTROPY_INDEX is a weighted average of the anisotropy values computed from cell clusters within the tumor stroma. The anisotropy for each cluster is measured as the ratio of the principal eigenvalue (reflecting the primary direction of variance in cell positions) to the total variance. This parameter quantifies how strongly the directional organization of cells deviates from randomness and is normalized to allow comparison across different patient cases and patches. |
| 1hkda6c727jq | TU,Th,Treg,B,P,M,MFp,MF,F,E | RANDOMIZED_ANISOTROPY | RANDOMIZED_ANISOTROPY is computed by applying the same anisotropy measurement process on a set of randomly generated cell positions within the stromal area. It serves as a baseline reference that captures the expected anisotropy if cells were distributed without any directional bias, ensuring the metric is normalized for comparative analysis. |
| 1hkda6c727jq | TU,Th,Treg,B,P,M,MFp,MF,F,E | NORMALIZED_ANISOTROPY | NORMALIZED_ANISOTROPY is derived as the ratio of the observed anisotropy (STROMAL_ANISOTROPY_INDEX) to the randomized anisotropy (RANDOMIZED_ANISOTROPY). This parameter provides a normalized metric that directly quantifies the deviation of the real cellular organization from a random distribution, making it suitable for comparisons between different patient cases. |
| 1hkda6c727jq | TU,Th,Treg,B,P,M,MFp,MF,F,E | MIN_CLUSTER_ANISOTROPY | MIN_CLUSTER_ANISOTROPY is defined as the smallest anisotropy value among all identified cell clusters within the stroma. It represents the least organized cluster in terms of directional alignment and, being a ratio metric, is normalized for comparative analysis across different tumor regions. |
| 1hkda6c727jq | TU,Th,Treg,B,P,M,MFp,MF,F,E | MAX_CLUSTER_ANISOTROPY | MAX_CLUSTER_ANISOTROPY measures the highest anisotropy value found among the clusters, corresponding to the cluster with the strongest directional organization. As a normalized ratio of principal variance to total variance, it facilitates direct comparison of directional organization intensity between different samples. |
| 1igp259cbdhq | Tc,Treg,B,P,M,G,MFp,MF,Ff,E,A | infiltration_index | The infiltration_index parameter represents the sum of the ratios of 11 different immune and stromal cell types relative to the total number of cells in the tumor region. It provides a normalized measure of overall cell infiltration, enabling comparisons across different patient samples. |
| 1igp259cbdhq | Tc,Treg,B,P,M,G,MFp,MF,Ff,E,A | ratio_Tc | The ratio_Tc parameter is a normalized metric indicating the proportion of CD8+ T cells (coded as 'Tc') in the tumor. It expresses the fraction of these cells relative to the total number of cells, allowing for meaningful comparisons between patients. |
| 1igp259cbdhq | Tc,Treg,B,P,M,G,MFp,MF,Ff,E,A | ratio_M | The ratio_M parameter quantifies the normalized fraction of macrophages (coded as 'M') within the tumor region. This parameter measures the macrophage infiltration as a ratio relative to the overall tumor cell count. |
| 1igp259cbdhq | Tc,Treg,B,P,M,G,MFp,MF,Ff,E,A | ratio_MFp | The ratio_MFp parameter denotes the normalized ratio of PDPN+ myofibroblasts (coded as 'MFp') compared to the total number of cells in the tumor. It provides insights into the presence of these specialized cells in a consistent and comparable manner. |
| 1igp259cbdhq | Tc,Treg,B,P,M,G,MFp,MF,Ff,E,A | ratio_MF | The ratio_MF parameter represents the normalized fraction of myofibroblasts (coded as 'MF') in the tumor compartment. It is computed as the ratio of myofibroblasts to the total cell count, ensuring it is a valid measure for comparing infiltration across cases. |
| 1o208kjmd7vm | M | MEDIAN_MACROPHAGE_NUCLEUS_ELONGATION_STROMA | This parameter represents the median nucleus elongation factor of macrophages located in the stromal compartment of breast cancer tissue patches. The elongation factor is computed as the ratio of the major axis length to the minor axis length of each macrophage nucleus, obtained by performing a principal component analysis on the polygonal outlines of the cells. This normalized numeric ratio provides a measure of nuclear shape heterogeneity which may indicate specific polarization states of macrophages related to tumor-promoting or tumor-inhibiting activities, thereby potentially influencing patient outcomes. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_weighted_betweenness | avg_weighted_betweenness: This parameter represents the average normalized betweenness centrality value across all cells in the patch. The betweenness centrality is computed on a Delaunay graph where cells serve as nodes and edges are weighted based on the Euclidean distance adjusted by cell type relevance, reflecting the overall communication influence in the tumor microenvironment. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | p75_weighted_betweenness | p75_weighted_betweenness: This parameter indicates the 75th percentile of the normalized weighted betweenness centrality values among all cells in the patch. It captures the threshold above which the top 25% of cells in terms of network centrality are found. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | p90_weighted_betweenness | p90_weighted_betweenness: This parameter represents the 90th percentile of the normalized weighted betweenness centrality distribution among cells. It highlights the value below which 90% of the cells fall, isolating the top 10% most central cells. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | high_bc_cells_p75_ratio | high_bc_cells_p75_ratio: This ratio measures the proportion of cells with a normalized betweenness centrality above the 75th percentile relative to the total number of cells, providing a normalized metric for assessing the prevalence of high-centrality cells. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | high_bc_cells_p90_ratio | high_bc_cells_p90_ratio: This ratio represents the fraction of cells whose normalized betweenness centrality exceeds the 90th percentile, offering insight into the relative abundance of extremely central cells in the network. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_bc_macrophage | avg_bc_macrophage: This parameter calculates the average normalized betweenness centrality for cells identified as macrophages. It quantifies the typical communication influence of macrophages within the tissue network. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_bc_epithelial_cell | avg_bc_epithelial_cell: This parameter is the average betweenness centrality among epithelial cells (commonly tumor cells), capturing their typical role as hubs in intercellular signaling within the patch. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_bc_endothelial_cell | avg_bc_endothelial_cell: This parameter represents the average normalized betweenness centrality for endothelial cells, which may reflect their connectivity in relation to blood vessel structures in the tumor region. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_bc_t_cell_cd8 | avg_bc_t_cell_cd8: This parameter indicates the average normalized betweenness centrality for CD8 T cells, highlighting their average involvement as communicative nodes in the network. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_bc_fibroblast | avg_bc_fibroblast: This parameter represents the average normalized betweenness centrality for fibroblast cells, reflecting their general role and connectivity within the tissue microenvironment. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_bc_myofibroblast | avg_bc_myofibroblast: This parameter measures the average normalized betweenness centrality for myofibroblasts, indicating how these cells typically contribute to network communication dynamics. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_bc_myofibroblast_pdpn | avg_bc_myofibroblast_pdpn: This parameter represents the average normalized betweenness centrality for PDPN-positive myofibroblasts, emphasizing the network influence of these specialized cells based on their specific marker expression. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_bc_t_cell_cd4 | avg_bc_t_cell_cd4: This parameter calculates the average normalized betweenness centrality for CD4 T helper cells, reflecting their typical role in mediating cell-to-cell interactions within the patch. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | max_bc_macrophage | max_bc_macrophage: This parameter indicates the maximum normalized betweenness centrality observed among macrophages, pinpointing the most central macrophage that may act as a crucial communication hub. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | max_bc_epithelial_cell | max_bc_epithelial_cell: This parameter represents the highest normalized betweenness centrality value among epithelial cells, identifying the most influential tumor cell in terms of network connectivity. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | max_bc_endothelial_cell | max_bc_endothelial_cell: This parameter captures the maximum normalized betweenness centrality observed in endothelial cells, highlighting the most connected cell within this category. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | max_bc_t_cell_cd8 | max_bc_t_cell_cd8: This parameter denotes the highest normalized betweenness centrality among CD8 T cells, marking the cell with the maximal influence in intercellular signaling in its group. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | max_bc_fibroblast | max_bc_fibroblast: This parameter represents the highest normalized betweenness centrality value within fibroblasts, reflecting the most influential fibroblast in terms of network connectivity. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | max_bc_myofibroblast | max_bc_myofibroblast: This parameter measures the maximum normalized betweenness centrality found among myofibroblasts, indicating the single most central cell within that cell type group. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | max_bc_myofibroblast_pdpn | max_bc_myofibroblast_pdpn: This parameter captures the maximum normalized betweenness centrality among PDPN-positive myofibroblasts, identifying the cell with the greatest network influence among this specialized subset. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | max_bc_t_cell_cd4 | max_bc_t_cell_cd4: This parameter denotes the highest normalized betweenness centrality among CD4 T helper cells, reflecting the single most central cell within this immune cell subset. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_bc_fibroblast_fsp1 | avg_bc_fibroblast_fsp1: This parameter represents the average normalized betweenness centrality for FSP1-positive fibroblasts, indicating their typical role in the tissue network. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | max_bc_fibroblast_fsp1 | max_bc_fibroblast_fsp1: This parameter captures the maximum normalized betweenness centrality value within FSP1-positive fibroblasts, highlighting the most central cell of this specific fibroblast subgroup. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_bc_plasma_cell | avg_bc_plasma_cell: This parameter calculates the average normalized betweenness centrality for plasma cells, reflecting their overall contribution to intercellular signal integration. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_bc_t_cell_reg | avg_bc_t_cell_reg: This parameter represents the average normalized betweenness centrality for regulatory T cells, providing a measure of their typical centrality in modulating network interactions. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_bc_b_cell | avg_bc_b_cell: This parameter indicates the average normalized betweenness centrality among B cells, capturing their overall role in the network. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_bc_ap_cell | avg_bc_ap_cell: This parameter reflects the average normalized betweenness centrality for antigen presenting cells, summarizing their typical influence in orchestrating immune interactions. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | max_bc_plasma_cell | max_bc_plasma_cell: This parameter denotes the maximum normalized betweenness centrality observed in plasma cells, pinpointing the most influential plasma cell within the patch. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | max_bc_t_cell_reg | max_bc_t_cell_reg: This parameter represents the highest normalized betweenness centrality among regulatory T cells, identifying the cell with the greatest potential impact on network signaling within this group. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | max_bc_b_cell | max_bc_b_cell: This parameter captures the maximum normalized betweenness centrality among B cells, indicating the most central B cell in the network. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | max_bc_ap_cell | max_bc_ap_cell: This parameter represents the highest normalized betweenness centrality found among antigen presenting cells, marking the cell with the maximal network influence in this category. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_bc_granulocyte | avg_bc_granulocyte: This parameter computes the average normalized betweenness centrality for granulocytes, reflecting their typical role in the intercellular communication network. |
| 1q4vfz0gxg3z | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | max_bc_granulocyte | max_bc_granulocyte: This parameter indicates the maximum normalized betweenness centrality among granulocytes, identifying the single most central granulocyte within the patch. |
| 1v6365tdzyws | MFp,Ff,Treg,P,B,G,E | overall_adjacency_ratio | The overall_adjacency_ratio measures the fraction of all target cells (the combined group of PDPN+ myofibroblasts, FSP1+ fibroblasts, regulatory T cells, plasma cells, B cells, granulocytes, and endothelial cells) that are immediately adjacent to tumor cells. It is normalized as it is expressed as a ratio, allowing comparisons across different patient cases or patches. |
| 1v6365tdzyws | MFp,Ff,Treg,P,B,G,E | myofibroblast_pdpn_adjacency_ratio | The myofibroblast_pdpn_adjacency_ratio represents the proportion of PDPN-positive myofibroblasts that are in direct contact or within a minimal distance threshold from tumor cells relative to the total PDPN+ myofibroblast count. This ratio is normalized to facilitate objective comparisons between different samples. |
| 1v6365tdzyws | MFp,Ff,Treg,P,B,G,E | endothelial_cell_adjacency_ratio | The endothelial_cell_adjacency_ratio indicates the proportion of endothelial cells that are adjacent to tumor cells compared to the total number of endothelial cells present. Like the other measures, it is normalized and expressed as a ratio, ensuring that it is suitable for comparing across diverse patient cases. |
| 1wh7pf5smpbp | TU | TUMOR_CELL_NUCLEUS_ORIENTATION_STD | The TUMOR_CELL_NUCLEUS_ORIENTATION_STD parameter measures the variability in the orientation angles (in degrees) of tumor cell nuclei within epithelial compartments for breast cancer cases. Each tumor cell’s nucleus is analyzed by first converting its shape into a minimum rotated rectangle, from which the longest edge is identified as representative of the nucleus's major axis. The angle of this edge is computed and normalized to a range of 0 to 180 degrees. The standard deviation of these orientation angles is then calculated using numerical methods, providing a normalized, numeric measure. Higher values indicate greater dispersion, suggesting a higher degree of disorganized growth, which may be linked to poorer clinical prognosis. |
| 24s116qqgvi6 | Treg,M,E | Treg_fraction | Treg_fraction represents the proportion of T regulatory cells relative to the total count of T regulatory cells, macrophages, and endothelial cells in tumor-associated regions. This normalized metric is calculated by dividing the count of T regulatory cells by the sum of the counts of these three cell types, thereby enabling direct comparisons of immune cell distributions across different patient samples. |
| 27df00e4zz1t | F | FIBROBLAST_NUCLEUS_MAJOR_AXIS_STD | FIBROBLAST_NUCLEUS_MAJOR_AXIS_STD quantifies the variability in the major axis lengths of fibroblast nuclei by computing the standard deviation of these lengths in the stromal compartments. This measure reflects heterogeneity in nucleus size that could indicate differing activation or differentiation states within the fibroblasts. |
| 27df00e4zz1t | F | FIBROBLAST_NUCLEUS_MAJOR_AXIS_MEAN | FIBROBLAST_NUCLEUS_MAJOR_AXIS_MEAN calculates the average major axis length of the fibroblast nuclei in the stromal compartments. It provides a central tendency measurement that summarizes the typical size of the nuclei and can be used for comparative analysis across patient cases. |
| 27df00e4zz1t | F | FIBROBLAST_NUCLEUS_MAJOR_AXIS_MIN | FIBROBLAST_NUCLEUS_MAJOR_AXIS_MIN identifies the smallest value among the major axis lengths of fibroblast nuclei measured in the stromal region. It serves as the lower bound indicator of nucleus elongation in the analyzed patch for normalization across cases. |
| 27df00e4zz1t | F | FIBROBLAST_NUCLEUS_MAJOR_AXIS_MAX | FIBROBLAST_NUCLEUS_MAJOR_AXIS_MAX captures the largest major axis length of fibroblast nuclei from the stromal areas, serving as the upper bound measurement that, together with other descriptive statistics, aids in comparing nucleus elongation features between different patient cases. |
| 28tvplxm4a9d | B | B_CELL_DENSITY_PER_BOUNDARY_LENGTH | B_CELL_DENSITY_PER_BOUNDARY_LENGTH is a normalized metric that represents the density of B cells along the tumor boundary. It is calculated by dividing the number of B cells in the stroma that are located within a 20-micrometer distance from the tumor boundary by the length of that boundary. This ratio allows for comparison across different patient cases by providing a value independent of absolute cell counts or boundary extents. |
| 29c73m788qye | TU,Tc,B,P,M,MFp,Ff,F,E,A | mean_synergy_index | mean_synergy_index represents the average synergy index computed from tumor-proximal clusters. The synergy index for each cluster is calculated as (fibroblast count * immune count) divided by the sum of fibroblast and immune counts, which quantifies the balance and intensity of interactions between fibroblasts and immune cells. Averaging these values produces a normalized metric that allows for comparison across different patient cases. |
| 29c73m788qye | TU,Tc,B,P,M,MFp,Ff,F,E,A | max_synergy_index | max_synergy_index is the highest synergy index observed among the tumor-proximal clusters. This value captures the maximum degree of fibroblast and immune cell interaction in any cluster within a patch, providing a normalized measure that is useful for comparative analyses across patient samples. |
| 29c73m788qye | TU,Tc,B,P,M,MFp,Ff,F,E,A | fibro_immune_ratio | fibro_immune_ratio is the ratio of the total number of fibroblasts to the total number of immune cells aggregated from tumor-proximal clusters. This parameter is expressed as a ratio, making it a normalized metric that reflects the balance between fibroblast and immune cell populations in the tumor microenvironment. |
| 2e6qldf971n7 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Tumor_Microenvironment_Balance_Index | The Tumor_Microenvironment_Balance_Index is a normalized ratio that quantifies the balance between tumor-favoring cells and cells involved in immune response and vascular function within a tumor patch. It is derived by dividing the count of tumor cells and fibroblast/myofibroblast cells by the count of immune cells and endothelial cells, ensuring comparability across different patient cases. This index provides a relative measure of how predominantly the tumor microenvironment is skewed towards supporting tumor progression versus eliciting an immune or vascular response. |
| 2iw9gjbold9l | Th,E | th_to_endo_overall_min_dist | th_to_endo_overall_min_dist measures the minimum Euclidean distance from any T helper cell in the stromal compartment to the nearest endothelial cell. This metric provides a sensitive measure of the closest spatial proximity between these immune and vascular cells across a tumor patch, ensuring comparability between different patient cases. |
| 2iw9gjbold9l | Th,E | th_to_endo_overall_median_dist | th_to_endo_overall_median_dist represents the median Euclidean distance from T helper cells in the stroma to their nearest endothelial cell. By summarizing the typical relationship of all measured cells in a patch, this parameter offers a robust, normalized metric that can be compared across patient samples. |
| 2iw9gjbold9l | Th,E | th_to_endo_adjacent_epi_min_dist | th_to_endo_adjacent_epi_min_dist captures the minimum distance from T helper cells that are adjacent to the epithelial boundary (defined as within 50 μm) to their nearest endothelial cell. This provides insight into the most immediate cell-to-cell proximity in regions where epithelial and stromal compartments interact. |
| 2iw9gjbold9l | Th,E | th_to_endo_adjacent_epi_median_dist | th_to_endo_adjacent_epi_median_dist calculates the median distance for T helper cells adjacent to the epithelial boundary to their closest endothelial cell. This metric summarizes the overall typical proximity for cells near the epithelial edge and allows for comparison across tumor patches. |
| 2iw9gjbold9l | Th,E | th_to_endo_nonadjacent_epi_min_dist | th_to_endo_nonadjacent_epi_min_dist measures the minimum distance from T helper cells that are not adjacent to the epithelial boundary (≥50 μm) to the nearest endothelial cell. This helps in assessing the closest spatial interaction within regions removed from the epithelial interface. |
| 2iw9gjbold9l | Th,E | th_to_endo_nonadjacent_epi_median_dist | th_to_endo_nonadjacent_epi_median_dist provides the median distance for T helper cells not adjacent to the epithelial boundary to their nearest endothelial cell, offering a normalized indication of typical spatial separation in the non-adjacent stromal compartment. |
| 2jmsx22ney4s | E | MAX_NUCLEAR_AXIS_LENGTH_ENDOTHELIAL | This parameter measures the maximum major axis length of any endothelial cell nucleus within a tumor patch. The process involves identifying endothelial cells based on their classification, computing the minimum rotated rectangle from each cell’s nuclear polygon to represent its geometry, and then calculating the Euclidean distances between consecutive vertices of the rectangle. The longest of these distances is taken as the cell’s nuclear major axis length, and the maximum value among all such cells in the patch is recorded. The measurement, expressed in micrometers, provides a comparative metric to assess features like active angiogenesis across different patient cases. |
| 2ldd1fbn5h75 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | nucleus_shape_factor_std | This parameter measures the standard deviation of nucleus shape factors calculated from the nuclei of valid cell types within a tumor patch. The nucleus shape factor is a dimensionless metric derived from each nucleus’s geometry using the formula (4 * π * area) / (perimeter²), where a value of 1 corresponds to a perfect circle. A higher standard deviation indicates greater heterogeneity in nuclear shapes, providing a normalized means to compare tumor regions across different patient cases. |
| 2nku0qcrsjld | M,A,E | MACROPHAGE_PROPORTION | MACROPHAGE_PROPORTION represents the normalized fraction of macrophages among the three cell types (macrophages, antigen presenting cells, and endothelial cells) found in the tumor epithelial compartment. It is calculated as the ratio of the number of macrophages to the total number of these cells, making it a normalized metric suitable for comparing different patient cases or image patches. |
| 2rtwx6tgbeep | M,B,F,MF | Macrophage_MEAN_AMPLITUDE | Macrophage_MEAN_AMPLITUDE represents the average nuclear boundary amplitude for macrophages in the stromal region. The amplitude is measured as the vertical distance between the highest and lowest positions of the nuclear boundary, capturing how pronounced the nuclear shape variation is in these cells. |
| 2rtwx6tgbeep | M,B,F,MF | Macrophage_STD_AMPLITUDE | Macrophage_STD_AMPLITUDE is the standard deviation of the nuclear boundary amplitude for macrophages. This parameter provides insight into the variability of the nuclear boundary measurements across individual macrophage cells within the stromal region. |
| 2rtwx6tgbeep | M,B,F,MF | B Cell_MEAN_AMPLITUDE | B Cell_MEAN_AMPLITUDE denotes the mean nuclear boundary amplitude for B cells in the stromal region. It quantifies the average vertical distance between the maximum and minimum y-values of the nuclear polygon across analyzed B cells. |
| 2rtwx6tgbeep | M,B,F,MF | B Cell_STD_AMPLITUDE | B Cell_STD_AMPLITUDE is the standard deviation of the nuclear boundary amplitude for B cells in the stromal area. It reflects the dispersion in amplitude measurements among B cells, indicating consistency or variability within the cell population. |
| 2rtwx6tgbeep | M,B,F,MF | Fibroblast FSP1-_MEAN_AMPLITUDE | Fibroblast FSP1-_MEAN_AMPLITUDE indicates the average nuclear boundary amplitude for fibroblasts that are FSP1 negative within the stroma. This measure is calculated as the mean vertical distance across the nuclear perimeters of the selected fibroblast population. |
| 2rtwx6tgbeep | M,B,F,MF | Fibroblast FSP1-_STD_AMPLITUDE | Fibroblast FSP1-_STD_AMPLITUDE represents the standard deviation in nuclear boundary amplitude for FSP1- fibroblasts. This provides an assessment of the variability of the nuclear shape characteristics among these fibroblasts. |
| 2rtwx6tgbeep | M,B,F,MF | PDPN- Myofibroblast_MEAN_AMPLITUDE | PDPN- Myofibroblast_MEAN_AMPLITUDE measures the mean nuclear boundary amplitude for PDPN negative myofibroblasts in the stromal region. This parameter captures the average vertical amplitude derived from the nuclear geometry of these specific cells. |
| 2rtwx6tgbeep | M,B,F,MF | PDPN- Myofibroblast_STD_AMPLITUDE | PDPN- Myofibroblast_STD_AMPLITUDE reflects the standard deviation of the nuclear boundary amplitude for PDPN- myofibroblasts, quantifying the variability in the nuclear boundary differences among these cells. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_eccentricity_variation_index | weighted_eccentricity_variation_index: A normalized index that quantifies the overall variability of nuclear eccentricity in a tissue patch. It is computed as the sum of the standard deviations of nuclear eccentricity for each cell type, each weighted by the proportion of that cell type within the patch. This index reflects the heterogeneity in nuclear shape, which may indicate genomic instability or aggressive tumor behavior. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | TU_eccentricity_std | TU_eccentricity_std: The standard deviation of the eccentricity values of the nuclei in tumor epithelial cells (TU). This parameter measures the variation in nuclear shape within this cell type, providing insight into the heterogeneity of tumor cells in a normalized manner. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | TU_proportion | TU_proportion: The normalized proportion of tumor epithelial cells (TU) within the analyzed tissue patch. It represents the fraction of these cells relative to the total number of cells, serving as a weighting factor in the overall variability index. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Tc_eccentricity_std | Tc_eccentricity_std: The standard deviation of the eccentricity values for cytotoxic T cells (Tc). It describes how much the nuclear shape of these cells varies, offering a normalized measure of dispersion for this immune cell subtype. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Tc_proportion | Tc_proportion: The normalized fraction of cytotoxic T cells (Tc) in the tissue patch. This proportion indicates the relative abundance of these cells compared to the overall cell population. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Th_eccentricity_std | Th_eccentricity_std: The standard deviation of eccentricity values for T helper cells (Th). It reflects the variability in nuclear shape among these cells on a normalized scale. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Th_proportion | Th_proportion: The proportion of T helper cells (Th) relative to the total cells in the patch, provided as a normalized value used in weighting the overall index. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Treg_eccentricity_std | Treg_eccentricity_std: The standard deviation of nuclear eccentricity for T regulatory cells (Treg). It measures the spread of nuclear shape values within this cell type, capturing their heterogeneity. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Treg_proportion | Treg_proportion: The normalized proportion of T regulatory cells (Treg) in the tissue sample, indicating their relative frequency in the analyzed patch. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | B_eccentricity_std | B_eccentricity_std: The standard deviation of the eccentricity measurements for B cells (B). This parameter captures the variability in the nuclear shape of B cells in a normalized manner. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | B_proportion | B_proportion: The normalized fraction of B cells (B) in the patch, expressing their relative abundance among all analyzed cells. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | P_eccentricity_std | P_eccentricity_std: The standard deviation of nuclear eccentricity for plasma cells (P). It quantifies the dispersion of eccentricity values, providing a normalized measure of morphological variability within this cell type. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | P_proportion | P_proportion: The normalized proportion of plasma cells (P) in the tissue patch, reflecting their relative contribution among all cell types. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | M_eccentricity_std | M_eccentricity_std: The standard deviation of eccentricity values for macrophages (M). It represents the normalized variability in the nuclear shape of macrophages. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | M_proportion | M_proportion: The normalized fraction of macrophages (M) present in the patch, indicating the relative frequency of these immune cells. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | G_eccentricity_std | G_eccentricity_std: The standard deviation of the eccentricity measurements for granulocytes (G). This parameter measures the spread in nuclear shape values in a normalized way. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | G_proportion | G_proportion: The normalized proportion of granulocytes (G) in the tissue region, used as a weight in composite variability measures. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MFp_eccentricity_std | MFp_eccentricity_std: The standard deviation of nuclear eccentricity for PDPN+ myofibroblasts (MFp). It reflects the variability in nuclear shape for this specialized cell type in a normalized format. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MFp_proportion | MFp_proportion: The normalized fraction of PDPN+ myofibroblasts (MFp) in the patch, highlighting their relative abundance. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MF_eccentricity_std | MF_eccentricity_std: The standard deviation of eccentricity for myofibroblasts (MF). This measure captures the normalized dispersion in the nuclear morphology of these cells. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MF_proportion | MF_proportion: The normalized proportion of myofibroblasts (MF) in the tissue patch, indicating their relative frequency among all cells. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Ff_eccentricity_std | Ff_eccentricity_std: The standard deviation of nuclear eccentricity for FSP1+ fibroblasts (Ff). It assesses the variability in nuclear shape of these fibroblasts in a normalized manner. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Ff_proportion | Ff_proportion: The normalized fraction of FSP1+ fibroblasts (Ff), representing their relative abundance in the analyzed area. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | F_eccentricity_std | F_eccentricity_std: The standard deviation of nuclear eccentricity for fibroblasts (F). This parameter measures the normalized variability in nuclear shape among fibroblasts. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | F_proportion | F_proportion: The normalized proportion of fibroblasts (F) in the tissue patch, used to reflect their relative frequency in the sample. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | E_eccentricity_std | E_eccentricity_std: The standard deviation of the eccentricity values for endothelial cells (E). It provides a normalized measure of the variability in the nuclear morphologies of these cells. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | E_proportion | E_proportion: The normalized proportion of endothelial cells (E) in the patch, representing their relative presence in the tissue. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | A_eccentricity_std | A_eccentricity_std: The standard deviation of nuclear eccentricity for antigen-presenting cells (A). This measure captures the normalized spread in the nuclear shape of these cells. |
| 2uydkrgg0ths | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | A_proportion | A_proportion: The normalized proportion of antigen-presenting cells (A) within the analyzed tissue patch, indicating their relative abundance. |
| 2zxb378zlqny | TU,Tc,Th,Treg,B,P,M,G,E | TU_heterogeneity_index | TU_heterogeneity_index represents the normalized difference in the distribution of epithelial (tumor) cells between the tumor and stroma compartments. It is calculated as the absolute difference between the counts in the two compartments divided by the total count of epithelial cells, ensuring that it is comparable across different patient cases. |
| 2zxb378zlqny | TU,Tc,Th,Treg,B,P,M,G,E | Tc_heterogeneity_index | Tc_heterogeneity_index represents the normalized difference in the distribution of CD8+ T cells between the tumor and stroma compartments. It is computed in a similar manner to reflect the imbalance in these cells across the two regions, making it a normalized metric suitable for cross-case comparisons. |
| 2zxb378zlqny | TU,Tc,Th,Treg,B,P,M,G,E | Th_heterogeneity_index | Th_heterogeneity_index reflects the normalized imbalance in the number of CD4+ T cells distributed between the tumor and stroma compartments. By normalizing the difference between the compartments with the total number of these cells, the metric allows for direct comparisons across different samples. |
| 2zxb378zlqny | TU,Tc,Th,Treg,B,P,M,G,E | Treg_heterogeneity_index | Treg_heterogeneity_index measures the normalized difference in the distribution of regulatory T cells between the tumor and stroma areas. The index is derived by taking the absolute difference in counts between the compartments and dividing by their sum, ensuring its normalized nature. |
| 2zxb378zlqny | TU,Tc,Th,Treg,B,P,M,G,E | B_heterogeneity_index | B_heterogeneity_index quantifies the normalized disparity in the spatial distribution of B cells between the tumor and stroma compartments. The normalization by the total B cell count in both regions makes it a robust measure for comparing different patient cases. |
| 2zxb378zlqny | TU,Tc,Th,Treg,B,P,M,G,E | P_heterogeneity_index | P_heterogeneity_index assesses the normalized difference in the number of plasma cells between the tumor and stroma compartments. The metric is obtained by dividing the absolute difference in plasma cell counts by the total plasma cell count, providing a standardized measure. |
| 2zxb378zlqny | TU,Tc,Th,Treg,B,P,M,G,E | M_heterogeneity_index | M_heterogeneity_index captures the normalized difference in macrophage distribution between the tumor and stroma compartments. By using normalization, it enables comparisons across patches from different tumors regardless of absolute macrophage counts. |
| 2zxb378zlqny | TU,Tc,Th,Treg,B,P,M,G,E | G_heterogeneity_index | G_heterogeneity_index represents the normalized imbalance in the distribution of granulocytes between the tumor and stroma areas. It is computed by comparing the absolute count differences with the total counts, ensuring a normalized metric that is comparable across cases. |
| 2zxb378zlqny | TU,Tc,Th,Treg,B,P,M,G,E | E_heterogeneity_index | E_heterogeneity_index reflects the normalized difference in endothelial cell distribution between the tumor and stroma compartments. This index is calculated by taking the absolute difference in counts divided by the combined count, making it suitable for comparison across different patient images. |
| 2zxb378zlqny | TU,Tc,Th,Treg,B,P,M,G,E | overall_heterogeneity_index | overall_heterogeneity_index is the average of the individual heterogeneity indices from the various cell phenotypes. It provides a combined measure of how unevenly the cell types are distributed between tumor and stroma compartments, thereby serving as a normalized overall metric for tumor-stroma cellular heterogeneity. |
| 344fx24fgauh | A,Tc,Th,Treg,E,M,B,P | APC_density | APC_density quantifies the density of antigen-presenting cells by dividing the number of APCs by the tissue area, providing a normalized measure (cells/μm²) that allows for comparison across different patient cases. |
| 344fx24fgauh | A,Tc,Th,Treg,E,M,B,P | T_cell_infiltration_index | T_cell_infiltration_index measures the proportion of T cells that are located within a threshold distance (20 μm) from the nearest APC. This normalized ratio reflects the degree of T cell coordination with APCs, indicating the strength of the local immune response. |
| 344fx24fgauh | A,Tc,Th,Treg,E,M,B,P | Macrophage_endothelial_adjacency_index | Macrophage_endothelial_adjacency_index represents the proportion of macrophages that are within a set distance (20 μm) from an endothelial cell, offering a normalized metric for assessing the interaction between macrophages and the vascular compartment. |
| 344fx24fgauh | A,Tc,Th,Treg,E,M,B,P | Composite_immune_response_index | Composite_immune_response_index is an integrated score that combines the normalized values of APC density, T cell infiltration index, and macrophage-endothelial adjacency index. It provides a comprehensive measure of the immune response within the tumor microenvironment, facilitating comparison between different patient cases. |
| 39i6b0c4pc96 | F,G,MFp,P,TU | dispersion_factor_all | dispersion_factor_all: This metric measures the overall dispersion of cell spatial distribution within the stroma by calculating the standard deviation of the nearest neighbor distances among all specified cell types combined. It reflects the variability in how cells are spaced relative to each other, making it suitable for comparing different patient cases. |
| 39i6b0c4pc96 | F,G,MFp,P,TU | mean_nn_distance | mean_nn_distance: This parameter represents the average of the nearest neighbor distances among all considered cell types within the stromal microenvironment. It provides a normalized measure of typical cell spacing that can be compared across patches and patient cases. |
| 39i6b0c4pc96 | F,G,MFp,P,TU | median_nn_distance | median_nn_distance: This is the median of all the computed nearest neighbor distances from the specified cell types in the stroma. It provides a robust central value for cell spacing that is less sensitive to extreme values, allowing for effective comparisons. |
| 39i6b0c4pc96 | F,G,MFp,P,TU | min_nn_distance | min_nn_distance: This value indicates the smallest nearest neighbor distance observed among all specified cell types within the stromal region. It reflects the minimum cell-to-cell proximity and is a normalized measure for intra-patch comparisons. |
| 39i6b0c4pc96 | F,G,MFp,P,TU | max_nn_distance | max_nn_distance: This parameter captures the largest nearest neighbor distance among all considered cell types in the stromal area, providing insight into the maximum spatial separation between cells in a patch. |
| 39i6b0c4pc96 | F,G,MFp,P,TU | cv_nn_distance | cv_nn_distance: The coefficient of variation for the nearest neighbor distances, calculated as the ratio of the standard deviation to the mean. This normalized metric offers a dimensionless measure of dispersion that facilitates comparison between different patches and patient samples. |
| 39i6b0c4pc96 | F,G,MFp,P,TU | dispersion_factor_G | dispersion_factor_G: This metric is the standard deviation of the nearest neighbor distances specifically for granulocytes in the stroma. It quantifies the variability in the spatial arrangement of granulocytes across different regions, allowing normalized comparisons. |
| 39i6b0c4pc96 | F,G,MFp,P,TU | dispersion_factor_P | dispersion_factor_P: This parameter calculates the standard deviation of the nearest neighbor distances for plasma cells, reflecting how varied their spatial distribution is within the stromal microenvironment. |
| 39i6b0c4pc96 | F,G,MFp,P,TU | dispersion_factor_F | dispersion_factor_F: This is the standard deviation of the nearest neighbor distances for fibroblasts in the stroma, measuring the heterogeneity of fibroblast spacing in a normalized manner. |
| 39i6b0c4pc96 | F,G,MFp,P,TU | dispersion_factor_MFp | dispersion_factor_MFp: This metric computes the standard deviation of the nearest neighbor distances for PDPN+ myofibroblasts, providing a normalized assessment of spatial dispersion for this specific cell type in the stromal region. |
| 39i6b0c4pc96 | F,G,MFp,P,TU | dispersion_factor_TU | dispersion_factor_TU: This parameter represents the standard deviation of the nearest neighbor distances for tumor cells within the stroma. It captures the variability of tumor cell spacing, making it useful for comparative analysis across cases. |
| 39l9kdzdpkth | Treg,G,Ff,MF,MFp | AGGREGATE_MORPH_SKEWNESS | AGGREGATE_MORPH_SKEWNESS measures the overall asymmetry in the distribution of nucleus areas across five defined cell types. It is obtained by computing the skewness of the nucleus area distribution for each cell type—regulatory T cells, granulocytes, FSP1+ fibroblasts, PDPN- myofibroblasts, and PDPN+ myofibroblasts—and then averaging these values. This metric is used to capture a normalized profile of morphological variance in tumor patches, making it suitable for comparing different patient cases. |
| 39l9kdzdpkth | Treg,G,Ff,MF,MFp | TREG_NUCLEUS_AREA_SKEWNESS | TREG_NUCLEUS_AREA_SKEWNESS quantifies the asymmetry (skewness) of the nucleus area distribution specifically for regulatory T cells. This numeric parameter reflects the extent to which the shape descriptor (nucleus area) deviates from a symmetric distribution in tumor regions. |
| 39l9kdzdpkth | Treg,G,Ff,MF,MFp | GRANULOCYTE_NUCLEUS_AREA_SKEWNESS | GRANULOCYTE_NUCLEUS_AREA_SKEWNESS calculates the skewness of the nucleus area distribution for granulocytes. It numerically represents how asymmetrically the nucleus area values are spread within these immune cells in tumor patches. |
| 39l9kdzdpkth | Treg,G,Ff,MF,MFp | FIBROBLAST_FSP1_NUCLEUS_AREA_SKEWNESS | FIBROBLAST_FSP1_NUCLEUS_AREA_SKEWNESS represents the skewness calculated from the nucleus area distribution of FSP1+ fibroblasts. This parameter highlights the degree of asymmetry in the cell morphology of these fibroblasts, offering a normalized measurement for comparison. |
| 39l9kdzdpkth | Treg,G,Ff,MF,MFp | MYOFIBROBLAST_NUCLEUS_AREA_SKEWNESS | MYOFIBROBLAST_NUCLEUS_AREA_SKEWNESS measures the asymmetry in the distribution of nucleus areas for PDPN- myofibroblasts. As a numeric parameter, it captures the standardized morphological deviations of these cells within the tumor microenvironment. |
| 39l9kdzdpkth | Treg,G,Ff,MF,MFp | MYOFIBROBLAST_PDPN_NUCLEUS_AREA_SKEWNESS | MYOFIBROBLAST_PDPN_NUCLEUS_AREA_SKEWNESS quantifies the skewness of the nucleus area distribution in PDPN+ myofibroblasts. This metric serves as a normalized indicator of the morphological distribution asymmetry in these cells, useful for comparative analysis across patient patches. |
| 3affiadj7277 | TU,MF | MEDIAN_FD_DIFFERENCE | MEDIAN_FD_DIFFERENCE represents the difference between the median fractal dimensions of tumor cell nuclei and PDPN- myofibroblast nuclei within the epithelial region. This parameter quantifies the relative complexity in nuclear architecture between the two cell types by subtracting the median value of myofibroblast fractal dimensions from that of tumor cells. |
| 3affiadj7277 | TU,MF | MEDIAN_TUMOR_FD | MEDIAN_TUMOR_FD measures the median fractal dimension of tumor cell nuclei. It reflects the central tendency of the geometrical complexity of tumor cell nuclear boundaries determined through a box-counting method. |
| 3affiadj7277 | TU,MF | MEDIAN_MYOFIBROBLAST_FD | MEDIAN_MYOFIBROBLAST_FD captures the median fractal dimension of PDPN- myofibroblast nuclei. This statistic summarizes the typical level of nuclear complexity in myofibroblasts using the same fractal analysis approach. |
| 3affiadj7277 | TU,MF | MEAN_TUMOR_FD | MEAN_TUMOR_FD is the average fractal dimension computed for tumor cell nuclei. It provides an overall assessment of the nuclear surface complexity across the tumor cell population. |
| 3affiadj7277 | TU,MF | MEAN_MYOFIBROBLAST_FD | MEAN_MYOFIBROBLAST_FD is the average fractal dimension of PDPN- myofibroblast nuclei. This parameter indicates the overall complexity of myofibroblast nuclear boundaries as derived from the individual measurements. |
| 3affiadj7277 | TU,MF | STD_TUMOR_FD | STD_TUMOR_FD represents the standard deviation of fractal dimensions among tumor cell nuclei. It quantifies the variability in nuclear complexity within the tumor cell group. |
| 3affiadj7277 | TU,MF | STD_MYOFIBROBLAST_FD | STD_MYOFIBROBLAST_FD is the standard deviation of fractal dimensions for PDPN- myofibroblast nuclei, showing how much variation exists in the measured nuclear complexity of these cells. |
| 3affiadj7277 | TU,MF | MAX_TUMOR_FD | MAX_TUMOR_FD is the highest fractal dimension observed among tumor cell nuclei. It indicates the maximum level of geometrical complexity detected in the tumor cells’ nuclear structures. |
| 3affiadj7277 | TU,MF | MIN_MYOFIBROBLAST_FD | MIN_MYOFIBROBLAST_FD is the lowest fractal dimension measured in PDPN- myofibroblast nuclei. This parameter identifies the minimum complexity value, reflecting the simplest nuclear boundary among these cells. |
| 3affiadj7277 | TU,MF | MAX_MYOFIBROBLAST_FD | MAX_MYOFIBROBLAST_FD represents the maximum fractal dimension recorded for PDPN- myofibroblast nuclei, highlighting the peak level of nuclear complexity in the myofibroblast population. |
| 3al07v3wttuk | P,F,MFp,A | MULTICELLULAR_ADJACENCY_RATIO | MULTICELLULAR_ADJACENCY_RATIO measures the proportion of observed physical cell-cell contacts (edges) among the selected cell types relative to the total number of unique possible pairwise contacts among them. This normalized ratio provides a comparative metric across different tumor regions or patient cases, reflecting how frequently the immune and stromal cells are in direct contact. |
| 3al07v3wttuk | P,F,MFp,A | AVG_CONNECTIONS_PER_CELL | AVG_CONNECTIONS_PER_CELL represents the average number of direct connections per cell within the defined group of selected cell types. Calculated as the mean degree in an adjacency graph constructed from detected cell contacts, this normalized value facilitates comparisons in cellular connectivity across various patches or patient samples. |
| 3dkq08lk34xs | TU,Tc,Th,M | SPATIAL_PROXIMITY_INDEX | SPATIAL_PROXIMITY_INDEX represents the average of the proximity ratios calculated for all immune cells in the tissue patch. Each ratio is derived by dividing the distance from an immune cell to the closest tumor cell by the distance from that cell to the nearest blood vessel, providing a normalized measure of spatial association. |
| 3dkq08lk34xs | TU,Tc,Th,M | MIN_PROXIMITY_RATIO | MIN_PROXIMITY_RATIO is the smallest proximity ratio observed among all immune cells, indicating the immune cell that is closest to tumor cells relative to its distance to vessels, which can be crucial for assessing direct tumor-immune interactions. |
| 3dkq08lk34xs | TU,Tc,Th,M | MAX_PROXIMITY_RATIO | MAX_PROXIMITY_RATIO is the highest proximity ratio among the immune cells, reflecting the immune cell with the greatest relative distance from tumor cells when compared to its distance from blood vessels, thus providing a measure of spatial heterogeneity. |
| 3dkq08lk34xs | TU,Tc,Th,M | MEDIAN_PROXIMITY_RATIO | MEDIAN_PROXIMITY_RATIO is the middle value of the proximity ratios when sorted, offering a robust central tendency measure that minimizes the effect of outliers in the spatial relationship data. |
| 3dkq08lk34xs | TU,Tc,Th,M | STD_PROXIMITY_RATIO | STD_PROXIMITY_RATIO quantifies the variability in the proximity ratios across all immune cells. A higher standard deviation indicates greater heterogeneity in the spatial arrangement of immune cells relative to tumor cells and vessels. |
| 3dkq08lk34xs | TU,Tc,Th,M | CD8_PROXIMITY_INDEX | CD8_PROXIMITY_INDEX is the average proximity ratio specifically for CD8+ cytotoxic T cells, calculated using the same method as the overall index. It provides insight into the spatial positioning of these key effector immune cells in relation to tumor cells and vessels. |
| 3dkq08lk34xs | TU,Tc,Th,M | CD4_PROXIMITY_INDEX | CD4_PROXIMITY_INDEX represents the average proximity ratio for CD4+ helper T cells, allowing for analysis of their spatial distribution relative to tumor cells and blood vessels, which can be important for understanding immune coordination. |
| 3dkq08lk34xs | TU,Tc,Th,M | MACROPHAGE_PROXIMITY_INDEX | MACROPHAGE_PROXIMITY_INDEX is the average proximity ratio computed for macrophages. This parameter aids in evaluating the spatial relationship of macrophages to tumor cells and vessels, which may have implications for their dual roles in tumor suppression or promotion. |
| 3dkq08lk34xs | TU,Tc,Th,M | PERCENT_IMMUNE_CELLS_DUAL_PROXIMITY | PERCENT_IMMUNE_CELLS_DUAL_PROXIMITY denotes the percentage of immune cells that are simultaneously within a defined proximity threshold (e.g., 50 micrometers) to both tumor cells and blood vessels. This normalized percentage highlights regions where immune-tumor interactions might be actively influenced by vascular supply. |
| 3f77atattshr | TU,MFp,M,Treg | MEAN_ORIENTATION_DIFF | MEAN_ORIENTATION_DIFF represents the average angular difference in degrees between the main orientation of spatially clustered tumor cells and PDPN+ myofibroblasts. It captures how aligned or misaligned these clusters are, providing an indication of the spatial relationship that may impact tumor progression. |
| 3f77atattshr | TU,MFp,M,Treg | WEIGHTED_MEAN_ORIENTATION_DIFF | WEIGHTED_MEAN_ORIENTATION_DIFF is a similar measure to the mean orientation difference, but it adjusts the metric according to the local immune context. Specifically, it weights each cluster pair’s orientation difference based on the local counts of macrophages and regulatory T cells, thereby incorporating the influence of the immune microenvironment on cell cluster alignment. |
| 3f77atattshr | TU,MFp,M,Treg | MAX_ORIENTATION_DIFF | MAX_ORIENTATION_DIFF denotes the maximum angular difference observed among all matched tumor-myofibroblast cluster pairs in a given patch. This parameter highlights the most extreme case of misalignment, which may be relevant for identifying regions with significant spatial heterogeneity. |
| 3f77atattshr | TU,MFp,M,Treg | MIN_ORIENTATION_DIFF | MIN_ORIENTATION_DIFF indicates the minimum angular difference among the matched cluster pairs. It reflects the closest alignment between tumor cell clusters and PDPN+ myofibroblast clusters and serves to identify areas where spatial organization is highly coordinated. |
| 3fb3v1hkjko0 | MF | MEDIAN_MIN_DISTANCE_PDPN_NEG_MF_TO_VESSELS | MEDIAN_MIN_DISTANCE_PDPN_NEG_MF_TO_VESSELS represents the median of the minimal Euclidean distances (measured in micrometers) from each PDPN-negative myofibroblast located in the stromal compartment to its nearest blood vessel. This parameter quantifies how close these myofibroblasts are to vascular structures, potentially indicating their influence on angiogenesis and tumor progression. The metric is computed on a per-patient (or per-patch within a whole-slide image) basis, making it normalized and suitable for comparative analysis across different patient cases. |
| 3hgve6x1jdj7 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | TU_deviation_index | TU_deviation_index measures the average absolute deviation of tumor cell (TU) spatial neighbors from what would be expected under a random distribution, normalizing the difference by the standard deviation from simulated random placements, thereby indicating the extent of non-random spatial organization in tumor regions. |
| 3hgve6x1jdj7 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | M_deviation_index | M_deviation_index quantifies the average absolute deviation for macrophages (M), computed by comparing the observed proximal co-localizations with other cell types against a randomized cell spatial simulation, providing a normalized metric that reflects their spatial interaction strength. |
| 3hgve6x1jdj7 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MF_deviation_index | MF_deviation_index assesses the deviation of myofibroblasts (MF) based on the difference between observed average neighboring cell counts and the average from simulated random distributions, normalized by the simulation’s standard deviation, which reflects non-random spatial patterning. |
| 3hgve6x1jdj7 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Tc_deviation_index | Tc_deviation_index is a normalized metric for cytotoxic T cells (Tc) that represents the average absolute deviation from a random spatial arrangement with other cell populations, indicating their potential involvement in structured spatial interactions. |
| 3hgve6x1jdj7 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | F_deviation_index | F_deviation_index calculates the normalized average absolute deviation for normal fibroblasts (F) by comparing their observed spatial proximities with those obtained from a randomized distribution, thus reflecting their degree of organized spatial arrangement. |
| 3hgve6x1jdj7 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | G_deviation_index | G_deviation_index evaluates the granulocyte (G) spatial distribution by measuring the absolute deviation from a randomly simulated neighborhood count and normalizing this deviation, thereby indicating the presence of distinct spatial organization patterns. |
| 3hgve6x1jdj7 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | E_deviation_index | E_deviation_index quantifies the degree of spatial organization for endothelial cells (E) by comparing observed neighbor counts with those from a simulation of random cell placement, normalizing the difference to reveal how distinctly these cells are spatially arranged. |
| 3hgve6x1jdj7 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | B_deviation_index | B_deviation_index measures the spatial co-localization deviation for B cells (B) by comparing their observed average number of neighboring cells with simulated values from random distributions, resulting in a normalized metric that indicates their non-random spatial interaction. |
| 3hgve6x1jdj7 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Th_deviation_index | Th_deviation_index represents the average normalized deviation for T helper cells (Th), computed as the absolute difference between observed and simulated neighbor counts divided by the simulation’s standard deviation, reflecting their distinct spatial co-localization patterns. |
| 3hgve6x1jdj7 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Ff_deviation_index | Ff_deviation_index indicates the normalized average absolute deviation for FSP1 positive fibroblasts (Ff) by comparing observed spatial neighbor counts with those generated from a randomized simulation, thereby measuring the strength of their non-random spatial interactions. |
| 3hgve6x1jdj7 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | A_deviation_index | A_deviation_index measures the deviation for antigen presenting cells (A) by assessing the absolute difference between observed and simulated average neighboring cell counts, normalized by the standard deviation of the simulation, which reflects their spatial organizational behavior. |
| 3hgve6x1jdj7 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MFp_deviation_index | MFp_deviation_index quantifies the spatial organization of myofibroblasts with high PDPN expression (MFp) by calculating the normalized absolute deviation from random cell distribution in terms of neighboring counts, indicating potential biological structuring. |
| 3hgve6x1jdj7 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Treg_deviation_index | Treg_deviation_index represents the normalized deviation for regulatory T cells (Treg) by measuring the difference between observed and simulated neighbor counts, normalized by the standard deviation in the simulation, thereby providing insight into their spatial arrangement. |
| 3hgve6x1jdj7 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | P_deviation_index | P_deviation_index reflects the average normalized absolute deviation for plasma cells (P) by comparing observed co-localization with randomized placements, which highlights their tendency to exhibit non-random spatial distributions. |
| 3hgve6x1jdj7 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | overall_deviation_index | overall_deviation_index is an aggregate measure that computes the overall degree of non-random spatial co-localization across all cell types within a patch by averaging the individual cell type deviation indices, thereby providing a comprehensive numeric summary of spatial organization. |
| 3hra4ynmhmzg | TU,Treg,M,Ff | median_indentation_tumor_cells | Median indentation depth for tumor cells, representing the central value of the differences computed between the convex hull area and the actual nuclear polygon area for tumor cells located in the epithelial compartment. This measurement quantifies nuclear shape irregularities and is appropriate for comparing distinct patient cases as it is derived from a normalization process (median of individual measurements within patches). |
| 3hra4ynmhmzg | TU,Treg,M,Ff | median_indentation_macrophages | Median indentation depth for macrophages, representing the central value of the differences computed between the convex hull area and the actual nuclear polygon area for macrophages located in the epithelial compartment. This provides a normalized numeric metric of macrophage nuclear indentation that facilitates comparison between different patient cases. |
| 3idezu06grd2 | Tc | mean_fractal_dimension | mean_fractal_dimension represents the average fractal dimension calculated from the nuclear boundaries of cytotoxic T cells located in the stromal compartment. This parameter quantifies the overall geometric complexity of the cell nuclei, providing insights into the irregular and intricate nature of the cytotoxic T cell membrane, and is normalized for comparison across different patient cases. |
| 3idezu06grd2 | Tc | std_fractal_dimension | std_fractal_dimension is the standard deviation of the fractal dimensions computed for each cytotoxic T cell in the stroma. It measures the variability or spread in the complexity of the nuclear boundaries among these cells, serving as an indicator of heterogeneity in nuclear morphology across different regions. |
| 3idezu06grd2 | Tc | min_fractal_dimension | min_fractal_dimension indicates the lowest fractal dimension value observed among the cytotoxic T cell nuclei in the stromal compartment. This parameter identifies the cell with the least complex nuclear boundary, providing a lower bound for the set of complexity measurements in a given tumor patch. |
| 3idezu06grd2 | Tc | max_fractal_dimension | max_fractal_dimension indicates the highest fractal dimension value observed among the cytotoxic T cell nuclei in the stromal compartment. It identifies the cell with the most complex nuclear boundary, establishing an upper bound for the complexity measurements in a given tumor patch. |
| 3k7q3ovtms3h | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff | silhouette_score | The silhouette_score parameter measures the overall quality of spatial clustering by quantifying how well-defined the clusters are. It is derived from the spatial coordinates of selected cell types and reflects the distinctness of the clusters, with values ranging between -1 and 1. Higher values indicate better-defined clusters and more distinct microenvironment niches, making this parameter normalized and suitable for comparing different patient cases. |
| 3lpt42dyr5yq | TU,Tc,B,P,M,MFp,MF,Ff,E,A | TU_infiltration_index | TU_infiltration_index represents the area-normalized infiltration index for epithelial cells (TU) within the stromal compartment. It is calculated by dividing the count of epithelial cells by the total stromal area in pixels, thus allowing comparison across patient cases. |
| 3lpt42dyr5yq | TU,Tc,B,P,M,MFp,MF,Ff,E,A | Tc_infiltration_index | Tc_infiltration_index represents the area-normalized infiltration index for CD8+ T cells (Tc) within the stromal compartment. It normalizes the cell count by the stromal area, enabling cross-sample comparisons. |
| 3lpt42dyr5yq | TU,Tc,B,P,M,MFp,MF,Ff,E,A | B_infiltration_index | B_infiltration_index represents the area-normalized infiltration index for B cells (B) within the stromal compartment. This index is computed by dividing the B cell count by the stromal area, ensuring it is comparable between different patient cases. |
| 3lpt42dyr5yq | TU,Tc,B,P,M,MFp,MF,Ff,E,A | P_infiltration_index | P_infiltration_index represents the area-normalized infiltration index for plasma cells (P) in the stromal compartment. It is derived by normalizing the plasma cell count to the stromal area, making the metric usable for comparative analysis. |
| 3lpt42dyr5yq | TU,Tc,B,P,M,MFp,MF,Ff,E,A | M_infiltration_index | M_infiltration_index represents the area-normalized infiltration index for macrophages (M) in the stromal compartment. It is the result of dividing the macrophage count by the stromal area, ensuring a standardized measure across patches. |
| 3lpt42dyr5yq | TU,Tc,B,P,M,MFp,MF,Ff,E,A | MFp_infiltration_index | MFp_infiltration_index represents the area-normalized infiltration index for PDPN+ myofibroblasts (MFp) within the stromal compartment. By normalizing the count to the stromal area, this index allows for consistent comparison between different tumor regions. |
| 3lpt42dyr5yq | TU,Tc,B,P,M,MFp,MF,Ff,E,A | MF_infiltration_index | MF_infiltration_index represents the area-normalized infiltration index for myofibroblasts (MF) in the stromal compartment. It is calculated by dividing the cell count by the stromal area, which facilitates meaningful comparisons across patients. |
| 3lpt42dyr5yq | TU,Tc,B,P,M,MFp,MF,Ff,E,A | Ff_infiltration_index | Ff_infiltration_index represents the area-normalized infiltration index for FSP1+ fibroblasts (Ff) within the stromal compartment. Normalizing the fibroblast count by the stromal area makes the parameter comparable between different patient cases. |
| 3lpt42dyr5yq | TU,Tc,B,P,M,MFp,MF,Ff,E,A | E_infiltration_index | E_infiltration_index represents the area-normalized infiltration index for endothelial cells (E) in the stromal compartment. It is computed by dividing the count of endothelial cells by the stromal area, thus providing a normalized measure for analysis. |
| 3lpt42dyr5yq | TU,Tc,B,P,M,MFp,MF,Ff,E,A | A_infiltration_index | A_infiltration_index represents the area-normalized infiltration index for antigen presenting cells (A) within the stromal compartment. This index divides the APC count by the stromal area, ensuring a normalized metric that can be compared across cases. |
| 3lpt42dyr5yq | TU,Tc,B,P,M,MFp,MF,Ff,E,A | global_immuno_fibroblastic_infiltration_index | global_immuno_fibroblastic_infiltration_index is the overall normalized index that combines the infiltration indices of all the examined cell types in the stromal compartment. By summing the individual normalized indices, it represents the cumulative level of immuno-fibroblastic infiltration, aiding in the assessment of tumor microenvironment differences across patient cases. |
| 3pwmrh3eiseo | Treg,F,A,E | Fibroblast_radial_infiltration_ratio | Fibroblast_radial_infiltration_ratio measures the relative density of fibroblasts (identified as FSP1- fibroblasts) in the inner tumor region compared to the outer region. The inner region is defined as the area within a radius that is half of the maximum distance from the tumor center, while the outer region covers the remaining area up to the maximum distance. This ratio is normalized by dividing the inner density (cells per unit area) by the outer density, providing a standardized measure that can be compared across different patient samples. |
| 3pwmrh3eiseo | Treg,F,A,E | APCell_radial_infiltration_ratio | APCell_radial_infiltration_ratio assesses the spatial distribution of antigen presenting cells by comparing their density in the inner tumor region to that in the outer tumor region. The ratio is computed by dividing the density of antigen presenting cells within the central area (using a defined radius threshold) by the density found in the peripheral area. This normalized ratio reflects immune activation gradients within the tumor and allows for comparison between patient cases. |
| 3pwmrh3eiseo | Treg,F,A,E | Endothelial_radial_infiltration_ratio | Endothelial_radial_infiltration_ratio quantifies the concentration of endothelial cells, indicative of vascular support, by comparing their density in the tumor core to that in its periphery. It is calculated as the ratio of the density of endothelial cells in the inner region (determined by a radial threshold from the tumor centroid) to that in the outer region. This normalized metric provides insight into the vascular distribution patterns within tumors across different patient samples. |
| 3qe1q9vezfym | E,Tc,Th,Treg,MFp,MF,Ff,F,G | fsp1_to_normal_ratio_bin1 | fsp1_to_normal_ratio_bin1 measures the ratio between the number of FSP1 positive fibroblasts and normal fibroblasts within the first defined distance bin from endothelial cells. It provides a normalized metric accounting for biological differences in cell subtype distribution across tumor patches. |
| 3qe1q9vezfym | E,Tc,Th,Treg,MFp,MF,Ff,F,G | fsp1_to_normal_ratio_bin2 | fsp1_to_normal_ratio_bin2 measures the ratio between the number of FSP1 positive fibroblasts and normal fibroblasts within the second distance bin from endothelial cells, allowing for comparison of fibroblast subtype dynamics in spatially distinct regions. |
| 3qe1q9vezfym | E,Tc,Th,Treg,MFp,MF,Ff,F,G | fsp1_to_normal_ratio_bin3 | fsp1_to_normal_ratio_bin3 measures the ratio between the number of FSP1 positive fibroblasts and normal fibroblasts within the third distance bin from endothelial cells, offering a normalized view of cell subtype proportions at an intermediate spatial range. |
| 3qe1q9vezfym | E,Tc,Th,Treg,MFp,MF,Ff,F,G | fsp1_to_normal_ratio_bin4 | fsp1_to_normal_ratio_bin4 measures the ratio between the number of FSP1 positive fibroblasts and normal fibroblasts within the fourth distance bin from endothelial cells, facilitating comparative analysis across tumor patches. |
| 3qe1q9vezfym | E,Tc,Th,Treg,MFp,MF,Ff,F,G | fsp1_to_normal_ratio_bin5 | fsp1_to_normal_ratio_bin5 measures the ratio between the number of FSP1 positive fibroblasts and normal fibroblasts within the fifth distance bin from endothelial cells, representing the spatial gradient at the farthest range from vascular structures. |
| 3qe1q9vezfym | E,Tc,Th,Treg,MFp,MF,Ff,F,G | tcell_to_fibroblast_ratio_bin1 | tcell_to_fibroblast_ratio_bin1 represents the normalized ratio of total T cells (combining CD8, CD4, and regulatory T cells) to the combined amount of fibroblast subtypes (FSP1 positive, normal, and PDPN positive myofibroblasts) in the first distance bin from endothelial cells. This ratio facilitates cross-case comparisons of immune to stromal cell balance. |
| 3qe1q9vezfym | E,Tc,Th,Treg,MFp,MF,Ff,F,G | tcell_to_fibroblast_ratio_bin2 | tcell_to_fibroblast_ratio_bin2 represents the normalized ratio of total T cells to the total fibroblast count in the second distance bin from endothelial cells, reflecting the relationship between immune infiltration and stromal components in that spatial segment. |
| 3qe1q9vezfym | E,Tc,Th,Treg,MFp,MF,Ff,F,G | tcell_to_fibroblast_ratio_bin3 | tcell_to_fibroblast_ratio_bin3 represents the normalized ratio of total T cells to total fibroblasts in the third distance bin from endothelial cells, providing insights into the immune-stroma interaction in regions with mid-range distance from vascular features. |
| 3qe1q9vezfym | E,Tc,Th,Treg,MFp,MF,Ff,F,G | tcell_to_fibroblast_ratio_bin4 | tcell_to_fibroblast_ratio_bin4 represents the normalized ratio of total T cells to total fibroblasts in the fourth distance bin from endothelial cells, allowing comparisons of T cell infiltration relative to fibroblast density in that spatial zone. |
| 3qe1q9vezfym | E,Tc,Th,Treg,MFp,MF,Ff,F,G | tcell_to_fibroblast_ratio_bin5 | tcell_to_fibroblast_ratio_bin5 represents the normalized ratio of total T cells to total fibroblasts in the fifth distance bin from endothelial cells, offering a normalized metric of the immune to stromal cell balance in the most distal spatial compartment. |
| 3v7aokjwif9r | M | percent_macrophages_in_clusters | percent_macrophages_in_clusters: This parameter represents the percentage of tumor-adjacent macrophages that are incorporated into identified clusters. It is derived by dividing the number of macrophages that have been grouped in clusters (excluding isolated cells marked by DBSCAN) by the total number of macrophages located within the tumor-adjacent stroma, and then multiplying by 100. Being a percentage, this metric is normalized, allowing for consistent comparisons across different patient cases. |
| 3v7aokjwif9r | M | mean_intercluster_distance | mean_intercluster_distance: This parameter measures the average Euclidean distance between the centroids of macrophage clusters identified within the tumor-adjacent stroma. Each cluster’s centroid is determined by averaging the spatial coordinates of the macrophages within it. The average of all pairwise distances among these centroids provides a normalized measure of how spread out the clusters are, enabling comparisons between different patches or patient samples. |
| 3v7aokjwif9r | M | min_intercluster_distance | min_intercluster_distance: This parameter indicates the smallest Euclidean distance recorded between any two distinct macrophage cluster centroids. By evaluating the pairwise distances between all clusters and selecting the minimum (excluding self-distances), the parameter offers insights into the closest spatial proximity among clusters. Its normalized nature makes it useful for comparing spatial patterns across different patient cases. |
| 3wmxbazni5rk | B | B_CELL_EPITHELIAL_PERIMETER_MEAN | B_CELL_EPITHELIAL_PERIMETER_MEAN measures the average perimeter length of B lymphocyte nuclei located within the epithelial (tumor) compartments. It provides an indication of the typical nucleus size in micrometers and allows comparison across different patient cases due to its derivation as an average value. |
| 3wmxbazni5rk | B | B_CELL_EPITHELIAL_PERIMETER_STD | B_CELL_EPITHELIAL_PERIMETER_STD quantifies the variability of the perimeter measurements of B cell nuclei within the epithelial regions. It represents the standard deviation in micrometers, offering insight into the dispersion of nucleus sizes in each analyzed patch. |
| 3wmxbazni5rk | B | B_CELL_EPITHELIAL_PERIMETER_CV | B_CELL_EPITHELIAL_PERIMETER_CV is the coefficient of variation calculated as the ratio of the standard deviation to the mean (with a small epsilon added to avoid division by zero). It is a dimensionless number that provides a normalized measure of the variability relative to the average perimeter. |
| 3wmxbazni5rk | B | B_CELL_EPITHELIAL_PERIMETER_MIN | B_CELL_EPITHELIAL_PERIMETER_MIN identifies the smallest perimeter value among the B cell nuclei in the epithelial compartments. This parameter helps define the lower bound of nucleus size distribution within each analyzed tumor patch. |
| 3wmxbazni5rk | B | B_CELL_EPITHELIAL_PERIMETER_MAX | B_CELL_EPITHELIAL_PERIMETER_MAX identifies the largest perimeter measurement of B cell nuclei in epithelial compartments, providing the upper bound of the size distribution in micrometers. |
| 3wmxbazni5rk | B | B_CELL_EPITHELIAL_PERIMETER_MEDIAN | B_CELL_EPITHELIAL_PERIMETER_MEDIAN represents the median value of the nucleus perimeters of epithelial B cells. It serves as a robust central tendency measure for comparing different patient's tumor patches. |
| 44kfxxutkoo9 | Tc,Th,Treg,B,P,M,G,MF,Ff,A | t_cell_cd8_outlier_fraction | t_cell_cd8_outlier_fraction: This parameter measures the proportion of CD8+ cytotoxic T cells that are identified as morphological outliers. The fraction is calculated by dividing the number of outlier cells, as determined by a robust Mahalanobis distance computed from area, eccentricity, and convexity of the cell polygon, by the total number of CD8+ cells. This normalization allows for comparison across different patient cases. |
| 44kfxxutkoo9 | Tc,Th,Treg,B,P,M,G,MF,Ff,A | t_cell_cd4_outlier_fraction | t_cell_cd4_outlier_fraction: This parameter represents the normalized fraction of CD4+ helper T cells exhibiting extreme morphological characteristics relative to the total number of CD4+ cells. It reflects the deviation in shape, size, and elongation by comparing robustly estimated Mahalanobis distances against a threshold based on a chi-square distribution. |
| 44kfxxutkoo9 | Tc,Th,Treg,B,P,M,G,MF,Ff,A | b_cell_outlier_fraction | b_cell_outlier_fraction: This metric indicates the fraction of B cells that are considered morphological outliers. It is derived by applying a multidimensional outlier detection method on features like cell area, eccentricity, and convexity, and then normalizing by the total B cell count in a given tumor patch. |
| 44kfxxutkoo9 | Tc,Th,Treg,B,P,M,G,MF,Ff,A | plasma_cell_outlier_fraction | plasma_cell_outlier_fraction: This parameter quantifies the proportion of plasma cells with unusual morphological features. The outlier detection is performed using robust covariance estimation and Mahalanobis distance, ensuring the fraction is normalized to enable comparison among different tumor regions. |
| 44kfxxutkoo9 | Tc,Th,Treg,B,P,M,G,MF,Ff,A | macrophage_outlier_fraction | macrophage_outlier_fraction: This value represents the normalized fraction of macrophages identified as outliers based on deviations in area, eccentricity, and convexity. It is calculated by dividing the number of outlier macrophages by the total count, facilitating consistent comparison across patient cases. |
| 44kfxxutkoo9 | Tc,Th,Treg,B,P,M,G,MF,Ff,A | myofibroblast_outlier_fraction | myofibroblast_outlier_fraction: This metric measures the fraction of myofibroblasts that have abnormal morphological attributes, determined via robust statistical methods. Being a normalized fraction, it reflects the ratio of outliers to total myofibroblasts in a tumor patch. |
| 44kfxxutkoo9 | Tc,Th,Treg,B,P,M,G,MF,Ff,A | fibroblast_fsp1_outlier_fraction | fibroblast_fsp1_outlier_fraction: This parameter indicates the proportion of FSP1+ fibroblasts that are classified as morphological outliers using features such as area, eccentricity, and convexity. The normalization process allows for comparisons across different cases by providing a ratio of outlier cells to the total count. |
| 44kfxxutkoo9 | Tc,Th,Treg,B,P,M,G,MF,Ff,A | ap_cell_outlier_fraction | ap_cell_outlier_fraction: This metric represents the normalized fraction of antigen presenting cells showing atypical morphological features. It is computed by evaluating the logical deviation using robust Mahalanobis distance metric and then dividing the resulting count by the total APC count in the region. |
| 4550ui5gpkp7 | A,Ff | APC_mean_vessel_distance | APC_mean_vessel_distance: Represents the average distance from the center of antigen presenting cells (APCs) in the stromal compartment to the nearest blood vessel, providing an estimate of how proximally these cells are located to the vascular network. |
| 4550ui5gpkp7 | A,Ff | FSP1_mean_vessel_distance | FSP1_mean_vessel_distance: Denotes the average distance from FSP1+ fibroblasts in the stromal region to the closest vessel, illustrating the vessel proximity for this cell type. |
| 4550ui5gpkp7 | A,Ff | APC_mean_epithelial_distance | APC_mean_epithelial_distance: Measures the average distance from APC cell centroids to the epithelial boundary (the interface between tumor and stroma), reflecting their spatial separation from the tumor mass. |
| 4550ui5gpkp7 | A,Ff | FSP1_mean_epithelial_distance | FSP1_mean_epithelial_distance: Indicates the average distance from FSP1+ fibroblast centroids to the epithelial boundary, portraying their overall positioning relative to the tumor edge. |
| 4550ui5gpkp7 | A,Ff | APC_mean_adjusted_distance | APC_mean_adjusted_distance: Computes the average vessel distance for APCs after adjusting for the distance to the epithelial boundary, thereby normalizing the vessel proximity measurement by accounting for epithelial influence. |
| 4550ui5gpkp7 | A,Ff | FSP1_mean_adjusted_distance | FSP1_mean_adjusted_distance: Represents the average adjusted vessel distance for FSP1+ fibroblasts, where the raw vessel distance is corrected by subtracting the proximity to the epithelial boundary. |
| 4550ui5gpkp7 | A,Ff | diff_mean_adjusted_distance | diff_mean_adjusted_distance: Reflects the difference between the mean adjusted vessel distances of APCs and FSP1+ fibroblasts, enabling a comparative analysis of their spatial distribution relative to the vasculature after correcting for epithelial boundary effects. |
| 4550ui5gpkp7 | A,Ff | APC_median_vessel_distance | APC_median_vessel_distance: Captures the median distance from APC cells to the nearest vessel, offering a robust measure that minimizes the influence of extreme values in vessel proximity. |
| 4550ui5gpkp7 | A,Ff | FSP1_median_vessel_distance | FSP1_median_vessel_distance: Denotes the median vessel distance for FSP1+ fibroblasts, serving as a central tendency measure of the spacing between these cells and the vessels. |
| 4550ui5gpkp7 | A,Ff | APC_median_epithelial_distance | APC_median_epithelial_distance: Provides the median distance from APCs to the epithelial boundary, summarizing the typical spatial relationship between these cells and the tumor-stroma interface. |
| 4550ui5gpkp7 | A,Ff | FSP1_median_epithelial_distance | FSP1_median_epithelial_distance: Represents the median distance from FSP1+ fibroblasts to the epithelial boundary, indicating the common separation value for these cells relative to tumor boundaries. |
| 4550ui5gpkp7 | A,Ff | APC_median_adjusted_distance | APC_median_adjusted_distance: Indicates the median vessel distance for APCs after adjusting for the distance to the epithelial boundary, yielding a robust metric for vessel proximity that is normalized against epithelial influence. |
| 4550ui5gpkp7 | A,Ff | FSP1_median_adjusted_distance | FSP1_median_adjusted_distance: Measures the median adjusted vessel distance for FSP1+ fibroblasts, computed by deducting the epithelial boundary distance from the raw vessel distance, to accurately reflect the spatial dynamics of these cells. |
| 4550ui5gpkp7 | A,Ff | diff_median_adjusted_distance | diff_median_adjusted_distance: Represents the difference between the median adjusted vessel distances of APCs and FSP1+ fibroblasts, thereby providing a comparative measure of how the two cell types differ in their vascular infiltration after adjusting for epithelial proximity. |
| 486cmyocoqia | M | MEAN_DISTANCE_MACROPHAGE_TO_TUMOR | MEAN_DISTANCE_MACROPHAGE_TO_TUMOR: Represents the average distance, measured in micrometers, from each macrophage located in the stromal compartment to the closest point on the tumor boundary. This parameter provides a normalized measure to compare spatial distributions across different patient cases. |
| 486cmyocoqia | M | MIN_DISTANCE_MACROPHAGE_TO_TUMOR | MIN_DISTANCE_MACROPHAGE_TO_TUMOR: Denotes the smallest distance, in micrometers, recorded between any macrophage in the stroma and the tumor boundary. It highlights the point of closest proximity, serving as an indicator of potential focal interaction zones. |
| 486cmyocoqia | M | MAX_DISTANCE_MACROPHAGE_TO_TUMOR | MAX_DISTANCE_MACROPHAGE_TO_TUMOR: Captures the greatest distance, measured in micrometers, from a macrophage in the stroma to the tumor boundary. This value helps to assess the extent of macrophage dispersion relative to tumor margin. |
| 486cmyocoqia | M | STD_DISTANCE_MACROPHAGE_TO_TUMOR | STD_DISTANCE_MACROPHAGE_TO_TUMOR: Measures the standard deviation of the distances (in micrometers) between stromal macrophages and the tumor boundary. This parameter reflects the variability and heterogeneity in the spatial relationships, allowing for normalized comparisons between cases. |
| 486cmyocoqia | M | MEDIAN_DISTANCE_MACROPHAGE_TO_TUMOR | MEDIAN_DISTANCE_MACROPHAGE_TO_TUMOR: Indicates the median distance, in micrometers, from stromal macrophages to the nearest tumor boundary. As a robust central tendency measure, it offers insight into the typical spatial arrangement of macrophages relative to tumor regions across different patient images. |
| 4egtw50tragu | Tc | MEAN_ASPECT_RATIO_CD8_TCELL_STROMA | MEAN_ASPECT_RATIO_CD8_TCELL_STROMA measures the average elongation of cytotoxic T lymphocyte nuclei in the stromal compartment by calculating the ratio of the major axis to the minor axis of the minimum rotated bounding rectangle that encloses each cell. The value is computed for each cell and then averaged per tumor patch, making it a normalized, numeric parameter that enables comparisons across different patient cases. |
| 4gq9r4y9arl8 | MFp,MF | density_ratio | density_ratio represents the normalized ratio of PDPN+ to PDPN- myofibroblasts near the epithelial-stromal interface. It is calculated by dividing the count of PDPN+ myofibroblasts by the count of PDPN- myofibroblasts, adjusted by a small constant to avoid division by zero. This ratio provides a comparative measure across different patient cases, making it suitable for cross-sample analysis despite variability in the raw cell counts. |
| 4kawhse2nx3a | Tc | proportion_clustered_t_cell_cd8 | The parameter 'proportion_clustered_t_cell_cd8' represents the normalized ratio of cytotoxic T lymphocytes (CD8+) in the stromal compartments that are part of multi-cell clusters. It is calculated by dividing the number of T cells within clusters (clusters defined as groups comprising two or more adjacent cells) by the total number of cytotoxic T cells in the stroma from a given tumor patch. This ratio allows for the comparison of clustering behavior across different patient cases and regions, as it is independent of the overall cell count. |
| 4kdypi1v9imp | Th,TU | MEDIAN_ROUNDNESS_T_HELPER | MEDIAN_ROUNDNESS_T_HELPER represents the median nuclear roundness of T helper cells in the stromal region. It is computed as the ratio of the minor axis length to the major axis length from the cell's minimum rotated rectangle, resulting in a normalized value between 0 and 1 where values closer to 1 indicate a rounder nucleus. |
| 4kdypi1v9imp | Th,TU | MEDIAN_ROUNDNESS_TUMOR | MEDIAN_ROUNDNESS_TUMOR represents the median nuclear roundness of tumor cells (epithelial cells) in the stromal region. Like the T helper cell metric, it is derived from the ratio of the minor to major axis lengths, yielding a normalized score between 0 and 1 that facilitates comparisons between patient cases. |
| 4kdypi1v9imp | Th,TU | ROUNDNESS_DIFFERENCE | ROUNDNESS_DIFFERENCE is calculated by subtracting the median roundness of tumor cells from that of T helper cells. This normalized value indicates whether T helper cells have a rounder nuclear morphology compared to tumor cells, with positive values signifying a higher roundness in T helper cells. |
| 4krjob0nfjbg | TU,Tc,Treg,B,P,M,Ff,F | fibroblast_FSP1_fraction | fibroblast_FSP1_fraction is a normalized metric representing the proportion of fibroblasts that are positive for the FSP1 marker. It is calculated by dividing the number of FSP1+ fibroblasts by the total count of fibroblast cells, allowing for comparisons across different patient cases or regions. |
| 4krjob0nfjbg | TU,Tc,Treg,B,P,M,Ff,F | tumor_immune_contact_fraction | tumor_immune_contact_fraction is a normalized parameter that quantifies the fraction of tumor cells that are in direct proximity to immune cells. It is determined by identifying tumor cells that have any immune cell (such as T cells, B cells, plasma cells, or macrophages) within 30 micrometers, and then calculating the ratio of these tumor cells to the total number of tumor cells. |
| 4krjob0nfjbg | TU,Tc,Treg,B,P,M,Ff,F | infiltration_ratio | infiltration_ratio is a composite, normalized measure that integrates the inflammatory profile of the tumor microenvironment. It is computed as the average of the fibroblast_FSP1_fraction and the tumor_immune_contact_fraction, providing a single metric to represent the combined extent of fibroblast FSP1 expression and tumor-immune cell interactions. |
| 4n66rlby59bp | M,Treg,Ff,MFp | CV_MACROPHAGE_NUCLEAR_ROUNDNESS | The CV_MACROPHAGE_NUCLEAR_ROUNDNESS parameter represents the coefficient of variation of the nuclear roundness values for macrophages located in stromal regions that include regulatory T lymphocytes (Tregs), FSP1+ fibroblasts, and PDPN+ myofibroblasts. It is calculated by first selecting stromal cells, confirming the presence of the required cell types to ensure the analysis is applicable, and then isolating macrophages from these regions. For each macrophage, the nuclear roundness is determined using the formula: (4 * π * area) / (perimeter^2), where area and perimeter are derived from the cell’s nuclear geometry. The parameter is then computed as the ratio of the standard deviation to the mean of these roundness values, ensuring normalization across different patient cases and image patches. This metric is numeric and normalized, suitable for comparing heterogeneity in macrophage nuclear morphology across tissue samples. |
| 4qacrli1tavl | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | epithelial_cell_mean_perimeter | epithelial_cell_mean_perimeter: Represents the average perimeter length of the nucleus polygons for all epithelial (tumor) cells, providing a normalized measurement of nuclear boundary size for comparison across different regions. |
| 4qacrli1tavl | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | t_cell_cd8_mean_perimeter | t_cell_cd8_mean_perimeter: Represents the average perimeter length of the nucleus polygons for all CD8+ T cells, capturing nuclear morphological features in a normalized numeric form. |
| 4qacrli1tavl | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | t_cell_cd4_mean_perimeter | t_cell_cd4_mean_perimeter: Represents the average perimeter length of the nucleus polygons for all CD4+ helper T cells, ensuring a normalized measurement for cross-case comparison. |
| 4qacrli1tavl | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | t_cell_reg_mean_perimeter | t_cell_reg_mean_perimeter: Represents the average perimeter length of the nucleus polygons for all regulatory T cells, providing a numeric and normalized parameter indicative of nuclear structure. |
| 4qacrli1tavl | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | b_cell_mean_perimeter | b_cell_mean_perimeter: Represents the average perimeter length of the nucleus polygons for all B cells, serving as a normalized metric for analyzing nuclear boundaries. |
| 4qacrli1tavl | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | plasma_cell_mean_perimeter | plasma_cell_mean_perimeter: Represents the average perimeter length of the nucleus polygons for all plasma cells, offering a numeric measurement that is normalized for comparative purposes. |
| 4qacrli1tavl | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | macrophage_mean_perimeter | macrophage_mean_perimeter: Represents the average perimeter length of the nucleus polygons for all macrophages, providing a normalized parameter to assess nuclear morphology across patches. |
| 4qacrli1tavl | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | granulocyte_mean_perimeter | granulocyte_mean_perimeter: Represents the average perimeter length of the nucleus polygons for all granulocytes, delivering a normalized numerical value for nuclear size. |
| 4qacrli1tavl | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | myofibroblast_pdpn_mean_perimeter | myofibroblast_pdpn_mean_perimeter: Represents the average perimeter length of the nucleus polygons for PDPN-positive myofibroblasts, offering a normalized and numeric metric of nuclear morphology. |
| 4qacrli1tavl | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | myofibroblast_mean_perimeter | myofibroblast_mean_perimeter: Represents the average perimeter length of the nucleus polygons for all myofibroblasts, providing a normalized quantitative measurement for analysis. |
| 4qacrli1tavl | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | fibroblast_fsp1_mean_perimeter | fibroblast_fsp1_mean_perimeter: Represents the average perimeter length of the nucleus polygons for FSP1-positive fibroblasts, ensuring a normalized measurement of nuclear boundaries. |
| 4qacrli1tavl | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | fibroblast_mean_perimeter | fibroblast_mean_perimeter: Represents the average perimeter length of the nucleus polygons for normal fibroblasts, offering a numeric and normalized parameter for comparative analysis. |
| 4qacrli1tavl | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | endothelial_cell_mean_perimeter | endothelial_cell_mean_perimeter: Represents the average perimeter length of the nucleus polygons for endothelial cells, providing a normalized and numeric metric of nuclear morphology. |
| 4qacrli1tavl | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | ap_cell_mean_perimeter | ap_cell_mean_perimeter: Represents the average perimeter length of the nucleus polygons for antigen presenting cells, delivering a normalized value useful for cross-sample comparisons. |
| 4qacrli1tavl | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | total_mean_perimeter_index | total_mean_perimeter_index: Represents the aggregate average of all valid cell type mean perimeters, calculated by averaging the non-missing values, thereby offering a normalized summary metric of nuclear morphology. |
| 4qacrli1tavl | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | sum_mean_perimeter_index | sum_mean_perimeter_index: Represents the cumulative sum of all valid cell type mean perimeters, providing an overall numeric aggregate measure of nuclear perimeters that is normalized for comparison. |
| 4v1pcsys20a7 | MFp,B | PDPN_MF_RECT_MEAN | PDPN_MF_RECT_MEAN represents the mean nucleus rectangularity for PDPN+ myofibroblasts found in the stromal compartment. It is computed as the ratio of the area of a nucleus polygon to the area of its minimum rotated bounding rectangle, providing a size-independent measure of nuclear shape. |
| 4v1pcsys20a7 | MFp,B | PDPN_MF_RECT_STD | PDPN_MF_RECT_STD is the standard deviation of the nucleus rectangularity values for PDPN+ myofibroblasts, describing the variability in nuclear shape within this cell group. |
| 4v1pcsys20a7 | MFp,B | PDPN_MF_RECT_MIN | PDPN_MF_RECT_MIN indicates the smallest observed nucleus rectangularity among PDPN+ myofibroblasts in the stroma, reflecting the lowest degree of shape regularity in the group. |
| 4v1pcsys20a7 | MFp,B | PDPN_MF_RECT_MAX | PDPN_MF_RECT_MAX denotes the largest observed nucleus rectangularity for PDPN+ myofibroblasts, representing the highest proportion of nucleus area relative to the minimum bounding rectangle area. |
| 4v1pcsys20a7 | MFp,B | B_CELL_RECT_MEAN | B_CELL_RECT_MEAN is the mean nucleus rectangularity for B cells in the stromal compartment. This metric provides an average measure of the nuclear shape regularity for this cell population. |
| 4v1pcsys20a7 | MFp,B | B_CELL_RECT_STD | B_CELL_RECT_STD is the standard deviation of nucleus rectangularity for B cells, capturing the degree of variation in nuclear shape among these cells. |
| 4v1pcsys20a7 | MFp,B | B_CELL_RECT_MIN | B_CELL_RECT_MIN represents the minimum nucleus rectangularity among B cells, indicating the lowest nuclear shape ratio observed. |
| 4v1pcsys20a7 | MFp,B | B_CELL_RECT_MAX | B_CELL_RECT_MAX reflects the maximum nucleus rectangularity among B cells, showing the highest nuclear shape regularity encountered. |
| 4v1pcsys20a7 | MFp,B | RECT_DIFF_PDPN_MF_VS_B | RECT_DIFF_PDPN_MF_VS_B is the difference between the mean nucleus rectangularity of PDPN+ myofibroblasts and that of B cells, offering a comparative metric to understand differences in nuclear morphology between the two cell types. |
| 52aocez8zxmu | TU,Tc,Th,Treg,B,P,M,Ff,E,A | IQR_orientation_TU | IQR_orientation_TU is the interquartile range of nuclear orientation angles for tumor cells (epithelial cells). It measures the spread between the 25th and 75th percentiles of these angles, computed from the major axis of each nucleus determined using principal component analysis on cell polygon coordinates. This normalized metric allows for comparisons across different patient cases and tumor regions. |
| 52aocez8zxmu | TU,Tc,Th,Treg,B,P,M,Ff,E,A | IQR_orientation_Tc | IQR_orientation_Tc is the interquartile range of nuclear orientation angles for CD8+ T cells. It quantifies the variability in the orientation of the nuclei by calculating the difference between the upper and lower quartiles of the angle measurements. This numeric parameter is designed for direct comparison between different patient samples. |
| 52aocez8zxmu | TU,Tc,Th,Treg,B,P,M,Ff,E,A | IQR_orientation_Th | IQR_orientation_Th is the interquartile range of nuclear orientation angles for CD4+ T helper cells. The parameter reflects the variation in the computed orientation angles, which are determined by assessing the major axis of the nucleus through principal component analysis. It is normalized to enable cross-sample comparisons. |
| 52aocez8zxmu | TU,Tc,Th,Treg,B,P,M,Ff,E,A | IQR_orientation_B | IQR_orientation_B is the interquartile range of nuclear orientation angles for B cells. It is calculated as the difference between the 75th and 25th percentiles of the orientation angles obtained from the nuclear geometry. This value serves as a normalized numeric indicator for comparing different patient cases. |
| 52aocez8zxmu | TU,Tc,Th,Treg,B,P,M,Ff,E,A | IQR_orientation_P | IQR_orientation_P is the interquartile range of nuclear orientation angles for plasma cells. The measure is derived from the variability in the nuclear orientation angles via principal component analysis, with the IQR capturing the dispersion between the first and third quartiles, providing a normalized parameter for inter-case analyses. |
| 52aocez8zxmu | TU,Tc,Th,Treg,B,P,M,Ff,E,A | IQR_orientation_M | IQR_orientation_M is the interquartile range of nuclear orientation angles for macrophages. This parameter is computed by determining the major axis orientation of the cell nuclei and assessing the spread of these angles, allowing for normalized comparisons between different tissue samples. |
| 52aocez8zxmu | TU,Tc,Th,Treg,B,P,M,Ff,E,A | IQR_orientation_Ff | IQR_orientation_Ff is the interquartile range of nuclear orientation angles for FSP1+ fibroblasts. It measures the dispersion of the angle values computed from the principal component analysis of the nuclear polygon coordinates, offering a normalized metric for comparing different patient patches. |
| 52aocez8zxmu | TU,Tc,Th,Treg,B,P,M,Ff,E,A | IQR_orientation_E | IQR_orientation_E is the interquartile range of nuclear orientation angles for endothelial cells. This value is calculated from the variability in the computed nuclear orientation angles, representing the difference between the 25th and 75th percentile measurements, thereby providing a numeric and normalized measure. |
| 52aocez8zxmu | TU,Tc,Th,Treg,B,P,M,Ff,E,A | IQR_orientation_A | IQR_orientation_A is the interquartile range of nuclear orientation angles for antigen presenting cells. It quantifies the spread in the orientation angles of these cells’ nuclei computed via PCA, serving as a numeric and normalized parameter suitable for comparing different patient outcomes. |
| 56efrj7vonwo | TU,Th,Treg,B,P,M,G,MFp,MF,F | TU_heterogeneity | TU_heterogeneity measures the coefficient of variation of tumor cell (epithelial cell) density across concentric rings defined around the largest vessel in a tumor region. It is a normalized metric, computed as the standard deviation divided by the mean of tumor cell densities in the rings, and facilitates comparing spatial heterogeneity across patient cases. |
| 56efrj7vonwo | TU,Th,Treg,B,P,M,G,MFp,MF,F | Th_heterogeneity | Th_heterogeneity measures the coefficient of variation of T helper cell density (mapped from CD4+ T cells) across concentric rings surrounding the largest vessel. This normalized parameter reflects the spatial variability in immune cell infiltration, aiding in inter-case comparisons. |
| 56efrj7vonwo | TU,Th,Treg,B,P,M,G,MFp,MF,F | Treg_heterogeneity | Treg_heterogeneity quantifies the coefficient of variation of T regulatory cell density across concentric rings around the largest vessel. By normalizing the variation in T regulatory cell densities, it can be compared across different patient cases to assess immune suppression characteristics. |
| 56efrj7vonwo | TU,Th,Treg,B,P,M,G,MFp,MF,F | B_heterogeneity | B_heterogeneity quantifies the coefficient of variation of B cell density across concentric rings around the largest vessel. This parameter normalizes cell density measures, allowing comparison of the spatial distribution of B cells among various tumor regions. |
| 56efrj7vonwo | TU,Th,Treg,B,P,M,G,MFp,MF,F | P_heterogeneity | P_heterogeneity measures the coefficient of variation of plasma cell density across concentric rings that encircle the largest vessel. It is normalized by using relative density variation, and thus can be compared between different patient cases. |
| 56efrj7vonwo | TU,Th,Treg,B,P,M,G,MFp,MF,F | M_heterogeneity | M_heterogeneity evaluates the coefficient of variation of macrophage density across concentric rings around the largest vessel. Being a normalized ratio reflecting spatial density variability, it supports cross-case analysis of macrophage distribution. |
| 56efrj7vonwo | TU,Th,Treg,B,P,M,G,MFp,MF,F | G_heterogeneity | G_heterogeneity calculates the coefficient of variation of granulocyte density in concentric rings around the largest vessel. The normalization process ensures that the metric reflects relative spatial heterogeneity, enabling comparisons among different tumor regions. |
| 56efrj7vonwo | TU,Th,Treg,B,P,M,G,MFp,MF,F | MFp_heterogeneity | MFp_heterogeneity quantifies the coefficient of variation of PDPN-positive myofibroblast density across concentric rings centered on the largest vessel. The metric is normalized by evaluating the ratio of standard deviation to mean density, facilitating comparative analysis across patient cases. |
| 56efrj7vonwo | TU,Th,Treg,B,P,M,G,MFp,MF,F | MF_heterogeneity | MF_heterogeneity computes the coefficient of variation of myofibroblast density across concentric rings around the largest vessel. This normalized parameter, based on the variation of cell densities, allows direct comparisons between different tumor patches. |
| 56efrj7vonwo | TU,Th,Treg,B,P,M,G,MFp,MF,F | F_heterogeneity | F_heterogeneity calculates the coefficient of variation of fibroblast density across concentric rings around the largest vessel in a tumor slide. By normalizing density variations, it offers a quantitative measure for comparing spatial heterogeneity across various patient cases. |
| 58r11osladoz | TU,M,Ff,A | nucleus_orientation_std_all | nucleus_orientation_std_all: This parameter quantifies the overall variability in nucleus orientation angles (in degrees) across all four cell types (tumor cells, macrophages, FSP1+ fibroblasts, and antigen presenting cells). It reflects the heterogeneity in nuclear alignment in the tumor microenvironment, providing a normalized metric to compare between different patient cases and spatial regions. |
| 58r11osladoz | TU,M,Ff,A | nucleus_orientation_std_TU | nucleus_orientation_std_TU: This parameter measures the standard deviation of the nuclear orientation angles for tumor cells only. It captures how much the tumor cells' nuclei deviate in orientation from one another, presenting a normalized value that can be compared across different samples. |
| 58r11osladoz | TU,M,Ff,A | nucleus_orientation_std_M | nucleus_orientation_std_M: This parameter calculates the variability in nuclear orientation (in degrees) solely within macrophages. It serves as a marker for the heterogeneity in cell alignment for macrophages within the tumor microenvironment and is normalized for comparative analysis. |
| 58r11osladoz | TU,M,Ff,A | nucleus_orientation_std_Ff | nucleus_orientation_std_Ff: This parameter represents the standard deviation of the nuclear orientation angles specifically for FSP1+ fibroblasts. It provides insight into the variability of fibroblast nuclear alignment and is considered normalized, making it useful for comparisons across different patient cases. |
| 58r11osladoz | TU,M,Ff,A | nucleus_orientation_std_A | nucleus_orientation_std_A: This parameter measures the standard deviation of nuclear orientation angles for antigen presenting cells. It quantifies the heterogeneity in nucleus orientation among these cells and yields a normalized measure for comparative analysis. |
| 5c2cnux8cz2e | G,Treg,F,A | granulocyte-granulocyte_K_100 | granulocyte-granulocyte_K_100: This parameter quantifies the normalized spatial clustering among granulocytes at a 100-pixel distance threshold. The value is derived by normalizing the observed number of granulocyte-granulocyte pairs using the stromal area and the total number of possible pairwise interactions, allowing comparisons across different patient cases. |
| 5c2cnux8cz2e | G,Treg,F,A | granulocyte-fibroblast_K_20 | granulocyte-fibroblast_K_20: This parameter measures the normalized degree of spatial proximity between granulocytes and fibroblasts at a distance threshold of 20 pixels. It is computed by normalizing the raw count of interacting granulocyte-fibroblast pairs based on the stromal area and the product of the cell counts. |
| 5c2cnux8cz2e | G,Treg,F,A | granulocyte-fibroblast_K_30 | granulocyte-fibroblast_K_30: This parameter assesses the normalized spatial association between granulocytes and fibroblasts at a 30-pixel threshold. The normalization ensures that variations in cell density and area do not affect cross-case comparisons. |
| 5c2cnux8cz2e | G,Treg,F,A | granulocyte-fibroblast_K_50 | granulocyte-fibroblast_K_50: This parameter evaluates the normalized clustering between granulocytes and fibroblasts at a distance threshold of 50 pixels. It incorporates normalization by the stromal area and cell number to provide a standardized measure. |
| 5c2cnux8cz2e | G,Treg,F,A | granulocyte-fibroblast_K_100 | granulocyte-fibroblast_K_100: This parameter quantifies the normalized spatial relationship between granulocytes and fibroblasts at a 100-pixel distance threshold. Its normalization facilitates reliable comparisons between different samples. |
| 5c2cnux8cz2e | G,Treg,F,A | t_cell_reg-t_cell_reg_K_100 | t_cell_reg-t_cell_reg_K_100: This parameter measures the normalized spatial clustering within regulatory T cells at a 100-pixel threshold. The normalization process (dividing by the adjusted cell pair count and stromal area) makes the metric comparable across different regions. |
| 5c2cnux8cz2e | G,Treg,F,A | t_cell_reg-fibroblast_K_30 | t_cell_reg-fibroblast_K_30: This parameter quantifies the normalized spatial association between regulatory T cells and fibroblasts at a distance threshold of 30 pixels. It integrates the stromal area and cell counts to provide a standardized measure. |
| 5c2cnux8cz2e | G,Treg,F,A | t_cell_reg-fibroblast_K_50 | t_cell_reg-fibroblast_K_50: This parameter assesses the normalized co-occurrence between regulatory T cells and fibroblasts at a 50-pixel threshold, ensuring that the measure accounts for differences in cell density and tissue area. |
| 5c2cnux8cz2e | G,Treg,F,A | t_cell_reg-fibroblast_K_100 | t_cell_reg-fibroblast_K_100: This parameter evaluates the normalized spatial interrelationship between regulatory T cells and fibroblasts at a threshold of 100 pixels, making the spatial metric comparable across diverse samples. |
| 5c2cnux8cz2e | G,Treg,F,A | t_cell_reg-ap_cell_K_20 | t_cell_reg-ap_cell_K_20: This parameter measures the normalized degree of spatial proximity between regulatory T cells and antigen presenting cells at a 20-pixel threshold. The computation normalizes for tissue area and cell numbers to allow robust cross-sample comparisons. |
| 5c2cnux8cz2e | G,Treg,F,A | t_cell_reg-ap_cell_K_30 | t_cell_reg-ap_cell_K_30: This parameter quantifies the normalized clustering between regulatory T cells and antigen presenting cells at a 30-pixel distance threshold, providing a standardized spatial metric through proper normalization. |
| 5c2cnux8cz2e | G,Treg,F,A | t_cell_reg-ap_cell_K_50 | t_cell_reg-ap_cell_K_50: This parameter assesses the normalized spatial association between regulatory T cells and antigen presenting cells at a 50-pixel threshold by accounting for stromal area and cell counts in the normalization. |
| 5c2cnux8cz2e | G,Treg,F,A | t_cell_reg-ap_cell_K_100 | t_cell_reg-ap_cell_K_100: This parameter evaluates the normalized spatial interrelationship between regulatory T cells and antigen presenting cells at a 100-pixel distance threshold, ensuring comparability across cases. |
| 5c2cnux8cz2e | G,Treg,F,A | fibroblast-fibroblast_K_10 | fibroblast-fibroblast_K_10: This parameter quantifies the normalized degree of spatial clustering among fibroblasts at a 10-pixel threshold. It is normalized by the stromal area and the number of unique cell pairs to enable comparison between different tumor patches. |
| 5c2cnux8cz2e | G,Treg,F,A | fibroblast-fibroblast_K_20 | fibroblast-fibroblast_K_20: This parameter measures the normalized spatial clustering of fibroblasts at a 20-pixel threshold, with normalization allowing for cross-sample analysis independent of raw cell counts. |
| 5c2cnux8cz2e | G,Treg,F,A | fibroblast-fibroblast_K_30 | fibroblast-fibroblast_K_30: This parameter assesses the normalized intratype clustering among fibroblasts at a 30-pixel distance threshold, standardized by the stromal area and cell counts. |
| 5c2cnux8cz2e | G,Treg,F,A | fibroblast-fibroblast_K_50 | fibroblast-fibroblast_K_50: This parameter evaluates the normalized spatial aggregation of fibroblasts at a 50-pixel threshold. Its normalization ensures that differences in cell density or tissue area do not affect comparisons. |
| 5c2cnux8cz2e | G,Treg,F,A | fibroblast-fibroblast_K_100 | fibroblast-fibroblast_K_100: This parameter quantifies the normalized spatial clustering within fibroblasts at a 100-pixel threshold, using a normalization approach based on the stromal area and the possible cell pair interactions. |
| 5c2cnux8cz2e | G,Treg,F,A | fibroblast-ap_cell_K_10 | fibroblast-ap_cell_K_10: This parameter measures the normalized spatial association between fibroblasts and antigen presenting cells at a 10-pixel threshold. The normalization enables the metric to be compared across regions with varying cell densities. |
| 5c2cnux8cz2e | G,Treg,F,A | fibroblast-ap_cell_K_20 | fibroblast-ap_cell_K_20: This parameter quantifies the normalized co-occurrence between fibroblasts and antigen presenting cells at a distance threshold of 20 pixels, accounting for tissue area and cell counts. |
| 5c2cnux8cz2e | G,Treg,F,A | fibroblast-ap_cell_K_30 | fibroblast-ap_cell_K_30: This parameter assesses the normalized spatial proximity between fibroblasts and antigen presenting cells at a 30-pixel threshold, ensuring a standardized measure through proper normalization. |
| 5c2cnux8cz2e | G,Treg,F,A | fibroblast-ap_cell_K_50 | fibroblast-ap_cell_K_50: This parameter evaluates the normalized spatial relationship between fibroblasts and antigen presenting cells at a 50-pixel threshold by adjusting for the stromal area and cell count variations. |
| 5c2cnux8cz2e | G,Treg,F,A | fibroblast-ap_cell_K_100 | fibroblast-ap_cell_K_100: This parameter measures the normalized degree of spatial association between fibroblasts and antigen presenting cells at a 100-pixel threshold, allowing reliable comparisons across different patient samples. |
| 5c2cnux8cz2e | G,Treg,F,A | ap_cell-ap_cell_K_10 | ap_cell-ap_cell_K_10: This parameter quantifies the normalized spatial clustering among antigen presenting cells at a 10-pixel threshold. It is normalized to the stromal area and the total number of unique cell pairs. |
| 5c2cnux8cz2e | G,Treg,F,A | ap_cell-ap_cell_K_20 | ap_cell-ap_cell_K_20: This parameter measures the normalized intra-type clustering of antigen presenting cells at a 20-pixel distance threshold, ensuring that the metric remains comparable between cases. |
| 5c2cnux8cz2e | G,Treg,F,A | ap_cell-ap_cell_K_30 | ap_cell-ap_cell_K_30: This parameter assesses the normalized spatial aggregation of antigen presenting cells at a 30-pixel threshold, calculated using normalization factors for area and cell number. |
| 5c2cnux8cz2e | G,Treg,F,A | ap_cell-ap_cell_K_50 | ap_cell-ap_cell_K_50: This parameter evaluates the normalized spatial relationship among antigen presenting cells at a 50-pixel threshold. The normalization renders the metric comparable across different tumor patches. |
| 5c2cnux8cz2e | G,Treg,F,A | ap_cell-ap_cell_K_100 | ap_cell-ap_cell_K_100: This parameter quantifies the normalized degree of spatial clustering within antigen presenting cells at a 100-pixel threshold, using standardized normalization procedures. |
| 5c2cnux8cz2e | G,Treg,F,A | composite_K_10 | composite_K_10: This composite parameter provides the average of the normalized Ripley’s K function values across all relevant cell type pairs at a 10-pixel threshold, offering an overall measure of spatial co-occurrence within the tumor stroma. |
| 5c2cnux8cz2e | G,Treg,F,A | composite_K_20 | composite_K_20: This composite parameter averages the normalized Ripley’s K function values across all cell type pairs at a 20-pixel threshold, reflecting the overall spatial relationship between different cell types in a normalized fashion. |
| 5c2cnux8cz2e | G,Treg,F,A | composite_K_30 | composite_K_30: This composite parameter represents the normalized average of Ripley’s K function values for all cell type pairs at a 30-pixel threshold, thereby summarizing overall spatial interactions in a standardized manner. |
| 5c2cnux8cz2e | G,Treg,F,A | composite_K_50 | composite_K_50: This composite parameter is the normalized average of Ripley’s K values across all cell type pairs at a 50-pixel threshold, providing a singular measure of overall spatial clustering. |
| 5c2cnux8cz2e | G,Treg,F,A | composite_K_100 | composite_K_100: This composite parameter computes the average of the normalized Ripley’s K function values for all cell type pairs at a 100-pixel threshold, offering a comprehensive and normalized measure of spatial co-occurrence across the tumor region. |
| 5c984ispfk4s | Th,B | avg_th_nuclear_perimeter | avg_th_nuclear_perimeter represents the average nuclear perimeter of T helper cells measured in a standardized unit. It is calculated by averaging the perimeters of T helper cells, which provides a normalized metric that can be compared across different tumor patches or patient cases. |
| 5c984ispfk4s | Th,B | avg_b_nuclear_perimeter | avg_b_nuclear_perimeter denotes the average nuclear perimeter of B cells. This value is derived from the average of the perimeters of B cells, offering a normalized morphological measure that facilitates comparisons between various patient samples or regions within the tumor. |
| 5c984ispfk4s | Th,B | th_b_perimeter_difference | th_b_perimeter_difference is the computed difference between the average nuclear perimeters of T helper cells and B cells, calculated as the value for T helper cells minus that for B cells. This parameter serves as a normalized indicator of the relative morphological differences between the two cell types in a way that supports comparative analysis across different patient cases. |
| 5k0bcf4wlfjp | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,F | TRICELL_ADJACENCY_FRACTION | TRICELL_ADJACENCY_FRACTION represents the normalized fraction of valid tri-cell groups among all possible combinations of three distinct cell types in a given tumor patch. It is calculated by dividing the number of tri-cell groups where every pair of cells is in close contact (either touching or within a set maximum distance of 10 micrometers) by the total number of possible triplets from the available cell types. This fraction is a dimensionless value that enables comparisons between different tumor regions or patient cases. |
| 5uc3f0p6fe91 | TU,Treg,Tc,MFp,MF,E | composite_score_with_endothelium | composite_score_with_endothelium is a normalized composite metric that quantifies the immune environment within a tumor region. It is derived by calculating the ratio of the sum of regulatory T cells and cytotoxic T cells to the sum of myofibroblasts (both PDPN+ and PDPN−), and then further normalizing this ratio by the count of tumor cells. This normalization makes the metric comparable across different patient cases and tissue patches, specifically for regions where endothelial cells are present. |
| 5v9pwhg2vz1f | TU,M,Tc,Treg,B,P,Ff,E | tumor_roundness_mean | tumor_roundness_mean: This parameter represents the average roundness value computed for tumor cells. It is a normalized metric derived from each tumor cell’s nucleus shape using a specific roundness formula based on the cell's area and perimeter, enabling comparisons across different tumor regions. |
| 5v9pwhg2vz1f | TU,M,Tc,Treg,B,P,Ff,E | tumor_roundness_median | tumor_roundness_median: This parameter provides the median roundness value measured for tumor cells. It is calculated from the individual nucleus roundness values and offers a central tendency measure that is robust to outliers, ensuring comparability among different patient cases. |
| 5v9pwhg2vz1f | TU,M,Tc,Treg,B,P,Ff,E | tumor_roundness_std | tumor_roundness_std: This parameter captures the standard deviation of roundness values for tumor cells. It reflects the variability in nuclear shape among tumor cells and serves as an indicator of heterogeneity within the tumor region. |
| 5v9pwhg2vz1f | TU,M,Tc,Treg,B,P,Ff,E | macrophages_roundness_mean | macrophages_roundness_mean: This metric is the mean roundness value for macrophages, computed from the roundness of individual cell nuclei. It allows for the assessment of the characteristic nuclear shape of macrophages relative to the tumor cells. |
| 5v9pwhg2vz1f | TU,M,Tc,Treg,B,P,Ff,E | macrophages_roundness_median | macrophages_roundness_median: This parameter denotes the median roundness value for macrophages. It provides a central value that is less influenced by extreme values and is useful for normalized comparisons in different tissue patches. |
| 5v9pwhg2vz1f | TU,M,Tc,Treg,B,P,Ff,E | macrophages_roundness_std | macrophages_roundness_std: This metric indicates the standard deviation of the roundness values for macrophages, offering insight into the degree of variability in their nuclear morphology. |
| 5v9pwhg2vz1f | TU,M,Tc,Treg,B,P,Ff,E | t_cells_roundness_mean | t_cells_roundness_mean: This parameter is the average roundness value for T cells, derived from the computed roundness values of both CD8 and regulatory T cell subtypes. It serves as a normalized measure to compare T cell nuclear shapes across different tumor patches. |
| 5v9pwhg2vz1f | TU,M,Tc,Treg,B,P,Ff,E | t_cells_roundness_median | t_cells_roundness_median: This metric provides the median roundness value for T cells, reflecting the central tendency of nuclear shape features in T cells while being robust to outliers. |
| 5v9pwhg2vz1f | TU,M,Tc,Treg,B,P,Ff,E | t_cells_roundness_std | t_cells_roundness_std: This parameter represents the standard deviation of the roundness values computed for T cells, highlighting the variability in T cell nuclear morphology in different patient cases. |
| 5v9pwhg2vz1f | TU,M,Tc,Treg,B,P,Ff,E | fibroblasts_roundness_mean | fibroblasts_roundness_mean: This parameter calculates the mean roundness value for fibroblasts, including both general fibroblasts and a specific fibroblast subtype. It is used to assess and compare the average nuclear morphology of fibroblasts in a normalized manner. |
| 5v9pwhg2vz1f | TU,M,Tc,Treg,B,P,Ff,E | fibroblasts_roundness_median | fibroblasts_roundness_median: This metric provides the median roundness value for fibroblasts, offering a robust central measure of nuclear roundness that aids in comparing fibroblast behavior among tumor regions. |
| 5v9pwhg2vz1f | TU,M,Tc,Treg,B,P,Ff,E | fibroblasts_roundness_std | fibroblasts_roundness_std: This parameter indicates the standard deviation in roundness values for fibroblasts, revealing the dispersion of nuclear shape features and enabling comparisons of variability between cases. |
| 5v9pwhg2vz1f | TU,M,Tc,Treg,B,P,Ff,E | macrophage_tumor_roundness_diff | macrophage_tumor_roundness_diff: This metric represents the absolute difference between the mean roundness of macrophages and the mean roundness of tumor cells. It is designed to quantify deviations in nuclear morphology between the immune component and tumor cells. |
| 5v9pwhg2vz1f | TU,M,Tc,Treg,B,P,Ff,E | macrophage_tumor_roundness_ratio | macrophage_tumor_roundness_ratio: This parameter is the ratio of the mean macrophage roundness to the mean tumor cell roundness. It normalizes the comparison of nuclear morphology between these two cell types, allowing for standardized assessments. |
| 5v9pwhg2vz1f | TU,M,Tc,Treg,B,P,Ff,E | tcell_tumor_roundness_diff | tcell_tumor_roundness_diff: This parameter measures the difference between the mean roundness of T cells and that of tumor cells, serving as a comparative metric to assess the disparity in nuclear roundness across cell types. |
| 5v9pwhg2vz1f | TU,M,Tc,Treg,B,P,Ff,E | tcell_tumor_roundness_ratio | tcell_tumor_roundness_ratio: This metric computes the ratio of the mean roundness of T cells to the mean tumor cell roundness. It is a normalized metric that standardizes the comparison of cell shape properties across different patches. |
| 5v9pwhg2vz1f | TU,M,Tc,Treg,B,P,Ff,E | fibroblast_tumor_roundness_diff | fibroblast_tumor_roundness_diff: This parameter denotes the difference in mean roundness between fibroblasts and tumor cells. It quantifies how much the nuclear morphology of fibroblasts deviates from that of tumor cells. |
| 5v9pwhg2vz1f | TU,M,Tc,Treg,B,P,Ff,E | fibroblast_tumor_roundness_ratio | fibroblast_tumor_roundness_ratio: This metric is the ratio of the mean fibroblast roundness value relative to the tumor cell roundness mean, providing a normalized measure to compare the nuclear shape features of fibroblasts with those of tumor cells. |
| 5vhmgbg0m0j9 | F,Ff,MFp,Tc,A,TU | mean_fibroblasts_per_cluster | mean_fibroblasts_per_cluster represents the average number of fibroblasts (including both fibroblast and fibroblast_fsp1 types) counted in each spatial cluster meeting the inclusion criteria. This parameter, being an average, adjusts for differences in total cell counts and allows comparison between different patient cases. |
| 5vhmgbg0m0j9 | F,Ff,MFp,Tc,A,TU | mean_pdpn_myofibroblasts_per_cluster | mean_pdpn_myofibroblasts_per_cluster indicates the average number of PDPN+ myofibroblasts per valid cluster. By averaging over clusters, this metric facilitates comparison across patches from different patient samples. |
| 5vhmgbg0m0j9 | F,Ff,MFp,Tc,A,TU | overall_fibroblast_to_pdpn_ratio | overall_fibroblast_to_pdpn_ratio is the dimensionless ratio computed by dividing the total number of fibroblasts by the total number of PDPN+ myofibroblasts across all valid clusters. This ratio normalizes differences in cell counts and provides a comparative measure of fibroblast dominance relative to PDPN+ myofibroblasts. |
| 5vhmgbg0m0j9 | F,Ff,MFp,Tc,A,TU | mean_fibroblast_to_pdpn_ratio | mean_fibroblast_to_pdpn_ratio is derived by calculating the fibroblast to PDPN+ myofibroblast ratio for each cluster and then averaging these ratios. This average ratio offers a normalized metric reflective of the relative abundance in each cluster, making it comparable between patient cases. |
| 5vhmgbg0m0j9 | F,Ff,MFp,Tc,A,TU | median_fibroblast_to_pdpn_ratio | median_fibroblast_to_pdpn_ratio provides the middle value of the distribution of fibroblast to PDPN+ myofibroblast ratios across all valid clusters. This robust statistic is less sensitive to outliers while still offering a normalized view of the relative cell proportions. |
| 5vhmgbg0m0j9 | F,Ff,MFp,Tc,A,TU | min_fibroblast_to_pdpn_ratio | min_fibroblast_to_pdpn_ratio captures the smallest observed fibroblast to PDPN+ myofibroblast ratio among the clusters, highlighting the lowest relative abundance of fibroblasts compared to PDPN+ myofibroblasts in any given cluster. |
| 5vhmgbg0m0j9 | F,Ff,MFp,Tc,A,TU | max_fibroblast_to_pdpn_ratio | max_fibroblast_to_pdpn_ratio identifies the highest observed ratio of fibroblasts to PDPN+ myofibroblasts in any valid cluster, indicating the maximum relative dominance of fibroblasts within the studied regions. |
| 5vhmgbg0m0j9 | F,Ff,MFp,Tc,A,TU | pct_high_ratio_clusters | pct_high_ratio_clusters expresses the percentage of clusters with a fibroblast to PDPN+ myofibroblast ratio greater than 2:1. As a percentage, this parameter is normalized and directly comparable across different patient cases. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | all_cell_type_weighted_multilayer_clustering | This parameter represents the weighted average of the multi-layer clustering coefficients across all cell types within a tumor patch. It is computed by weighting each cell type's average clustering value by its relative abundance, resulting in a normalized metric that enables comparison across different patient cases. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | overall_clustering_mean | This parameter conveys the arithmetic mean of the multi-layer clustering coefficients calculated for every cell in a tumor patch. It provides a normalized measure of the typical cross-layer clustering behavior without additional weighting. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | TU_clustering_mean | This parameter captures the mean multi-layer clustering coefficient for tumor (TU) cells. It reflects the average degree of spatial clustering exhibited by tumor cells as they interact with both similar and different cell types, providing a normalized metric of their coordinated behavior. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | TU_clustering_std | This parameter measures the standard deviation of the multi-layer clustering coefficients for tumor (TU) cells. It quantifies the variability in spatial clustering among tumor cells within a tumor patch in a normalized fashion. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Tc_clustering_mean | This parameter represents the average multi-layer clustering coefficient for cytotoxic T (Tc) cells. It indicates the typical level of spatial organization these cells achieve when interacting with cells across different layers, normalized for cross-case comparison. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Tc_clustering_std | This parameter reflects the standard deviation of the multi-layer clustering coefficients for cytotoxic T (Tc) cells, highlighting the variability in their spatial clustering patterns within the tumor microenvironment. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Th_clustering_mean | This parameter captures the average multi-layer clustering coefficient for T helper (Th) cells, providing a normalized insight into the typical spatial clustering and coordinated interactions these cells exhibit. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Th_clustering_std | This parameter quantifies the standard deviation of the multi-layer clustering coefficients for T helper (Th) cells. It reflects the dispersion in clustering measurements among these cells across the tumor patch. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Treg_clustering_mean | This parameter measures the average multi-layer clustering coefficient for regulatory T (Treg) cells, offering a normalized indicator of how these cells spatially cluster with both similar and diverse cell types. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Treg_clustering_std | This parameter represents the standard deviation of the multi-layer clustering coefficients for regulatory T (Treg) cells, thereby demonstrating the variability in the extent of their spatial interactions. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | B_clustering_mean | This parameter denotes the average multi-layer clustering coefficient for B cells. It is a normalized metric that quantifies the typical spatial clustering behavior of B cells within a tumor patch. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | B_clustering_std | This parameter represents the standard deviation of the multi-layer clustering coefficients for B cells, measuring the variation in their clustering behavior across different regions. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | P_clustering_mean | This parameter captures the average multi-layer clustering coefficient for plasma (P) cells, providing a normalized assessment of their spatial organization among interacting cell types. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | P_clustering_std | This parameter describes the standard deviation of the multi-layer clustering coefficients for plasma (P) cells, indicating the variability in their spatial clustering behavior. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | M_clustering_mean | This parameter quantifies the average multi-layer clustering coefficient for macrophages (M), serving as a normalized measure of their typical spatial aggregation in the tumor microenvironment. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | M_clustering_std | This parameter reflects the standard deviation of the multi-layer clustering coefficients for macrophages (M), offering insight into the heterogeneity of their spatial interactions. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | G_clustering_mean | This parameter denotes the average multi-layer clustering coefficient for granulocytes (G), providing a normalized metric that illustrates how these cells typically cluster spatially with surrounding cells. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | G_clustering_std | This parameter captures the standard deviation of the multi-layer clustering coefficients for granulocytes (G), highlighting the variability in their clustering patterns across a tumor patch. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MFp_clustering_mean | This parameter represents the average multi-layer clustering coefficient for PDPN+ myofibroblasts (MFp), providing a normalized measure of their spatial clustering characteristics within the tumor region. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MFp_clustering_std | This parameter quantifies the standard deviation of the multi-layer clustering coefficients for PDPN+ myofibroblasts (MFp), which indicates the variance in spatial clustering among these cells. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MF_clustering_mean | This parameter describes the mean multi-layer clustering coefficient for myofibroblasts (MF), offering a normalized metric of the average spatial organization of these cells in the tumor microenvironment. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MF_clustering_std | This parameter denotes the standard deviation of the multi-layer clustering coefficients for myofibroblasts (MF), thereby capturing the variability of their spatial clustering behavior. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Ff_clustering_mean | This parameter reflects the average multi-layer clustering coefficient for FSP1+ fibroblasts (Ff), providing a normalized assessment of the degree of spatial clustering for these cells. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Ff_clustering_std | This parameter measures the standard deviation of the multi-layer clustering coefficients for FSP1+ fibroblasts (Ff), indicating how consistently these cells cluster across the tumor patch. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | F_clustering_mean | This parameter represents the mean multi-layer clustering coefficient for fibroblasts (F), capturing the average normalized spatial clustering behavior of these cells within the tissue microenvironment. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | F_clustering_std | This parameter captures the standard deviation of the multi-layer clustering coefficients for fibroblasts (F), thereby reflecting the dispersion in their spatial clustering measurements. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | E_clustering_mean | This parameter measures the average multi-layer clustering coefficient for endothelial cells (E), providing a normalized metric of the typical spatial interaction strength among these cells. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | E_clustering_std | This parameter represents the standard deviation of the multi-layer clustering coefficients for endothelial cells (E), highlighting the variability of their spatial clustering within the tumor patch. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | A_clustering_mean | This parameter represents the average multi-layer clustering coefficient for antigen-presenting cells (A), indicating the normalized level of spatial clustering exhibited by these cells in the tumor microenvironment. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | A_clustering_std | This parameter conveys the standard deviation of the multi-layer clustering coefficients for antigen-presenting cells (A), capturing the variability in their spatial clustering behavior. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | TU_Tc_pair_clustering | This parameter measures the clustering coefficient specifically quantifying how cytotoxic T (Tc) cells spatially cluster around tumor (TU) cells. It provides a normalized indicator of intercellular interaction between these two pivotal cell types in the tumor context. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | TU_M_pair_clustering | This parameter captures the clustering metric that quantifies the spatial interaction between tumor (TU) cells and macrophages (M). It reflects the normalized extent of coordinated spatial organization between these cell types within a tumor patch. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | TU_F_pair_clustering | This parameter signifies the clustering coefficient that assesses the spatial interactions between tumor (TU) cells and fibroblasts (F). It is normalized and indicative of the degree to which these cells exhibit coordinated spatial clustering. |
| 5wyjafognl5s | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | M_Tc_pair_clustering | This parameter measures the clustering coefficient for interactions between macrophages (M) and cytotoxic T (Tc) cells. It provides a normalized metric reflecting the level of spatial coordination between these two cell types. |
| 5zdwa9c5p2gr | TU,Treg,B,A,G,MFp | IQR_Roundness_TU | IQR_Roundness_TU represents the interquartile range of the nucleus roundness values for tumor cells. Nucleus roundness is calculated by the formula 4 π multiplied by the area divided by the square of the perimeter. This parameter captures the variability in cell shape among tumor cells in a given patch, making it a normalized metric suitable for comparing different patient cases. |
| 5zdwa9c5p2gr | TU,Treg,B,A,G,MFp | IQR_Roundness_B | IQR_Roundness_B represents the interquartile range of nucleus roundness for B cells. It is derived from the same normalized calculation of nucleus roundness and reflects the spread in the morphological metric among B cells within the tumor patch, allowing for meaningful comparisons in downstream analyses. |
| 5zdwa9c5p2gr | TU,Treg,B,A,G,MFp | IQR_Roundness_A | IQR_Roundness_A represents the interquartile range of nucleus roundness for antigen presenting cells. This metric quantifies the dispersion in the nucleus roundness, calculated as described, and serves as a normalized measurement that can be compared across various patient tumor patches. |
| 5zdwa9c5p2gr | TU,Treg,B,A,G,MFp | IQR_Roundness_MFp | IQR_Roundness_MFp represents the interquartile range of nucleus roundness for PDPN+ myofibroblasts. It measures how widely the nucleus roundness values are spread for these cells using the normalized formula, ensuring that the metric is comparable across different cases. |
| 61lya8vlnula | Th,MF | mean_distance_th_to_pdpn_neg_mf | mean_distance_th_to_pdpn_neg_mf represents the average Euclidean distance between T helper cells and PDPN-negative myofibroblasts located at or near the epithelial-stromal boundary. This metric is calculated by taking all pairwise distances between these two cell types within a given patch and computing the mean value, making it a normalized measure that is comparable across different patient cases. |
| 61lya8vlnula | Th,MF | min_distance_th_to_pdpn_neg_mf | min_distance_th_to_pdpn_neg_mf indicates the smallest Euclidean distance found among all pairs of T helper cells and PDPN-negative myofibroblasts at the epithelial-stromal boundary. This measure reflects the closest proximity between the cells, which can be an indicator of potential direct cellular interactions. |
| 61lya8vlnula | Th,MF | max_distance_th_to_pdpn_neg_mf | max_distance_th_to_pdpn_neg_mf denotes the largest Euclidean distance recorded between any T helper cell and PDPN-negative myofibroblast pair at the boundary. It provides insight into the extent of spatial distribution of these cells in the tissue context. |
| 61lya8vlnula | Th,MF | std_distance_th_to_pdpn_neg_mf | std_distance_th_to_pdpn_neg_mf quantifies the variability in the distances calculated between T helper cells and PDPN-negative myofibroblasts at the boundary. A higher standard deviation indicates greater heterogeneity in cell spacing across the analyzed patches, further supporting comparative analysis across multiple patient cases. |
| 68nwn7fwjprq | Tc | std_circularity_cd8_t_stroma | The parameter 'std_circularity_cd8_t_stroma' measures the standard deviation of the nuclear circularity values for all CD8+ T cells located in the stroma region of breast cancer tissue. It quantifies the variability in nuclear shape, which provides insights into the heterogeneity of cytotoxic T cell morphology that could reflect diverse activation states or functional differentiation. This measure is calculated by determining the circularity of each T cell nucleus from its polygonal representation and then computing the sample standard deviation over these values. Being a normalized statistic, it is suitable for comparing different patient cases. |
| 6aysuupmssmq | TU,Treg,B,P,M,G,MFp,MF,Ff,E | skewness_TU | skewness_TU measures the skewness of the nuclear polygon area distribution for epithelial (tumor) cells. It quantifies the asymmetry in the distribution of the cell nucleus areas, allowing comparison across different tumor patches. |
| 6aysuupmssmq | TU,Treg,B,P,M,G,MFp,MF,Ff,E | skewness_Treg | skewness_Treg measures the skewness of the nuclear polygon area distribution for T regulatory cells. It assesses the deviation from symmetry in the distribution of nucleus areas for these immune cells across tumor regions. |
| 6aysuupmssmq | TU,Treg,B,P,M,G,MFp,MF,Ff,E | skewness_B | skewness_B measures the skewness of the nuclear polygon area distribution for B cells. This parameter reflects how the distribution of nuclear areas for B cells is skewed, indicating potential heterogeneity in cell size. |
| 6aysuupmssmq | TU,Treg,B,P,M,G,MFp,MF,Ff,E | skewness_P | skewness_P measures the skewness of the nuclear polygon area distribution for plasma cells. It indicates the degree of asymmetry in the nuclear area distribution for plasma cells detected in a tumor patch. |
| 6aysuupmssmq | TU,Treg,B,P,M,G,MFp,MF,Ff,E | skewness_M | skewness_M measures the skewness of the nuclear polygon area distribution for macrophages. This parameter captures the asymmetry in the distribution of nuclear areas for macrophages, serving as a potential marker of cell heterogeneity. |
| 6aysuupmssmq | TU,Treg,B,P,M,G,MFp,MF,Ff,E | skewness_G | skewness_G measures the skewness of the nuclear polygon area distribution for granulocytes. It quantifies how the distribution of granulocyte nuclear areas deviates from symmetry, supporting normalized comparisons across samples. |
| 6aysuupmssmq | TU,Treg,B,P,M,G,MFp,MF,Ff,E | skewness_MFp | skewness_MFp measures the skewness of the nuclear polygon area distribution for PDPN-positive myofibroblasts. This numeric parameter reveals the asymmetry in nuclear area distribution specific to these cells within a tumor region. |
| 6aysuupmssmq | TU,Treg,B,P,M,G,MFp,MF,Ff,E | skewness_MF | skewness_MF measures the skewness of the nuclear polygon area distribution for myofibroblasts. It provides a normalized measure of the asymmetry in the distribution of nuclear areas for these cells across different patches. |
| 6aysuupmssmq | TU,Treg,B,P,M,G,MFp,MF,Ff,E | skewness_Ff | skewness_Ff measures the skewness of the nuclear polygon area distribution for FSP1-positive fibroblasts. It captures the degree of asymmetry in the distribution of nuclear areas for these fibroblasts and enables cross-patient comparisons. |
| 6aysuupmssmq | TU,Treg,B,P,M,G,MFp,MF,Ff,E | skewness_E | skewness_E measures the skewness of the nuclear polygon area distribution for endothelial cells. This parameter quantifies the asymmetry in the distribution of nuclear areas and is used to assess differences between tumor patches. |
| 6j2r1s1e9vve | TU,B | Tumor_Cell_Median_Solidity | Tumor_Cell_Median_Solidity represents the median value of the nuclear solidity for tumor cells in the epithelial region of a tumor patch. Nuclear solidity is computed as the ratio of the area of the nucleus to the area of its convex hull, providing a normalized measurement that allows for reliable comparisons across different patient cases. This parameter reflects variations in nuclear morphology that may be linked to tumor aggressiveness, making it suitable for further analysis. |
| 6pkak032ictn | TU,Th,B,Treg,M | TU_cv | TU_cv represents the coefficient of variation of the nuclear perimeters for tumor cells. This parameter is computed as the ratio of the standard deviation to the mean of nuclear perimeters, providing a normalized measure of dispersion that allows comparisons across different patient cases. |
| 6pkak032ictn | TU,Th,B,Treg,M | Th_cv | Th_cv represents the coefficient of variation of the nuclear perimeters for helper T cells. It quantifies the relative variability in nuclear shapes by normalizing the standard deviation by the mean, making it suitable for comparing tumor regions from different patients. |
| 6pkak032ictn | TU,Th,B,Treg,M | B_cv | B_cv represents the coefficient of variation of the nuclear perimeters for B cells. This metric, calculated as the standard deviation divided by the mean of the perimeters, serves as a normalized indicator of cellular heterogeneity for cross-case analysis. |
| 6pkak032ictn | TU,Th,B,Treg,M | Treg_cv | Treg_cv represents the coefficient of variation of the nuclear perimeters for regulatory T cells. It provides a normalized measurement of variability in nuclear contours by dividing the standard deviation by the mean, enabling reliable comparisons between different tumor patches. |
| 6pkak032ictn | TU,Th,B,Treg,M | M_cv | M_cv represents the coefficient of variation of the nuclear perimeters for macrophages. By normalizing the standard deviation by the mean perimeter, this parameter delivers a robust, numerical measure of the variability in nuclear shape that can be compared across patient cases. |
| 6t6yt01gq0fj | TU,MFp,MF,Ff,F,M,G,Th,Tc | NORMALIZED_TUMOR_FIBROBLAST_BOUNDARY_LENGTH | This parameter represents the average length of the direct contact boundaries between tumor cells and fibroblasts. The measurement is obtained by calculating the total tumor-fibroblast contact boundary length and then normalizing it by dividing by the number of tumor cells. The normalization ensures that variations in tumor cell numbers across different patient cases or patches are accounted for, making the metric comparable across different cases. |
| 70xykv723ujn | M,MF | MACRO_MF_CURV_DIFF | MACRO_MF_CURV_DIFF is the difference between the mean nuclear curvature of macrophages and the mean nuclear curvature of PDPN- myofibroblasts in the stromal compartment. The parameter is computed by first determining the curvature of each cell's nuclear boundary using the turning angles relative to the segment lengths, then averaging these curvatures across the two cell types, and finally calculating the difference between these means. This metric allows for normalized comparison across different patient cases. |
| 70xykv723ujn | M,MF | MACRO_MEAN_CURV | MACRO_MEAN_CURV represents the average nuclear curvature calculated from the macrophages in the stromal compartment. The curvature for each cell is obtained from its boundary geometry and the average of these curvature measurements provides a normalized indicator of nuclear shape characteristics. |
| 70xykv723ujn | M,MF | MF_MEAN_CURV | MF_MEAN_CURV represents the average nuclear curvature for PDPN- myofibroblasts in the stromal region. Similar to MACRO_MEAN_CURV, this parameter averages the curvature measurements derived from the nuclear boundary geometry of each myofibroblast, resulting in a normalized measure suitable for cross-sample comparisons. |
| 70xykv723ujn | M,MF | MACRO_STD_CURV | MACRO_STD_CURV is the standard deviation of nuclear curvature values among macrophages in the stromal compartment. This parameter quantifies the variability in nuclear curvature measurements, providing insight into the heterogeneity of cell shape within this cell type. |
| 70xykv723ujn | M,MF | MF_STD_CURV | MF_STD_CURV is the standard deviation of nuclear curvature measurements for PDPN- myofibroblasts in the stromal compartment. It measures the variability in the nuclear curvature values of these cells, indicating the degree of heterogeneity within the cell population. |
| 73s631jk93nd | TU,Tc,Th,Treg,B,P,M,MFp | MAX_CHAIN_DEPTH | MAX_CHAIN_DEPTH is the maximum depth found among cell chains that spatially bridge the tumor and stroma compartments. It is computed as the longest shortest path (graph diameter) in any valid connected component and reflects the extent of spatial connectivity between the compartments. |
| 73s631jk93nd | TU,Tc,Th,Treg,B,P,M,MFp | MAX_CHAIN_DEPTH_MIN_2_SUBSETS | MAX_CHAIN_DEPTH_MIN_2_SUBSETS measures the maximum chain depth among the cell chains that include at least two distinct cell subsets. This parameter emphasizes the spatial connectivity in regions where diversity in cell types is present across the tumor and stromal regions. |
| 73s631jk93nd | TU,Tc,Th,Treg,B,P,M,MFp | MAX_CHAIN_DEPTH_2_SUBSETS | MAX_CHAIN_DEPTH_2_SUBSETS represents the maximum chain depth observed among chains composed of exactly two unique cell subsets. It quantifies the longest spatial chain when only two different cell types are involved. |
| 73s631jk93nd | TU,Tc,Th,Treg,B,P,M,MFp | MAX_CHAIN_DEPTH_3_SUBSETS | MAX_CHAIN_DEPTH_3_SUBSETS is the maximum chain depth calculated for chains made up of exactly three distinct cell subsets, indicating the extent of multi-cell interactions when three different cell types participate. |
| 73s631jk93nd | TU,Tc,Th,Treg,B,P,M,MFp | MAX_CHAIN_DEPTH_4_SUBSETS | MAX_CHAIN_DEPTH_4_SUBSETS denotes the longest chain depth among chains that include exactly four unique cell types, serving as a measure of spatial complexity with moderate cell subset diversity. |
| 73s631jk93nd | TU,Tc,Th,Treg,B,P,M,MFp | MAX_CHAIN_DEPTH_5_SUBSETS | MAX_CHAIN_DEPTH_5_SUBSETS is defined as the maximum chain depth among cell chains composed of exactly five different cell subsets. It reflects deeper multi-cell connectivity when a moderate to high degree of cell type diversity is observed. |
| 73s631jk93nd | TU,Tc,Th,Treg,B,P,M,MFp | MAX_CHAIN_DEPTH_7_SUBSETS | MAX_CHAIN_DEPTH_7_SUBSETS captures the maximum chain depth among chains that consist of exactly seven unique cell subsets, highlighting extensive spatial integration across a high number of different cell types. |
| 78r5sfbjbf6r | Tc,Treg,MFp | tri_ripley_k_25um | tri_ripley_k_25um: This parameter represents the normalized tri-variate Ripley’s K function value computed at a 25 μm radius. It measures the spatial clustering of cytotoxic T cells, regulatory T cells, and PDPN+ myofibroblasts in the stromal region by counting the number of neighboring cells from the other two cell types within the specified radius, normalizing this count by the area of the circle defined by a 25 μm radius, and averaging over the relevant cells. |
| 78r5sfbjbf6r | Tc,Treg,MFp | tri_ripley_k_50um | tri_ripley_k_50um: This parameter represents the normalized tri-variate Ripley’s K function value computed at a 50 μm radius. It quantifies the co-localization and clustering of the three specified immune and stromal cell populations within a 50 μm circular area, with counts normalized by the corresponding area and averaged across all cells considered. |
| 78r5sfbjbf6r | Tc,Treg,MFp | tri_ripley_k_75um | tri_ripley_k_75um: This parameter represents the normalized tri-variate Ripley’s K function value computed at a 75 μm radius. It evaluates the spatial clustering pattern of cytotoxic T cells, regulatory T cells, and PDPN+ myofibroblasts in the stroma, using a normalization based on the area of a circle with a 75 μm radius and averaging the results over the cells of interest. |
| 78r5sfbjbf6r | Tc,Treg,MFp | tri_ripley_k_100um | tri_ripley_k_100um: This parameter represents the normalized tri-variate Ripley’s K function value computed at a 100 μm radius. It measures the degree of spatial interplay among cytotoxic T cells, regulatory T cells, and PDPN+ myofibroblasts by counting nearby cells from the other populations within a 100 μm radius, normalizing by the circle’s area and averaging the measure across the population. |
| 78r5sfbjbf6r | Tc,Treg,MFp | tri_ripley_k_150um | tri_ripley_k_150um: This parameter represents the normalized tri-variate Ripley’s K function value computed at a 150 μm radius. It captures the clustering behavior of the three cell types over a broader spatial scale by normalizing the cell count within a 150 μm radius area and averaging the resulting values, providing an evaluation of co-localization in a larger tissue context. |
| 78r5sfbjbf6r | Tc,Treg,MFp | tri_ripley_k_integrated | tri_ripley_k_integrated: This parameter is the integrated value of the tri-variate Ripley’s K function over the range of distance bins (25, 50, 75, 100, and 150 μm). It summarizes the overall spatial clustering pattern of cytotoxic T cells, regulatory T cells, and PDPN+ myofibroblasts in the stromal compartment by computing the area under the curve of the K function values across the various radii, thereby providing a single summary metric that encapsulates multi-scale clustering behavior. |
| 7a3yg8qpno81 | G,Treg,Th,M,MFp,MF,Ff | MEAN_FD_Granulocytes | MEAN_FD_Granulocytes quantifies the average fractal dimension of the nuclei boundaries in granulocyte cells located in the stroma. This parameter reflects the geometric complexity of the nuclear periphery measured via a box-counting method, enabling comparisons across tumor patches. |
| 7a3yg8qpno81 | G,Treg,Th,M,MFp,MF,Ff | MEAN_FD_Treg | MEAN_FD_Treg measures the mean fractal dimension for T regulatory cells (Treg) in the stromal compartment. It provides a normalized, numeric value that captures the intricacy of the nuclear boundaries based on the regression slope derived from log-log analysis. |
| 7a3yg8qpno81 | G,Treg,Th,M,MFp,MF,Ff | MEAN_FD_Helper_T | MEAN_FD_Helper_T represents the average fractal dimension of the nuclei for helper T cells within the stroma. It reflects the level of complexity of nuclear contours obtained through box-counting and subsequent averaging over the analyzed patches. |
| 7a3yg8qpno81 | G,Treg,Th,M,MFp,MF,Ff | MEAN_FD_Macrophages | MEAN_FD_Macrophages assesses the mean fractal dimension of macrophage nuclei in the stromal region. It delivers a numeric value indicating the complexity of the nuclear boundary, making it suitable for comparing different patient cases. |
| 7a3yg8qpno81 | G,Treg,Th,M,MFp,MF,Ff | MEAN_FD_PDPN_Pos_Myofibroblasts | MEAN_FD_PDPN_Pos_Myofibroblasts captures the average fractal dimension of nuclei for PDPN-positive myofibroblasts in the stroma. By employing a robust box-counting algorithm, it quantifies the complexity of nuclear structure in a normalized manner. |
| 7a3yg8qpno81 | G,Treg,Th,M,MFp,MF,Ff | MEAN_FD_PDPN_Neg_Myofibroblasts | MEAN_FD_PDPN_Neg_Myofibroblasts quantifies the mean fractal dimension of nuclei for PDPN-negative myofibroblasts in the stroma. This parameter measures nuclear boundary complexity using a normalized approach, allowing inter-patient comparisons. |
| 7a3yg8qpno81 | G,Treg,Th,M,MFp,MF,Ff | MEAN_FD_FSP1_Pos_Fibroblasts | MEAN_FD_FSP1_Pos_Fibroblasts calculates the average fractal dimension for FSP1-positive fibroblast nuclei in the stromal region. It numerically represents the level of complexity in the nuclear boundary formation derived from a box-counting method. |
| 7a3yg8qpno81 | G,Treg,Th,M,MFp,MF,Ff | COMBINED_STROMAL_FD_INDEX | COMBINED_STROMAL_FD_INDEX is a composite index that averages the mean fractal dimensions of all the specified stromal cell types. This normalized parameter provides an overall measure of nuclear boundary complexity across different cell populations within the tumor stroma. |
| 7b1dh9sh1qch | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | WEIGHTED_TERTIARY_LYMPHOID_CLUSTER_FREQUENCY | This parameter measures the frequency of tertiary lymphoid-like structures within a tumor patch by summing the weights of all valid clusters. Each valid cluster is one that contains at least one B cell, one T cell (including CD8, CD4, or regulatory T cells), and one antigen-presenting cell. The weight of a cluster is computed as the ratio of the number of primary immune cells in that cluster (B cells, T cells, and APCs) to the total count of primary immune cells in the entire patch. This normalization allows for comparison across different patient cases, reflecting the relative density and frequency of these immune clusters, which may indicate robust immune infiltration in the tumor microenvironment. |
| 7b94o2ls3ddn | TU,Tc,Th,Treg,B,M,G,Ff | CONVEX_HULL_AREA | CONVEX_HULL_AREA quantifies the spatial distribution of selected immune and fibroblast cells within a tumor patch by calculating the area of the convex polygon that minimally encloses their positions. Measured in square micrometers, this parameter reflects the spread of these cells and is suitable for inter-patient comparisons because it is derived from spatial measurements rather than being a raw cell count. |
| 7g5b29ahrlfq | MFp | PROP_PDPN_MF_ELONG_NEAR_VESSEL | PROP_PDPN_MF_ELONG_NEAR_VESSEL represents the normalized proportion of PDPN+ myofibroblasts in the stromal compartments that exhibit highly elongated nuclei and are in close proximity to vessel structures. The proportion is calculated by taking the number of cells that meet both the elongation criteria and the vessel proximity criteria and dividing it by the total number of PDPN+ myofibroblasts in the stroma, thus providing a normalized metric that can be compared across different patient cases. |
| 7iki6eki09xv | TU | Tumor_Cell_Nuclear_Perimeter_Variance | Tumor_Cell_Nuclear_Perimeter_Variance represents the sample variance of the nuclear perimeter values measured from tumor cells located within epithelial compartments. This parameter quantifies the heterogeneity in the shape of tumor cell nuclei by statistically measuring how much the nuclear perimeters differ from each other within a given tumor patch. It is computed by first filtering epithelial tumor cells with confirmed tumor markers, extracting the length of each cell's nucleus outline, and then calculating the variance using a sample variance approach. The resulting metric is numeric and is designed to be comparable across different patient cases, assisting in the identification of potential aggressive cancer phenotypes where a higher variance indicates greater morphological variability. |
| 7nave1ki3xt0 | TU,Tc,B,P,MFp,MF,E | TU_epithelial_large_nucleus_proportion | TU_epithelial_large_nucleus_proportion measures the fraction of tumor cells within the epithelial compartment that have a nucleus area equal to or exceeding the predefined threshold. This normalized parameter is calculated as the number of tumor cells with a large nucleus divided by the total number of tumor cells in the epithelial region, enabling robust comparisons between different patient cases. |
| 7nave1ki3xt0 | TU,Tc,B,P,MFp,MF,E | TU_stromal_large_nucleus_proportion | TU_stromal_large_nucleus_proportion quantifies the ratio of tumor cells with large nuclei in the stromal compartment. It is computed by dividing the count of tumor cells with a nucleus area above the threshold by the total tumor cell count in the stromal area, yielding a normalized metric suitable for inter-case analysis. |
| 7nave1ki3xt0 | TU,Tc,B,P,MFp,MF,E | MF_stromal_large_nucleus_proportion | MF_stromal_large_nucleus_proportion represents the fraction of PDPN- myofibroblasts within the stromal compartment that exhibit large nuclei. This parameter is derived by dividing the number of stromal myofibroblasts with a nucleus area meeting or exceeding the threshold by the total number of stromal myofibroblasts, providing a normalized value for comparative studies. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | global_contact_proportion | global_contact_proportion measures the ratio of observed direct intercellular contacts to the maximum possible number of unique cell pairings among the filtered cells within a tissue patch. This normalized value, which ranges between 0 and 1, provides an overall view of cellular connectivity in the tumor microenvironment. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | TU_Tc_proportion | TU_Tc_proportion represents the normalized frequency of direct contacts between tumor cells (TU) and cytotoxic T cells (Tc) relative to all observed contacts. It highlights the interaction level between these two cell types. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | M_TU_proportion | M_TU_proportion quantifies the proportion of contacts between macrophages (M) and tumor cells (TU) compared to all intercellular contacts, reflecting potential interactions between the immune and tumor compartments. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MFp_TU_proportion | MFp_TU_proportion measures the normalized frequency of contacts between myofibroblasts with podoplanin (MFp) and tumor cells (TU), offering insight into stromal and tumor cell interactions. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MF_TU_proportion | MF_TU_proportion determines the proportion of contacts between myofibroblasts (MF) and tumor cells (TU) among all detected contacts, providing an indicator of stromal influence on tumor behavior. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | F_TU_proportion | F_TU_proportion calculates the normalized frequency of direct contacts between fibroblasts (F) and tumor cells (TU) in a tissue patch, indicating aspects of the tumor microenvironment related to stromal-tumor interactions. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | E_TU_proportion | E_TU_proportion represents the proportion of contacts between endothelial cells (E) and tumor cells (TU) relative to the total number of contacts, which may reflect vascular-tumor interactions within the tissue. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Tc_Th_proportion | Tc_Th_proportion measures the ratio of contacts between cytotoxic T cells (Tc) and helper T cells (Th) normalized by all observed interactions. It provides insight into the interplay between different T cell subtypes in the immune response. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | M_Tc_proportion | M_Tc_proportion quantifies the normalized proportion of contacts between macrophages (M) and cytotoxic T cells (Tc), highlighting interactions that can influence tumor immunity. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MFp_Tc_proportion | MFp_Tc_proportion computes the frequency of direct contacts between myofibroblasts with podoplanin (MFp) and cytotoxic T cells (Tc) relative to the overall cell contact network, suggesting potential stromal-immune interactions. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MF_Tc_proportion | MF_Tc_proportion determines the proportion of interactions between myofibroblasts (MF) and cytotoxic T cells (Tc) normalized by all detected contacts, reflecting aspects of the immune microenvironment. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | F_Tc_proportion | F_Tc_proportion records the normalized frequency of contacts between fibroblasts (F) and cytotoxic T cells (Tc), offering insights into how stromal cells may interact with immune cells within the tumor. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | M_Th_proportion | M_Th_proportion measures the proportion of direct contacts between macrophages (M) and helper T cells (Th), normalized by total contacts, thereby indicating cross-talk within the immune cell population. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MF_Th_proportion | MF_Th_proportion quantifies the normalized frequency of interactions between myofibroblasts (MF) and helper T cells (Th), providing another perspective on immune-stromal cell interaction. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | F_Th_proportion | F_Th_proportion determines the proportion of direct contacts between fibroblasts (F) and helper T cells (Th) relative to all intercellular interactions, reflecting potential stromal influences on immune activity. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | M_MFp_proportion | M_MFp_proportion measures the normalized frequency of contacts between macrophages (M) and myofibroblasts with podoplanin (MFp), highlighting interactions that may play a role in shaping the tumor microenvironment. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | M_MF_proportion | M_MF_proportion quantifies the proportion of contacts between macrophages (M) and myofibroblasts (MF) relative to the entire set of interactions, indicating aspects of cellular cross-talk in the tissue. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | F_M_proportion | F_M_proportion calculates the normalized frequency of contacts between fibroblasts (F) and macrophages (M), which may be important for understanding the interplay between stromal and immune components. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | A_M_proportion | A_M_proportion represents the normalized ratio of contacts between antigen presenting cells (A) and macrophages (M) relative to all cellular interactions, providing insights into immune cell communication. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MF_MFp_proportion | MF_MFp_proportion measures the proportion of interactions between myofibroblasts (MF) and myofibroblasts with podoplanin (MFp) normalized to the total number of contacts, suggesting heterogeneity within the stromal compartment. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | F_MFp_proportion | F_MFp_proportion quantifies the normalized frequency of contacts between fibroblasts (F) and myofibroblasts with podoplanin (MFp), offering insights into stromal cell interactions in the tumor microenvironment. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | E_MFp_proportion | E_MFp_proportion computes the proportion of direct contacts between endothelial cells (E) and myofibroblasts with podoplanin (MFp) normalized by total contacts, which may be indicative of vascular-stromal interactions. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | F_MF_proportion | F_MF_proportion measures the normalized frequency of contacts between fibroblasts (F) and myofibroblasts (MF) relative to all interactions, reflecting aspects of stromal organization. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | E_MF_proportion | E_MF_proportion quantifies the proportion of direct contacts between endothelial cells (E) and myofibroblasts (MF) normalized to the overall contact count, possibly indicating influences on tumor vascularization. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | E_F_proportion | E_F_proportion calculates the normalized frequency of contacts between endothelial cells (E) and fibroblasts (F), providing a measure of interactions that may be critical in vascular support. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | TU_TU_proportion | TU_TU_proportion quantifies the normalized rate of tumor cell (TU) self-interactions by computing the proportion of tumor-to-tumor contacts among all observed contacts, which can shed light on tumor clustering. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Tc_Tc_proportion | Tc_Tc_proportion measures the normalized frequency of contacts among cytotoxic T cells (Tc) relative to total interactions, reflecting intra-lineage cell communication within the immune compartment. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | M_M_proportion | M_M_proportion computes the normalized proportion of macrophage-to-macrophage contacts, giving insight into the level of macrophage clustering within the tissue. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MFp_MFp_proportion | MFp_MFp_proportion represents the normalized frequency of self-interactions among myofibroblasts with podoplanin (MFp), indicating contact density within this specific stromal cell type. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MF_MF_proportion | MF_MF_proportion quantifies the normalized proportion of contacts among myofibroblasts (MF) relative to all cellular interactions, reflecting the degree of self-association within this cell population. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | F_F_proportion | F_F_proportion measures the normalized rate of fibroblast-to-fibroblast contacts, providing insight into the clustering behavior of fibroblasts within the tumor microenvironment. |
| 7p8gz1o7a7y0 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | E_E_proportion | E_E_proportion computes the normalized frequency of contacts among endothelial cells (E), indicating the degree of endothelial cell connectivity in the tissue. |
| 7pswufg727sq | MFp | median_nucleus_diameter_pdpn_myofibroblasts_stroma | This parameter quantifies the median nucleus diameter (in micrometers) for PDPN+ myofibroblasts located in the stromal regions of breast cancer tissues. It is derived by filtering cell data to include only those cells classified as PDPN-positive myofibroblasts that are situated in the stroma, measuring each nucleus by calculating its area based on the polygonal representation, and then converting this area into an equivalent diameter using the formula for a circle. The resulting diameters are collected and the median value is computed, providing a normalized numerical measure that is comparable across different patient cases and tissue patches. This metric is used to assess nuclear size, which may correlate with an activated cellular phenotype involved in tumor progression. |
| 7sa9vjsulcdh | TU,Tc,Th,Treg,B,P,M,MFp,Ff,A | TU_level1_H_energy | For cell type TU (tumor cells): The metrics TU_levelX_H_energy, TU_levelX_V_energy, TU_levelX_D_energy, and TU_levelX_A_energy (with X representing decomposition levels 1, 2, and 3) quantify the energy derived from the wavelet transform of a Gaussian-smoothed cell density map in the stromal compartment. The horizontal (H), vertical (V), and diagonal (D) energies capture directional texture features at each scale, while the approximation (A) energy reflects the overall density pattern. |
| 7sa9vjsulcdh | TU,Tc,Th,Treg,B,P,M,MFp,Ff,A | TU_level1_V_energy | For cell type Tc (cytotoxic T cells): The parameters Tc_levelX_H_energy, Tc_levelX_V_energy, Tc_levelX_D_energy, and Tc_levelX_A_energy measure the scale-specific wavelet energy features that describe the spatial infiltration patterns of cytotoxic T cells. They reflect the strength of horizontal, vertical, and diagonal fluctuations, as well as the general density structure at each decomposition level. |
| 7sa9vjsulcdh | TU,Tc,Th,Treg,B,P,M,MFp,Ff,A | TU_level1_D_energy | For cell type Th (helper T cells): The metrics Th_levelX_H_energy, Th_levelX_V_energy, Th_levelX_D_energy, and Th_levelX_A_energy capture the directional energy components and overall approximation energy computed from the multiscale 2D wavelet transform. They represent the textural and distributional properties of helper T cells in the tissue environment. |
| 7sa9vjsulcdh | TU,Tc,Th,Treg,B,P,M,MFp,Ff,A | TU_level1_A_energy | For cell type Treg (regulatory T cells): The parameters Treg_levelX_H_energy, Treg_levelX_V_energy, Treg_levelX_D_energy, and Treg_levelX_A_energy are obtained by summing the squared wavelet coefficients from the Gaussian smoothed density maps. They characterize the directional detail (horizontal, vertical, diagonal) and overall approximation energies indicative of the spatial arrangement of regulatory T cells. |
| 7sa9vjsulcdh | TU,Tc,Th,Treg,B,P,M,MFp,Ff,A | TU_level2_H_energy | For cell type B (B cells): The features B_levelX_H_energy, B_levelX_V_energy, B_levelX_D_energy, and B_levelX_A_energy reflect the multiscale spatial variability of B cell distributions. The computed energies from the 2D wavelet transform serve to quantify both directional (H, V, D) details and the general approximation pattern of the cell density map. |
| 7sa9vjsulcdh | TU,Tc,Th,Treg,B,P,M,MFp,Ff,A | TU_level2_V_energy | For cell type P (plasma cells): The parameters P_levelX_H_energy, P_levelX_V_energy, P_levelX_D_energy, and P_levelX_A_energy measure the spatial texture characteristics of plasma cells by computing the energy in the horizontal, vertical, diagonal, and overall approximation components from a multiscale wavelet analysis of their distribution. |
| 7sa9vjsulcdh | TU,Tc,Th,Treg,B,P,M,MFp,Ff,A | TU_level2_D_energy | For cell type M (macrophages): The metrics M_levelX_H_energy, M_levelX_V_energy, M_levelX_D_energy, and M_levelX_A_energy are derived from a 2D wavelet transform applied to the Gaussian-smoothed density map of macrophages. They quantify how energy is distributed across different directions and scales, representing the infiltration pattern of these cells. |
| 7sa9vjsulcdh | TU,Tc,Th,Treg,B,P,M,MFp,Ff,A | TU_level2_A_energy | For cell type MFp (myofibroblasts with PDPN): The features MFp_levelX_H_energy, MFp_levelX_V_energy, MFp_levelX_D_energy, and MFp_levelX_A_energy capture the specific multiscale energy distribution associated with myofibroblast patterns. These parameters reflect the directional details and the overall approximation energy from the wavelet decomposition of their spatial distribution. |
| 7sa9vjsulcdh | TU,Tc,Th,Treg,B,P,M,MFp,Ff,A | TU_level3_H_energy | For cell type Ff (FSP1 positive fibroblasts): The parameters Ff_levelX_H_energy, Ff_levelX_V_energy, Ff_levelX_D_energy, and Ff_levelX_A_energy represent the wavelet energies computed from the fibroblast density heatmap. They provide a quantitative assessment of horizontal, vertical, and diagonal texture features as well as the general density pattern at each scale. |
| 7sa9vjsulcdh | TU,Tc,Th,Treg,B,P,M,MFp,Ff,A | TU_level3_V_energy | For cell type A (antigen presenting cells): The metrics A_levelX_H_energy, A_levelX_V_energy, A_levelX_D_energy, and A_levelX_A_energy summarize the multiscale spatial characteristics of antigen presenting cells. Through the energy of horizontal, vertical, and diagonal detail coefficients along with the approximation energy, these parameters measure the infiltration patterns and density distribution within the stromal compartment. |
| 7xsjpiepaqm0 | TU,Tc,Treg,B,P,M,G,MFp,E | Tc_median_depth | Tc_median_depth: Represents the median distance measured from the centroid of CD8+ T cells to the tumor boundary. This metric summarizes the typical infiltration depth of these immune cells within the tumor microenvironment. |
| 7xsjpiepaqm0 | TU,Tc,Treg,B,P,M,G,MFp,E | Treg_median_depth | Treg_median_depth: Indicates the median minimal Euclidean distance of regulatory T cells from the tumor border. It captures the central tendency of their spatial penetration into the tumor region. |
| 7xsjpiepaqm0 | TU,Tc,Treg,B,P,M,G,MFp,E | B_median_depth | B_median_depth: Reports the median distance from the tumor boundary to the centroids of B cells. It reflects how deeply B cells infiltrate the tumor area. |
| 7xsjpiepaqm0 | TU,Tc,Treg,B,P,M,G,MFp,E | P_median_depth | P_median_depth: Measures the median penetration depth of plasma cells by calculating the median of the minimal distances from their centroids to the tumor boundary. |
| 7xsjpiepaqm0 | TU,Tc,Treg,B,P,M,G,MFp,E | M_median_depth | M_median_depth: Provides the median minimal distance of macrophages from the tumor boundary, serving as an indicator of their depth of infiltration in the tissue. |
| 7xsjpiepaqm0 | TU,Tc,Treg,B,P,M,G,MFp,E | G_median_depth | G_median_depth: Denotes the median penetration depth of granulocytes, derived from the central tendency of the minimal Euclidean distances between granulocyte centroids and the tumor boundary. |
| 7xsjpiepaqm0 | TU,Tc,Treg,B,P,M,G,MFp,E | MFp_median_depth | MFp_median_depth: Captures the median distance of PDPN+ myofibroblasts from the tumor edge. This parameter reflects the typical infiltration level of this stromal cell subtype. |
| 7xsjpiepaqm0 | TU,Tc,Treg,B,P,M,G,MFp,E | E_median_depth | E_median_depth: Reflects the median penetration depth of endothelial cells from the tumor boundary, summarizing their position relative to the tumor border. |
| 7xsjpiepaqm0 | TU,Tc,Treg,B,P,M,G,MFp,E | TU_mean_depth | TU_mean_depth: Represents the average distance of epithelial tumor cells from the tumor boundary calculated over all such cells, indicating overall tumor cell infiltration depth. |
| 7xsjpiepaqm0 | TU,Tc,Treg,B,P,M,G,MFp,E | Tc_mean_depth | Tc_mean_depth: Measures the average penetration depth of CD8+ T cells by computing the mean of minimal distances from their centroids to the tumor boundary. |
| 7xsjpiepaqm0 | TU,Tc,Treg,B,P,M,G,MFp,E | Treg_mean_depth | Treg_mean_depth: Indicates the average minimal distance of regulatory T cells from the tumor border, providing insight into their collective infiltration behavior. |
| 7xsjpiepaqm0 | TU,Tc,Treg,B,P,M,G,MFp,E | B_mean_depth | B_mean_depth: Reports the mean penetration depth of B cells, summarizing the overall extent to which these cells are found deeper within the tumor region. |
| 7xsjpiepaqm0 | TU,Tc,Treg,B,P,M,G,MFp,E | P_mean_depth | P_mean_depth: Captures the average minimal distance from the tumor boundary for plasma cells, reflecting the overall infiltration pattern of these cells. |
| 7xsjpiepaqm0 | TU,Tc,Treg,B,P,M,G,MFp,E | M_mean_depth | M_mean_depth: Represents the mean penetration depth of macrophages, which is calculated as the average of their minimal distances to the tumor boundary. |
| 7xsjpiepaqm0 | TU,Tc,Treg,B,P,M,G,MFp,E | G_mean_depth | G_mean_depth: Denotes the average penetration depth of granulocytes based on their minimal Euclidean distances, reflecting their typical spatial distribution within the tumor. |
| 7xsjpiepaqm0 | TU,Tc,Treg,B,P,M,G,MFp,E | MFp_mean_depth | MFp_mean_depth: Measures the mean penetration depth of PDPN+ myofibroblasts, indicating their average distance from the tumor border across the analyzed region. |
| 7xsjpiepaqm0 | TU,Tc,Treg,B,P,M,G,MFp,E | E_mean_depth | E_mean_depth: Reflects the average minimal distance of endothelial cells from the tumor boundary, summarizing their spatial positioning relative to the tumor edge. |
| 7xsjpiepaqm0 | TU,Tc,Treg,B,P,M,G,MFp,E | composite_penetration_index | composite_penetration_index: A composite metric computed as the average of the median penetration depths across all targeted cell subtypes. This index provides an overall, normalized measure of cell infiltration depth, facilitating comparisons across different patient cases and tissue patches. |
| 7zlh26nztsrt | B,MFp | pdpn_mfb_density_epithelial | The parameter 'pdpn_mfb_density_epithelial' represents the normalized density of PDPN+ myofibroblasts in the epithelial compartment. It is computed by dividing the number of PDPN+ myofibroblasts identified within the epithelial area by the total epithelial area (measured as pixels). This normalization allows for direct comparison across different patient cases and tissue patches as it adjusts for variations in the size of the epithelial region analysed. |
| 7zs5vnjntrh7 | Treg | MEAN_TREG_NUCLEUS_LACUNARITY | MEAN_TREG_NUCLEUS_LACUNARITY measures the average lacunarity value computed from the nuclei of regulatory T cells located in the stromal compartment. This average provides an estimation of the overall chromatin organization pattern, enabling comparison across different patient cases by reflecting the structural heterogeneity of cell nuclei. |
| 7zs5vnjntrh7 | Treg | STD_TREG_NUCLEUS_LACUNARITY | STD_TREG_NUCLEUS_LACUNARITY represents the standard deviation of lacunarity values calculated for the regulatory T cell nuclei in the stroma. It quantifies the variability of chromatin organization among these cells, allowing researchers to gauge how consistently structured the nuclei are within a tumor patch. |
| 7zs5vnjntrh7 | Treg | MIN_TREG_NUCLEUS_LACUNARITY | MIN_TREG_NUCLEUS_LACUNARITY captures the lowest lacunarity value observed among the regulatory T cell nuclei in the stromal compartment. This metric highlights the instance of the most homogeneous chromatin structure, serving as a relative indicator of nuclear uniformity. |
| 7zs5vnjntrh7 | Treg | MAX_TREG_NUCLEUS_LACUNARITY | MAX_TREG_NUCLEUS_LACUNARITY records the highest lacunarity value from the set of regulatory T cell nuclei within the stroma. It identifies the most heterogeneous nucleus in terms of chromatin organization, providing insight into cellular diversity within the tumor area. |
| 7zs5vnjntrh7 | Treg | VALID_TREG_CELL_PERCENTAGE | VALID_TREG_CELL_PERCENTAGE calculates the proportion, expressed as a percentage, of regulatory T cells in the stromal region that yield valid lacunarity measurements. By normalizing the count of cells with computable results against the total number of such cells, this parameter supports consistent comparisons across different tumor regions and patient cases. |
| 7zy1gw0ekxmf | TU,MFp | mean_area_tumor_cells | mean_area_tumor_cells is the average nuclear area of tumor cells (epithelial cells) calculated by measuring the area of each cell nucleus from its polygon representation and then computing the arithmetic mean. This metric is normalized per patch, allowing for comparisons across different patient cases. |
| 7zy1gw0ekxmf | TU,MFp | mean_area_pdpn_mf | mean_area_pdpn_mf represents the average nuclear area of PDPN+ myofibroblasts. It is determined by calculating the nuclear area of each PDPN+ myofibroblast and averaging these values, making it a normalized measure suitable for comparing regions from various patient samples. |
| 7zy1gw0ekxmf | TU,MFp | area_difference | area_difference is the computed difference between the mean nuclear area of tumor cells and that of PDPN+ myofibroblasts. It is derived by subtracting the mean area of PDPN+ myofibroblasts from the mean area of tumor cells, and it serves as a normalized indicator of the morphological disparity between these cell types in tumor regions. |
| 82wwhoqn8izj | P,MFp | PDPN_MYOFIB_MEAN_PERIMETER | PDPN_MYOFIB_MEAN_PERIMETER represents the average nuclear perimeter of the PDPN+ myofibroblasts in the epithelial tumor region. This parameter is calculated by measuring the perimeter of each cell's nucleus and then averaging these measures, offering a normalized metric that is comparable across different patient cases. |
| 82wwhoqn8izj | P,MFp | PDPN_MYOFIB_MEDIAN_PERIMETER | PDPN_MYOFIB_MEDIAN_PERIMETER indicates the median value of nuclear perimeters for PDPN+ myofibroblasts within the epithelial region. By using the median, this parameter provides a robust central tendency measure that minimizes the impact of outliers, ensuring a normalized and reliable comparison across samples. |
| 8ahph8i3y7cv | Treg,Th | MEDIAN_DISTANCE_TREG_TO_TH | MEDIAN_DISTANCE_TREG_TO_TH represents the median of all computed Euclidean distances between regulatory T cells and helper T cells within the stromal compartment. This parameter provides a normalized measure of the typical spatial proximity between these two cell types, making it comparable across different patient cases and tumor regions. |
| 8ahph8i3y7cv | Treg,Th | MIN_DISTANCE_TREG_TO_TH | MIN_DISTANCE_TREG_TO_TH is the minimum distance recorded among all pairwise Euclidean distances between regulatory T cells and helper T cells in the stroma. It reflects the closest observed interaction between these cell types, and being based on spatial measurement, it is normalized for comparison across different samples. |
| 8ahph8i3y7cv | Treg,Th | MAX_DISTANCE_TREG_TO_TH | MAX_DISTANCE_TREG_TO_TH indicates the maximum distance between any regulatory T cell and helper T cell pair within the stromal compartment. This parameter highlights the spread or dispersion of the cells and, as a normalized spatial metric, can be compared across patches from different patients. |
| 8ahph8i3y7cv | Treg,Th | MEAN_DISTANCE_TREG_TO_TH | MEAN_DISTANCE_TREG_TO_TH calculates the average of all pairwise Euclidean distances between regulatory T cells and helper T cells in the stroma. This measure gives an overall sense of the spatial separation between the two cell populations in a given tumor region, which is normalized and suitable for cross-sample comparison. |
| 8ahph8i3y7cv | Treg,Th | STD_DISTANCE_TREG_TO_TH | STD_DISTANCE_TREG_TO_TH is the standard deviation of the spatial distances measured between regulatory T cells and helper T cells. It quantifies the variability in the spatial distribution of the cells, offering insights into how uniformly the cells are positioned relative to each other across different tumor regions. |
| 8cy4v93sig6h | G | PROPORTION_GRANULOCYTES_NEAR_VESSELS | This parameter represents the normalized percentage of stromal granulocytes that are located within 15 µm of any vessel. It is calculated by determining the proportion of granulocytes in the stroma that fall below the 15 µm distance threshold from the nearest vessel, making it suitable for comparing different patient cases. |
| 8d561r9a6y0n | B,F,MF,TU,Tc | median_nuclear_aspect_ratio_TU | median_nuclear_aspect_ratio_TU: This parameter measures the median nuclear aspect ratio for tumor cells in the stromal compartment. It is determined by fitting the minimum rotated rectangle around each nucleus, calculating the major (longer) and minor (shorter) side lengths, and then computing the ratio of these two values. The computed median provides a normalized, numeric metric that can be compared across different patient cases. |
| 8d561r9a6y0n | B,F,MF,TU,Tc | median_nuclear_aspect_ratio_Tc | median_nuclear_aspect_ratio_Tc: This parameter measures the median nuclear aspect ratio for cytotoxic T cells in the stromal compartment. The aspect ratio is obtained by fitting a minimum rotated rectangle to the nucleus of each cell and calculating the ratio of the longest side to the shortest side. The resulting median value serves as a normalized, numeric measure for comparing nuclear shape alterations across cases. |
| 8d561r9a6y0n | B,F,MF,TU,Tc | median_nuclear_aspect_ratio_F | median_nuclear_aspect_ratio_F: This parameter measures the median nuclear aspect ratio for fibroblasts (FSP1-) in the stromal compartment. Each nucleus’s shape is quantified by computing the ratio of its major axis to its minor axis from the minimum rotated rectangle. The median of these values yields a normalized and numeric parameter, enabling valid comparisons between patient samples. |
| 8d561r9a6y0n | B,F,MF,TU,Tc | median_nuclear_aspect_ratio_MF | median_nuclear_aspect_ratio_MF: This parameter measures the median nuclear aspect ratio for PDPN- myofibroblasts in the stromal compartment. It is calculated by determining the ratio between the longest and shortest sides of the minimum rotated rectangle fitted around each nucleus and then taking the median of these ratios. The result is a normalized numeric parameter suitable for cross-case analysis. |
| 8d561r9a6y0n | B,F,MF,TU,Tc | median_nuclear_aspect_ratio_B | median_nuclear_aspect_ratio_B: This parameter measures the median nuclear aspect ratio for B lymphocytes in the stromal compartment. It involves fitting a minimum rotated rectangle around each nucleus to compute the ratio of the major axis to the minor axis, followed by the calculation of a median value. The outcome is a normalized, numeric measure that aids in the comparative evaluation of nuclear shape modifications among patients. |
| 8n4x1sn2cp0g | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_knn_distance_variance | weighted_knn_distance_variance represents the weighted variance of distances to the kth nearest neighbor for cells within a tumor patch. This parameter is calculated by first computing the kth distance for each cell based on spatial coordinates, then weighting each distance by the proportion of its cell type within the region, and finally determining the variance of these weighted distances. This measure reflects how variable the distances are, offering insight into the heterogeneity of the spatial distribution of various cell types. As a derived statistical measure, it is normalized and comparable across different patches and patient cases. |
| 8n4x1sn2cp0g | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_knn_distance_std | weighted_knn_distance_std is the square root of the weighted variance of kth nearest neighbor distances. It provides the dispersion of these distances in the same physical units as the measurements (such as micrometers), offering a direct and interpretable measure of spatial heterogeneity. Like its variance counterpart, this parameter is normalized, numeric, and suitable for comparison across different tumor regions. |
| 8nmj331xxc99 | MFp,MF,Ff,F,M,G,A,Th,B | min_hotspot_distance | min_hotspot_distance represents the smallest Euclidean distance calculated between a fibroblast hotspot and its nearest immune hotspot within a tumor patch. This metric enables comparison across different patient cases by indicating the closest interaction point between these cellular clusters. |
| 8nmj331xxc99 | MFp,MF,Ff,F,M,G,A,Th,B | max_hotspot_distance | max_hotspot_distance is the largest Euclidean distance observed between any fibroblast hotspot and its nearest immune hotspot in a patch. It provides insight into the maximum spatial separation in the tumor microenvironment, facilitating normalized comparisons across cases. |
| 8nmj331xxc99 | MFp,MF,Ff,F,M,G,A,Th,B | mean_hotspot_distance | mean_hotspot_distance is the average Euclidean distance between fibroblast hotspots and their closest immune hotspots, summarizing the overall proximity between these cell groups within a tumor patch. As an averaged metric, it is normalized and allows direct comparison across different patient tissues. |
| 8nmj331xxc99 | MFp,MF,Ff,F,M,G,A,Th,B | median_hotspot_distance | median_hotspot_distance calculates the middle value of the sorted distances from fibroblast hotspots to their nearest immune hotspots. This robust measure of central tendency minimizes the effect of extreme values and is normalized for comparing spatial relationships across patches. |
| 8nmj331xxc99 | MFp,MF,Ff,F,M,G,A,Th,B | weighted_mean_distance | weighted_mean_distance is the average distance between fibroblast and immune hotspots weighted by the product of their hotspot sizes. This normalization gives greater influence to larger clusters, providing a balanced metric that can be compared across different tumor samples. |
| 8nmj331xxc99 | MFp,MF,Ff,F,M,G,A,Th,B | std_hotspot_distance | std_hotspot_distance is the standard deviation of distances between fibroblast hotspots and their closest immune hotspots. It quantifies the variability in distances across a patch and, as a normalized dispersion metric, enables comparison of spatial heterogeneity between patient cases. |
| 8nmj331xxc99 | MFp,MF,Ff,F,M,G,A,Th,B | fibroblast_to_immune_ratio | fibroblast_to_immune_ratio is the ratio of the number of fibroblast cells to immune cells within the stroma of a tumor patch. As a relative measure, it is normalized and facilitates comparative analysis of cell population balance across different patient cases. |
| 8ovmv3uqzkrx | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | SHANNON_DIVERSITY_INDEX | SHANNON_DIVERSITY_INDEX is a normalized and numeric metric that measures the diversity of cell types in a tumor patch. It is derived by first computing the fraction of each of the 14 predefined cell types among the total cells, and then applying a formula where each fraction is multiplied by the natural logarithm of itself (with the summed product negated) to yield the diversity index. Higher values indicate a more even and heterogeneous distribution of different cell types, reflecting a potentially more adaptable tumor microenvironment, while lower values suggest that a few cell types are predominant. |
| 8s9jc92xi07o | Tc,B,F,MFp | mean_alignment_index | mean_alignment_index measures the average cosine similarity between the dipole vectors of neighboring cells near vessels. This value, ranging from 0 to 1, provides an overall indicator of how consistently the cell orientations align, making it suitable for comparing different patient cases. |
| 8s9jc92xi07o | Tc,B,F,MFp | median_alignment_index | median_alignment_index represents the middle value in the distribution of cosine similarities between neighboring cells' dipole vectors near vessels. It offers a robust summary of the alignment, less affected by extreme values, and is normalized for effective cross-case comparisons. |
| 8s9jc92xi07o | Tc,B,F,MFp | min_alignment_index | min_alignment_index captures the smallest cosine similarity value observed among neighboring cell pairs near vessels. This parameter highlights the region with the least cell orientation coordination and, being derived from normalized alignment values, is suitable for comparative analysis. |
| 8s9jc92xi07o | Tc,B,F,MFp | max_alignment_index | max_alignment_index denotes the highest cosine similarity observed among neighboring cell pairs near vessels, indicating the area with the most aligned cell orientations. As it is normalized, it can be reliably used for comparison across different patient cases. |
| 8s9jc92xi07o | Tc,B,F,MFp | std_alignment_index | std_alignment_index quantifies the variability or dispersion of the cosine similarity values between neighboring cell pairs near vessels. It provides insights into the consistency of cell alignment within a patch and is normalized to allow comparisons between different cases. |
| 8uyssp3wmkk6 | TU,Tc,F,MF | BOUNDARY_IRREGULARITY_INDEX | BOUNDARY_IRREGULARITY_INDEX is the average ratio computed by dividing the perimeter of the cluster’s unified cell boundary by the perimeter of its convex hull. This normalized metric reflects how irregular the boundaries of the cell clusters are, where higher values indicate greater irregularity and potential biological implications in tumor tissue remodeling. |
| 8uyssp3wmkk6 | TU,Tc,F,MF | MEAN_PERIMETER | MEAN_PERIMETER represents the average length of the perimeters of the clusters formed by the union of cell polygons. This metric provides a quantitative measure in micrometers of the boundary length of clusters, capturing the physical extent of the cell groupings. |
| 8uyssp3wmkk6 | TU,Tc,F,MF | MEAN_CONVEX_HULL_PERIMETER | MEAN_CONVEX_HULL_PERIMETER is the average perimeter of the convex hulls calculated for each cell cluster. The convex hull perimeter serves as a reference to understand the overall roughness and spread of the cluster shape. |
| 8uyssp3wmkk6 | TU,Tc,F,MF | MAX_IRREGULARITY | MAX_IRREGULARITY is the highest value of the boundary irregularity index observed among all clusters. It emphasizes the most irregular cluster shape in relation to its convex hull and can signal extreme instances of morphological variation. |
| 8uyssp3wmkk6 | TU,Tc,F,MF | MIN_IRREGULARITY | MIN_IRREGULARITY is the lowest boundary irregularity index value among the clusters, identifying the cluster whose boundary is closest to its convex hull, thereby representing the most regular structure within the examined region. |
| 8uyssp3wmkk6 | TU,Tc,F,MF | STD_IRREGULARITY | STD_IRREGULARITY is the standard deviation of the boundary irregularity indices across all clusters. This metric quantifies the variability in irregularity among clusters, providing insights into the consistency or heterogeneity of the cell clustering patterns. |
| 915p00bsybtz | TU,Tc,M,MFp,MF,Ff,F | AVG_DISTANCE_TO_TUMOR | AVG_DISTANCE_TO_TUMOR measures the mean distance, in micrometers, from each stromal-immune cell to its closest tumor cell. This metric is determined by calculating the minimum Euclidean distance from each targeted stromal-immune cell to all tumor cell centroids within each analyzed patch, providing an aggregated value that reflects the overall spatial proximity between immune-stromal cells and tumor cells. |
| 915p00bsybtz | TU,Tc,M,MFp,MF,Ff,F | COEF_VARIATION_DISTANCE | COEF_VARIATION_DISTANCE represents the coefficient of variation of the distances from stromal-immune cells to their nearest tumor cell. It is computed as the ratio of the standard deviation to the mean of these distances, offering a normalized, dimensionless measure that quantifies the degree of spatial heterogeneity in the distribution of stromal-immune cells relative to tumor cells across different patient cases. |
| 91yy5teas6va | TU,Tc,Th,B,P,M,MFp,MF,Ff,E | average_nuclear_perimeter | The average nuclear perimeter parameter quantifies the mean length of the perimeters of cell nuclei from a specific set of cell types, including epithelial cells, CD8+ T cells, CD4+ T cells, B cells, plasma cells, macrophages, PDPN+ myofibroblasts, myofibroblasts, fibroblasts expressing FSP1, and endothelial cells. This parameter is calculated by summing the perimeters of individual nuclei, which are determined using their polygon boundaries, and dividing this total by the count of valid cells within a patch. As an averaged measure, it is normalized and comparable across different patient samples and tumor regions, providing insights into variations in nuclear morphology that may correlate with tumor aggressiveness and immune response patterns. |
| 95tqiq971b79 | MF | skewness_pdpn_neg_mf_nucleus_area | This parameter represents the skewness of the nucleus area distribution for PDPN-negative myofibroblasts found in epithelial (tumor) compartments. It quantifies the asymmetry of the distribution, where a positive value indicates a right-skewed distribution with a predominance of smaller nuclei and a tail extending towards larger sizes, and a negative value indicates a left-skewed distribution. As a normalized and numeric measure, it facilitates comparisons across different patient cases. |
| 9bdwjpv1fmdm | TU,Tc,Th,Treg,B,P,M,G,MF,Ff,A | correlation_coefficient | correlation_coefficient quantifies the linear relationship between the bounding box aspect ratios of neighboring cells of different types. This normalized metric, computed via the Pearson correlation method, reflects coordinated morphological adaptations in tumor regions, enabling meaningful comparisons across different patient cases. |
| 9d00z9xtifzo | Th,B,F,M | Th_density_0_20 | Th_density_0_20: This parameter represents the normalized density of helper T cells within a spatial ring spanning from 0 to 20 micrometers from the epithelial boundary. The value is calculated by dividing the count of helper T cells in this narrow ring by the area (converted to mm²) of that ring, allowing for standardized comparisons across different tumor patches. |
| 9d00z9xtifzo | Th,B,F,M | B_density_0_20 | B_density_0_20: This parameter denotes the normalized density of B cells measured in the 0 to 20 micrometer ring adjacent to the epithelial boundary. The computation involves normalizing the count of B cells in that ring by the corresponding area, resulting in a density expressed as cells per mm². |
| 9d00z9xtifzo | Th,B,F,M | F_density_0_20 | F_density_0_20: This parameter measures the normalized density of fibroblasts (FSP1-) found in the 0 to 20 micrometer ring from the epithelial boundary. The density is obtained by dividing the number of fibroblasts within the ring by its area (in mm²), thus providing a comparable metric across patient cases. |
| 9d00z9xtifzo | Th,B,F,M | M_density_0_20 | M_density_0_20: This parameter provides the normalized density of macrophages in the 0 to 20 micrometer ring from the epithelial boundary. It is derived by normalizing the count of macrophages by the area of the ring, yielding a density in cells per mm². |
| 9d00z9xtifzo | Th,B,F,M | Th_density_20_40 | Th_density_20_40: This parameter quantifies the normalized density of helper T cells in the 20 to 40 micrometer ring from the epithelial boundary. The value is computed by dividing the number of helper T cells in this ring by its area (converted to mm²), ensuring comparability across subjects. |
| 9d00z9xtifzo | Th,B,F,M | F_density_20_40 | F_density_20_40: This parameter reflects the normalized density of fibroblasts (FSP1-) in the 20 to 40 micrometer ring from the epithelial boundary. The density is determined by normalizing the cell count by the area of the ring, expressed as cells per mm². |
| 9d00z9xtifzo | Th,B,F,M | M_density_20_40 | M_density_20_40: This parameter represents the normalized density of macrophages present in the 20 to 40 micrometer ring from the epithelial boundary. It is calculated by dividing the macrophage count by the ring’s area, with the result given in cells per mm². |
| 9d00z9xtifzo | Th,B,F,M | Th_density_40_60 | Th_density_40_60: This parameter captures the normalized density of helper T cells in the 40 to 60 micrometer ring from the epithelial boundary. It is computed by taking the count of helper T cells and normalizing it to the measured area of the ring (mm²), thus allowing comparisons between cases. |
| 9d00z9xtifzo | Th,B,F,M | F_density_40_60 | F_density_40_60: This parameter denotes the normalized density of fibroblasts (FSP1-) in the 40 to 60 micrometer ring from the epithelial boundary. The density is calculated by dividing the number of fibroblasts by the area of the ring, resulting in a value in cells per mm². |
| 9d00z9xtifzo | Th,B,F,M | M_density_40_60 | M_density_40_60: This parameter defines the normalized density of macrophages in the 40 to 60 micrometer ring from the epithelial boundary. The value is obtained by normalizing the count of macrophages by the area of the ring (mm²), facilitating cross-case analysis. |
| 9d00z9xtifzo | Th,B,F,M | Th_density_60_80 | Th_density_60_80: This parameter indicates the normalized density of helper T cells in the 60 to 80 micrometer ring from the epithelial boundary. The density is determined by dividing the helper T cell count by the ring area, yielding a standardized metric in cells per mm². |
| 9d00z9xtifzo | Th,B,F,M | B_density_60_80 | B_density_60_80: This parameter represents the normalized density of B cells in the 60 to 80 micrometer ring from the epithelial boundary. The measurement normalizes the B cell count against the corresponding area of the ring (in mm²), making it suitable for comparative studies. |
| 9d00z9xtifzo | Th,B,F,M | F_density_60_80 | F_density_60_80: This parameter measures the normalized density of fibroblasts (FSP1-) in the 60 to 80 micrometer ring from the epithelial boundary. The density is computed by normalizing the fibroblast count by the area of the ring, resulting in units of cells per mm². |
| 9d00z9xtifzo | Th,B,F,M | M_density_60_80 | M_density_60_80: This parameter quantifies the normalized density of macrophages in the 60 to 80 micrometer ring from the epithelial boundary. It is calculated by dividing the macrophage count by the area of the ring, with the result expressed in cells per mm². |
| 9d00z9xtifzo | Th,B,F,M | Th_density_80_100 | Th_density_80_100: This parameter quantifies the normalized density of helper T cells located within the 80 to 100 micrometer ring from the epithelial boundary. The calculation involves normalizing the cell count to the ring's area, resulting in a comparable density measure in cells per mm². |
| 9d00z9xtifzo | Th,B,F,M | B_density_80_100 | B_density_80_100: This parameter reflects the normalized density of B cells measured in the 80 to 100 micrometer ring from the epithelial boundary. The value is obtained by dividing the number of B cells by the area of the ring (mm²), ensuring the metric is normalized. |
| 9d00z9xtifzo | Th,B,F,M | F_density_80_100 | F_density_80_100: This parameter indicates the normalized density of fibroblasts (FSP1-) in the 80 to 100 micrometer ring from the epithelial boundary. The density is computed by normalizing the fibroblast count by the area of the ring, expressed as cells per mm². |
| 9d00z9xtifzo | Th,B,F,M | M_density_80_100 | M_density_80_100: This parameter represents the normalized density of macrophages found within the 80 to 100 micrometer ring from the epithelial boundary. The metric is derived by dividing the macrophage count by the corresponding ring area, yielding a density in cells per mm². |
| 9d00z9xtifzo | Th,B,F,M | Th_density_100_120 | Th_density_100_120: This parameter captures the normalized density of helper T cells in the 100 to 120 micrometer ring from the epithelial boundary. It is computed by normalizing the helper T cell number by the area of the ring (mm²), thus providing a standardized metric. |
| 9d00z9xtifzo | Th,B,F,M | B_density_100_120 | B_density_100_120: This parameter denotes the normalized density of B cells in the 100 to 120 micrometer ring from the epithelial boundary. The density is calculated by dividing the B cell count by the area of the ring, resulting in a value expressed in cells per mm². |
| 9d00z9xtifzo | Th,B,F,M | F_density_100_120 | F_density_100_120: This parameter measures the normalized density of fibroblasts (FSP1-) in the 100 to 120 micrometer ring from the epithelial boundary. The density is determined by normalizing the number of fibroblasts to the area of the ring (converted to mm²). |
| 9d00z9xtifzo | Th,B,F,M | M_density_100_120 | M_density_100_120: This parameter indicates the normalized density of macrophages in the 100 to 120 micrometer ring from the epithelial boundary. It is calculated by dividing the macrophage count by the corresponding ring area, yielding a density value in cells per mm². |
| 9d00z9xtifzo | Th,B,F,M | Th_density_120_140 | Th_density_120_140: This parameter represents the normalized density of helper T cells within the 120 to 140 micrometer ring from the epithelial boundary. The density value is derived by normalizing the count of helper T cells by the area of the ring, ensuring comparability in cells per mm². |
| 9d00z9xtifzo | Th,B,F,M | B_density_120_140 | B_density_120_140: This parameter quantifies the normalized density of B cells in the 120 to 140 micrometer ring from the epithelial boundary. It is computed by dividing the B cell count by the area of the ring (mm²), producing a standardized density measure. |
| 9d00z9xtifzo | Th,B,F,M | F_density_120_140 | F_density_120_140: This parameter reflects the normalized density of fibroblasts (FSP1-) in the 120 to 140 micrometer ring from the epithelial boundary. The density is obtained by normalizing the fibroblast count to the area of the ring, with the result expressed as cells per mm². |
| 9d00z9xtifzo | Th,B,F,M | M_density_120_140 | M_density_120_140: This parameter defines the normalized density of macrophages in the 120 to 140 micrometer ring from the epithelial boundary. It is calculated by dividing the macrophage count by the corresponding ring area (mm²), thereby providing a normalized metric. |
| 9d00z9xtifzo | Th,B,F,M | Th_density_140_160 | Th_density_140_160: This parameter indicates the normalized density of helper T cells in the 140 to 160 micrometer ring from the epithelial boundary. The value is determined by dividing the cell count of helper T cells by the area of the ring, yielding a density expressed in cells per mm². |
| 9d00z9xtifzo | Th,B,F,M | B_density_140_160 | B_density_140_160: This parameter represents the normalized density of B cells measured in the 140 to 160 micrometer ring from the epithelial boundary. The density is calculated by normalizing the B cell count with the area of the ring, resulting in cells per mm². |
| 9d00z9xtifzo | Th,B,F,M | F_density_140_160 | F_density_140_160: This parameter quantifies the normalized density of fibroblasts (FSP1-) in the 140 to 160 micrometer ring from the epithelial boundary. It is computed by dividing the fibroblast count by the area of the ring (converted to mm²), ensuring a normalized measure across samples. |
| 9d00z9xtifzo | Th,B,F,M | M_density_140_160 | M_density_140_160: This parameter measures the normalized density of macrophages in the 140 to 160 micrometer ring from the epithelial boundary. The density value is derived by dividing the number of macrophages by the area of the ring, thereby facilitating comparisons among tumor patches. |
| 9d00z9xtifzo | Th,B,F,M | Th_density_160_180 | Th_density_160_180: This parameter captures the normalized density of helper T cells within the 160 to 180 micrometer ring from the epithelial boundary. It is calculated by normalizing the count of helper T cells by the ring’s area (in mm²), providing a standardized metric. |
| 9d00z9xtifzo | Th,B,F,M | B_density_160_180 | B_density_160_180: This parameter represents the normalized density of B cells in the 160 to 180 micrometer ring from the epithelial boundary. The measurement is achieved by dividing the B cell count by the corresponding area of the ring, yielding a density in cells per mm². |
| 9d00z9xtifzo | Th,B,F,M | F_density_160_180 | F_density_160_180: This parameter indicates the normalized density of fibroblasts (FSP1-) in the 160 to 180 micrometer ring from the epithelial boundary. The density is computed by normalizing the fibroblast count by the area of the ring (mm²), ensuring a comparable metric across patient cases. |
| 9d00z9xtifzo | Th,B,F,M | M_density_160_180 | M_density_160_180: This parameter defines the normalized density of macrophages in the 160 to 180 micrometer ring from the epithelial boundary. It is determined by dividing the number of macrophages by the measured ring area, resulting in a density expressed in cells per mm². |
| 9d00z9xtifzo | Th,B,F,M | Th_density_180_200 | Th_density_180_200: This parameter denotes the normalized density of helper T cells present in the 180 to 200 micrometer ring from the epithelial boundary. The value is derived by normalizing the helper T cell count by the area of the ring, producing a density metric expressed as cells per mm². |
| 9d00z9xtifzo | Th,B,F,M | B_density_180_200 | B_density_180_200: This parameter quantifies the normalized density of B cells in the 180 to 200 micrometer ring from the epithelial boundary. It is calculated by dividing the B cell count by the corresponding ring area (converted to mm²), ensuring the metric is normalized. |
| 9d00z9xtifzo | Th,B,F,M | F_density_180_200 | F_density_180_200: This parameter reflects the normalized density of fibroblasts (FSP1-) found within the 180 to 200 micrometer ring from the epithelial boundary. The density is computed by normalizing the fibroblast count by the ring's area, yielding a value in cells per mm². |
| 9d00z9xtifzo | Th,B,F,M | M_density_180_200 | M_density_180_200: This parameter measures the normalized density of macrophages in the 180 to 200 micrometer ring from the epithelial boundary. It is derived by dividing the macrophage count by the area of the ring (mm²), resulting in a density value that facilitates comparisons across different patient cases. |
| 9g3fjeog5hmt | TU,Tc,Th,Treg,B,P,M,MFp,MF,Ff,E | TU_zone_gradient_ratio | TU_zone_gradient_ratio measures the ratio of tumor cell counts in the innermost tumor zone to the counts in the outermost stroma zone, thereby providing a normalized indicator of the direct spatial gradient for tumor cells. |
| 9g3fjeog5hmt | TU,Tc,Th,Treg,B,P,M,MFp,MF,Ff,E | TU_cumulative_gradient | TU_cumulative_gradient represents the ratio of the cumulative tumor cell count from the stroma through the tumor zones to the cumulative count in the outermost stroma zone, offering a normalized measure of overall tumor cell infiltration. |
| 9g3fjeog5hmt | TU,Tc,Th,Treg,B,P,M,MFp,MF,Ff,E | Tc_cumulative_gradient | Tc_cumulative_gradient quantifies the normalized cumulative infiltration of cytotoxic T cells (Tc) by comparing their cumulative counts from the stroma to the innermost tumor zone. |
| 9g3fjeog5hmt | TU,Tc,Th,Treg,B,P,M,MFp,MF,Ff,E | M_cumulative_gradient | M_cumulative_gradient provides a normalized measure of macrophage (M) infiltration by calculating the cumulative ratio of their counts from the stromal region to the tumor epithelium. |
| 9g3fjeog5hmt | TU,Tc,Th,Treg,B,P,M,MFp,MF,Ff,E | MF_zone_gradient_ratio | MF_zone_gradient_ratio computes the ratio of myofibroblast (MF) counts in the innermost tumor zone relative to those in the outermost stroma zone, yielding a normalized gradient metric. |
| 9g3fjeog5hmt | TU,Tc,Th,Treg,B,P,M,MFp,MF,Ff,E | MF_cumulative_gradient | MF_cumulative_gradient reflects the normalized cumulative count ratio for myofibroblasts from the stroma to the tumor, summarizing their overall infiltration pattern. |
| 9g3fjeog5hmt | TU,Tc,Th,Treg,B,P,M,MFp,MF,Ff,E | Ff_zone_gradient_ratio | Ff_zone_gradient_ratio indicates the normalized ratio of fibroblast (Ff) counts between the innermost tumor zone and the outermost stroma zone, capturing the direct spatial gradient. |
| 9g3fjeog5hmt | TU,Tc,Th,Treg,B,P,M,MFp,MF,Ff,E | Ff_cumulative_gradient | Ff_cumulative_gradient represents the normalized cumulative ratio of fibroblast counts across zones from stroma to tumor, thereby describing their infiltration pattern. |
| 9g3fjeog5hmt | TU,Tc,Th,Treg,B,P,M,MFp,MF,Ff,E | E_zone_gradient_ratio | E_zone_gradient_ratio measures the ratio of endothelial cell (E) counts in the innermost tumor zone to those in the outermost stroma zone, serving as a normalized indicator of their spatial gradient. |
| 9g3fjeog5hmt | TU,Tc,Th,Treg,B,P,M,MFp,MF,Ff,E | E_cumulative_gradient | E_cumulative_gradient quantifies the overall normalized infiltration pattern of endothelial cells by computing the cumulative ratio from the stroma to the tumor epithelium. |
| 9htsfwblqf9b | G | GRANULOCYTE_DENSITY_GRADIENT_SLOPE | GRANULOCYTE_DENSITY_GRADIENT_SLOPE measures the slope coefficient from a linear regression that fits granulocyte density values calculated across 10 concentric annular bands from the tumor center to its boundary. This normalized parameter indicates how granulocyte density changes with increasing radial distance, with a positive value signifying a rising density toward the periphery. |
| 9htsfwblqf9b | G | GRADIENT_R_SQUARED | GRADIENT_R_SQUARED represents the coefficient of determination of the linear regression model applied to the granulocyte density gradient data. It is a normalized statistic, ranging from 0 to 1, that quantifies the proportion of variance in the granulocyte density explained by changes in radial distance. |
| 9htsfwblqf9b | G | BAND_1_RADIAL_DISTANCE | BAND_1_RADIAL_DISTANCE is the central (midpoint) radial distance of the innermost annular band from the tumor center. It is determined by averaging the inner and outer radii of the band, providing a standardized spatial measure of the region. |
| 9htsfwblqf9b | G | BAND_2_RADIAL_DISTANCE | BAND_2_RADIAL_DISTANCE denotes the midpoint radial distance for the second annular region from the tumor center, calculated in a similar way to offer a consistent measure across different tumors. |
| 9htsfwblqf9b | G | BAND_3_RADIAL_DISTANCE | BAND_3_RADIAL_DISTANCE captures the central radial distance of the third concentric band from the tumor centroid, reflecting the spatial positioning of that band relative to the core. |
| 9htsfwblqf9b | G | BAND_4_RADIAL_DISTANCE | BAND_4_RADIAL_DISTANCE represents the average radial distance of the fourth annular band from the tumor center, determined by the band's defined inner and outer limits. |
| 9htsfwblqf9b | G | BAND_5_RADIAL_DISTANCE | BAND_5_RADIAL_DISTANCE measures the midpoint radial distance for the fifth band, providing a normalized spatial metric as a function of tumor geometry. |
| 9htsfwblqf9b | G | BAND_6_RADIAL_DISTANCE | BAND_6_RADIAL_DISTANCE conveys the central distance of the sixth annular region from the tumor centroid, computed similarly to the other bands to maintain consistency. |
| 9htsfwblqf9b | G | BAND_7_DENSITY | BAND_7_DENSITY quantifies the density of granulocytes within the seventh annular band. This value is calculated as the number of cells per unit area, rendering it a normalized metric that accounts for the irregular area of the band. |
| 9htsfwblqf9b | G | BAND_7_RADIAL_DISTANCE | BAND_7_RADIAL_DISTANCE provides the central (midpoint) radial distance of the seventh band from the tumor center, serving as a standardized spatial measure for that region. |
| 9htsfwblqf9b | G | BAND_8_RADIAL_DISTANCE | BAND_8_RADIAL_DISTANCE is the computed midpoint radial distance of the eighth band, which aids in spatial mapping of the density gradient across the tumor region. |
| 9htsfwblqf9b | G | BAND_9_RADIAL_DISTANCE | BAND_9_RADIAL_DISTANCE denotes the central radial distance of the ninth annular band from the tumor core, offering a consistent and comparative spatial metric. |
| 9htsfwblqf9b | G | BAND_10_RADIAL_DISTANCE | BAND_10_RADIAL_DISTANCE represents the midpoint radial distance for the outermost (tenth) band from the tumor center, reflecting the spatial extent at the tumor periphery. |
| 9i2il6ue83er | B,E,G,MFp,Tc | MST_LENGTH_PER_CELL | MST_LENGTH_PER_CELL is a normalized metric that measures the total edge length of the Minimum Spanning Tree (MST) constructed from target cell centroids within a tumor's stromal patch and then divides this total length by the number of cells analyzed. This normalization allows for comparisons across different patches or patient cases regardless of the absolute number of cells found. |
| 9i2il6ue83er | B,E,G,MFp,Tc | MST_LENGTH_PER_AREA | MST_LENGTH_PER_AREA is a normalized metric that calculates the total MST edge length and then divides it by the measured stromal area (the number of pixels corresponding to the stroma). This density-normalized measurement enables comparisons across patches with varying stromal areas, making it suitable for assessing spatial organization in a standardized manner. |
| 9i7j2li19588 | Tc,Treg,B,Ff,MFp,TU | Tc_norm_boundary_tumor | Tc_norm_boundary_tumor: Represents the normalized density of cytotoxic T cells (Tc) in the tumor boundary zone. It is calculated by dividing the count of Tc cells within a 50μm boundary region from the tumor by the estimated tumor boundary area, making it comparable across different patient cases. |
| 9i7j2li19588 | Tc,Treg,B,Ff,MFp,TU | Tc_norm_boundary_stroma | Tc_norm_boundary_stroma: Represents the normalized density of cytotoxic T cells (Tc) in the stroma boundary zone. This parameter assesses the density of Tc cells normalized by the stroma boundary area, allowing cross-case comparisons. |
| 9i7j2li19588 | Tc,Treg,B,Ff,MFp,TU | Treg_norm_boundary_stroma | Treg_norm_boundary_stroma: Represents the normalized density of regulatory T cells (Treg) in the stroma boundary zone. It quantifies the presence of Treg cells relative to the stroma boundary area, thus enabling standardized comparisons. |
| 9i7j2li19588 | Tc,Treg,B,Ff,MFp,TU | B_norm_boundary_stroma | B_norm_boundary_stroma: Represents the normalized density of B cells in the stroma boundary zone, calculated by dividing the cell count by the stroma boundary area to allow comparative analysis between cases. |
| 9i7j2li19588 | Tc,Treg,B,Ff,MFp,TU | Ff_norm_boundary_stroma | Ff_norm_boundary_stroma: Represents the normalized density of FSP1+ fibroblasts (Ff) in the stroma boundary zone. By normalizing the cell count to the area of the stroma boundary, it facilitates reliable cross-patient comparisons. |
| 9i7j2li19588 | Tc,Treg,B,Ff,MFp,TU | MFp_norm_boundary_tumor | MFp_norm_boundary_tumor: Represents the normalized density of PDPN+ myofibroblasts (MFp) within the tumor boundary zone. The value is derived by normalizing the cell count with the tumor boundary area. |
| 9i7j2li19588 | Tc,Treg,B,Ff,MFp,TU | MFp_norm_boundary_stroma | MFp_norm_boundary_stroma: Represents the normalized density of PDPN+ myofibroblasts (MFp) in the stroma boundary zone. It is computed as the cell count divided by the corresponding stroma area to enable standardized analysis. |
| 9i7j2li19588 | Tc,Treg,B,Ff,MFp,TU | TU_norm_boundary_tumor | TU_norm_boundary_tumor: Represents the normalized density of tumor (epithelial) cells (TU) in the tumor boundary zone. The metric is based on the count normalized to the relevant tumor boundary area. |
| 9i7j2li19588 | Tc,Treg,B,Ff,MFp,TU | TU_norm_boundary_stroma | TU_norm_boundary_stroma: Represents the normalized density of tumor (epithelial) cells (TU) in the stroma boundary zone, calculated by dividing the cell count by the stroma boundary area. |
| 9i7j2li19588 | Tc,Treg,B,Ff,MFp,TU | Tc_flux_index | Tc_flux_index: Represents the flux index for cytotoxic T cells (Tc), calculated as the difference between their normalized densities in the tumor and stroma boundary zones. This index indicates the directional shift of cell distribution along the tumor-stroma interface. |
| 9i7j2li19588 | Tc,Treg,B,Ff,MFp,TU | Treg_flux_index | Treg_flux_index: Represents the flux index for regulatory T cells (Treg) measured as the difference between their normalized densities on the tumor side and the stroma side of the boundary, reflecting spatial distribution differences. |
| 9i7j2li19588 | Tc,Treg,B,Ff,MFp,TU | B_flux_index | B_flux_index: Represents the flux index for B cells, derived by subtracting the normalized density in the stroma boundary zone from that in the tumor boundary zone. It highlights disparities in cell distribution across regions. |
| 9i7j2li19588 | Tc,Treg,B,Ff,MFp,TU | Ff_flux_index | Ff_flux_index: Represents the flux index for FSP1+ fibroblasts (Ff), calculated as the difference between their normalized densities in the tumor and stroma boundary zones, offering insight into spatial cellular dynamics. |
| 9i7j2li19588 | Tc,Treg,B,Ff,MFp,TU | MFp_flux_index | MFp_flux_index: Represents the flux index for PDPN+ myofibroblasts (MFp). It quantifies the difference in normalized densities between the tumor and stroma sides of the boundary, thereby reflecting patterns in cellular migration or accumulation. |
| 9i7j2li19588 | Tc,Treg,B,Ff,MFp,TU | TU_flux_index | TU_flux_index: Represents the flux index for tumor (epithelial) cells (TU), computed as the difference in their normalized densities between the tumor and stroma boundary zones. |
| 9i7j2li19588 | Tc,Treg,B,Ff,MFp,TU | composite_flux_index | composite_flux_index: Represents an overall flux measure computed as the average of individual flux indices for all cell types. This composite parameter provides a consolidated view of the directional differences in cell distributions across the tumor-stroma boundary. |
| 9i7j2li19588 | Tc,Treg,B,Ff,MFp,TU | immune_mf_ratio_tumor_boundary | immune_mf_ratio_tumor_boundary: Represents the ratio of immune cells (combining cytotoxic T, regulatory T, and B cells) to PDPN+ myofibroblasts in the tumor boundary zone. This metric assesses the balance between immune infiltration and myofibroblast presence in the tumor region. |
| 9i7j2li19588 | Tc,Treg,B,Ff,MFp,TU | immune_mf_ratio_stroma_boundary | immune_mf_ratio_stroma_boundary: Represents the ratio of immune cells to PDPN+ myofibroblasts in the stroma boundary zone, providing an indicator of the relative abundance of immune cells compared to myofibroblasts. |
| 9i7j2li19588 | Tc,Treg,B,Ff,MFp,TU | immune_mf_ratio_difference | immune_mf_ratio_difference: Represents the difference between the immune to myofibroblast ratios of the tumor boundary zone and the stroma boundary zone, illustrating the change in immune cell balance across the tumor-stroma interface. |
| 9kflbc4g3c73 | Tc,Th,Treg,B,P,MF,Ff,M | MAX_IMMUNE_STROMAL_SUBSET_COUNT_PERIVASCULAR | This parameter measures the highest number of distinct immune and stromal cell types (from the eight defined subsets: Tc, Th, Treg, B, P, MF, Ff, and M) that are found to co-occur within any 50 μm radius neighborhood centered on an immune or stromal cell within the perivascular region. The computed value, ranging from 0 to 8, reflects a normalized and spatially contextualized metric that facilitates comparison across different patient cases and tumor patches by focusing on local cellular diversity rather than raw cell counts. |
| 9kqgmg00m29p | B,Treg | median_min_distance_b_to_treg | This parameter represents the median of the minimum Euclidean distances from each B cell to the nearest regulatory T cell within the stromal compartment of a tumor patch. It quantifies the typical spatial proximity between B cells and regulatory T cells, offering insights into potential immunosuppressive niches in breast cancer. As a normalized, numeric metric derived by comparing distances within each image patch, it facilitates reliable comparisons across different patient cases. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | TU_mean_aspect_ratio | TU_mean_aspect_ratio: For the cell type TU, this parameter calculates the average nuclear aspect ratio, defined as the ratio of the larger to the smaller dimension of the nucleus. It is a normalized, dimensionless measurement reflecting nuclear shape and potential morphological changes influenced by the local tumor microenvironment. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | TU_mean_local_density | TU_mean_local_density: For the cell type TU, this parameter represents the average number of neighboring cells found within a fixed 50μm radius. Although it originates from cell counts, the use of a fixed neighborhood area makes it comparable across different patient cases as a measure of localized cell crowding. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | TU_correlation_coefficient | TU_correlation_coefficient: For the cell type TU, this parameter is the Pearson correlation coefficient quantifying the linear relationship between the nuclear aspect ratio and the local cell density. Its value, ranging between -1 and 1, indicates the strength and direction of the association. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | TU_p_value | TU_p_value: For the cell type TU, this parameter indicates the statistical significance of the observed Pearson correlation between nuclear aspect ratio and local density. A lower p-value provides strong evidence that the correlation is not due to random chance. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | Th_mean_aspect_ratio | Th_mean_aspect_ratio: For the cell type Th, this parameter computes the average nuclear aspect ratio based on the ratio of the larger to the smaller nuclear dimension, serving as a normalized indicator of nuclear morphology within the tumor patch. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | Th_mean_local_density | Th_mean_local_density: For the cell type Th, this parameter represents the mean count of neighboring cells within a 50μm radius. The fixed search area ensures that this metric is standardized and comparable across different tumor regions. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | Th_correlation_coefficient | Th_correlation_coefficient: For the cell type Th, this parameter calculates the Pearson correlation coefficient between nuclear aspect ratio and local cell density, providing a normalized measure of the linear association between cell morphology and the local cellular environment. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | Th_p_value | Th_p_value: For the cell type Th, this parameter indicates the statistical significance of the correlation between nuclear aspect ratio and local density, with lower values signifying a stronger and more reliable association. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | Treg_mean_aspect_ratio | Treg_mean_aspect_ratio: For the cell type Treg, this parameter determines the average nuclear aspect ratio, a dimensionless measurement derived from the geometry of the nucleus, which helps in assessing morphological variations in relation to the tumor microenvironment. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | Treg_mean_local_density | Treg_mean_local_density: For the cell type Treg, this parameter is the normalized average number of cells found within a 50μm radius, providing a standardized measure of local density across different patient patches. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | Treg_correlation_coefficient | Treg_correlation_coefficient: For the cell type Treg, this parameter computes the Pearson correlation coefficient between nuclear aspect ratio and local density. This normalized measure reflects the degree and direction of the association between nuclear shape and cell crowding. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | Treg_p_value | Treg_p_value: For the cell type Treg, this parameter denotes the statistical significance of the computed correlation, indicating the robustness of the relationship between nucleus morphology and local cellular density. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | B_mean_aspect_ratio | B_mean_aspect_ratio: For the cell type B, this parameter calculates the mean nuclear aspect ratio, a normalized measure of nuclear shape that is obtained by dividing the larger dimension by the smaller dimension of the nucleus. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | B_mean_local_density | B_mean_local_density: For the cell type B, this parameter reflects the average count of neighboring cells within a fixed 50μm radius, serving as a standardized measure of local cell density. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | B_correlation_coefficient | B_correlation_coefficient: For the cell type B, this parameter is the Pearson correlation coefficient that quantifies the linear relationship between the nuclear aspect ratio and local cell density, resulting in a normalized correlation value. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | B_p_value | B_p_value: For the cell type B, this parameter represents the statistical significance of the observed correlation between nuclear aspect ratio and local density, with lower values reinforcing the reliability of the association. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | P_mean_aspect_ratio | P_mean_aspect_ratio: For the cell type P, this parameter computes the average nuclear aspect ratio by evaluating the ratio of the longer to the shorter nuclear dimension, providing a normalized metric reflective of cellular morphology. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | P_mean_local_density | P_mean_local_density: For the cell type P, this parameter measures the mean local density by averaging the count of neighboring cells within a 50μm radius, ensuring comparability across tumor patches. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | P_correlation_coefficient | P_correlation_coefficient: For the cell type P, this parameter calculates the Pearson correlation coefficient between the nuclear aspect ratio and local cell density, offering a normalized assessment of the association between these two features. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | P_p_value | P_p_value: For the cell type P, this parameter indicates the p-value associated with the Pearson correlation, highlighting the statistical significance of the relation between nuclear morphology and local density. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | M_mean_aspect_ratio | M_mean_aspect_ratio: For the cell type M, this parameter determines the mean nuclear aspect ratio by analyzing the proportions of the nucleus, yielding a normalized, dimensionless value that describes nuclear shape. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | M_mean_local_density | M_mean_local_density: For the cell type M, this parameter represents the average number of neighboring cells within a fixed 50μm radius, thus providing a standardized measure of the local cellular environment. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | M_correlation_coefficient | M_correlation_coefficient: For the cell type M, this parameter is the Pearson correlation coefficient that quantitatively assesses the linear relationship between nuclear aspect ratio and the local cell density, resulting in a normalized metric. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | M_p_value | M_p_value: For the cell type M, this parameter reflects the statistical significance (p-value) of the correlation between the nuclear aspect ratio and local density, with lower values indicating a robust association. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | G_mean_aspect_ratio | G_mean_aspect_ratio: For the cell type G, this parameter calculates the average nuclear aspect ratio as a normalized value, representing the ratio of the larger to the smaller dimension of the nucleus and offering insights into nuclear morphology. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | G_mean_local_density | G_mean_local_density: For the cell type G, this parameter represents the mean local density by averaging the number of neighboring cells within a fixed 50μm radius, ensuring the metric is standardized across different samples. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | G_correlation_coefficient | G_correlation_coefficient: For the cell type G, this parameter computes the Pearson correlation coefficient between the nuclear aspect ratio and local cell density, providing a normalized indicator of the linear association between these properties. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | G_p_value | G_p_value: For the cell type G, this parameter denotes the p-value associated with the computed correlation, serving as a measure of the statistical significance of the observed relationship. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | MFp_mean_aspect_ratio | MFp_mean_aspect_ratio: For the cell type MFp, this parameter calculates the mean nuclear aspect ratio, which is a normalized, dimensionless measure derived from comparing the nucleus’ larger and smaller dimensions, reflecting cell morphology. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | MFp_mean_local_density | MFp_mean_local_density: For the cell type MFp, this parameter assesses the average number of cells within a defined 50μm radius, resulting in a standardized measure of local cell density across tumor patches. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | MFp_correlation_coefficient | MFp_correlation_coefficient: For the cell type MFp, this parameter is the Pearson correlation coefficient between the nuclear aspect ratio and local density, yielding a normalized metric that describes the strength and direction of their relationship. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | MFp_p_value | MFp_p_value: For the cell type MFp, this parameter indicates the statistical significance (p-value) of the correlation between nuclear shape and local cell density, validating the robustness of the association. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | MF_mean_aspect_ratio | MF_mean_aspect_ratio: For the cell type MF, this parameter calculates the average nuclear aspect ratio as the ratio of the larger to the smaller dimension of the nucleus, providing a normalized measurement of nuclear morphology. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | MF_mean_local_density | MF_mean_local_density: For the cell type MF, this parameter represents the mean local density by averaging the number of neighboring cells within a 50μm radius, ensuring that the metric is comparable across different cases. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | MF_correlation_coefficient | MF_correlation_coefficient: For the cell type MF, this parameter computes the Pearson correlation coefficient between nuclear aspect ratio and local density, offering a normalized measure of the linear relationship between these variables. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | MF_p_value | MF_p_value: For the cell type MF, this parameter reflects the statistical significance of the correlation between nuclear aspect ratio and local density through its p-value, with lower values indicating a more reliable association. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | Ff_mean_aspect_ratio | Ff_mean_aspect_ratio: For the cell type Ff, this parameter calculates the mean nuclear aspect ratio by evaluating the shape of the nucleus (the ratio of its larger to smaller dimension), resulting in a normalized measure of cellular morphology. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | Ff_mean_local_density | Ff_mean_local_density: For the cell type Ff, this parameter represents the average count of neighboring cells within a 50μm radius, computed over the cell population to provide a standardized assessment of local density. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | Ff_correlation_coefficient | Ff_correlation_coefficient: For the cell type Ff, this parameter is the Pearson correlation coefficient that quantifies the strength and direction of the linear relationship between the nuclear aspect ratio and the local cell density, yielding a normalized metric. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | Ff_p_value | Ff_p_value: For the cell type Ff, this parameter indicates the p-value associated with the computed correlation, serving as a measure of statistical significance for the relationship between nuclear morphology and local density. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | E_mean_aspect_ratio | E_mean_aspect_ratio: For the cell type E, this parameter calculates the average nuclear aspect ratio, a normalized measure obtained by comparing the nucleus’s larger and smaller dimensions, which reflects changes in cell shape. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | E_mean_local_density | E_mean_local_density: For the cell type E, this parameter represents the mean local density by averaging the number of neighboring cells within a fixed 50μm radius, ensuring a standardized density measure across patches. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | E_correlation_coefficient | E_correlation_coefficient: For the cell type E, this parameter computes the Pearson correlation coefficient between nuclear aspect ratio and local density, providing a normalized value that describes the intensity and direction of their linear relationship. |
| 9mp42ayyvnj7 | TU,Th,Treg,B,P,M,G,MFp,MF,Ff,E | E_p_value | E_p_value: For the cell type E, this parameter denotes the statistical significance (p-value) of the observed correlation between nuclear aspect ratio and local density, with lower p-values indicating a stronger, more significant relationship. |
| 9ptownf05oj4 | TU,Tc,Th,Treg,B,P,M,G,MFp | GRANULOCYTE_DOMINANCE_INDEX | GRANULOCYTE_DOMINANCE_INDEX represents a normalized ratio measuring the relative abundance of granulocytes compared to the total number of cells across nine specific cancer cell subpopulations. This index facilitates comparison between different patient cases or tumor regions, as it is derived by dividing the granulocyte count by the total cell count (with an epsilon adjustment to avoid division by zero). |
| 9ptownf05oj4 | TU,Tc,Th,Treg,B,P,M,G,MFp | EPITHELIAL_CELL_PERCENT | EPITHELIAL_CELL_PERCENT indicates the percentage of epithelial cells within the nine analyzed subpopulations. It provides a normalized measure of the fraction of epithelial cells relative to the total cell count, enabling comparisons across different samples. |
| 9ptownf05oj4 | TU,Tc,Th,Treg,B,P,M,G,MFp | T_CELL_CD8_PERCENT | T_CELL_CD8_PERCENT is the percentage of CD8-positive cytotoxic T cells among the nine cell subpopulations. This normalized parameter reflects the relative abundance of these immune cells in a given tumor patch. |
| 9ptownf05oj4 | TU,Tc,Th,Treg,B,P,M,G,MFp | T_CELL_CD4_PERCENT | T_CELL_CD4_PERCENT represents the percentage of CD4-positive helper T cells within the total cell count of the nine subpopulations. It normalizes the contribution of these cells, allowing for inter-sample comparison. |
| 9ptownf05oj4 | TU,Tc,Th,Treg,B,P,M,G,MFp | T_CELL_REG_PERCENT | T_CELL_REG_PERCENT measures the percentage of regulatory T cells among the nine subpopulations. This normalized value indicates the proportion of immunosuppressive T cells relative to the total cell population. |
| 9ptownf05oj4 | TU,Tc,Th,Treg,B,P,M,G,MFp | B_CELL_PERCENT | B_CELL_PERCENT is the percentage of B lymphocytes within the nine evaluated cell subpopulations. It is calculated by normalizing the raw count of B cells with the overall cell count, providing a comparative metric. |
| 9ptownf05oj4 | TU,Tc,Th,Treg,B,P,M,G,MFp | PLASMA_CELL_PERCENT | PLASMA_CELL_PERCENT indicates the percentage of plasma cells among the nine cell subpopulations. It offers a normalized perspective on plasma cell abundance in relation to the total cell count. |
| 9ptownf05oj4 | TU,Tc,Th,Treg,B,P,M,G,MFp | MACROPHAGE_PERCENT | MACROPHAGE_PERCENT represents the normalized percentage of macrophages in the tumor region, computed as the proportion of macrophages out of the total cell count of the nine subpopulations. |
| 9ptownf05oj4 | TU,Tc,Th,Treg,B,P,M,G,MFp | GRANULOCYTE_PERCENT | GRANULOCYTE_PERCENT is the normalized percentage of granulocytes within the nine subpopulations. It provides insight into the contribution of granulocytes relative to the overall cell count, which is crucial for understanding inflammatory responses. |
| 9ptownf05oj4 | TU,Tc,Th,Treg,B,P,M,G,MFp | MYOFIBROBLAST_PDPN_PERCENT | MYOFIBROBLAST_PDPN_PERCENT is the normalized percentage of PDPN-positive myofibroblasts among the nine subpopulations. This parameter quantifies the proportion of these specific stromal cells compared to the total cell count. |
| 9trkbtgxup5l | B,M,MF | COLOC_INDEX_OVERALL | COLOC_INDEX_OVERALL represents the overall spatial co-localization index for B cells, macrophages, and PDPN- myofibroblasts in the epithelial region. It is calculated by averaging the transformed spatial metrics (L-functions) derived from pairwise K-function analyses across a range of evaluation distances. The method incorporates normalization through area adjustment, ensuring that the resulting value is comparable across different patient cases and tissue patches. |
| 9trkbtgxup5l | B,M,MF | COLOC_INDEX_LONG_RANGE | COLOC_INDEX_LONG_RANGE quantifies the degree of cellular co-localization at long spatial distances (greater than 100μm) within the epithelial region. It reflects broader tissue organization patterns by averaging the L-function values computed over these long-range distances, and its normalization allows effective comparison between different tumors. |
| 9trkbtgxup5l | B,M,MF | COLOC_INDEX_MACRO_MYOFIB | COLOC_INDEX_MACRO_MYOFIB specifically measures the spatial co-localization between macrophages and PDPN- myofibroblasts. This parameter is derived by calculating and averaging the transformed L-function values for the macrophage-myofibroblast cell pair across the evaluation distances, with normalization achieved through adjusting for cell counts and the epithelial area, making it suitable for inter-sample comparisons. |
| 9ybb0p1lhow1 | P | PLASMA_CELL_NUCLEUS_CONVEXITY_VARIANCE | This parameter measures the variance in nuclear convexity across all plasma cell nuclei within a TMA patch. The convexity for each nucleus is calculated as the ratio of the area of the nucleus to the area of its convex hull, resulting in a normalized and dimensionless value that reflects the irregularity or smoothness of the nuclear shape. A high variance indicates a greater heterogeneity in the nuclear shapes among plasma cells, which may suggest differences in cellular maturation states impacting their functional roles in antibody production and antitumor response. |
| a0mshf28cqgv | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | TU_DILATION_EROSION_RATIO | TU_DILATION_EROSION_RATIO: This parameter quantifies the morphological behavior of the TU (epithelial cell) population by calculating the ratio of the area obtained after performing a binary dilation operation to the area obtained after a binary erosion operation. The ratio serves as a normalized metric that captures the expansion versus contraction behavior of the cell's spatial distribution, allowing for comparisons across different patient cases. |
| a0mshf28cqgv | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | TU_WEIGHTED_RATIO | TU_WEIGHTED_RATIO: This parameter represents the weighted contribution of the TU cell type's dilation-erosion ratio by factoring in its prevalence within the tumor patch. It is computed by multiplying the individual TU dilation-erosion ratio with the relative frequency of TU cells, ensuring normalization and enabling comparative analyses between different patient samples. |
| a0mshf28cqgv | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | COMPOSITE_DILATION_EROSION_RATIO | COMPOSITE_DILATION_EROSION_RATIO: This overall tissue-level parameter is derived by summing the weighted dilation-erosion ratios of all analyzed cell types. It serves as an aggregate and normalized measurement of the tissue's morphological characteristics, reflecting the combined effects of individual cell type behaviors in a standardized manner across different tumor regions. |
| a1msuh24zfpk | Th,E,F,TU | helper T cells_slope | helper T cells_slope: This parameter represents the slope obtained from a linear regression analysis investigating the relationship between the distance of helper T cells from vessels and their cell boundary roughness. The roughness metric is normalized by comparing the cell perimeter with that of a perfect circle of the same area. |
| a1msuh24zfpk | Th,E,F,TU | helper T cells_pvalue | helper T cells_pvalue: This numeric parameter provides the p-value from the linear regression performed for helper T cells, indicating the statistical significance of the relationship between vessel distance and cell boundary roughness. |
| a1msuh24zfpk | Th,E,F,TU | helper T cells_r_squared | helper T cells_r_squared: This parameter represents the R-squared value for the regression analysis of helper T cells, measuring the proportion of variance in the cell boundary roughness that can be explained by the vessel distance. |
| a1msuh24zfpk | Th,E,F,TU | endothelial cells_slope | endothelial cells_slope: This parameter indicates the slope from a linear regression between the vessel distance and normalized cell boundary roughness specifically for endothelial cells, reflecting how changes in vessel proximity might influence cell shape irregularities. |
| a1msuh24zfpk | Th,E,F,TU | endothelial cells_pvalue | endothelial cells_pvalue: This numeric parameter gives the p-value derived from the regression analysis for endothelial cells, serving as a measure of the statistical significance associated with the observed relationship. |
| a1msuh24zfpk | Th,E,F,TU | endothelial cells_r_squared | endothelial cells_r_squared: This parameter is the R-squared value for the endothelial cells regression, indicating the strength of the goodness-of-fit between vessel distance and cell boundary roughness. |
| a1msuh24zfpk | Th,E,F,TU | fibroblasts FSP1-_slope | fibroblasts FSP1-_slope: Representing the slope from the regression analysis for fibroblasts FSP1-, this parameter quantifies the association between the distance to the nearest vessel and the normalized cell boundary roughness of these cells. |
| a1msuh24zfpk | Th,E,F,TU | fibroblasts FSP1-_pvalue | fibroblasts FSP1-_pvalue: This numeric parameter provides the p-value for the regression analysis of fibroblasts FSP1-, thereby measuring the statistical significance of the correlation between vessel proximity and cell boundary roughness. |
| a1msuh24zfpk | Th,E,F,TU | fibroblasts FSP1-_r_squared | fibroblasts FSP1-_r_squared: This parameter describes the R-squared value from the regression analysis for fibroblasts FSP1-, indicating the proportion of variance in cell roughness explained by the vessel distance. |
| a1msuh24zfpk | Th,E,F,TU | tumor cells_slope | tumor cells_slope: This numeric parameter represents the slope from the linear regression applied to tumor cells, quantitatively expressing the variation in normalized cell boundary roughness as a function of vessel distance. |
| a1msuh24zfpk | Th,E,F,TU | tumor cells_pvalue | tumor cells_pvalue: This parameter specifies the p-value from the regression analysis for tumor cells, providing a measure for the statistical significance of the relationship under investigation. |
| a1msuh24zfpk | Th,E,F,TU | tumor cells_r_squared | tumor cells_r_squared: This parameter is the R-squared value for the tumor cells regression analysis, indicating the extent to which variations in vessel distance can explain the changes in the normalized cell boundary roughness. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Tc_density_slope | Tc_density_slope: Measures the rate at which CD8+ T cell density changes across concentric radial zones from the tumor boundary. This slope is derived by computing cell densities (cell counts normalized by zone area) and applying linear regression using the midpoints of each zone, resulting in a normalized parameter that reflects spatial distribution. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Th_density_slope | Th_density_slope: Quantifies the change in CD4+ T helper cell density across successive radial zones from the tumor margin. The computed slope indicates how the density of these cells increases or decreases with distance, making it comparable across different tumor regions. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Treg_density_slope | Treg_density_slope: Represents the rate of change in regulatory T cell density across predefined concentric zones from the tumor boundary. It is calculated via linear regression on area-normalized densities, offering insight into the spatial dynamics of immunosuppressive cells. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | B_density_slope | B_density_slope: Captures the slope of B cell density change across the radial zones extending from the tumor. This parameter normalizes cell counts by the respective area of each zone and employs regression to assess the spatial gradient of B cell presence. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | P_density_slope | P_density_slope: Indicates the gradient of plasma cell density across concentric zones radiating from the tumor boundary. The slope reflects the rate of density change, computed from normalized values that account for the area of each zone. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | M_density_slope | M_density_slope: Measures the rate at which macrophage density changes with increasing distance from the tumor. It is derived from linear regression applied to densities calculated as cell counts per unit area in each radial zone. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | G_density_slope | G_density_slope: Reflects the change in granulocyte density across the zones surrounding the tumor. This slope is calculated by comparing normalized densities (cell count divided by zone area) across concentric annular regions. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MFp_density_slope | MFp_density_slope: Represents the slope of PDPN+ myofibroblast density change across radial zones from the tumor boundary. The computed parameter is based on area-normalized cell counts and provides a spatial gradient measurement of these specific cells. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MF_density_slope | MF_density_slope: Quantifies the rate of change in myofibroblast density across defined radial zones from the tumor. Derived from linear regression on normalized densities, it indicates how the distribution of myofibroblasts varies with distance. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Ff_density_slope | Ff_density_slope: Measures the slope of FSP1+ fibroblast density across concentric zones surrounding the tumor. This parameter is calculated using normalized densities (cell count per zone area) and serves as an index of spatial variation. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | F_density_slope | F_density_slope: Indicates the rate at which overall fibroblast density changes across the tumor’s radial zones. The slope is determined by performing linear regression on densities that have been normalized by zone area, ensuring comparability across regions. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | E_density_slope | E_density_slope: Reflects the gradient in endothelial cell density measured from the tumor boundary outward. The parameter is computed by regressing area-normalized densities and illustrates the spatial distribution of vascular cells. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | A_density_slope | A_density_slope: Captures the rate of change in antigen presenting cell density across concentric zones starting from the tumor margin. This normalized slope provides insight into the spatial alteration of immune surveillance cells. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Tc_weighted_slope | Tc_weighted_slope: Provides a normalized metric for CD8+ T cells by weighting the density slope with the relative abundance of these cells among all immune cells. This combines both spatial gradient and frequency information for cross-patient comparability. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Th_weighted_slope | Th_weighted_slope: Offers a weighted measure for CD4+ T helper cells by multiplying their density slope by the cell’s proportion among total immune cells. This normalization allows consistent comparisons across different tumor regions. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Treg_weighted_slope | Treg_weighted_slope: Computes a weighted slope for regulatory T cells by combining the density slope with the cell’s relative frequency. This approach normalizes the parameter, facilitating comparisons based on both spatial distribution and cell prevalence. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | B_weighted_slope | B_weighted_slope: Represents a normalized metric for B cells by multiplying the density slope by the relative abundance of B cells in the analyzed patch. The weighted slope reflects both spatial variation and prevalence. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | P_weighted_slope | P_weighted_slope: Indicates the weighted metric for plasma cells by integrating the density slope with the relative frequency of plasma cells. This normalization aids in comparing spatial gradients across different patient cases. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | M_weighted_slope | M_weighted_slope: Provides a weighted measure for macrophages by multiplying the density slope by the cell’s relative abundance. This parameter reflects the normalized spatial distribution of macrophages within tumor regions. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | G_weighted_slope | G_weighted_slope: Computes a weighted slope for granulocytes by combining the regression-derived density slope with their relative abundance in the immune cell population, yielding a normalized measure. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MFp_weighted_slope | MFp_weighted_slope: Offers a weighted measure for PDPN+ myofibroblasts, integrating the density slope with the cell’s proportion among immune cells. The resulting normalized parameter reflects the spatial gradient of these cells. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MF_weighted_slope | MF_weighted_slope: Captures the spatial gradient for myofibroblasts through a weighted slope, where the density slope is multiplied by the relative abundance. This normalization facilitates comparison across heterogeneous samples. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Ff_weighted_slope | Ff_weighted_slope: Represents a weighted metric for FSP1+ fibroblasts by combining their density slope with the relative frequency of these cells in the patch. The parameter is normalized to allow cross-patient analysis. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | F_weighted_slope | F_weighted_slope: Provides a normalized weighted slope for fibroblasts by integrating the rate of change in density with the relative abundance. This metric allows objectives comparisons of fibroblast spatial patterns. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | E_weighted_slope | E_weighted_slope: Offers a weighted, normalized measure for endothelial cells by multiplying the slope of density change by the cell's relative abundance. This parameter reflects vascular distribution dynamics. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | A_weighted_slope | A_weighted_slope: Computes a weighted slope for antigen presenting cells by factoring the density slope with the cells’ relative frequency. This normalized measure facilitates comparison of immune gradients across different cases. |
| a478gvrcyen5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | all_cell_weighted_slope | all_cell_weighted_slope: Sums the weighted slopes across all immune cell types to generate an overall normalized metric of the immune gradient. It reflects the aggregated spatial change in immune cell densities from the tumor boundary, enabling robust inter-patient comparisons. |
| a5o01qoonv76 | G | MEAN_GRANULOCYTE_NUCLEAR_PERIMETER | MEAN_GRANULOCYTE_NUCLEAR_PERIMETER measures the average perimeter of granulocyte nuclei within each tumor patch. It aggregates the individual perimeters of granulocyte nuclei and computes a mean value, allowing for normalized comparison across different patient cases. |
| a5o01qoonv76 | G | STD_GRANULOCYTE_NUCLEAR_PERIMETER | STD_GRANULOCYTE_NUCLEAR_PERIMETER quantifies the variability in nuclear perimeters of granulocytes in each patch. It calculates the standard deviation of the perimeter measurements, providing insight into the distribution and consistency of nuclear sizes between different patches. |
| a5o01qoonv76 | G | MIN_GRANULOCYTE_NUCLEAR_PERIMETER | MIN_GRANULOCYTE_NUCLEAR_PERIMETER captures the smallest nuclear perimeter among the granulocyte cells measured in a tumor patch. By identifying the minimum value, it helps to establish the lower boundary of nuclear size in the sampled area. |
| a5o01qoonv76 | G | MAX_GRANULOCYTE_NUCLEAR_PERIMETER | MAX_GRANULOCYTE_NUCLEAR_PERIMETER captures the largest nuclear perimeter among the granulocyte cells in a patch. This parameter provides information on the maximum nuclear size and contributes to a comprehensive understanding of the nuclear size range within the tumor region. |
| aav60os6mfai | TU,Treg,Ff,MFp,M | TRIANGULATION_IRREGULARITY_INDEX | TRIANGULATION_IRREGULARITY_INDEX is the average ratio of the longest to the shortest edge in each triangle computed via Delaunay triangulation of stromal cell centroids. This normalized metric reflects the overall degree of irregularity in cell spatial distribution and enables comparison between different patient cases. |
| aav60os6mfai | TU,Treg,Ff,MFp,M | TRIANGULATION_IRREGULARITY_STD | TRIANGULATION_IRREGULARITY_STD measures the standard deviation of the irregularity ratios across all triangles, providing insight into the variability of triangle shapes and the consistency of the spatial irregularity across the patch. |
| aav60os6mfai | TU,Treg,Ff,MFp,M | TRIANGULATION_IRREGULARITY_MIN | TRIANGULATION_IRREGULARITY_MIN represents the smallest ratio found among all triangles, indicating the least distorted triangle in the triangulation and serving as a normalized metric of cell spatial arrangement. |
| aav60os6mfai | TU,Treg,Ff,MFp,M | TRIANGULATION_IRREGULARITY_MAX | TRIANGULATION_IRREGULARITY_MAX represents the largest ratio observed among the triangles, capturing the most severely distorted triangle and serving as a normalized measure of local spatial irregularity. |
| aav60os6mfai | TU,Treg,Ff,MFp,M | TRIANGULATION_IRREGULARITY_MEDIAN | TRIANGULATION_IRREGULARITY_MEDIAN is the median value of the irregularity ratios, offering a robust central tendency measure of the distortion in the spatial arrangement of stromal cells. |
| amerb2788yh1 | F | FSP1_NEG_FIBROBLAST_RATIO | The FSP1_NEG_FIBROBLAST_RATIO parameter measures the proportion of FSP1-negative fibroblasts relative to the total fibroblast population in the tumor core area. This normalized value is calculated by dividing the count of FSP1-negative fibroblasts by the overall count of fibroblasts (including both FSP1-negative and FSP1-positive cells). Its normalized nature allows for valid comparisons across different patient cases and tissue patches. |
| anprv90d3sun | Tc,MFp | PROPORTION_TC_NEAR_PDPN_MF | This parameter measures the fraction of cytotoxic T lymphocytes in the stroma that are located within 30 µm of at least one PDPN-positive myofibroblast. The calculation is based on determining, for each T cell in the stromal compartment, whether there exists a PDPN+ myofibroblast within the specified spatial distance. The number of T cells meeting this condition is then normalized by dividing by the total number of cytotoxic T cells in the stroma. This normalization allows for comparisons between different patient cases and patch-level regions, ensuring that the metric is a comparable, numeric ratio reflecting spatial interactions that could influence immune modulation and tumor progression. |
| as599rdlkatj | Tc,Th,Treg,M,B,P,E,MFp,TU | Tc_median_core_area | Tc_median_core_area: This parameter quantifies the median nucleus area, measured in square micrometers, of CD8 T cells located in the tumor core. The tumor core is defined by cells whose Euclidean distance from the tumor centroid is less than or equal to the median distance of all tumor cells. This normalization allows for comparison between different patient patches. |
| as599rdlkatj | Tc,Th,Treg,M,B,P,E,MFp,TU | Tc_median_periphery_area | Tc_median_periphery_area: This parameter represents the median nucleus area of CD8 T cells found in the tumor periphery, which is the region beyond the median distance from the tumor centroid. It is expressed in square micrometers and normalized to enable comparisons across patient cases. |
| as599rdlkatj | Tc,Th,Treg,M,B,P,E,MFp,TU | Tc_gradient_score | Tc_gradient_score: This parameter is the computed difference between the median nucleus area of CD8 T cells in the tumor core and that in the tumor periphery (core minus periphery). A positive score indicates larger nuclei in the core compared to the periphery, and it is a numeric, normalized measure. |
| as599rdlkatj | Tc,Th,Treg,M,B,P,E,MFp,TU | Th_median_core_area | Th_median_core_area: This parameter measures the median nucleus area of CD4 T cells (helper T cells) within the tumor core. The core is defined using distance criteria from the tumor centroid, making the measurement normalized and numeric. |
| as599rdlkatj | Tc,Th,Treg,M,B,P,E,MFp,TU | Th_median_periphery_area | Th_median_periphery_area: This parameter indicates the median nucleus area of CD4 T cells located in the tumor periphery. It is calculated in square micrometers with the same spatial definition as the core, ensuring normalization across different patient patches. |
| as599rdlkatj | Tc,Th,Treg,M,B,P,E,MFp,TU | Th_gradient_score | Th_gradient_score: This parameter captures the difference between the median nucleus areas of CD4 T cells in the tumor core and periphery (core minus periphery). It serves as an indicator of spatial differences in nuclear morphology and is numeric and normalized. |
| as599rdlkatj | Tc,Th,Treg,M,B,P,E,MFp,TU | Treg_median_core_area | Treg_median_core_area: This parameter reflects the median nucleus area of regulatory T cells within the tumor core region. The region is defined based on the calculated Euclidean distances from the tumor centroid, and the value is normalized and numeric. |
| as599rdlkatj | Tc,Th,Treg,M,B,P,E,MFp,TU | Treg_median_periphery_area | Treg_median_periphery_area: This parameter denotes the median nucleus area of regulatory T cells in the tumor periphery. It is expressed in square micrometers and normalized for comparison across different tumor patches. |
| as599rdlkatj | Tc,Th,Treg,M,B,P,E,MFp,TU | M_median_core_area | M_median_core_area: This parameter represents the median nucleus area of macrophages located within the tumor core (cells with distances less than or equal to the median tumor cell distance). It is a normalized numeric measure. |
| as599rdlkatj | Tc,Th,Treg,M,B,P,E,MFp,TU | M_median_periphery_area | M_median_periphery_area: This parameter measures the median nucleus area of macrophages present in the tumor periphery, defined as cells situated beyond the median distance from the tumor centroid. The measurement is numeric and standardized. |
| as599rdlkatj | Tc,Th,Treg,M,B,P,E,MFp,TU | M_gradient_score | M_gradient_score: This parameter is the numerical difference between the median nucleus areas of macrophages in the tumor core and tumor periphery (core minus periphery). It is designed to be a normalized metric indicating spatial differences in nuclear size. |
| as599rdlkatj | Tc,Th,Treg,M,B,P,E,MFp,TU | B_median_core_area | B_median_core_area: This parameter quantifies the median nucleus area of B cells within the tumor core. It is calculated based on the spatial division of the tumor region and is normalized, allowing cross-case comparisons. |
| as599rdlkatj | Tc,Th,Treg,M,B,P,E,MFp,TU | B_median_periphery_area | B_median_periphery_area: This parameter denotes the median nucleus area of B cells in the tumor periphery. Using the predefined spatial threshold related to the tumor centroid, the measurement is numeric and normalized. |
| as599rdlkatj | Tc,Th,Treg,M,B,P,E,MFp,TU | B_gradient_score | B_gradient_score: This parameter reflects the difference between the median nucleus areas of B cells in the tumor core and periphery (core minus periphery). The gradient score is a normalized numeric value that highlights spatial differences in B cell nuclear morphology. |
| as599rdlkatj | Tc,Th,Treg,M,B,P,E,MFp,TU | P_median_core_area | P_median_core_area: This parameter measures the median nucleus area of plasma cells within the tumor core region. The value is computed from cells within a defined distance from the tumor centroid and is expressed in a normalized, numeric format. |
| as599rdlkatj | Tc,Th,Treg,M,B,P,E,MFp,TU | P_median_periphery_area | P_median_periphery_area: This parameter represents the median nucleus area of plasma cells found in the tumor periphery. The areas are computed in a standardized way (using the established spatial threshold) and are numeric. |
| as599rdlkatj | Tc,Th,Treg,M,B,P,E,MFp,TU | P_gradient_score | P_gradient_score: This parameter is the difference between the median nucleus area of plasma cells in the tumor core and that in the tumor periphery (core minus periphery). It is a normalized numeric metric useful for comparing tumor microenvironments. |
| as599rdlkatj | Tc,Th,Treg,M,B,P,E,MFp,TU | E_median_core_area | E_median_core_area: This parameter captures the median nucleus area of endothelial cells within the tumor core. The tumor core is defined via a calculated threshold based on distances from the tumor centroid, ensuring normalization across patient cases. |
| as599rdlkatj | Tc,Th,Treg,M,B,P,E,MFp,TU | E_median_periphery_area | E_median_periphery_area: This parameter indicates the median nucleus area of endothelial cells in the tumor periphery. It is derived based on consistent spatial criteria and is a numeric, normalized measure. |
| as599rdlkatj | Tc,Th,Treg,M,B,P,E,MFp,TU | E_gradient_score | E_gradient_score: This parameter provides the computed difference between the median nucleus areas of endothelial cells in the tumor core and periphery (core minus periphery). It is a normalized, numeric value that reflects spatial distribution differences. |
| as599rdlkatj | Tc,Th,Treg,M,B,P,E,MFp,TU | MFp_median_core_area | MFp_median_core_area: This parameter represents the median nucleus area of myofibroblasts (pdpn positive) within the tumor core. The measurement is based on a defined geometric threshold relative to the tumor centroid and is normalized. |
| as599rdlkatj | Tc,Th,Treg,M,B,P,E,MFp,TU | MFp_median_periphery_area | MFp_median_periphery_area: This parameter measures the median nucleus area of myofibroblasts in the tumor periphery. Using uniform spatial criteria from the tumor centroid, it yields a numeric, normalized value. |
| as599rdlkatj | Tc,Th,Treg,M,B,P,E,MFp,TU | MFp_gradient_score | MFp_gradient_score: This parameter is the difference between the median nucleus areas of myofibroblasts in the tumor core and periphery (core minus periphery), providing a normalized numeric score that indicates the direction and magnitude of spatial variation. |
| as599rdlkatj | Tc,Th,Treg,M,B,P,E,MFp,TU | TU_median_core_area | TU_median_core_area: This parameter quantifies the median nucleus area of epithelial cells within the tumor core. The tumor core is defined based on cells' Euclidean distance relative to the tumor centroid, ensuring that the measurement is numeric and normalized. |
| as599rdlkatj | Tc,Th,Treg,M,B,P,E,MFp,TU | TU_median_periphery_area | TU_median_periphery_area: This parameter denotes the median nucleus area of epithelial cells located in the tumor periphery. With the standardized spatial definition, it is a normalized, numeric value. |
| as599rdlkatj | Tc,Th,Treg,M,B,P,E,MFp,TU | TU_gradient_score | TU_gradient_score: This parameter represents the difference in median nucleus areas of epithelial cells between the tumor core and periphery (core minus periphery). It is a normalized numerical metric that enables comparison of nuclear morphology across patches. |
| az4bseyukwz7 | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | mean_dist_Tc | mean_dist_Tc: This parameter measures the average distance between CD8+ T cells and their nearest tumor cell, expressed in micrometers. It provides insight into the spatial relationship and potential interaction between cytotoxic T cells and tumor cells in a given patch. |
| az4bseyukwz7 | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | mean_dist_Th | mean_dist_Th: This parameter quantifies the average distance between CD4+ T helper cells and their closest tumor cell, expressed in micrometers. It serves as an indicator of how helper T cells are spatially distributed relative to tumor regions. |
| az4bseyukwz7 | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | mean_dist_Treg | mean_dist_Treg: This parameter calculates the mean distance from T regulatory cells to the nearest tumor cell, measured in micrometers. It reflects the spatial positioning of regulatory T cells in the tumor microenvironment. |
| az4bseyukwz7 | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | mean_dist_B | mean_dist_B: This parameter represents the average distance from B cells to their nearest tumor cell, expressed in micrometers. It is used to assess the proximity of B cells in relation to tumor cells within each image patch. |
| az4bseyukwz7 | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | mean_dist_P | mean_dist_P: This parameter measures the average distance from plasma cells to the nearest tumor cell in micrometers. It provides a metric for evaluating the spatial organization of plasma cells relative to tumor cell clusters. |
| az4bseyukwz7 | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | mean_dist_M | mean_dist_M: This parameter determines the mean distance between macrophages and their nearest tumor cell, expressed in micrometers. It helps in understanding the interaction and infiltration of macrophages in the tumor milieu. |
| az4bseyukwz7 | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | mean_dist_MFp | mean_dist_MFp: This parameter computes the mean distance from PDPN+ myofibroblasts to the nearest tumor cell, measured in micrometers. It offers insights into the positioning of these stromal cells within the tumor microenvironment. |
| az4bseyukwz7 | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | mean_dist_Ff | mean_dist_Ff: This parameter calculates the average distance from FSP1+ fibroblasts to the nearest tumor cell in micrometers. It provides a measure of the spatial arrangement of fibroblasts relative to tumor cells. |
| az4bseyukwz7 | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | mean_dist_E | mean_dist_E: This parameter represents the mean distance from endothelial cells to the nearest tumor cell, expressed in micrometers. It is used to evaluate the spatial relationship between blood vessel lining cells and tumor cells. |
| az4bseyukwz7 | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | distance_variation_index | distance_variation_index: This parameter is the coefficient of variation (standard deviation divided by mean) calculated from the average distances of the various non-tumor cell types to tumor cells. It is a normalized metric that captures the diversity in spatial organization across different cell types, facilitating comparisons across different patient cases. |
| b46v0wukyo8h | F,Ff,MFp,E | ENTROPY_F | ENTROPY_F is a normalized entropy value (ranging from 0 to 1) for FSP1- fibroblasts. It quantifies the variation in cell shape complexity by computing a shape descriptor based on the ratio of the cell's perimeter to the square root of its area, organizing these descriptors into a histogram, and then calculating a normalized Shannon entropy. Higher values indicate a more diverse range of cell shapes, while lower values reflect greater uniformity. |
| b46v0wukyo8h | F,Ff,MFp,E | ENTROPY_Ff | ENTROPY_Ff is a normalized entropy value (ranging from 0 to 1) for FSP1+ fibroblasts. It measures the diversity in cell morphology by using the shape descriptors calculated from the cell's geometric properties. The derived values are binned into a histogram and a normalized Shannon entropy is computed, with higher entropy corresponding to more variability in shapes. |
| b46v0wukyo8h | F,Ff,MFp,E | ENTROPY_MFp | ENTROPY_MFp is a normalized entropy value (ranging from 0 to 1) for PDPN+ myofibroblasts. This parameter assesses the morphological divergence among these cells using a similar methodology where the shape descriptor, derived from the cell's perimeter and area, is distributed into bins and processed through a normalized entropy calculation, reflecting the extent of morphological variation. |
| b46v0wukyo8h | F,Ff,MFp,E | ENTROPY_E | ENTROPY_E is a normalized entropy metric (ranging from 0 to 1) for endothelial cells. The measure is computed by evaluating the complexity of cell shape through a pre-defined shape descriptor, creating a histogram, and using normalized Shannon entropy to quantify the morphological variability. Higher values denote a wider range of shape complexities. |
| b7nhzk69aamo | TU,Tc,Th,Treg,B,P,M,G,MFp,F | CELL_DENSITY | CELL_DENSITY measures the overall density of the selected tumor and immune cell types by normalizing the total number of filtered cells by the tissue area; the unit is cells per square micrometer, which allows for comparisons across patient cases. |
| b7nhzk69aamo | TU,Tc,Th,Treg,B,P,M,G,MFp,F | DENSITY_CORRIDOR_COVERAGE | DENSITY_CORRIDOR_COVERAGE quantifies the proportion of the tissue area that is covered by high-density corridors. It is computed by dividing the area of the largest connected high-density region by the total tissue area, making it a normalized metric suitable for cross-case comparisons. |
| b7nhzk69aamo | TU,Tc,Th,Treg,B,P,M,G,MFp,F | AVG_CORRIDOR_WIDTH | AVG_CORRIDOR_WIDTH represents the average width of the high-density corridors. It is calculated as the ratio of the total area of the corridors to their combined length, yielding a measurement in micrometers that is independent of absolute dimensions and thus normalized for comparative analysis. |
| bcr9kwcsaf02 | Ff,MF,Treg,A | Fibroblast_Band_Thickness | Fibroblast_Band_Thickness quantifies the radial extent of fibroblast presence around epithelial tumor regions. This metric is computed by first identifying fibroblast cells within the stroma that express markers such as FSP1 or are classified as myofibroblasts. The spatial distances from these cells to the tumor boundary, delineated from the tumor mask, are calculated. To mitigate the influence of outlier values, the 90th percentile of these distances is taken, which represents the effective thickness of the fibroblast band. Being based on relative distances rather than raw counts, this parameter is a normalized numerical measure that facilitates comparisons across different patient cases and tumor patches. |
| bdn7hxs7f9ng | A,Th | PERIVASCULAR_APC_DENSITY | PERIVASCULAR_APC_DENSITY: This parameter measures the density of antigen presenting cells in the perivascular region by dividing the number of APCs within that region by the total perivascular area. This normalized measure allows for reliable comparisons across different patient cases and patches. |
| bdn7hxs7f9ng | A,Th | PERIVASCULAR_TH_DENSITY | PERIVASCULAR_TH_DENSITY: This parameter represents the density of T helper cells in the perivascular area by calculating the number of T helper cells per unit area. Its normalization through division by area makes it suitable for comparing different patient samples. |
| bdn7hxs7f9ng | A,Th | PERIVASCULAR_APC_TH_DENSITY_RATIO | PERIVASCULAR_APC_TH_DENSITY_RATIO: This parameter is the ratio of the antigen presenting cell density to the T helper cell density in the perivascular region. By comparing two normalized densities, it offers a robust, relative measure that can be reliably compared between different patient cases. |
| bdn7hxs7f9ng | A,Th | PERIVASCULAR_APC_TH_COUNT_RATIO | PERIVASCULAR_APC_TH_COUNT_RATIO: This parameter represents the ratio of the count of antigen presenting cells to T helper cells within the perivascular region. Although derived from raw counts, the ratio itself is a dimensionless, relative measure that enables standardized comparisons across samples. |
| bgr9l3avupxb | TU,G,Treg,B,Th,Ff,F | mean_shape_factor | mean_shape_factor: This parameter represents the average tumor cell shape factor, calculated using the formula (4π * area divided by perimeter squared). The shape factor measures how close a cell is to being a perfect circle, with a value of 1 indicating an ideal circle. Being normalized, it allows comparison between different tumor regions across patient cases. |
| bgr9l3avupxb | TU,G,Treg,B,Th,Ff,F | std_shape_factor | std_shape_factor: This parameter quantifies the variability (standard deviation) of the tumor cell shape factor across the analyzed patch. It provides insight into the dispersion of cell shapes, and since it is derived from a normalized shape factor, it is suitable for comparing different patient cases. |
| bgr9l3avupxb | TU,G,Treg,B,Th,Ff,F | mean_shape_factor_high_granulocyte | mean_shape_factor_high_granulocyte: This parameter calculates the average tumor cell shape factor specifically for cells that are surrounded by a granulocyte count above the median in their local neighborhood. It aims to capture the influence of granulocyte infiltration on tumor cell morphology in a normalized manner. |
| bgr9l3avupxb | TU,G,Treg,B,Th,Ff,F | mean_shape_factor_high_t_cell_reg | mean_shape_factor_high_t_cell_reg: This parameter reflects the average tumor cell shape factor for those tumor cells that are located in areas with T regulatory cell counts exceeding the median. It is used to assess the impact of T regulatory cells on cell shape and is normalized for inter-sample comparison. |
| bgr9l3avupxb | TU,G,Treg,B,Th,Ff,F | mean_shape_factor_high_b_cell | mean_shape_factor_high_b_cell: This parameter assesses the average shape factor of tumor cells in environments where the B cell count is higher than the median. It indicates potential morphological changes due to a higher B cell presence and is normalized for comparing different patches. |
| bgr9l3avupxb | TU,G,Treg,B,Th,Ff,F | mean_shape_factor_high_t_cell_cd4 | mean_shape_factor_high_t_cell_cd4: This parameter measures the average tumor cell shape factor for cells in regions with an above-median count of helper T cells. It helps evaluate the effect of these immune cells on cell morphology, with normalization ensuring comparability across cases. |
| bgr9l3avupxb | TU,G,Treg,B,Th,Ff,F | mean_shape_factor_high_fibroblast_fsp1 | mean_shape_factor_high_fibroblast_fsp1: This parameter denotes the average shape factor of tumor cells found in patches where the count of FSP1+ fibroblasts is above the median. It provides insight into fibroblast influence on tumor cell shape under normalized conditions. |
| bgr9l3avupxb | TU,G,Treg,B,Th,Ff,F | mean_shape_factor_high_fibroblast | mean_shape_factor_high_fibroblast: This parameter calculates the average tumor cell shape factor for cells in regions with above-median counts of FSP1- fibroblasts. It is a normalized metric used to analyze the impact of these fibroblasts on tumor morphology. |
| bgr9l3avupxb | TU,G,Treg,B,Th,Ff,F | correlation_shape_granulocyte | correlation_shape_granulocyte: This parameter represents the correlation coefficient between tumor cell shape factor and granulocyte count in the local neighborhood. The coefficient, ranging from -1 to 1, is normalized to enable comparison across patient cases, indicating the strength and direction of the association. |
| bgr9l3avupxb | TU,G,Treg,B,Th,Ff,F | correlation_shape_t_cell_reg | correlation_shape_t_cell_reg: This parameter quantifies the correlation between tumor cell shape factor and T regulatory cell counts. As a normalized correlation metric, it reveals whether increases or decreases in T regulatory cell infiltration are associated with changes in cell morphology. |
| bgr9l3avupxb | TU,G,Treg,B,Th,Ff,F | correlation_shape_b_cell | correlation_shape_b_cell: This parameter is the correlation coefficient between tumor cell shape factor and the B cell count in the surrounding neighborhood. Its normalized value helps determine the relationship between B cell presence and cell circularity. |
| bgr9l3avupxb | TU,G,Treg,B,Th,Ff,F | correlation_shape_t_cell_cd4 | correlation_shape_t_cell_cd4: This parameter represents the correlation between tumor cell shape factor and helper T cell counts, providing insights into the association between helper T cell infiltration and tumor cell morphology. It is normalized for comparative analysis. |
| bgr9l3avupxb | TU,G,Treg,B,Th,Ff,F | correlation_shape_fibroblast_fsp1 | correlation_shape_fibroblast_fsp1: This parameter measures the correlation coefficient between tumor cell shape factor and FSP1+ fibroblast counts. Being normalized, it quantifies how changes in the local concentration of FSP1+ fibroblasts relate to alterations in cell shape. |
| bgr9l3avupxb | TU,G,Treg,B,Th,Ff,F | correlation_shape_fibroblast | correlation_shape_fibroblast: This parameter represents the correlation between tumor cell shape factor and FSP1- fibroblast counts. It is normalized and serves to evaluate the association between fibroblast presence and tumor cell morphology. |
| bgvd8hmyrwf4 | Tc,Th,Treg,F | Tc_mean_distance | Tc_mean_distance is the average radial distance measured from the centroids of cytotoxic T-cells to the tumor nest boundary. This value quantifies how far, on average, these cells reside from the tumor, offering a normalized measure for comparing spatial distribution across different patient patches. |
| bgvd8hmyrwf4 | Tc,Th,Treg,F | Tc_layering_index | Tc_layering_index represents a weighted average radial distance of cytotoxic T-cells from the tumor boundary. It is calculated by assigning cell counts to fixed-width concentric rings and then normalizing the weighted sum by the total number of binned cells, thereby capturing the pattern of spatial layering in a normalized fashion. |
| bgvd8hmyrwf4 | Tc,Th,Treg,F | Th_mean_distance | Th_mean_distance is the average radial distance of helper T-cells from the tumor boundary. It expresses the mean separation of these immune cells from the tumor nests and facilitates cross-patient comparisons by normalizing the measurement. |
| bgvd8hmyrwf4 | Tc,Th,Treg,F | Th_layering_index | Th_layering_index is a weighted average measure of the radial distribution of helper T-cells. By calculating a weighted sum of distances based on their distribution among concentric rings around the tumor, this parameter quantitatively reflects the immune cell layering and is normalized across different patches. |
| bgvd8hmyrwf4 | Tc,Th,Treg,F | Treg_mean_distance | Treg_mean_distance quantifies the average distance of regulatory T-cells from the tumor boundary. This normalized metric provides insight into the spatial placement of these cells relative to tumor nests, enabling comparisons between different patient cases. |
| bgvd8hmyrwf4 | Tc,Th,Treg,F | Treg_layering_index | Treg_layering_index is a weighted average radial distance that captures the distribution of regulatory T-cells around tumor nests. The calculation, based on cell counts in predefined concentric rings, results in a normalized measure that describes the layering pattern. |
| bgvd8hmyrwf4 | Tc,Th,Treg,F | F_mean_distance | F_mean_distance is the average distance of fibroblasts from the tumor boundary, offering a normalized spatial metric that reflects the typical separation of fibroblasts from tumor nests, which can be used to compare different samples. |
| bgvd8hmyrwf4 | Tc,Th,Treg,F | F_layering_index | F_layering_index is the weighted average radial distance for fibroblasts. By summing the product of cell counts in fixed radial bins and normalizing by the total number of binned fibroblasts, this parameter gives a normalized indication of fibroblast layering around tumor areas. |
| bk6ba4leget9 | Tc,P | MEAN_CYTOTOXIC_T_CIRCULARITY | MEAN_CYTOTOXIC_T_CIRCULARITY measures the average circularity of the nuclei in cytotoxic T cells. This parameter is computed by calculating the circularity for each cell based on its area and perimeter, and then taking the mean value, making it suitable for comparing across different patient cases and tissue regions. |
| bk6ba4leget9 | Tc,P | MEDIAN_CYTOTOXIC_T_CIRCULARITY | MEDIAN_CYTOTOXIC_T_CIRCULARITY represents the median circularity of cytotoxic T cells. It provides a robust central tendency measure that is less influenced by outliers in the circularity values of these cells. |
| bk6ba4leget9 | Tc,P | MEAN_PLASMA_CIRCULARITY | MEAN_PLASMA_CIRCULARITY calculates the average nuclear circularity for plasma cells. Like the cytotoxic T cell mean, it is derived by averaging individual circularity measurements and is normalized for comparison between different patient samples. |
| bk6ba4leget9 | Tc,P | MEDIAN_PLASMA_CIRCULARITY | MEDIAN_PLASMA_CIRCULARITY is the median value of nuclear circularity for plasma cells, offering a resilient central measure that reduces the effect of extreme values within the dataset. |
| bk6ba4leget9 | Tc,P | MEAN_CIRCULARITY_DIFFERENCE | MEAN_CIRCULARITY_DIFFERENCE quantifies the difference between the mean circularity of cytotoxic T cells and plasma cells. This parameter facilitates comparative analysis by showing how the average nuclear shapes differ between these two cell types. |
| bk6ba4leget9 | Tc,P | MEDIAN_CIRCULARITY_DIFFERENCE | MEDIAN_CIRCULARITY_DIFFERENCE represents the difference between the median circularity values of cytotoxic T cells and plasma cells, providing a robust comparison metric that highlights the central tendency differences in nuclear morphology between the cell populations. |
| bth0xsp46xys | TU,Treg,F,Ff,A | boundary_ratio | boundary_ratio: This parameter represents the ratio of cells of interest located at the epithelial-stromal boundary relative to the total number of cells in an adjacent area. It is normalized because it compares the boundary cell count to the overall adjacent cell count, enabling comparisons across different patient cases. |
| bth0xsp46xys | TU,Treg,F,Ff,A | TU_ratio | TU_ratio: This normalized ratio indicates the proportion of tumor cells at the boundary relative to the total cells in the adjacent area, thereby allowing for standard comparisons by eliminating biases caused by patch size differences. |
| bth0xsp46xys | TU,Treg,F,Ff,A | Treg_ratio | Treg_ratio: This parameter provides a normalized measure of the proportion of regulatory T cells at the boundary in relation to the total cell count in the adjacent area, which aids in comparing immune cell distributions in different cases. |
| bth0xsp46xys | TU,Treg,F,Ff,A | F_ratio | F_ratio: This ratio reflects the proportion of FSP1- fibroblasts at the boundary relative to the total number of cells in the adjacent area; it is normalized and can be used to compare different tumor regions. |
| bth0xsp46xys | TU,Treg,F,Ff,A | Ff_ratio | Ff_ratio: This normalized ratio measures the relative presence of FSP1+ fibroblasts at the boundary, divided by the total cells in the adjacent area, ensuring comparability across different image patches. |
| bth0xsp46xys | TU,Treg,F,Ff,A | A_ratio | A_ratio: This parameter captures the proportion of antigen presenting cells at the boundary in relation to the total cells in the adjacent area, offering a normalized metric for cross-case analysis. |
| bth0xsp46xys | TU,Treg,F,Ff,A | TU_prop | TU_prop: This proportion describes the fraction of tumor cells among all the cells of interest found at the boundary. It provides insight into the relative composition of tumor cells independent of absolute cell numbers. |
| bth0xsp46xys | TU,Treg,F,Ff,A | Treg_prop | Treg_prop: This parameter expresses the proportion of regulatory T cells among the boundary cells of interest, normalizing the count to reflect their relative contribution in the cell population at the interface. |
| bth0xsp46xys | TU,Treg,F,Ff,A | F_prop | F_prop: This proportion represents the fraction of FSP1- fibroblasts within the cells of interest at the boundary, offering a normalized insight into their relative abundance. |
| bth0xsp46xys | TU,Treg,F,Ff,A | Ff_prop | Ff_prop: This parameter defines the proportion of FSP1+ fibroblasts among the boundary cells of interest, calculated as a normalized fraction to facilitate comparisons across different regions. |
| bth0xsp46xys | TU,Treg,F,Ff,A | A_prop | A_prop: This metric indicates the proportion of antigen presenting cells among the selected boundary cells of interest, providing a normalized measure of their representation at the compartment interface. |
| bth0xsp46xys | TU,Treg,F,Ff,A | Treg_APC_ratio | Treg_APC_ratio: This ratio is a combined normalized measure specifying the sum of counts of regulatory T cells and antigen presenting cells at the boundary divided by the total number of cells in the adjacent area. It provides an overall density metric for immunomodulatory cells. |
| bth0xsp46xys | TU,Treg,F,Ff,A | Treg_APC_prop | Treg_APC_prop: This parameter reflects the proportion of combined regulatory T cells and antigen presenting cells among all boundary cells of interest. It normalizes their combined count to give a relative representation within the cell population at the boundary. |
| bth0xsp46xys | TU,Treg,F,Ff,A | Fibroblast_ratio | Fibroblast_ratio: This normalized ratio represents the combined presence of both types of fibroblasts (FSP1- and FSP1+) at the boundary, relative to the total cell count in the adjacent area, allowing for standardized comparisons. |
| bth0xsp46xys | TU,Treg,F,Ff,A | Fibroblast_prop | Fibroblast_prop: This proportion measures the relative contribution of the combined fibroblast counts among the boundary cells of interest, normalizing the value to show their share in the interfacial microenvironment. |
| bth0xsp46xys | TU,Treg,F,Ff,A | tumor_immune_fibroblast_index | tumor_immune_fibroblast_index: This composite index quantifies the interaction between tumor cells, immune cells (specifically regulatory T cells and antigen presenting cells), and fibroblasts at the boundary. It is calculated by normalizing the product of these cell counts with the square of the total boundary cell count, ensuring it can be used for comparative analysis across different patient cases. |
| bu2fneg4ynzb | B,P,MFp,A | B_cells_asymmetry_index | B_cells_asymmetry_index quantifies the uneven distribution of B lymphocytes around tumor cell clusters. It is computed by dividing the difference between the maximum and minimum cell densities across angular sectors by the mean density, providing a normalized metric that can be compared across different patient cases. |
| bu2fneg4ynzb | B,P,MFp,A | Plasma_cells_asymmetry_index | Plasma_cells_asymmetry_index measures the variation in plasma cell density around tumor clusters. The index is derived by calculating the difference between the highest and lowest plasma cell counts in the predefined angular bins relative to the average count, resulting in a normalized number that reflects distribution asymmetry. |
| bu2fneg4ynzb | B,P,MFp,A | PDPN_myofibroblasts_asymmetry_index | PDPN_myofibroblasts_asymmetry_index calculates the asymmetry in the spatial distribution of PDPN-positive myofibroblasts around tumor regions. The metric is derived by taking the difference between the maximum and minimum counts in the angular compartments and normalizing it by the overall mean, thereby providing a comparable measure across different cases. |
| bu2fneg4ynzb | B,P,MFp,A | AP_cells_asymmetry_index | AP_cells_asymmetry_index provides a normalized measure of the irregular distribution of antigen presenting cells around tumor clusters. It is computed as the ratio of the difference between the highest and lowest angular counts to the mean count, indicating the degree of asymmetry in spatial distribution. |
| bvzrgumohy70 | Tc,Th,B,Ff | HARMONIC_MEAN_INTERCELL_DISTANCE | HARMONIC_MEAN_INTERCELL_DISTANCE measures the harmonic mean of the Euclidean distances computed for all unique pairs of cytotoxic T cells, helper T cells, B lymphocytes, and FSP1+ fibroblasts located in the stromal compartment. This parameter provides a normalized distance metric per patch that enables comparisons across different patient cases, highlighting the spatial proximity and potential interactions among these cells in the tumor microenvironment. |
| byeata0qnbcz | TU,Tc,Th,Treg,B,P,M,MFp,MF,Ff | vessel_proximity_cross_entropy | vessel_proximity_cross_entropy: A normalized metric derived from the cross entropy calculation that measures the divergence between the local cell type probability distribution near vessels and the overall cell distribution across the entire TMA spot. It quantifies how different the local composition is compared to the global reference. |
| byeata0qnbcz | TU,Tc,Th,Treg,B,P,M,MFp,MF,Ff | vessel_proximity_TU_percent | vessel_proximity_TU_percent: The percentage of tumor cells (epithelial cells) among all cells located in the vessel proximity region, providing a normalized measure of tumor cell infiltration related to vessel areas. |
| byeata0qnbcz | TU,Tc,Th,Treg,B,P,M,MFp,MF,Ff | vessel_proximity_Tc_percent | vessel_proximity_Tc_percent: The percentage of CD8+ T cells among the cells in the vessel proximity region, serving as a normalized indicator of cytotoxic immune cell representation near vessels. |
| byeata0qnbcz | TU,Tc,Th,Treg,B,P,M,MFp,MF,Ff | vessel_proximity_Th_percent | vessel_proximity_Th_percent: The percentage of CD4+ T cells within the vessel proximity region, offering a normalized view of helper T cell infiltration associated with vessels. |
| byeata0qnbcz | TU,Tc,Th,Treg,B,P,M,MFp,MF,Ff | vessel_proximity_Treg_percent | vessel_proximity_Treg_percent: The percentage of regulatory T cells among local cells close to vessels, calculated as a normalized value to indicate the immune suppressive component in the vessel vicinity. |
| byeata0qnbcz | TU,Tc,Th,Treg,B,P,M,MFp,MF,Ff | vessel_proximity_B_percent | vessel_proximity_B_percent: The percentage of B cells present in the vessel proximity area, offering a normalized metric for the relative abundance of these cells near the vessels. |
| byeata0qnbcz | TU,Tc,Th,Treg,B,P,M,MFp,MF,Ff | vessel_proximity_P_percent | vessel_proximity_P_percent: The percentage of plasma cells among the cells in the vessel proximity region, yielding a normalized quantification of these antibody-producing cells near vessel structures. |
| byeata0qnbcz | TU,Tc,Th,Treg,B,P,M,MFp,MF,Ff | vessel_proximity_M_percent | vessel_proximity_M_percent: The percentage of macrophages within the vessel proximity region, providing a normalized measure of these immune cells in the local vascular context. |
| byeata0qnbcz | TU,Tc,Th,Treg,B,P,M,MFp,MF,Ff | vessel_proximity_MFp_percent | vessel_proximity_MFp_percent: The percentage of PDPN+ myofibroblasts in the vessel proximity area, representing the normalized contribution of this cell type near blood vessels. |
| byeata0qnbcz | TU,Tc,Th,Treg,B,P,M,MFp,MF,Ff | vessel_proximity_MF_percent | vessel_proximity_MF_percent: The percentage of myofibroblasts among the local cell population adjacent to vessels, calculated as a normalized metric to facilitate comparisons between cases. |
| byeata0qnbcz | TU,Tc,Th,Treg,B,P,M,MFp,MF,Ff | vessel_proximity_Ff_percent | vessel_proximity_Ff_percent: The percentage of FSP1+ fibroblasts present in the vessel proximity region, delivering a normalized measure of fibroblastic cell infiltration near vessels. |
| byeata0qnbcz | TU,Tc,Th,Treg,B,P,M,MFp,MF,Ff | vessel_proximity_cell_density | vessel_proximity_cell_density: The density of cells in the vessel proximity region defined as the number of cells per square micrometer. This metric is normalized by the area, allowing comparison across different patient cases. |
| c3gx00i4v22h | Th,Treg,B,M,G,MFp,Ff,F | perc_tiles_with_cells | perc_tiles_with_cells: This metric quantifies the percentage of spatial tiles that contain at least one of the target cell types relative to all tiles generated from the tissue sample. It is normalized, providing a comparative measure of tissue coverage across patient cases. |
| c3gx00i4v22h | Th,Treg,B,M,G,MFp,Ff,F | global_entropy | global_entropy: This parameter represents the average Shannon entropy calculated across all spatial tiles. It reflects the diversity and overall disorder of the immune-fibroblast cell composition within the tissue, allowing for normalized comparisons across samples. |
| c3gx00i4v22h | Th,Treg,B,M,G,MFp,Ff,F | entropy_std | entropy_std: This metric measures the standard deviation of the Shannon entropy values across all tiles, indicating the variability in cell distribution patterns within the tissue. Its normalized nature helps in assessing heterogeneity between different patient cases. |
| c3gx00i4v22h | Th,Treg,B,M,G,MFp,Ff,F | entropy_max | entropy_max: This parameter captures the maximum Shannon entropy value among all tiles, identifying the patch with the most heterogeneous and diverse cell composition. It is normalized and useful for cross-sample comparisons. |
| c3gx00i4v22h | Th,Treg,B,M,G,MFp,Ff,F | avg_Th_per_tile | avg_Th_per_tile: This metric provides the average number of T helper cells (Th) per spatial tile. Since it is averaged over uniformly sized tiles, it serves as a normalized measure that can be compared across different tissue samples. |
| c3gx00i4v22h | Th,Treg,B,M,G,MFp,Ff,F | avg_Treg_per_tile | avg_Treg_per_tile: This parameter indicates the average count of T regulatory cells (Treg) per tile, derived from dividing cell counts by the number of tiles. Its normalized format makes it suitable for comparing immune profiles across patient cases. |
| c3gx00i4v22h | Th,Treg,B,M,G,MFp,Ff,F | avg_B_per_tile | avg_B_per_tile: This metric computes the average number of B cells per tile. By expressing cell counts on a per-tile basis, it normalizes the data, enabling reliable comparisons between different tissue samples. |
| c3gx00i4v22h | Th,Treg,B,M,G,MFp,Ff,F | avg_M_per_tile | avg_M_per_tile: This parameter is the average number of macrophages (M) per tile. Normalizing the cell count by the number of tiles allows for meaningful comparisons regarding macrophage distribution across patients. |
| c3gx00i4v22h | Th,Treg,B,M,G,MFp,Ff,F | avg_G_per_tile | avg_G_per_tile: This metric represents the average number of granulocytes (G) per tile, providing a normalized assessment of granulocyte density within the tissue sample. |
| c3gx00i4v22h | Th,Treg,B,M,G,MFp,Ff,F | avg_MFp_per_tile | avg_MFp_per_tile: This parameter calculates the average count of PDPN-positive myofibroblasts (MFp) per tile. The normalization by tile enables comparative analysis of myofibroblast distribution across different cases. |
| c3gx00i4v22h | Th,Treg,B,M,G,MFp,Ff,F | avg_Ff_per_tile | avg_Ff_per_tile: This metric reflects the average number of FSP1-positive fibroblasts (Ff) per tile. As a normalized average, it facilitates comparisons of fibroblast density between patient samples. |
| c3gx00i4v22h | Th,Treg,B,M,G,MFp,Ff,F | avg_F_per_tile | avg_F_per_tile: This parameter indicates the average number of fibroblasts (F) per tile. By averaging over uniformly sized tiles, it provides a normalized and comparable measure of fibroblast presence across tissues. |
| c6h4kypb4jyl | Tc,B,A,MFp | tumor_prop_cytotoxic_t | tumor_prop_cytotoxic_t: This parameter measures the normalized proportion of cytotoxic T cells (CD8+) in the tumor compartment. It is computed by dividing the count of cytotoxic T cells by the total number of cells in the tumor, with a small constant added to the denominator to avoid division by zero. This normalization allows for direct comparisons between different patient samples. |
| c6h4kypb4jyl | Tc,B,A,MFp | tumor_prop_myofibroblasts_pdpn | tumor_prop_myofibroblasts_pdpn: This parameter represents the normalized fraction of PDPN+ myofibroblasts within the tumor compartment. It is obtained by dividing the count of these myofibroblasts by the overall cell count in the tumor, enabling comparisons across diverse patient cases. |
| c6h4kypb4jyl | Tc,B,A,MFp | stroma_prop_cytotoxic_t | stroma_prop_cytotoxic_t: This parameter indicates the normalized proportion of cytotoxic T cells in the stroma compartment. The value is derived by dividing the cytotoxic T cell count by the total number of cells in the stroma, making it suitable for cross-sample analysis. |
| c6h4kypb4jyl | Tc,B,A,MFp | stroma_prop_b_cells | stroma_prop_b_cells: This parameter measures the normalized proportion of B cells in the stroma. It is calculated as the number of B cells divided by the total cell count in the stroma, offering a standardized metric for comparing different tumor cases. |
| c6h4kypb4jyl | Tc,B,A,MFp | stroma_prop_ap_cells | stroma_prop_ap_cells: This parameter reflects the normalized fraction of antigen presenting cells in the stroma. It is computed by dividing the count of antigen presenting cells by the overall number of cells in the stroma, which allows for effective comparison across samples. |
| c6h4kypb4jyl | Tc,B,A,MFp | stroma_prop_myofibroblasts_pdpn | stroma_prop_myofibroblasts_pdpn: This parameter quantifies the normalized proportion of PDPN+ myofibroblasts in the stroma compartment by dividing their count by the total cell count in the stroma. This normalization facilitates comparison across various patient cases. |
| c6h4kypb4jyl | Tc,B,A,MFp | ratio_tumor_stroma_cytotoxic_t_cells | ratio_tumor_stroma_cytotoxic_t_cells: This parameter is the ratio of the normalized proportion of cytotoxic T cells between the tumor and stroma compartments. It is obtained by dividing the tumor proportion by the stroma proportion (with an adjustment to prevent division by zero), thereby offering a comparative metric between the two tissue compartments. |
| c6h4kypb4jyl | Tc,B,A,MFp | ratio_tumor_stroma_myofibroblasts_pdpn | ratio_tumor_stroma_myofibroblasts_pdpn: This parameter measures the ratio of the normalized proportion of PDPN+ myofibroblasts in the tumor compartment to that in the stroma. Calculated by dividing the tumor proportion by the stroma proportion (with a slight adjustment to avoid division by zero), it provides a direct comparison of myofibroblast distribution between compartments. |
| c6s8kv09oo8a | TU,A,MF,Ff,B | tri_cell_normalized_by_cells | tri_cell_normalized_by_cells represents the frequency of tri-cell contacts among the three distinct types of cells in the stromal compartment. It is normalized by dividing the raw count of tri-cell contacts by the total number of filtered stromal cells, thus allowing a comparison between different patient cases regardless of differences in cellular density. |
| c6s8kv09oo8a | TU,A,MF,Ff,B | tri_cell_density_per_1000squm | tri_cell_density_per_1000squm measures the density of tri-cell contacts per 1000 square micrometers of stromal area. By normalizing the raw tri-cell contact count with the size of the stromal region, this parameter facilitates meaningful comparisons across tumor samples with varying tissue areas. |
| c9to1xcdn3vh | Tc | proportion_aligned_cytotoxic_t_cells | proportion_aligned_cytotoxic_t_cells represents the fraction of cytotoxic T lymphocytes in the stromal compartment that are aligned with their nearest blood vessel. The alignment is based on comparing the orientation of the cell's nucleus and the vessel's major axis, with an alignment threshold of 30 degrees applied to the angular difference. This metric is normalized, meaning it provides a relative measurement (a proportion) rather than a raw count, making it suitable for comparisons across different patient cases or image patches. |
| caqz7q9hh21x | Ff,Treg,A,G | FIBROBLAST_FSP1_SMOOTHNESS_MEAN | FIBROBLAST_FSP1_SMOOTHNESS_MEAN represents the average nuclear contour smoothness of FSP1-positive fibroblasts in the stromal region. It is calculated by measuring the coefficient of variation (ratio of the standard deviation to the mean) of the distances from the nucleus centroid to its polygon vertices. This normalized metric allows comparisons across patient cases by averaging over the analyzed cells in each patch. |
| caqz7q9hh21x | Ff,Treg,A,G | T_CELL_REG_SMOOTHNESS_MEAN | T_CELL_REG_SMOOTHNESS_MEAN represents the average nuclear contour smoothness of regulatory T cells located in the stromal region. The measure is computed by calculating a coefficient of variation for each cell’s nuclear contour and then averaging these values. Being normalized over the number of cells, it is suitable for comparisons between different tumor regions. |
| caqz7q9hh21x | Ff,Treg,A,G | AP_CELL_SMOOTHNESS_MEAN | AP_CELL_SMOOTHNESS_MEAN represents the average nuclear contour smoothness of antigen presenting cells in the stromal region. It is derived by computing the coefficient of variation for the cellular nuclear contour and aggregating these values. This normalized metric reflects the morphological irregularity of nuclei in these immune cells across patches. |
| caqz7q9hh21x | Ff,Treg,A,G | GRANULOCYTE_SMOOTHNESS_MEAN | GRANULOCYTE_SMOOTHNESS_MEAN represents the average nuclear contour smoothness of granulocytes in the stromal region. Similar to the other cell types, the coefficient of variation of distances from the nucleus centroid to the contour vertices is computed per cell and then averaged, providing a normalized measure to compare cellular irregularity. |
| caqz7q9hh21x | Ff,Treg,A,G | IMMUNE_CELLS_SMOOTHNESS_MEAN | IMMUNE_CELLS_SMOOTHNESS_MEAN is the composite average of the mean smoothness values of the three immune cell types: regulatory T cells, antigen presenting cells, and granulocytes. This parameter provides a consolidated, normalized measure of nuclear contour irregularity across immune cells in the stromal region, facilitating comparison across different patches or patient cases. |
| caqz7q9hh21x | Ff,Treg,A,G | SMOOTHNESS_RATIO | SMOOTHNESS_RATIO represents the ratio of the fibroblast FSP1-positive cell smoothness to the average smoothness of the immune cells (calculated from T cell regulatory, antigen presenting cells, and granulocytes). This normalized parameter indicates the relative difference in nuclear contour irregularity between fibroblasts and immune cells, thus serving as a comparative metric across patient cases. |
| cena9qdsbt8f | TU,Ff | MEDIAN_VESSEL_PROXIMAL_TU_FSP1_DENSITY_RATIO | This parameter measures the median ratio of tumor cell density to FSP1+ fibroblast density within vessel-proximal stromal regions. For each vessel, a surrounding stromal area is defined by buffering the vessel polygon and intersecting it with the stromal compartment. The densities of tumor cells and FSP1+ fibroblasts are calculated by dividing their counts by the area of this defined region, and the ratio of these densities is computed. The final parameter is the median of all such ratios across vessels, providing a normalized numeric measure that can be compared across different patient cases. A higher ratio suggests a relative predominance of tumor cells, which may indicate an aggressive, invasive phenotype with potential for vascular dissemination. |
| cm1w7cbq98m5 | Ff,G | fsp1_mean_form_factor | fsp1_mean_form_factor: This parameter is the average nuclear form factor of FSP1+ fibroblasts in the stromal compartment. The nuclear form factor is computed by a normalized formula (4 * π * area) / (perimeter^2) for each cell, ensuring comparability across different patient cases. |
| cm1w7cbq98m5 | Ff,G | fsp1_median_form_factor | fsp1_median_form_factor: This parameter represents the median nuclear form factor of FSP1+ fibroblasts. It is derived using the same normalized nuclear form factor calculation and provides a robust measure of central tendency in cell morphology. |
| cm1w7cbq98m5 | Ff,G | granulocyte_mean_form_factor | granulocyte_mean_form_factor: This parameter is the mean nuclear form factor of granulocytes within the stromal compartment. It is calculated from the normalized ratio of nuclear area to the square of its perimeter, making it comparable across different tissue patches. |
| cm1w7cbq98m5 | Ff,G | granulocyte_median_form_factor | granulocyte_median_form_factor: This parameter denotes the median nuclear form factor of granulocytes. Like its fibroblast counterpart, it is calculated from the normalized form factor formula, offering a robust metric for comparing nuclear shape features. |
| cm1w7cbq98m5 | Ff,G | mean_form_factor_difference | mean_form_factor_difference: This parameter measures the difference between the mean nuclear form factors of FSP1+ fibroblasts and granulocytes. It reflects the comparative change in nuclear shape attributes between the two cell types across different patches. |
| cm1w7cbq98m5 | Ff,G | median_form_factor_difference | median_form_factor_difference: This parameter quantifies the difference between the median nuclear form factors of FSP1+ fibroblasts and granulocytes. It is used to assess the comparative differences in nuclear morphology in a robust, normalized manner. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_TU_TU | corr_TU_TU: This parameter measures the Pearson correlation coefficient between the radial density profile of epithelial cells (TU) with itself, serving as an internal consistency check of the density measurements across defined concentric bins. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_TU_Tc | corr_TU_Tc: This parameter measures the Pearson correlation coefficient between the radial density profiles of epithelial cells (TU) and cytotoxic T cells (Tc). It quantifies the degree to which the spatial distribution of these two cell types changes in tandem across radial bins. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_TU_Th | corr_TU_Th: This parameter measures the Pearson correlation coefficient between the radial density profiles of epithelial cells (TU) and helper T cells (Th), indicating how similarly their densities vary from the center to the periphery. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_TU_Treg | corr_TU_Treg: This parameter measures the Pearson correlation coefficient between the radial density profiles of epithelial cells (TU) and regulatory T cells (Treg), reflecting their spatial co-distribution patterns within the tissue region. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_TU_B | corr_TU_B: This parameter measures the Pearson correlation coefficient between the radial density profiles of epithelial cells (TU) and B cells (B), assessing how the variations in cell density for these types correlate across the annular bins. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_TU_P | corr_TU_P: This parameter measures the Pearson correlation coefficient between the radial density profiles of epithelial cells (TU) and plasma cells (P), providing insight into the spatial relationship between these cell types. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_TU_M | corr_TU_M: This parameter measures the Pearson correlation coefficient between the radial density profiles of epithelial cells (TU) and macrophages (M), indicating the degree of synchronized spatial distribution. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_TU_MFp | corr_TU_MFp: This parameter measures the Pearson correlation coefficient between the radial density profiles of epithelial cells (TU) and myofibroblasts (MFp), quantifying the linear relationship in density patterns along the radial bins. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_TU_MF | corr_TU_MF: This parameter measures the Pearson correlation coefficient between the radial density profiles of epithelial cells (TU) and myofibroblasts (MF), reflecting the similarity in their spatial gradients across the tumor region. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_TU_E | corr_TU_E: This parameter measures the Pearson correlation coefficient between the radial density profiles of epithelial cells (TU) and endothelial cells (E), thereby assessing the degree of co-localization in their radial distributions. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_Tc_Tc | corr_Tc_Tc: This parameter measures the Pearson correlation coefficient between the radial density profile of cytotoxic T cells (Tc) with itself, ensuring internal consistency in the spatial density measurements for this cell type. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_Tc_Th | corr_Tc_Th: This parameter measures the Pearson correlation coefficient between the radial density profiles of cytotoxic T cells (Tc) and helper T cells (Th), indicating how their spatial distributions correlate across the tissue patch. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_Tc_Treg | corr_Tc_Treg: This parameter measures the Pearson correlation coefficient between the radial density profiles of cytotoxic T cells (Tc) and regulatory T cells (Treg), providing insight into their potential coordinated spatial behavior. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_Tc_B | corr_Tc_B: This parameter measures the Pearson correlation coefficient between the radial density profiles of cytotoxic T cells (Tc) and B cells (B), capturing the association between their distributions across radial bins. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_Tc_P | corr_Tc_P: This parameter measures the Pearson correlation coefficient between the radial density profiles of cytotoxic T cells (Tc) and plasma cells (P), reflecting the degree of linear association in their spatial patterns. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_Tc_M | corr_Tc_M: This parameter measures the Pearson correlation coefficient between the radial density profiles of cytotoxic T cells (Tc) and macrophages (M), indicating the extent to which their density variations align over the radial intervals. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_Tc_MFp | corr_Tc_MFp: This parameter measures the Pearson correlation coefficient between the radial density profiles of cytotoxic T cells (Tc) and myofibroblasts (MFp), revealing the linear relationship in their spatial distributions. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_Tc_MF | corr_Tc_MF: This parameter measures the Pearson correlation coefficient between the radial density profiles of cytotoxic T cells (Tc) and myofibroblasts (MF), showing how similarly their densities change radially. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_Tc_E | corr_Tc_E: This parameter measures the Pearson correlation coefficient between the radial density profiles of cytotoxic T cells (Tc) and endothelial cells (E), thereby quantifying their spatial correlation. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_Th_Th | corr_Th_Th: This parameter measures the Pearson correlation coefficient of the radial density profile of helper T cells (Th) with itself, serving as a consistency measure for its density across the bins. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_Th_Treg | corr_Th_Treg: This parameter measures the Pearson correlation coefficient between the radial density profiles of helper T cells (Th) and regulatory T cells (Treg), assessing the similarity of their radial spatial trends. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_Th_B | corr_Th_B: This parameter measures the Pearson correlation coefficient between the radial density profiles of helper T cells (Th) and B cells (B), indicating how their distributions co-vary across the annular bins. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_Th_P | corr_Th_P: This parameter measures the Pearson correlation coefficient between the radial density profiles of helper T cells (Th) and plasma cells (P), reflecting the degree of association between their spatial patterns. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_Th_M | corr_Th_M: This parameter measures the Pearson correlation coefficient between the radial density profiles of helper T cells (Th) and macrophages (M), thereby quantifying their spatial interrelationship. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_Th_MFp | corr_Th_MFp: This parameter measures the Pearson correlation coefficient between the radial density profiles of helper T cells (Th) and myofibroblasts (MFp), showing the linear relationship in their density distributions. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_Th_MF | corr_Th_MF: This parameter measures the Pearson correlation coefficient between the radial density profiles of helper T cells (Th) and myofibroblasts (MF), capturing the extent of their coordinated spatial variation. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_Th_E | corr_Th_E: This parameter measures the Pearson correlation coefficient between the radial density profiles of helper T cells (Th) and endothelial cells (E), indicating the level of resemblance in their radial distribution patterns. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_Treg_Treg | corr_Treg_Treg: This parameter measures the Pearson correlation coefficient of the radial density profile of regulatory T cells (Treg) with itself, confirming the consistency of its spatial measurements. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_Treg_B | corr_Treg_B: This parameter measures the Pearson correlation coefficient between the radial density profiles of regulatory T cells (Treg) and B cells (B), illustrating the degree to which their spatial distributions are aligned. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_Treg_P | corr_Treg_P: This parameter measures the Pearson correlation coefficient between the radial density profiles of regulatory T cells (Treg) and plasma cells (P), assessing their co-distribution across the concentric bins. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_Treg_M | corr_Treg_M: This parameter measures the Pearson correlation coefficient between the radial density profiles of regulatory T cells (Treg) and macrophages (M), reflecting how similarly their densities vary across the tumor patch. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_Treg_MFp | corr_Treg_MFp: This parameter measures the Pearson correlation coefficient between the radial density profiles of regulatory T cells (Treg) and myofibroblasts (MFp), quantifying the linear relationship in their spatial distributions. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_Treg_MF | corr_Treg_MF: This parameter measures the Pearson correlation coefficient between the radial density profiles of regulatory T cells (Treg) and myofibroblasts (MF), indicating the degree of synchronized spatial variation. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_Treg_E | corr_Treg_E: This parameter measures the Pearson correlation coefficient between the radial density profiles of regulatory T cells (Treg) and endothelial cells (E), thereby capturing their spatial correlation. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_B_B | corr_B_B: This parameter measures the Pearson correlation coefficient of the radial density profile of B cells (B) with itself, ensuring reliable density measurement across the bins. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_B_P | corr_B_P: This parameter measures the Pearson correlation coefficient between the radial density profiles of B cells (B) and plasma cells (P), revealing the degree of similarity in their spatial trends. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_B_M | corr_B_M: This parameter measures the Pearson correlation coefficient between the radial density profiles of B cells (B) and macrophages (M), indicating the synchronized variation in their density distributions. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_B_MFp | corr_B_MFp: This parameter measures the Pearson correlation coefficient between the radial density profiles of B cells (B) and myofibroblasts (MFp), quantifying the linear relationship between their spatial patterns. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_B_MF | corr_B_MF: This parameter measures the Pearson correlation coefficient between the radial density profiles of B cells (B) and myofibroblasts (MF), showing the extent of their correlated spatial behavior. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_B_E | corr_B_E: This parameter measures the Pearson correlation coefficient between the radial density profiles of B cells (B) and endothelial cells (E), reflecting how similarly their densities change radially. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_P_P | corr_P_P: This parameter measures the Pearson correlation coefficient of the radial density profile of plasma cells (P) with itself, serving as an internal consistency measure for plasma cell density. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_P_M | corr_P_M: This parameter measures the Pearson correlation coefficient between the radial density profiles of plasma cells (P) and macrophages (M), assessing the degree of co-variation in their spatial distributions. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_P_MFp | corr_P_MFp: This parameter measures the Pearson correlation coefficient between the radial density profiles of plasma cells (P) and myofibroblasts (MFp), indicating the linear association in their density patterns. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_P_MF | corr_P_MF: This parameter measures the Pearson correlation coefficient between the radial density profiles of plasma cells (P) and myofibroblasts (MF), reflecting the similarity in their spatial gradients. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_P_E | corr_P_E: This parameter measures the Pearson correlation coefficient between the radial density profiles of plasma cells (P) and endothelial cells (E), thereby quantifying their spatial relation. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_M_M | corr_M_M: This parameter measures the Pearson correlation coefficient of the radial density profile of macrophages (M) with itself, ensuring consistency in the measurement of macrophage density across bins. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_M_MFp | corr_M_MFp: This parameter measures the Pearson correlation coefficient between the radial density profiles of macrophages (M) and myofibroblasts (MFp), capturing the linear relationship between their spatial distributions. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_M_MF | corr_M_MF: This parameter measures the Pearson correlation coefficient between the radial density profiles of macrophages (M) and myofibroblasts (MF), indicating the extent to which their density changes are aligned. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_M_E | corr_M_E: This parameter measures the Pearson correlation coefficient between the radial density profiles of macrophages (M) and endothelial cells (E), reflecting their spatial co-variation. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_MFp_MFp | corr_MFp_MFp: This parameter measures the Pearson correlation coefficient of the radial density profile of myofibroblasts (MFp) with itself, confirming the internal consistency of their density data. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_MFp_MF | corr_MFp_MF: This parameter measures the Pearson correlation coefficient between the radial density profiles of myofibroblasts (MFp) and myofibroblasts (MF), quantifying the degree of their spatial association. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_MFp_E | corr_MFp_E: This parameter measures the Pearson correlation coefficient between the radial density profiles of myofibroblasts (MFp) and endothelial cells (E), indicating how similarly their densities vary radially. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_MF_MF | corr_MF_MF: This parameter measures the Pearson correlation coefficient of the radial density profile of myofibroblasts (MF) with itself, ensuring the reliability of the spatial density measurement for this cell type. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_MF_E | corr_MF_E: This parameter measures the Pearson correlation coefficient between the radial density profiles of myofibroblasts (MF) and endothelial cells (E), reflecting the relationship between their spatial distributions. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | corr_E_E | corr_E_E: This parameter measures the Pearson correlation coefficient of the radial density profile of endothelial cells (E) with itself, confirming the consistency of the density information across the bins. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | TU_mean_density | TU_mean_density: This parameter represents the average normalized density (cells per square micrometer) of epithelial cells (TU) across all concentric radial bins of the tissue patch, enabling comparison between patient cases. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | TU_max_density | TU_max_density: This parameter indicates the maximum normalized density observed for epithelial cells (TU) in any radial bin, highlighting the region of peak cell concentration. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | TU_radial_gradient | TU_radial_gradient: This parameter captures the slope of the linear regression fitted to the radial density profile of epithelial cells (TU). A positive gradient indicates increasing density towards the periphery, while a negative gradient indicates a decrease. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | Tc_mean_density | Tc_mean_density: This parameter represents the average normalized density of cytotoxic T cells (Tc) across the radial bins, providing a standardized measure of their spatial distribution. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | Tc_max_density | Tc_max_density: This parameter indicates the maximum normalized density of cytotoxic T cells (Tc) in any of the annular bins, reflecting the highest concentration region within the patch. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | Tc_radial_gradient | Tc_radial_gradient: This parameter captures the trend of cytotoxic T cell (Tc) distribution by providing the slope of the linear regression of its radial density profile, which signals whether density increases or decreases from the center outward. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | Th_mean_density | Th_mean_density: This parameter represents the average normalized density of helper T cells (Th) across the defined radial bins, allowing for comparison across cases. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | Th_max_density | Th_max_density: This parameter indicates the highest normalized density of helper T cells (Th) within any radial bin, pinpointing the area with the most concentrated cell presence. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | Th_radial_gradient | Th_radial_gradient: This parameter measures the slope of the linear fit to the radial density profile of helper T cells (Th), with the sign of the slope indicating the direction of density change from the center to the periphery. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | Treg_mean_density | Treg_mean_density: This parameter represents the average normalized density of regulatory T cells (Treg) across the tissue patch’s radial bins, ensuring normalization for comparison across samples. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | Treg_max_density | Treg_max_density: This parameter indicates the maximum normalized density of regulatory T cells (Treg) observed in any radial bin, marking the peak level of cellular concentration. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | Treg_radial_gradient | Treg_radial_gradient: This parameter captures the radial trend of regulatory T cell (Treg) density by providing the slope of the linear regression on its density profile, with positive slopes indicating an increase towards the edge. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | B_mean_density | B_mean_density: This parameter represents the average normalized density of B cells (B) across all radial bins of the patch, standardized to the annular areas for valid inter-sample comparisons. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | B_max_density | B_max_density: This parameter indicates the peak normalized density of B cells (B) within any specific radial bin, reflecting the area of highest B cell concentration. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | B_radial_gradient | B_radial_gradient: This parameter measures the slope of the linear regression fitted to the B cell (B) radial density profile, identifying whether their density increases or decreases from the center towards the periphery. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | P_mean_density | P_mean_density: This parameter represents the average normalized density of plasma cells (P) across the concentric bins of the tissue patch, enabling comparison across different patient cases. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | P_max_density | P_max_density: This parameter indicates the highest normalized density of plasma cells (P) observed in any annular bin, identifying the compartment with maximum concentration. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | P_radial_gradient | P_radial_gradient: This parameter captures the spatial trend of plasma cell (P) distribution by providing the slope of the linear fit to its density profile, with the value indicating the directional change from the center outward. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | M_mean_density | M_mean_density: This parameter represents the average normalized density of macrophages (M) calculated over all radial bins, ensuring that the measurement is normalized by area. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | M_max_density | M_max_density: This parameter indicates the maximum normalized density of macrophages (M) in any radial bin, thus identifying the region of peak macrophage accumulation within the tissue patch. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | M_radial_gradient | M_radial_gradient: This parameter measures the slope of the linear regression line fitted to the macrophage (M) density profile across the radial bins, reflecting whether their density increases or decreases towards the periphery. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | MFp_mean_density | MFp_mean_density: This parameter represents the average normalized density of myofibroblasts marked as MFp across all concentric bins, normalized by the area of each bin, facilitating cross-case comparisons. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | MFp_max_density | MFp_max_density: This parameter indicates the maximum normalized density of MFp cells observed in any radial bin, highlighting the area of highest cell concentration. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | MFp_radial_gradient | MFp_radial_gradient: This parameter captures the rate of change in the density of MFp cells across the radial bins through the slope of a linear regression, indicating spatial trends from the center outward. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | MF_mean_density | MF_mean_density: This parameter represents the average normalized density of myofibroblasts (MF) across the tissue patch’s radial bins, standardized by area for consistent comparisons. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | MF_max_density | MF_max_density: This parameter indicates the peak normalized density of myofibroblasts (MF) in any annular bin, reflecting the highest local concentration of these cells. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | MF_radial_gradient | MF_radial_gradient: This parameter measures the slope of the linear regression fitted to the radial density profile of myofibroblasts (MF), indicating the tendency of their density to increase or decrease from the center to the periphery. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | E_mean_density | E_mean_density: This parameter represents the average normalized density of endothelial cells (E) across all radial bins, with normalization allowing for valid comparisons across samples. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | E_max_density | E_max_density: This parameter indicates the maximum normalized density of endothelial cells (E) observed in any radial bin, identifying the region with the highest endothelial cell concentration. |
| crecbc67jue4 | TU,Tc,Th,Treg,B,P,M,MFp,MF,E | E_radial_gradient | E_radial_gradient: This parameter captures the directional trend in the density of endothelial cells (E) by providing the slope of the linear regression applied to their radial density profile, where the sign of the slope reflects whether density increases or decreases toward the tissue periphery. |
| csnzzcliltti | TU,Tc,Th,Treg,B,M,Ff,E | TU_close_avg_perimeter | TU_close_avg_perimeter measures the average nucleus perimeter of tumor epithelial cells (TU) that are located within 50 pixels of a vessel. This normalized metric allows comparison across different patient cases by averaging the per-cell measurements. |
| csnzzcliltti | TU,Tc,Th,Treg,B,M,Ff,E | TU_far_avg_perimeter | TU_far_avg_perimeter measures the average nucleus perimeter of tumor epithelial cells (TU) found beyond the 50 pixel threshold from the nearest vessel, providing a normalized assessment of cell morphology in more distal regions. |
| csnzzcliltti | TU,Tc,Th,Treg,B,M,Ff,E | TU_perimeter_ratio | TU_perimeter_ratio provides the normalized ratio of the average nucleus perimeter of tumor epithelial cells (TU) close to vessels relative to those far from vessels, highlighting potential morphological shifts with proximity. |
| csnzzcliltti | TU,Tc,Th,Treg,B,M,Ff,E | Tc_close_avg_perimeter | Tc_close_avg_perimeter represents the average nucleus perimeter of CD8 positive T cells (Tc) that are within 50 pixels of a vessel, offering a normalized morphological measurement for these immune cells in close vicinity to vessels. |
| csnzzcliltti | TU,Tc,Th,Treg,B,M,Ff,E | Tc_far_avg_perimeter | Tc_far_avg_perimeter represents the average nucleus perimeter of CD8 positive T cells (Tc) located beyond 50 pixels from a vessel, enabling comparison of nuclear morphology based on vessel proximity. |
| csnzzcliltti | TU,Tc,Th,Treg,B,M,Ff,E | Tc_perimeter_ratio | Tc_perimeter_ratio is the ratio of the average nucleus perimeter for CD8 positive T cells (Tc) near vessels versus those further away, providing a relative, normalized metric of their morphological differences. |
| csnzzcliltti | TU,Tc,Th,Treg,B,M,Ff,E | Th_close_avg_perimeter | Th_close_avg_perimeter indicates the average nucleus perimeter of CD4 positive T cells (Th) that are within the 50 pixel threshold from a vessel, representing a normalized metric for these cells in vessel proximal areas. |
| csnzzcliltti | TU,Tc,Th,Treg,B,M,Ff,E | Th_far_avg_perimeter | Th_far_avg_perimeter indicates the average nucleus perimeter of CD4 positive T cells (Th) located more than 50 pixels away from a vessel, facilitating normalized comparisons based on proximity. |
| csnzzcliltti | TU,Tc,Th,Treg,B,M,Ff,E | Th_perimeter_ratio | Th_perimeter_ratio is the ratio comparing the average nucleus perimeter of CD4 positive T cells (Th) in close proximity to vessels against those located further away, serving as a normalized indicator of spatial morphological variation. |
| csnzzcliltti | TU,Tc,Th,Treg,B,M,Ff,E | Treg_close_avg_perimeter | Treg_close_avg_perimeter measures the average nucleus perimeter of regulatory T cells (Treg) that are situated within 50 pixels of a vessel, providing a normalized criterion for analyzing cellular morphology in proximity to vascular structures. |
| csnzzcliltti | TU,Tc,Th,Treg,B,M,Ff,E | B_close_avg_perimeter | B_close_avg_perimeter quantifies the average nucleus perimeter of B cells that are found within 50 pixels of a vessel, ensuring normalization by averaging individual cell measurements across patches. |
| csnzzcliltti | TU,Tc,Th,Treg,B,M,Ff,E | B_far_avg_perimeter | B_far_avg_perimeter quantifies the average nucleus perimeter of B cells located beyond the 50 pixel threshold from a vessel, offering a normalized measure to compare with vessel-adjacent regions. |
| csnzzcliltti | TU,Tc,Th,Treg,B,M,Ff,E | B_perimeter_ratio | B_perimeter_ratio provides the normalized ratio of average nucleus perimeter of B cells close to vessels relative to those found further away, highlighting differences in cellular morphology based on spatial factors. |
| csnzzcliltti | TU,Tc,Th,Treg,B,M,Ff,E | M_close_avg_perimeter | M_close_avg_perimeter measures the average nucleus perimeter of macrophages (M) that are within 50 pixels of a vessel, yielding a normalized metric for comparing macrophage morphology across different patient patches. |
| csnzzcliltti | TU,Tc,Th,Treg,B,M,Ff,E | M_far_avg_perimeter | M_far_avg_perimeter measures the average nucleus perimeter of macrophages (M) located more than 50 pixels from a vessel, providing a normalized comparison basis for cellular morphology. |
| csnzzcliltti | TU,Tc,Th,Treg,B,M,Ff,E | M_perimeter_ratio | M_perimeter_ratio is the ratio of the average nucleus perimeter of macrophages (M) close to vessels to those far from vessels, offering a normalized measure of morphological disparity relative to vessel proximity. |
| csnzzcliltti | TU,Tc,Th,Treg,B,M,Ff,E | Ff_close_avg_perimeter | Ff_close_avg_perimeter calculates the average nucleus perimeter of fibroblasts (Ff) within 50 pixels of a vessel, serving as a normalized measure of their nuclear morphology in vessel-adjacent zones. |
| csnzzcliltti | TU,Tc,Th,Treg,B,M,Ff,E | Ff_far_avg_perimeter | Ff_far_avg_perimeter calculates the average nucleus perimeter of fibroblasts (Ff) situated beyond 50 pixels from a vessel, providing a normalized metric to assess morphology in more distal regions. |
| csnzzcliltti | TU,Tc,Th,Treg,B,M,Ff,E | Ff_perimeter_ratio | Ff_perimeter_ratio provides the ratio of average nucleus perimeter for fibroblasts (Ff) near vessels compared to those further away, yielding a normalized indicator of morphological change with spatial context. |
| csnzzcliltti | TU,Tc,Th,Treg,B,M,Ff,E | E_close_avg_perimeter | E_close_avg_perimeter measures the average nucleus perimeter of endothelial cells (E) that are located within 50 pixels of a vessel, offering a normalized assessment relevant for vessel-proximal cellular analysis. |
| csnzzcliltti | TU,Tc,Th,Treg,B,M,Ff,E | E_far_avg_perimeter | E_far_avg_perimeter measures the average nucleus perimeter of endothelial cells (E) located beyond 50 pixels from a vessel, providing a normalized metric for comparing morphological features based on proximity. |
| csnzzcliltti | TU,Tc,Th,Treg,B,M,Ff,E | E_perimeter_ratio | E_perimeter_ratio provides the ratio of average nucleus perimeter for endothelial cells (E) in close proximity to vessels relative to those far from vessels, serving as a normalized indicator of spatial morphological variation. |
| cuvxkl3yu725 | Tc | Median_Nucleus_Perimeter | The parameter represents the median value of the perimeters of the nuclei from cytotoxic T lymphocytes (CD8+ T cells) located in the stroma of breast cancer tissue. It is computed by measuring the perimeter of each cell nucleus in the designated region and calculating the median of these values, providing a normalized numeric metric that can be compared across different patient cases. |
| cxfbv6rrc5c7 | Treg,Th,Tc,B,M,A | Treg_overlap_proportion | Treg_overlap_proportion measures the normalized fraction of regulatory T cells that intersect with the defined epithelial-stromal boundary region. It is calculated by dividing the number of overlapping Treg cells by the total number of Treg cells, allowing for a consistent comparison across different patient patches. |
| cxfbv6rrc5c7 | Treg,Th,Tc,B,M,A | Helper T Cells_overlap_proportion | Helper T Cells_overlap_proportion measures the normalized fraction of helper T cells that intersect with the defined boundary region between the epithelial and stromal compartments. This parameter is computed by determining the ratio of helper T cells overlapping the boundary to the total helper T cells in the patch. |
| cxfbv6rrc5c7 | Treg,Th,Tc,B,M,A | Cytotoxic T Cells_overlap_proportion | Cytotoxic T Cells_overlap_proportion measures the normalized fraction of cytotoxic T cells that intersect with the epithelial-stromal boundary region. It is obtained by dividing the count of cytotoxic T cells that overlap with the boundary by their total count, making it comparable across different cases. |
| cxfbv6rrc5c7 | Treg,Th,Tc,B,M,A | B Cells_overlap_proportion | B Cells_overlap_proportion measures the normalized fraction of B cells that intersect with the defined boundary between the epithelial and stromal tissue compartments. The value is derived by the ratio of overlapping B cells to the total available B cells in the analyzed region. |
| cxfbv6rrc5c7 | Treg,Th,Tc,B,M,A | Macrophages_overlap_proportion | Macrophages_overlap_proportion measures the normalized fraction of macrophages that intersect with the epithelial-stromal boundary region. It is defined as the proportion of macrophages overlapping the sensitive boundary relative to the overall count of macrophages, ensuring cross-case comparability. |
| cxfbv6rrc5c7 | Treg,Th,Tc,B,M,A | APC_overlap_proportion | APC_overlap_proportion measures the normalized fraction of antigen-presenting cells (APCs) that intersect with the epithelial-stromal boundary. It is calculated by dividing the number of APCs overlapping the boundary by the total number of APCs, providing a normalized metric. |
| cxfbv6rrc5c7 | Treg,Th,Tc,B,M,A | total_overlap_proportion | total_overlap_proportion is a composite metric that sums the individual normalized overlap proportions of the immune cell types of interest (Treg, Helper T Cells, Cytotoxic T Cells, B Cells, Macrophages, and APC). This aggregated measure provides an overall estimate of immune cell interaction at the epithelial-stromal boundary, enabling cross-patient and cross-patch comparisons. |
| d0sm327jlo54 | TU,Tc,Th,Treg,M,MFp,Ff,E,A | TU_avg_degree | TU_avg_degree: Represents the normalized average number of edges per epithelial cell (TU) in the spatial graph. It is computed by dividing the sum of all connections within the epithelial cell network by the number of epithelial cells, allowing comparison among different tumor patches. |
| d0sm327jlo54 | TU,Tc,Th,Treg,M,MFp,Ff,E,A | TU_clustering_coef | TU_clustering_coef: Represents the normalized average clustering coefficient for the epithelial cell group (TU). It indicates the tendency of epithelial cells to cluster together within the spatial graph, providing a measure between 0 and 1. |
| d0sm327jlo54 | TU,Tc,Th,Treg,M,MFp,Ff,E,A | TU_connectivity_score | TU_connectivity_score: Calculated as the product of TU_avg_degree and TU_clustering_coef, this metric provides an integrated, normalized measure of the connectivity of the epithelial cell network. |
| d0sm327jlo54 | TU,Tc,Th,Treg,M,MFp,Ff,E,A | Tc_avg_degree | Tc_avg_degree: Represents the normalized average number of connections per t-cell CD8 (Tc) within their spatial graph. It allows for consistent comparison of connectivity among different patches. |
| d0sm327jlo54 | TU,Tc,Th,Treg,M,MFp,Ff,E,A | Tc_clustering_coef | Tc_clustering_coef: Represents the normalized average clustering coefficient for t-cell CD8 (Tc) networks. It quantifies how locally interconnected these cells are within the spatial configuration. |
| d0sm327jlo54 | TU,Tc,Th,Treg,M,MFp,Ff,E,A | Tc_connectivity_score | Tc_connectivity_score: This metric is the product of Tc_avg_degree and Tc_clustering_coef, offering a combined, normalized measure of connectivity for t-cell CD8 cells. |
| d0sm327jlo54 | TU,Tc,Th,Treg,M,MFp,Ff,E,A | Th_avg_degree | Th_avg_degree: Represents the normalized average degree for t-cell CD4 (Th), indicating how many connections t-cell CD4 cells have on average within the spatial graph. |
| d0sm327jlo54 | TU,Tc,Th,Treg,M,MFp,Ff,E,A | M_avg_degree | M_avg_degree: Represents the normalized average number of connections per macrophage (M) in the spatial graph, thus allowing for meaningful comparisons across patches. |
| d0sm327jlo54 | TU,Tc,Th,Treg,M,MFp,Ff,E,A | M_clustering_coef | M_clustering_coef: Represents the normalized average clustering coefficient for macrophages (M), indicating the level of local interconnectivity among these cells. |
| d0sm327jlo54 | TU,Tc,Th,Treg,M,MFp,Ff,E,A | M_connectivity_score | M_connectivity_score: Calculated as the product of M_avg_degree and M_clustering_coef, this metric provides an integrated, normalized measure of connectivity for macrophages. |
| d0sm327jlo54 | TU,Tc,Th,Treg,M,MFp,Ff,E,A | MFp_avg_degree | MFp_avg_degree: Represents the normalized average number of connections per myofibroblast (MFp) within the spatial graph, conveying average connectivity. |
| d0sm327jlo54 | TU,Tc,Th,Treg,M,MFp,Ff,E,A | MFp_clustering_coef | MFp_clustering_coef: Represents the normalized average clustering coefficient for myofibroblasts (MFp), quantifying how closely these cells are grouped together spatially. |
| d0sm327jlo54 | TU,Tc,Th,Treg,M,MFp,Ff,E,A | MFp_connectivity_score | MFp_connectivity_score: This metric is calculated as the product of MFp_avg_degree and MFp_clustering_coef, providing an integrated, normalized measure of connectivity for myofibroblasts. |
| d0sm327jlo54 | TU,Tc,Th,Treg,M,MFp,Ff,E,A | E_avg_degree | E_avg_degree: Represents the normalized average number of connections per endothelial cell (E) in the spatial graph. It is used to assess the average connectivity level in a standardized way. |
| d0sm327jlo54 | TU,Tc,Th,Treg,M,MFp,Ff,E,A | E_clustering_coef | E_clustering_coef: Represents the normalized average clustering coefficient for endothelial cells (E), indicating the degree of local interconnectivity among these cells. |
| d0sm327jlo54 | TU,Tc,Th,Treg,M,MFp,Ff,E,A | E_connectivity_score | E_connectivity_score: Calculated as the product of E_avg_degree and E_clustering_coef, this metric provides an overall, normalized measure of endothelial cell connectivity. |
| d0sm327jlo54 | TU,Tc,Th,Treg,M,MFp,Ff,E,A | A_avg_degree | A_avg_degree: Represents the normalized average number of connections per apical cell (A) in the spatial graph, ensuring consistency across different patches. |
| d0sm327jlo54 | TU,Tc,Th,Treg,M,MFp,Ff,E,A | A_clustering_coef | A_clustering_coef: Represents the normalized average clustering coefficient for apical cells (A), reflecting the tendency of these cells to form clusters in the spatial organization. |
| d0sm327jlo54 | TU,Tc,Th,Treg,M,MFp,Ff,E,A | A_connectivity_score | A_connectivity_score: This metric is the product of A_avg_degree and A_clustering_coef, offering an integrated, normalized measure of connectivity for apical cells. |
| d0sm327jlo54 | TU,Tc,Th,Treg,M,MFp,Ff,E,A | overall_connectivity_score | overall_connectivity_score: Represents the normalized overall connectivity across all cell types within a tumor patch. It is computed as the mean of the individual connectivity scores of all valid cell subsets, providing a single standardized measure for comparative analysis. |
| d0urolexk31y | TU,Tc,Th,B,P,M,G,MFp,MF,F | ECCENTRICITY_TU | ECCENTRICITY_TU: This parameter represents the normalized mean eccentricity of epithelial (tumor) cell nuclei. It is derived by calculating the eccentricity of each epithelial cell's nucleus shape based on its polygon coordinates, and then averaging these values over the patch. |
| d0urolexk31y | TU,Tc,Th,B,P,M,G,MFp,MF,F | ECCENTRICITY_Tc | ECCENTRICITY_Tc: This parameter denotes the normalized mean eccentricity of CD8+ T cell nuclei. It is calculated by evaluating the eccentricity from the nuclear polygon shape for each CD8+ T cell and then determining the average across all such cells in a patch. |
| d0urolexk31y | TU,Tc,Th,B,P,M,G,MFp,MF,F | ECCENTRICITY_Th | ECCENTRICITY_Th: This parameter reflects the normalized mean eccentricity of CD4+ T cell nuclei. It is obtained by calculating the nucleus shape eccentricity for each CD4+ T cell and averaging these values over the area of interest. |
| d0urolexk31y | TU,Tc,Th,B,P,M,G,MFp,MF,F | ECCENTRICITY_B | ECCENTRICITY_B: This parameter measures the normalized mean eccentricity of B cell nuclei. The computation involves analyzing the polygon shape of each B cell nucleus and deriving the average eccentricity as a robust morphological metric. |
| d0urolexk31y | TU,Tc,Th,B,P,M,G,MFp,MF,F | ECCENTRICITY_P | ECCENTRICITY_P: This parameter quantifies the normalized mean eccentricity of plasma cell nuclei. It is determined by calculating the eccentricity for each plasma cell's nucleus and then averaging these values, capturing morphological deviations. |
| d0urolexk31y | TU,Tc,Th,B,P,M,G,MFp,MF,F | ECCENTRICITY_M | ECCENTRICITY_M: This parameter represents the normalized mean eccentricity of macrophage nuclei. The eccentricity is computed from the polygonal outline of each macrophage nucleus and averaged to compare tumor regions. |
| d0urolexk31y | TU,Tc,Th,B,P,M,G,MFp,MF,F | ECCENTRICITY_G | ECCENTRICITY_G: This parameter indicates the normalized mean eccentricity of granulocyte nuclei. It involves the measurement of nuclear polygon eccentricity for each granulocyte followed by an average, providing a standardized measure. |
| d0urolexk31y | TU,Tc,Th,B,P,M,G,MFp,MF,F | ECCENTRICITY_MFp | ECCENTRICITY_MFp: This parameter defines the normalized mean eccentricity of PDPN+ myofibroblast nuclei. It is calculated by evaluating the nuclear eccentricity for each PDPN+ myofibroblast and obtaining the mean value for the patch. |
| d0urolexk31y | TU,Tc,Th,B,P,M,G,MFp,MF,F | ECCENTRICITY_MF | ECCENTRICITY_MF: This parameter captures the normalized mean eccentricity of myofibroblast nuclei. It is derived from the shape analysis of each myofibroblast nucleus and represents the average eccentricity across the region. |
| d0urolexk31y | TU,Tc,Th,B,P,M,G,MFp,MF,F | ECCENTRICITY_F | ECCENTRICITY_F: This parameter represents the normalized mean eccentricity of fibroblast nuclei. It is computed by measuring the eccentricity of the nuclear polygon for each fibroblast and averaging these values. |
| d0urolexk31y | TU,Tc,Th,B,P,M,G,MFp,MF,F | ECCENTRICITY_ALL | ECCENTRICITY_ALL: This parameter is a global metric representing the normalized mean eccentricity across all analyzed cell types. It is computed by aggregating the eccentricity values from each cell and then averaging them, providing an overall morphological characterization. |
| d1abc0ngtvvw | P,MF | P_solidity_bin_0-50 | P_solidity_bin_0-50 represents the mean nucleus solidity of plasma cells that are located within 0-50 pixels from the epithelial boundary. Nucleus solidity is calculated as the ratio of the cell's nuclear area to the area of its convex hull, providing a normalized metric of the nuclear shape. |
| d1abc0ngtvvw | P,MF | MF_solidity_bin_0-50 | MF_solidity_bin_0-50 represents the mean nucleus solidity of PDPN- myofibroblasts within 0-50 pixels from the epithelial boundary. It gives a normalized value that reflects the relationship between the nuclear area and the convex hull area of these cells. |
| d1abc0ngtvvw | P,MF | MF_solidity_bin_50-100 | MF_solidity_bin_50-100 represents the mean nucleus solidity of PDPN- myofibroblasts within 50-100 pixels from the epithelial boundary. This parameter is a normalized measurement indicating the average solidity of the nuclei in that specific distance range. |
| d1abc0ngtvvw | P,MF | MF_solidity_bin_100-150 | MF_solidity_bin_100-150 represents the mean nucleus solidity of PDPN- myofibroblasts within 100-150 pixels from the epithelial boundary. It is computed as a normalized ratio of the nuclear area to its convex hull area, serving as a standardized metric for comparison. |
| d2eymx18hfaj | MFp | PDPN_myofibroblast_density | PDPN_myofibroblast_density represents the normalized density of PDPN-positive myofibroblasts within the stromal compartment. This parameter is calculated by first counting the number of myofibroblasts that are positive for PDPN in tissue regions designated as stroma. The raw cell count is then normalized by dividing by the stromal area, which is computed by identifying all pixels representing stroma in a tissue mask and converting the pixel count into an area measurement. The resulting value, expressed in cells per square millimeter, provides a numeric and normalized measure that allows for comparisons across different patient cases. |
| d7cq1jpvtqmt | TU,Tc,Th,Treg,M,MFp,MF,F,E,G | avg_cluster_size | avg_cluster_size represents the average number of cells per identified cluster in the perivascular regions, providing a normalized metric of cell clustering that is comparable across tumor patches. |
| d7cq1jpvtqmt | TU,Tc,Th,Treg,M,MFp,MF,F,E,G | TU_avg_cluster_size | TU_avg_cluster_size is the average cluster size for epithelial cells (TU) located in the perivascular zone, computed by averaging the sizes of clusters in which these cells occur. |
| d7cq1jpvtqmt | TU,Tc,Th,Treg,M,MFp,MF,F,E,G | Tc_avg_cluster_size | Tc_avg_cluster_size is the average cluster size for cytotoxic T cells (Tc) within the perivascular area, offering a normalized measurement of the clustering behavior of these cells. |
| d7cq1jpvtqmt | TU,Tc,Th,Treg,M,MFp,MF,F,E,G | Th_avg_cluster_size | Th_avg_cluster_size indicates the average number of helper T cells (Th) per cluster in the perivascular region, reflecting the degree of their aggregation around vessels. |
| d7cq1jpvtqmt | TU,Tc,Th,Treg,M,MFp,MF,F,E,G | Treg_avg_cluster_size | Treg_avg_cluster_size measures the average cluster size for regulatory T cells (Treg) identified in perivascular regions, helping to standardize comparisons across different patient cases. |
| d7cq1jpvtqmt | TU,Tc,Th,Treg,M,MFp,MF,F,E,G | M_avg_cluster_size | M_avg_cluster_size is the average cluster size for macrophages (M) in the perivascular zones, reflecting the clustering dynamics of these immune cells. |
| d7cq1jpvtqmt | TU,Tc,Th,Treg,M,MFp,MF,F,E,G | MFp_avg_cluster_size | MFp_avg_cluster_size denotes the average cluster size for myofibroblasts expressing pdpn (MFp) in perivascular regions, offering a normalized insight into their aggregation. |
| d7cq1jpvtqmt | TU,Tc,Th,Treg,M,MFp,MF,F,E,G | MF_avg_cluster_size | MF_avg_cluster_size represents the average cluster size for myofibroblasts (MF) found in the perivascular area, computed by averaging the sizes of clusters containing these cells. |
| d7cq1jpvtqmt | TU,Tc,Th,Treg,M,MFp,MF,F,E,G | F_avg_cluster_size | F_avg_cluster_size is the average cluster size for traditional fibroblasts (F) in the perivascular regions, providing a normalized metric that can be used for comparing different tumor patches. |
| d7cq1jpvtqmt | TU,Tc,Th,Treg,M,MFp,MF,F,E,G | E_avg_cluster_size | E_avg_cluster_size measures the average cluster size for endothelial cells (E) around vessels, offering a standardized assessment of their clustering behavior. |
| d7cq1jpvtqmt | TU,Tc,Th,Treg,M,MFp,MF,F,E,G | G_avg_cluster_size | G_avg_cluster_size represents the average cluster size for granulocytes (G) detected in the perivascular region, allowing for cross-patient comparisons through its normalized value. |
| d8vxequu15qb | Tc,B,F,MFp | Tc_B_correlation | Tc_B_correlation: This parameter quantifies the Pearson correlation coefficient between the nucleus roundness of CD8+ T cells and B cells in the stromal compartment. The correlation is derived from pairing the nucleus roundness of each cell with that of its nearest neighbor in the opposite group. It reflects how the morphological features of these two cell types are related. |
| d8vxequu15qb | Tc,B,F,MFp | Tc_F_correlation | Tc_F_correlation: This parameter measures the Pearson correlation coefficient between the nucleus roundness of CD8+ T cells and FSP1- fibroblasts in tumor stroma. The value represents the degree to which the roundness of CD8+ T cells is associated with that of fibroblasts when cells are paired based on proximity. |
| d8vxequu15qb | Tc,B,F,MFp | Tc_MFp_correlation | Tc_MFp_correlation: This parameter is the Pearson correlation coefficient between the nucleus roundness of CD8+ T cells and PDPN+ myofibroblasts. It captures the strength of the morphological relationship between these two cell types in the stromal patch by analyzing their nearest neighbor associations. |
| d8vxequu15qb | Tc,B,F,MFp | B_F_correlation | B_F_correlation: This parameter represents the Pearson correlation coefficient between the nucleus roundness of B cells and FSP1- fibroblasts. It is calculated by pairing the roundness measurements from each cell in the B cell group with that of its nearest fibroblast neighbor, thereby summarizing their morphological coordination. |
| d8vxequu15qb | Tc,B,F,MFp | B_MFp_correlation | B_MFp_correlation: This parameter quantifies the Pearson correlation coefficient between the nucleus roundness measurements of B cells and PDPN+ myofibroblasts. It provides a numerical measure of the association between these cells' morphological features based on their proximity correspondence. |
| d8vxequu15qb | Tc,B,F,MFp | F_MFp_correlation | F_MFp_correlation: This parameter calculates the Pearson correlation coefficient between the nucleus roundness of FSP1- fibroblasts and PDPN+ myofibroblasts. It assesses the degree to which the nuclear shape of these two stromal cell types is correlated by analyzing nearest neighbor pairs. |
| d8vxequu15qb | Tc,B,F,MFp | mutual_correlation_index | mutual_correlation_index: This parameter is the average of the six pairwise Pearson correlation coefficients computed among CD8+ T cells, B cells, FSP1- fibroblasts, and PDPN+ myofibroblasts. It serves as an overall indicator of the mutual morphological correlation among the stromal cell types in a tumor patch, allowing for comparisons across different patient cases. |
| dj0ajcy4uesb | B,P,M,Ff | macrophage_ratio | The 'macrophage_ratio' parameter represents the proportion of macrophages within the tumor compartment relative to the total cell count in that compartment. It is derived by dividing the number of cells classified as macrophages by the total number of cells present in the tumor area (with a small epsilon added to prevent division by zero), making it a normalized metric suitable for comparing different patient cases and tumor patches. |
| du70lswfg3ei | M,Treg,Ff,E | total_colocalization_percent | total_colocalization_percent: Represents the percentage of target cells in the tumor-stroma interface that are spatially adjacent to at least one cell of a different target type. This normalized percentage enables comparison across different patient cases. |
| du70lswfg3ei | M,Treg,Ff,E | M_percent | M_percent: Represents the percentage of macrophages among all target cells in the tumor-stroma interface. As a normalized value, it facilitates comparisons regardless of variations in the total cell count of each case. |
| du70lswfg3ei | M,Treg,Ff,E | Treg_percent | Treg_percent: Represents the percentage of regulatory T cells among all target cells in the tumor-stroma interface. This normalized percentage allows for fair comparison between different cases. |
| du70lswfg3ei | M,Treg,Ff,E | Ff_percent | Ff_percent: Represents the percentage of FSP1+ fibroblasts among all target cells in the tumor-stroma interface. It is computed by normalizing the fibroblast count by the total target cell count to allow cross-sample comparison. |
| du70lswfg3ei | M,Treg,Ff,E | E_percent | E_percent: Represents the percentage of endothelial cells among all target cells in the tumor-stroma interface. The normalization ensures that the metric is comparable across different tumor samples. |
| du70lswfg3ei | M,Treg,Ff,E | M_Treg | M_Treg: Represents the percentage of macrophages that are spatially colocalized with at least one regulatory T cell in the tumor-stroma interface. This normalized metric reflects the interaction level between these cell types across patient cases. |
| du70lswfg3ei | M,Treg,Ff,E | M_Ff | M_Ff: Represents the percentage of macrophages that are spatially colocalized with at least one FSP1+ fibroblast. By expressing the number as a percentage of total macrophages, this parameter is normalized for cross-case analysis. |
| du70lswfg3ei | M,Treg,Ff,E | M_E | M_E: Represents the percentage of macrophages that are spatially colocalized with at least one endothelial cell. This normalization (percentage) allows for an equitable comparison among different cases. |
| du70lswfg3ei | M,Treg,Ff,E | Ff_E | Ff_E: Represents the percentage of FSP1+ fibroblasts that are spatially colocalized with at least one endothelial cell. This percentage-based measurement is normalized to facilitate comparison across different patient cases. |
| dvngosqm09o2 | Tc,TU,Ff,MF,M | MEAN_GEODESIC_DISTANCE | MEAN_GEODESIC_DISTANCE represents the average length of the paths computed between cytotoxic T cells and their nearest tumor cells. It is derived by calculating the geodesic path through a designated navigable region within a tumor patch and then averaging these distance values. This parameter is numeric and normalized, as it is computed as a mean value over all valid paths in the patch, making it suitable for comparing measurements across different patient cases. |
| e94k8c7tmupq | TU,B,P | PLASMA_CELL_FRACTION | The PLASMA_CELL_FRACTION parameter represents the ratio of plasma cells to the total number of B lineage cells (including both B cells and plasma cells) that are found in close proximity to tumor cells. This normalized measure is calculated by dividing the count of tumor-proximal plasma cells by the total count of tumor-proximal B lineage cells, thereby allowing for meaningful comparisons across different patient cases. |
| e9khs0pokurj | TU,Tc,Th,Treg,B,M,MFp,MF,Ff,E | median_nuclear_convexity_TU | median_nuclear_convexity_TU: This parameter measures the median nuclear convexity score for tumor cells. It quantifies the regularity of the nucleus shape by calculating the ratio of the nucleus's polygon area to its convex hull area, thereby normalizing the measurement to be comparable across different cases. |
| e9khs0pokurj | TU,Tc,Th,Treg,B,M,MFp,MF,Ff,E | median_nuclear_convexity_Tc | median_nuclear_convexity_Tc: This parameter measures the median nuclear convexity score for cytotoxic T cells. It reflects the cellular regularity by comparing the nucleus area with its convex hull area, resulting in a normalized ratio that can be compared between patient cases. |
| e9khs0pokurj | TU,Tc,Th,Treg,B,M,MFp,MF,Ff,E | median_nuclear_convexity_Th | median_nuclear_convexity_Th: This parameter measures the median nuclear convexity score for T helper cells. By computing the ratio of the nucleus polygon area to its convex hull area for these cells, it provides a normalized metric to assess nuclear regularity. |
| e9khs0pokurj | TU,Tc,Th,Treg,B,M,MFp,MF,Ff,E | median_nuclear_convexity_Treg | median_nuclear_convexity_Treg: This parameter measures the median nuclear convexity score for regulatory T cells. It is calculated as the ratio of the cell nucleus area to its convex hull area, offering a normalized value that can be used to compare cellular morphology across different tumor regions. |
| e9khs0pokurj | TU,Tc,Th,Treg,B,M,MFp,MF,Ff,E | median_nuclear_convexity_B | median_nuclear_convexity_B: This parameter measures the median nuclear convexity score for B cells. It represents the ratio between the measured nucleus polygon area and the corresponding convex hull area, yielding a normalized value to evaluate the regularity of the nucleus shape. |
| e9khs0pokurj | TU,Tc,Th,Treg,B,M,MFp,MF,Ff,E | median_nuclear_convexity_M | median_nuclear_convexity_M: This parameter measures the median nuclear convexity score for macrophages. It is derived by computing the ratio of the cell nucleus area to its convex hull area, resulting in a normalized score that reflects nuclear shape regularity. |
| e9khs0pokurj | TU,Tc,Th,Treg,B,M,MFp,MF,Ff,E | median_nuclear_convexity_MFp | median_nuclear_convexity_MFp: This parameter measures the median nuclear convexity score for PDPN-positive myofibroblasts. It normalizes the assessment of nuclear shape by calculating the ratio of the nucleus area to its convex hull area, with values close to 1 indicating more regular nuclei. |
| e9khs0pokurj | TU,Tc,Th,Treg,B,M,MFp,MF,Ff,E | median_nuclear_convexity_MF | median_nuclear_convexity_MF: This parameter measures the median nuclear convexity score for myofibroblasts. It is determined by the ratio of the cell nucleus area to the convex hull area of the nucleus, providing a normalized metric that reflects nuclear regularity. |
| e9khs0pokurj | TU,Tc,Th,Treg,B,M,MFp,MF,Ff,E | median_nuclear_convexity_Ff | median_nuclear_convexity_Ff: This parameter measures the median nuclear convexity score for fibroblasts. It quantifies the degree of nuclear convexity via the ratio of the nucleus's polygon area to its convex hull area, yielding a normalized value that facilitates comparison across cases. |
| e9khs0pokurj | TU,Tc,Th,Treg,B,M,MFp,MF,Ff,E | median_nuclear_convexity_E | median_nuclear_convexity_E: This parameter measures the median nuclear convexity score for endothelial cells. It calculates the ratio of the nucleus area to its convex hull area, providing a normalized measurement of nuclear regularity that can be compared across different tumor patches. |
| e9rw0vkverzg | TU,A | Avg_Ellipticity_Tumor | Avg_Ellipticity_Tumor measures the average ellipticity of tumor cell nuclei within a patch by computing the ratio of the fitted ellipse's major axis to its minor axis. This ratio is dimensionless and normalized, allowing for comparisons across different patient cases. |
| e9rw0vkverzg | TU,A | Avg_Ellipticity_APC | Avg_Ellipticity_APC measures the average ellipticity of antigen presenting cell nuclei within a patch, derived similarly by fitting ellipses to nuclear polygons and calculating the ratio of major to minor axis. This normalized metric facilitates comparisons across cases. |
| e9rw0vkverzg | TU,A | Difference_in_Ellipticity | Difference_in_Ellipticity represents the difference between the average ellipticity of tumor cells and that of antigen presenting cells, computed as (Avg_Ellipticity_Tumor - Avg_Ellipticity_APC). This normalized value highlights relative morphological differences between the two cell populations. |
| e9rw0vkverzg | TU,A | Std_Ellipticity_Tumor | Std_Ellipticity_Tumor denotes the standard deviation of the ellipticity values for tumor cell nuclei, providing insight into the variability of nuclear shapes within a tumor region. This statistical measure is normalized and numeric. |
| e9rw0vkverzg | TU,A | Std_Ellipticity_APC | Std_Ellipticity_APC denotes the standard deviation of the ellipticity values for antigen presenting cell nuclei, indicating variability in their nuclear shapes. It is a normalized numeric parameter for comparative analysis. |
| e9rw0vkverzg | TU,A | Max_Ellipticity_Tumor | Max_Ellipticity_Tumor captures the maximum ellipticity value observed among tumor cell nuclei in a patch, reflecting the most extreme elongation in nuclear shape. This normalized ratio is useful in identifying outliers or significant morphological features. |
| e9rw0vkverzg | TU,A | Max_Ellipticity_APC | Max_Ellipticity_APC captures the maximum ellipticity value observed in antigen presenting cell nuclei, indicating the highest ratio of major to minor axis among these cells in a patch. The metric is normalized for cross-case comparisons. |
| e9rw0vkverzg | TU,A | Min_Ellipticity_Tumor | Min_Ellipticity_Tumor identifies the minimum ellipticity value among tumor cell nuclei, representing the least elongated or more rounded nuclear shape within a patch. This normalized parameter helps establish the range of nuclear morphology. |
| e9rw0vkverzg | TU,A | Min_Ellipticity_APC | Min_Ellipticity_APC identifies the minimum ellipticity value among antigen presenting cell nuclei in a patch, describing the lower end of the nuclear shape spectrum. As a normalized parameter, it supports comparative analyses between different regions. |
| ecd2gbxb84mr | Th,Treg,M,F,Ff | Th_M_Ratio | Th_M_Ratio: This parameter represents the normalized ratio of adjacent pairs between helper T cells and macrophages within a tumor patch. It is computed by identifying how many helper T cells are within a specified distance of macrophages relative to the total possible pairs, ensuring the metric is numeric and normalized for cross-patient comparison. |
| ecd2gbxb84mr | Th,Treg,M,F,Ff | Th_F_Ratio | Th_F_Ratio: This parameter quantifies the normalized frequency of adjacency between helper T cells and FSP1- fibroblasts in the stromal area of the tumor. It is calculated as the number of adjacent cell pairs divided by the total expected pairs, making it a numeric and normalized measure. |
| ecd2gbxb84mr | Th,Treg,M,F,Ff | Th_Ff_Ratio | Th_Ff_Ratio: This metric measures the normalized frequency of cell-cell contact between helper T cells and FSP1+ fibroblasts within a tumor patch. By counting adjacent cells within a uniform distance threshold and normalizing by the possible pairs, the ratio facilitates comparisons across different instances. |
| ecd2gbxb84mr | Th,Treg,M,F,Ff | Treg_M_Ratio | Treg_M_Ratio: This parameter represents the normalized ratio of adjacent pairs between regulatory T cells and macrophages. It is derived by counting adjacent occurrences and normalizing against all possible pair combinations, providing a numeric value that is directly comparable between different patient cases. |
| ecd2gbxb84mr | Th,Treg,M,F,Ff | M_F_Ratio | M_F_Ratio: This parameter captures the normalized frequency of adjacency between macrophages and FSP1- fibroblasts in a tumor patch. The calculation involves dividing the count of adjacent cell pairs by the total number of pairwise combinations, ensuring the value is both numeric and normalized. |
| ecd2gbxb84mr | Th,Treg,M,F,Ff | M_Ff_Ratio | M_Ff_Ratio: This metric measures the normalized adjacency frequency between macrophages and FSP1+ fibroblasts. It provides a numeric value by calculating the ratio of observed adjacent pairs to the total possible pairs, enabling standardized comparisons between tumor samples. |
| ecd2gbxb84mr | Th,Treg,M,F,Ff | F_Ff_Ratio | F_Ff_Ratio: This parameter quantifies the normalized ratio of adjacent pairs between FSP1- fibroblasts and FSP1+ fibroblasts. The computed ratio, which is the count of adjacent cells divided by the total possible pairings, is numeric and normalized for consistent cross-sample evaluation. |
| ecd2gbxb84mr | Th,Treg,M,F,Ff | Mean_Adjacency_Ratio | Mean_Adjacency_Ratio: This overall parameter is the mean of all individual normalized pairwise adjacency ratios. It aggregates the coordinated cell-cell contacts among various pairs, providing a single numeric value that reflects the overall spatial interaction within a tumor patch. |
| emecucik2svh | M,TU,MF,Ff | mean_distance_to_tumor | mean_distance_to_tumor measures the average minimum Euclidean distance in micrometers from the centroid of each macrophage to the nearest tumor cell (identified as an epithelial cell). This parameter reflects the spatial proximity between macrophages and tumor cells across different tissue patches, making it suitable for comparing patient cases. |
| emecucik2svh | M,TU,MF,Ff | mean_distance_to_myofibroblast | mean_distance_to_myofibroblast measures the average minimum Euclidean distance in micrometers from the centroid of each macrophage to the closest PDPN- myofibroblast. It quantifies the spatial relationship between macrophages and a specific fibroblast subtype, enabling normalized comparisons between patient samples. |
| emecucik2svh | M,TU,MF,Ff | mean_distance_to_fibroblast | mean_distance_to_fibroblast measures the average minimum Euclidean distance in micrometers from the centroid of each macrophage to the nearest FSP1+ fibroblast. This parameter indicates the spatial proximity of macrophages to FSP1+ fibroblasts, supporting comparisons across different patient and tissue patch analyses. |
| et2z1ho7bp78 | Treg,Th,A,Ff,MFp,TU | mean_entropy | mean_entropy: The average Shannon entropy calculated from the radial distribution of immune and stromal cells around tumor clusters. This measure summarizes the overall disorder in the spatial arrangement of cells by averaging the entropy values obtained for each tumor cluster, enabling normalized comparisons across different patient cases. |
| et2z1ho7bp78 | Treg,Th,A,Ff,MFp,TU | median_entropy | median_entropy: The median value of the Shannon entropy measurements derived from the radial distributions around tumor clusters. This statistic highlights the central tendency of the entropy values and provides a robust, normalized metric that is less sensitive to extreme values across different samples. |
| et2z1ho7bp78 | Treg,Th,A,Ff,MFp,TU | min_entropy | min_entropy: The lowest Shannon entropy value observed among the tumor clusters. This parameter identifies the region with the most organized (least random) distribution of immune and stromal cells around a tumor cluster, and represents a normalized measurement of spatial organization. |
| et2z1ho7bp78 | Treg,Th,A,Ff,MFp,TU | max_entropy | max_entropy: The highest Shannon entropy value recorded among the tumor clusters. It reflects the tumor cluster with the most disorderly distribution of immune and stromal cells, serving as a normalized indicator of spatial randomness within the analyzed regions. |
| et2z1ho7bp78 | Treg,Th,A,Ff,MFp,TU | std_entropy | std_entropy: The standard deviation of the Shannon entropy values across all tumor clusters. This parameter quantifies the variability in cell distribution patterns around tumor clusters, providing a normalized measure of heterogeneity in the spatial organization across different patient patches. |
| evh28l1vu4co | TU,MFp,MF,Ff,F,M,G,E,A | mean_CV_MFp | mean_CV_MFp: This parameter represents the average coefficient of variation of PDPN+ myofibroblast densities measured across predefined radial distance bins around vessels. It captures the normalized variation in cell density, allowing for comparison across different tumor patches. |
| evh28l1vu4co | TU,MFp,MF,Ff,F,M,G,E,A | std_CV_MFp | std_CV_MFp: This parameter is the standard deviation of the coefficient of variation for PDPN+ myofibroblast densities. It quantifies the dispersion in the variation measures across the vessels, indicating the consistency or variability of spatial distribution. |
| evh28l1vu4co | TU,MFp,MF,Ff,F,M,G,E,A | mean_CV_MF | mean_CV_MF: This parameter reflects the average coefficient of variation of PDPN- myofibroblast densities across the same radial bins. It serves as a normalized assessment of the heterogeneity in PDPN- cell distribution around vessels. |
| evh28l1vu4co | TU,MFp,MF,Ff,F,M,G,E,A | std_CV_MF | std_CV_MF: This parameter is the standard deviation of the coefficient of variation for PDPN- myofibroblast densities. It provides insight into the variability of spatial heterogeneity among different vessels. |
| evh28l1vu4co | TU,MFp,MF,Ff,F,M,G,E,A | median_CV_MFp | median_CV_MFp: This parameter is the median coefficient of variation of PDPN+ myofibroblast densities. It offers a robust measure of the central tendency of spatial variation, reducing the impact of outliers. |
| evh28l1vu4co | TU,MFp,MF,Ff,F,M,G,E,A | median_CV_MF | median_CV_MF: This parameter denotes the median coefficient of variation of PDPN- myofibroblast densities, summarizing the central trend of heterogeneity in their spatial distribution. |
| evh28l1vu4co | TU,MFp,MF,Ff,F,M,G,E,A | max_CV_MFp | max_CV_MFp: This parameter is defined as the maximum coefficient of variation observed among all vessels for PDPN+ myofibroblast densities. It highlights the extreme cases of spatial heterogeneity within the tissue region. |
| evh28l1vu4co | TU,MFp,MF,Ff,F,M,G,E,A | max_CV_MF | max_CV_MF: This parameter represents the maximum coefficient of variation for PDPN- myofibroblast densities observed across vessels, indicating the highest level of uneven distribution encountered. |
| ewt4zcy21gp3 | TU,Tc,F,A | global_entropy | global_entropy represents the weighted average of the Shannon entropy values calculated from local cell type distributions in each grid region of the tumor tissue. This parameter reflects the overall diversity of cell types (tumor cells, cytotoxic T cells, fibroblasts, and antigen presenting cells) while accounting for the number of cells in each grid patch, making it comparable across different patient cases. |
| ewt4zcy21gp3 | TU,Tc,F,A | min_region_entropy | min_region_entropy is the minimum Shannon entropy observed among all analyzed grid regions (patches). It identifies the region with the least diversity in cell type composition, indicating an area where one cell type predominates or where cell distribution is most skewed. |
| ewt4zcy21gp3 | TU,Tc,F,A | max_region_entropy | max_region_entropy denotes the maximum Shannon entropy value among the grid regions. It captures the region exhibiting the highest diversity in cell type distribution, suggesting a more balanced or heterogeneous mix of cell populations. |
| ewt4zcy21gp3 | TU,Tc,F,A | mean_region_entropy | mean_region_entropy is the simple average of the Shannon entropy values calculated for each grid region containing cells. This parameter provides an overall measure of tissue heterogeneity by averaging the diversity measures across all regions. |
| ewt4zcy21gp3 | TU,Tc,F,A | std_region_entropy | std_region_entropy is the standard deviation of the regional Shannon entropy values. It quantifies the variability in cell type diversity among different grid regions, indicating the consistency or spread of the local entropy measurements across the tumor tissue. |
| ex1gmix3s4zp | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_nucleus_complexity_index | weighted_nucleus_complexity_index: This parameter measures the overall nucleus polygon complexity across all considered cell types. It is obtained by computing a weighted average of individual cell type irregularity metrics, where each type’s average irregularity is weighted by its cell count. The division by the total number of cells ensures that the metric is normalized across samples. |
| ex1gmix3s4zp | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | TU_avg_irregularity | TU_avg_irregularity: This parameter represents the average irregularity metric of the nucleus polygons specifically for Tumor cells. It is calculated as the mean of the irregularity values, which indicate deviations from a perfect circular shape. The normalization by averaging makes it comparable across different patient samples. |
| ex1gmix3s4zp | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Tc_avg_irregularity | Tc_avg_irregularity: This parameter quantifies the average geometric irregularity of nucleus boundaries for Cytotoxic T cells. It is derived by averaging the irregularity metric computed for each cell, providing a normalized measure that facilitates comparison between cases. |
| ex1gmix3s4zp | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Th_avg_irregularity | Th_avg_irregularity: This parameter measures the average nucleus polygon irregularity for T helper cells. Being an average of the individual cell irregularities, it is normalized and thus can be used to compare across different tumor regions or patient samples. |
| ex1gmix3s4zp | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Treg_avg_irregularity | Treg_avg_irregularity: This parameter represents the normalized average nucleus irregularity for T regulator cells. It is computed as the mean irregularity value for these cells, providing an indicator of the morphological irregularities that can be compared across different patient cases. |
| ex1gmix3s4zp | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | B_avg_irregularity | B_avg_irregularity: This parameter represents the average irregularity of nucleus polygons for B cells. The computed mean serves as a normalized metric, allowing comparisons between different tumor regions or patient cases regarding B cell nuclear morphology. |
| ex1gmix3s4zp | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | P_avg_irregularity | P_avg_irregularity: This parameter quantifies the average nucleus polygon irregularity for Plasma cells. It is normalized through averaging the irregularity values of individual cells, thereby supporting comparative analysis across different samples. |
| ex1gmix3s4zp | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | M_avg_irregularity | M_avg_irregularity: This parameter indicates the average irregularity metric for Macrophages. By computing the mean of the irregularity values, it becomes a normalized measure that allows the evaluation of nuclear morphological irregularity in macrophages across different patients. |
| ex1gmix3s4zp | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | G_avg_irregularity | G_avg_irregularity: This parameter reflects the average nucleus polygon irregularity for Granulocytes. The averaging process normalizes the measure, enabling reliable comparisons in nucleus complexity among different patient samples. |
| ex1gmix3s4zp | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MFp_avg_irregularity | MFp_avg_irregularity: This parameter measures the average irregularity of nucleus borders for Myofibroblasts with high PDPN expression. The normalization by average calculation permits consistent inter-sample comparisons of nuclear boundary complexity. |
| ex1gmix3s4zp | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MF_avg_irregularity | MF_avg_irregularity: This parameter quantifies the average nucleus polygon irregularity for Myofibroblasts. Since it is an average of computed irregularity metrics, it provides a normalized value that can be used to compare different cases. |
| ex1gmix3s4zp | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Ff_avg_irregularity | Ff_avg_irregularity: This parameter represents the normalized average irregularity of nucleus polygons for FSP1 positive Fibroblasts. It reflects the deviation from a perfect circle and is computed in a way that allows comparisons across different patient cases. |
| ex1gmix3s4zp | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | F_avg_irregularity | F_avg_irregularity: This parameter indicates the average nucleus irregularity metric for Normal fibroblasts. Its normalized average value facilitates comparative analyses between different patient tissue samples. |
| ex1gmix3s4zp | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | E_avg_irregularity | E_avg_irregularity: This parameter captures the average irregularity of nucleus polygons for Endothelial cells. The average is normalized, making it suitable for comparing nuclear morphology across samples. |
| ex1gmix3s4zp | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | A_avg_irregularity | A_avg_irregularity: This parameter reflects the normalized average irregularity of nucleus boundaries for Antigen Presenting cells. Calculated as a mean of irregularity metrics, it effectively serves as a comparative measure across different patient cases. |
| f0opndgcgi1f | TU,Treg,M,P,MFp,E,MF | TU_mean_alignment | TU_mean_alignment: Mean alignment score (in degrees, normalized to a range between 0 and 90) calculated across all tumor cells by comparing each cell's nuclear orientation with the orientation of its nearest neighboring cell of a different type. |
| f0opndgcgi1f | TU,Treg,M,P,MFp,E,MF | TU_median_alignment | TU_median_alignment: Median alignment score for tumor cells, indicating the central tendency of the angular differences between tumor cell orientations and that of their closest non-tumor cell neighbor. |
| f0opndgcgi1f | TU,Treg,M,P,MFp,E,MF | TU_std_alignment | TU_std_alignment: Standard deviation of alignment scores for tumor cells, quantifying the variability in the angular differences measured between tumor cells and their nearest neighboring cells. |
| f0opndgcgi1f | TU,Treg,M,P,MFp,E,MF | Treg_mean_alignment | Treg_mean_alignment: Mean alignment score for T regulatory cells, computed as the average minimal angular difference between the nuclear orientation of each T regulatory cell and the orientation of its nearest cell of a different type. |
| f0opndgcgi1f | TU,Treg,M,P,MFp,E,MF | Treg_median_alignment | Treg_median_alignment: Median alignment score for T regulatory cells, representing the central value in the distribution of angular differences from the pairing of T regulatory cells with their nearest non-identical neighbors. |
| f0opndgcgi1f | TU,Treg,M,P,MFp,E,MF | Treg_std_alignment | Treg_std_alignment: Standard deviation of T regulatory cell alignment scores, reflecting the degree of variability in the angular alignment differences relative to the mean score. |
| f0opndgcgi1f | TU,Treg,M,P,MFp,E,MF | M_mean_alignment | M_mean_alignment: Mean alignment score for macrophages, calculated as the average minimal angular difference between each macrophage's nuclear orientation and that of its nearest neighbor belonging to another cell type. |
| f0opndgcgi1f | TU,Treg,M,P,MFp,E,MF | M_median_alignment | M_median_alignment: Median alignment score for macrophages, indicating the middle value of the alignment score distribution derived from comparing macrophage orientations with those of nearby cells of different types. |
| f0opndgcgi1f | TU,Treg,M,P,MFp,E,MF | M_std_alignment | M_std_alignment: Standard deviation of macrophage alignment scores, which measures the spread of the angular differences around the average, thereby highlighting variability in alignment. |
| f0opndgcgi1f | TU,Treg,M,P,MFp,E,MF | P_mean_alignment | P_mean_alignment: Mean alignment score for plasma cells, defined as the average minimal angular difference found when comparing each plasma cell's nuclear orientation to that of its closest neighboring cell from a different type. |
| f0opndgcgi1f | TU,Treg,M,P,MFp,E,MF | P_median_alignment | P_median_alignment: Median alignment score for plasma cells, reflecting the central tendency of the alignment values generated from the angular differences between plasma cells and their nearest different-type neighbors. |
| f0opndgcgi1f | TU,Treg,M,P,MFp,E,MF | P_std_alignment | P_std_alignment: Standard deviation of alignment scores for plasma cells, quantifying how spread out the angular alignment differences are relative to the mean for plasma cells. |
| f0opndgcgi1f | TU,Treg,M,P,MFp,E,MF | MFp_mean_alignment | MFp_mean_alignment: Mean alignment score for PDPN+ myofibroblasts, computed as the average minimal angular difference between the nuclear orientation of PDPN+ myofibroblasts and that of their nearest neighbor of a different cell type. |
| f0opndgcgi1f | TU,Treg,M,P,MFp,E,MF | MFp_median_alignment | MFp_median_alignment: Median alignment score for PDPN+ myofibroblasts, representing the central measure of the angular differences observed between PDPN+ myofibroblasts and their nearest neighboring cell of another type. |
| f0opndgcgi1f | TU,Treg,M,P,MFp,E,MF | MFp_std_alignment | MFp_std_alignment: Standard deviation of alignment scores for PDPN+ myofibroblasts, which reflects the variability in alignment by measuring how individual angular differences deviate from the mean. |
| f0opndgcgi1f | TU,Treg,M,P,MFp,E,MF | E_mean_alignment | E_mean_alignment: Mean alignment score for endothelial cells, calculated as the average minimal angular difference between each endothelial cell's orientation and that of its nearest neighbor belonging to a different cell subtype. |
| f0opndgcgi1f | TU,Treg,M,P,MFp,E,MF | E_median_alignment | E_median_alignment: Median alignment score for endothelial cells, indicating the central value of the angular alignment scores computed from pairing endothelial cells with adjacent cells of another type. |
| f0opndgcgi1f | TU,Treg,M,P,MFp,E,MF | E_std_alignment | E_std_alignment: Standard deviation of alignment scores for endothelial cells, showing the spread of angular differences in the alignment measurements relative to the average. |
| f0opndgcgi1f | TU,Treg,M,P,MFp,E,MF | MF_mean_alignment | MF_mean_alignment: Mean alignment score for PDPN- myofibroblasts, representing the average minimal difference in nuclear orientation angles between these cells and their nearest neighboring cell of a different type. |
| f0opndgcgi1f | TU,Treg,M,P,MFp,E,MF | MF_median_alignment | MF_median_alignment: Median alignment score for PDPN- myofibroblasts, reflecting the central tendency of alignment measurements derived from the angular differences between PDPN- myofibroblasts and their nearest neighbors. |
| f0opndgcgi1f | TU,Treg,M,P,MFp,E,MF | MF_std_alignment | MF_std_alignment: Standard deviation of alignment scores for PDPN- myofibroblasts, quantifying the variability in the angular alignment differences around the mean value. |
| f0opndgcgi1f | TU,Treg,M,P,MFp,E,MF | overall_mean_alignment | overall_mean_alignment: Mean alignment score across all cell types, computed as the overall average of the minimal angular differences between each cell's orientation and the orientation of its nearest non-identical neighbor. |
| f0opndgcgi1f | TU,Treg,M,P,MFp,E,MF | overall_median_alignment | overall_median_alignment: Median alignment score across all cell types, representing the central tendency of the pooled alignment measurements from all evaluated cell pairs in the study. |
| f0opndgcgi1f | TU,Treg,M,P,MFp,E,MF | overall_std_alignment | overall_std_alignment: Standard deviation of alignment scores across all cell types, reflecting the overall variability in the nuclear orientation differences calculated from all cell pair comparisons. |
| f1ffae3x4cbj | M,MFp,TU | M_VESSEL_ADJ_MEAN_DIST | M_VESSEL_ADJ_MEAN_DIST represents the average infiltration distance from the centroids of macrophages that are adjacent to vessels to their nearest tumor cell, measured in micrometers. This parameter is calculated by taking the Euclidean distances of each vessel-adjacent macrophage to the closest tumor cell and then computing the mean, allowing for normalized comparisons across different patches. |
| f1ffae3x4cbj | M,MFp,TU | M_VESSEL_NADJ_MEAN_DIST | M_VESSEL_NADJ_MEAN_DIST is the average infiltration distance for macrophages that are not adjacent to vessels. It is computed similarly by measuring the minimum distance from each non-vessel-adjacent macrophage to the nearest tumor cell and taking the mean, resulting in a normalized measure of spatial relationship. |
| f1ffae3x4cbj | M,MFp,TU | MFp_VESSEL_ADJ_MEAN_DIST | MFp_VESSEL_ADJ_MEAN_DIST denotes the mean infiltration distance from PDPN+ myofibroblasts that are adjacent to vessels to the nearest tumor cell. This measure captures the spatial positioning of these cells relative to tumor cells in vessel-adjacent regions and provides a normalized value for inter-case comparisons. |
| f1ffae3x4cbj | M,MFp,TU | MFp_VESSEL_NADJ_MEAN_DIST | MFp_VESSEL_NADJ_MEAN_DIST represents the average distance from PDPN+ myofibroblasts that are not adjacent to vessels to the nearest tumor cell. This parameter is derived by averaging the minimal Euclidean distances for this group and is suitable for comparing spatial infiltration across different tumor patches. |
| f1ffae3x4cbj | M,MFp,TU | M_MFp_VESSEL_ADJ_DIFF | M_MFp_VESSEL_ADJ_DIFF is the normalized difference in mean infiltration distances between macrophages and PDPN+ myofibroblasts that are adjacent to vessels. It is calculated as the difference between the macrophage mean and the myofibroblast mean in vessel-adjacent regions, highlighting relative spatial differences. |
| f1ffae3x4cbj | M,MFp,TU | M_MFp_VESSEL_NADJ_DIFF | M_MFp_VESSEL_NADJ_DIFF is the normalized difference in mean infiltration distances between macrophages and PDPN+ myofibroblasts not adjacent to vessels. It is derived by subtracting the mean distance of PDPN+ myofibroblasts from that of macrophages in non-vessel-adjacent areas, providing a comparative measure of spatial infiltration. |
| f6w81e7o0w2v | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,A | TU_mean_fractal_dim | TU_mean_fractal_dim: Represents the mean fractal dimension of nuclear boundaries for tumor cells. This parameter quantifies the complexity of the nuclear boundary using a normalized box-counting method and is computed as the average across tumor cells, making it comparable across different patient cases. |
| f6w81e7o0w2v | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,A | Tc_mean_fractal_dim | Tc_mean_fractal_dim: Represents the mean fractal dimension of nuclear boundaries for cytotoxic T cells. Calculated by averaging the computed fractal dimensions from these cells, this normalized metric reflects the complexity of their nuclear outlines and is suitable for cross-patient comparisons. |
| f6w81e7o0w2v | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,A | Th_mean_fractal_dim | Th_mean_fractal_dim: Represents the averaged fractal dimension for T helper cells. It is computed using a normalized fractal analysis method (box-counting) on the cells' nuclear boundaries, capturing the geometric irregularities in a standardized way. |
| f6w81e7o0w2v | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,A | Treg_mean_fractal_dim | Treg_mean_fractal_dim: Denotes the mean fractal dimension measured on the nuclear boundaries of T regulatory cells. By applying a normalized box-counting calculation per cell and averaging the results, this parameter provides a consistent measure of boundary complexity. |
| f6w81e7o0w2v | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,A | B_mean_fractal_dim | B_mean_fractal_dim: Reflects the mean fractal dimension of nuclear boundaries for B cells. It is derived by assessing the boundary complexity through a normalized fractal analysis approach, ensuring that the measurement is comparable across samples. |
| f6w81e7o0w2v | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,A | P_mean_fractal_dim | P_mean_fractal_dim: Indicates the average fractal dimension for plasma cells' nuclear boundaries. This parameter captures the morphological complexity of plasma cell nuclei using a box-counting technique in a normalized manner, facilitating meaningful comparisons. |
| f6w81e7o0w2v | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,A | M_mean_fractal_dim | M_mean_fractal_dim: Represents the mean fractal dimension computed for the nuclear boundaries of macrophages. The parameter is normalized through a standardized statistical approach (box-counting) to quantify the shape irregularity of the nuclei. |
| f6w81e7o0w2v | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,A | G_mean_fractal_dim | G_mean_fractal_dim: Denotes the averaged fractal dimension of nuclear boundaries for granulocytes. This normalized measure of boundary complexity is obtained by applying a box-counting method to granulocyte nuclei, allowing for comparison between patient cases. |
| f6w81e7o0w2v | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,A | MFp_mean_fractal_dim | MFp_mean_fractal_dim: Indicates the mean fractal dimension for myofibroblasts, computed by analyzing the complexity of the cell nuclear boundaries with a normalized fractal analysis method. It provides a scale-invariant metric that is comparable among samples. |
| f6w81e7o0w2v | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,A | Ff_mean_fractal_dim | Ff_mean_fractal_dim: Represents the average fractal dimension of fibroblast nuclear boundaries. By quantifying the geometric irregularity using a normalized method, this parameter allows for the comparison of fibroblast morphology across patient cases. |
| f6w81e7o0w2v | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,A | A_mean_fractal_dim | A_mean_fractal_dim: Captures the mean fractal dimension of nuclear boundaries for antigen presenting cells. This parameter, derived from a normalized box-counting method applied to the nuclear periphery, measures boundary complexity in a comparable manner. |
| f6w81e7o0w2v | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,A | overall_mean_fractal_dim | overall_mean_fractal_dim: Reflects the overall average fractal dimension computed across all evaluated cell types. Being the aggregate of the individual normalized measures, it serves as a comprehensive metric for nuclear boundary complexity across a tumor region. |
| fawv7f4xc8wt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | ANGULAR_DISPERSION_MEAN | ANGULAR_DISPERSION_MEAN measures the weighted average of the variability in the angles calculated from triplets of cells. The dispersion in each triangle is derived as the standard deviation of the angles within that triangle (converted to degrees), and the weighted mean is computed using a normalization based on the diversity of cell types present in the triangle, making the parameter normalized across different patient cases. |
| fawv7f4xc8wt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | ANGULAR_DISPERSION_STD | ANGULAR_DISPERSION_STD represents the standard deviation of the dispersion values calculated for all triangles in a tissue patch. It quantifies how much the angular dispersion values vary across the entire sample, reflecting the consistency or variability of the cell spatial organization. |
| fawv7f4xc8wt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | ANGULAR_DISPERSION_MIN | ANGULAR_DISPERSION_MIN captures the smallest dispersion value among all triangles in the patch. This value identifies the triangle with the most regular angular organization, serving as a baseline for the minimum level of cell arrangement irregularity. |
| fawv7f4xc8wt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | ANGULAR_DISPERSION_MAX | ANGULAR_DISPERSION_MAX denotes the largest dispersion value observed among all triangles. It indicates the most irregular or chaotic triangle formation in terms of angular differences, providing insight into the extreme end of tissue disorganization. |
| fawv7f4xc8wt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | ANGULAR_DISPERSION_MEDIAN | ANGULAR_DISPERSION_MEDIAN provides the median angular dispersion value across all triangles. As a robust measure of central tendency, it reflects the typical level of angular irregularity in the tissue without being influenced by outlier values. |
| fawv7f4xc8wt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | CELL_TYPE_ENTROPY | CELL_TYPE_ENTROPY quantifies the average number of unique cell types present within each triangle. By averaging these diversity counts (ranging from 1 to 3), this parameter offers a normalized measure of cellular heterogeneity in the spatial organization, making it comparable across different patient cases. |
| fdohtw36xz2b | P | MEDIAN_NUCLEUS_CONTOUR_ROUGHNESS_PLASMA_CELLS_STROMA | MEDIAN_NUCLEUS_CONTOUR_ROUGHNESS_PLASMA_CELLS_STROMA measures the median value of the ratio between the actual nuclear perimeter and the perimeter of its convex hull for plasma cells within stromal compartments. This parameter provides a normalized metric of nuclear contour roughness, allowing for comparisons across different tumor patches and patient cases to assess the irregularity of nuclear boundaries. |
| ff92vcrwbtcf | TU,Tc,Th,Treg,B,M,MFp,MF,F,Ff | freq_1 | freq_1 to freq_20: Normalized frequencies of the top twenty quadruple motifs. Each 'freq_i' parameter quantifies the proportion of the total motifs that correspond to the i-th most frequent motif, allowing standardized comparison across different tumor patches despite variations in the raw count of motifs. |
| ff92vcrwbtcf | TU,Tc,Th,Treg,B,M,MFp,MF,F,Ff | freq_2 | motif_entropy: The Shannon entropy of the distribution of motif frequencies. This metric measures the diversity and unpredictability in the motif composition within a given tumor patch, with higher values indicating a more heterogeneous set of interactions. |
| ff92vcrwbtcf | TU,Tc,Th,Treg,B,M,MFp,MF,F,Ff | freq_3 | dominant_motif_freq: The normalized frequency of the most prevalent quadruple motif in a sample. It reflects the dominance of a specific cell adjacency pattern relative to the total motif count, enabling meaningful inter-sample comparisons. |
| ff92vcrwbtcf | TU,Tc,Th,Treg,B,M,MFp,MF,F,Ff | freq_4 | tumor_immune_motif_freq: The normalized frequency of motifs that include both tumor cells and immune cells (such as T cells or B cells). This parameter assesses the extent of tumor-immune interactions in a standardized manner. |
| ff92vcrwbtcf | TU,Tc,Th,Treg,B,M,MFp,MF,F,Ff | freq_5 | tumor_stromal_motif_freq: The normalized frequency of motifs that incorporate tumor cells along with stromal cells (for instance, fibroblasts or myofibroblasts). It provides insight into the interactions between tumor and stromal components on a comparable scale across samples. |
| ff92vcrwbtcf | TU,Tc,Th,Treg,B,M,MFp,MF,F,Ff | freq_6 | immune_rich_motif_freq: The normalized frequency of motifs containing at least three immune cells. This parameter highlights immune-dense regions by standardizing the count of these motifs against the total, enabling cross-patient analysis. |
| ff92vcrwbtcf | TU,Tc,Th,Treg,B,M,MFp,MF,F,Ff | freq_7 | stromal_rich_motif_freq: The normalized frequency of motifs enriched with at least three stromal cells. This measure offers a consistent comparison of stromal cell prevalence in the motif distribution across different tumor patches. |
| ffw91ce9ocix | Th,E,MFp | MFP_DENSITY_EPITHELIAL | MFP_DENSITY_EPITHELIAL represents the density of PDPN+ myofibroblasts in the epithelial compartment. This parameter is computed by counting the number of PDPN+ myofibroblasts in the tumor region and normalizing that count by the total epithelial area (in pixels). As such, it yields a numeric value that is directly comparable across different patient cases and imaging patches, ensuring that the results reflect a standardized measurement of cellular infiltration. |
| fgteux7hybui | G,MFp | GRAN_MFP_MAX_CLUSTERING_INDEX | GRAN_MFP_MAX_CLUSTERING_INDEX represents the peak strength of spatial co-clustering between granulocytes and PDPN+ myofibroblasts by reporting the maximum L-function value across all tested distance thresholds. A higher value indicates a stronger deviation from random distribution, signifying enhanced clustering. |
| fgteux7hybui | G,MFp | GRAN_MFP_MEAN_CLUSTERING_INDEX | GRAN_MFP_MEAN_CLUSTERING_INDEX is the average L-function value calculated over all considered distance thresholds. This parameter provides an overall normalized measure of the spatial clustering between the two cell types, facilitating comparison across different patient samples. |
| fgteux7hybui | G,MFp | GRAN_MFP_SHORT_RANGE_INDEX | GRAN_MFP_SHORT_RANGE_INDEX computes the mean L-function value for short distances (up to 30 μm) between granulocytes and PDPN+ myofibroblasts. It captures immediate cell-cell interaction and local clustering phenomena. |
| fgteux7hybui | G,MFp | GRAN_MFP_MID_RANGE_INDEX | GRAN_MFP_MID_RANGE_INDEX represents the average L-function value for medium-range distances (31-60 μm), highlighting the intensity of co-distribution between the cell types at an intermediate spatial scale. |
| fgteux7hybui | G,MFp | GRAN_MFP_LONG_RANGE_INDEX | GRAN_MFP_LONG_RANGE_INDEX calculates the average L-function value for long distances (greater than 60 μm), reflecting broader spatial patterns of clustering between granulocytes and PDPN+ myofibroblasts. |
| fgteux7hybui | G,MFp | GRAN_MFP_L_10 | GRAN_MFP_L_10 denotes the L-function value at a 10 μm distance threshold, quantifying the degree of cell clustering at a very short range. It is a normalized metric that shows how the observed spatial arrangement deviates from randomness at this scale. |
| fgteux7hybui | G,MFp | GRAN_MFP_L_20 | GRAN_MFP_L_20 indicates the L-function value computed at a 20 μm threshold. This measurement reflects clustering trends between the cell populations at this specific distance, supporting detailed spatial analysis. |
| fgteux7hybui | G,MFp | GRAN_MFP_L_30 | GRAN_MFP_L_30 provides the L-function value at a 30 μm distance threshold. It captures the normalized clustering effect between granulocytes and PDPN+ myofibroblasts at this near-range distance. |
| fgteux7hybui | G,MFp | GRAN_MFP_L_40 | GRAN_MFP_L_40 records the L-function value at a 40 μm threshold, offering a measure of spatial co-localization that can be compared across different tissue samples. |
| fgteux7hybui | G,MFp | GRAN_MFP_L_50 | GRAN_MFP_L_50 reflects the L-function value at 50 μm, used to assess the clustering behavior between the two cell types at an intermediate distance. |
| fgteux7hybui | G,MFp | GRAN_MFP_L_60 | GRAN_MFP_L_60 represents the L-function value computed at a 60 μm distance, aiding in the evaluation of spatial relationships at this longer scale. |
| fgteux7hybui | G,MFp | GRAN_MFP_L_70 | GRAN_MFP_L_70 provides the L-function value at a 70 μm threshold, supporting the analysis of cell distribution trends over a wider range. |
| fgteux7hybui | G,MFp | GRAN_MFP_L_80 | GRAN_MFP_L_80 indicates the L-function value at an 80 μm distance threshold, offering another normalized metric for examining spatial clustering. |
| fgteux7hybui | G,MFp | GRAN_MFP_L_90 | GRAN_MFP_L_90 denotes the L-function value at a 90 μm threshold, which further contributes to the assessment of long-range cell clustering patterns. |
| fgteux7hybui | G,MFp | GRAN_MFP_L_100 | GRAN_MFP_L_100 calculates the L-function value at a 100 μm threshold, summarizing the clustering behavior at the maximum analyzed distance and serving as a robust indicator of overall spatial interaction. |
| fhbp7a85aea0 | MF,Ff,P,Th,TU | SERPENTINE_TUMOR | SERPENTINE_TUMOR represents the average serpentine index for tumor cells. This index is computed by squaring the perimeter of the tumor cell nucleus and dividing by its area, providing a normalized measure of nuclear shape complexity that allows for comparisons across different patient cases. |
| fhbp7a85aea0 | MF,Ff,P,Th,TU | SERPENTINE_THELPER | SERPENTINE_THELPER represents the average serpentine index for helper T cells. The index is determined by assessing the perimeter and area of each cell's nuclear polygon to measure its shape complexity, resulting in a normalized metric applicable for cross-patient comparisons. |
| fhbp7a85aea0 | MF,Ff,P,Th,TU | SERPENTINE_PLASMA | SERPENTINE_PLASMA represents the average serpentine index for plasma cells. It is calculated by evaluating the perimeters and areas of their nuclei and averaging the resulting complexity values, thereby normalizing the measure for comparison between different patients. |
| fhbp7a85aea0 | MF,Ff,P,Th,TU | SERPENTINE_MYOFIBROBLAST | SERPENTINE_MYOFIBROBLAST represents the average serpentine index for myofibroblasts. The value is derived from calculating the shape complexity (using perimeter squared over area) of each nuclear outline and then averaging these values, ensuring normalization across samples. |
| fhbp7a85aea0 | MF,Ff,P,Th,TU | SERPENTINE_FIBROBLAST_FSP1 | SERPENTINE_FIBROBLAST_FSP1 represents the average serpentine index for FSP1-positive fibroblasts. This metric is obtained by measuring the nuclei's perimeter and area to compute a complexity index, and then averaging these values for normalization across patient cases. |
| fhbp7a85aea0 | MF,Ff,P,Th,TU | SERPENTINE_COMPOSITE | SERPENTINE_COMPOSITE is a composite measure of nuclear shape complexity calculated as the mean of the average serpentine indices of the individual cell types. This composite index provides an overall normalized assessment of nuclear morphology across different cell populations for a given patch. |
| fkti0ldo05wk | F,MFp,Tc,B | KOLMOGOROV_COMPLEXITY | KOLMOGOROV_COMPLEXITY is a normalized measure that represents the complexity of the spatial arrangement of selected cell types along the tumor boundary. This metric is calculated by first converting the spatial cell distribution into a symbolic sequence where each symbol corresponds to a specific cell type. The sequence is then compressed using a Lempel-Ziv algorithm, and the length of the compressed output is divided by the sequence length to produce a normalized value. This normalization allows for meaningful comparisons across different patient cases and tissue patches. |
| fuwikxormvjy | G,E | GRAN_ENDO_NUCLEUS_AXIS_DIFF | GRAN_ENDO_NUCLEUS_AXIS_DIFF measures the difference between the average major axis lengths of granulocyte and endothelial cell nuclei. This value is derived by calculating the mean measurements from polygon-based analyses of each nucleus and then computing the difference between these averages, making it comparable across different patient samples. |
| fuwikxormvjy | G,E | GRAN_AVG_NUCLEUS_AXIS | GRAN_AVG_NUCLEUS_AXIS represents the average major axis length of granulocyte nuclei. This parameter is computed by measuring the longest distance (major axis) within the polygon of each granulocyte nucleus and then averaging these values within a patch, providing a normalized measure for comparison. |
| fuwikxormvjy | G,E | ENDO_AVG_NUCLEUS_AXIS | ENDO_AVG_NUCLEUS_AXIS indicates the average major axis length of endothelial cell nuclei. It is calculated similarly by determining the major axis from each cell's polygon and taking the mean, which allows for standardized comparison between different patient cases. |
| fuwikxormvjy | G,E | GRAN_MIN_NUCLEUS_AXIS | GRAN_MIN_NUCLEUS_AXIS records the minimum major axis length observed among granulocyte nuclei. This parameter is derived from the set of measured major axis lengths within a patch, providing insight into the lower bound of nuclear size variability in granulocytes. |
| fuwikxormvjy | G,E | GRAN_MAX_NUCLEUS_AXIS | GRAN_MAX_NUCLEUS_AXIS captures the maximum major axis length among granulocyte nuclei. It is determined by identifying the largest measured major axis within a patch, serving as an indicator of the upper bound of nuclear size variation. |
| fuwikxormvjy | G,E | GRAN_STD_NUCLEUS_AXIS | GRAN_STD_NUCLEUS_AXIS quantifies the standard deviation of granulocyte nuclei major axis lengths. This statistical measure reflects the variability and dispersion of nuclear size measurements, offering a normalized metric that is useful for comparing heterogeneity across samples. |
| fuwikxormvjy | G,E | ENDO_MIN_NUCLEUS_AXIS | ENDO_MIN_NUCLEUS_AXIS represents the minimum major axis length among endothelial cell nuclei. It is obtained by selecting the smallest value from the set of measurements, thereby providing a comparable metric across different patient regions. |
| fuwikxormvjy | G,E | ENDO_MAX_NUCLEUS_AXIS | ENDO_MAX_NUCLEUS_AXIS denotes the maximum major axis length among endothelial cell nuclei. The parameter identifies the largest measurement in the set of endothelial nucleus sizes, aiding in the comparison of extreme cellular dimensions between cases. |
| fuwikxormvjy | G,E | ENDO_STD_NUCLEUS_AXIS | ENDO_STD_NUCLEUS_AXIS measures the standard deviation of the major axis lengths of endothelial cell nuclei. This value describes the spread of the nuclear size measurements and is a normalized parameter that supports inter-sample comparison. |
| fwgf4guk0o78 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | ANISOTROPY_INDEX | ANISOTROPY_INDEX measures the non-uniformity of cell distribution around the tumor center by calculating the coefficient of variation of cell proportions across defined angular segments. It provides a dimensionless value that facilitates comparison between different patient cases. |
| fwgf4guk0o78 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MAX_PROP_DIFF | MAX_PROP_DIFF quantifies the range of variation in cell distribution by calculating the difference between the maximum and minimum proportion of cells across the angular segments. This normalized value reflects the extent of variability in cell presence within the tumor microenvironment. |
| fwgf4guk0o78 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | ENTROPY | ENTROPY uses the Shannon entropy formula to assess the randomness or disorder in the cell distribution among the angular segments. A higher entropy indicates a more unpredictable cell distribution pattern, while a lower entropy reflects a more even distribution. |
| fwgf4guk0o78 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | GINI_COEFFICIENT | GINI_COEFFICIENT evaluates the inequality in the distribution of cells across the angular segments by comparing all pairwise differences of cell proportions. This parameter provides a normalized measure of dispersion, indicating how evenly (or unevenly) the cells are distributed. |
| fwgf4guk0o78 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | SEGMENT_0_PROPORTION | SEGMENT_0_PROPORTION represents the fraction of total cells that are located within the 0th angular segment, providing a normalized measure of cell density in that specific area of the tumor region. |
| fwgf4guk0o78 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | SEGMENT_1_PROPORTION | SEGMENT_1_PROPORTION represents the fraction of total cells within the 1st angular segment, indicating the proportion of cells in that specific partition relative to the entire tumor region. |
| fwgf4guk0o78 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | SEGMENT_2_PROPORTION | SEGMENT_2_PROPORTION represents the fraction of total cells within the 2nd angular segment, offering a normalized measure of cell density in that particular region. |
| fwgf4guk0o78 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | SEGMENT_3_PROPORTION | SEGMENT_3_PROPORTION represents the fraction of total cells in the 3rd angular segment, facilitating comparison of regional cell distribution within the tumor microenvironment. |
| fwgf4guk0o78 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | SEGMENT_4_PROPORTION | SEGMENT_4_PROPORTION represents the fraction of total cells in the 4th angular segment, providing insight into the localized cell density relative to the overall cell count. |
| fwgf4guk0o78 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | SEGMENT_5_PROPORTION | SEGMENT_5_PROPORTION represents the fraction of total cells in the 5th angular segment, enabling the assessment of cell distribution uniformity across the tumor. |
| fwgf4guk0o78 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | SEGMENT_6_PROPORTION | SEGMENT_6_PROPORTION represents the fraction of total cells in the 6th angular segment, serving as a normalized metric to compare cell presence among different tumor regions. |
| fwgf4guk0o78 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | SEGMENT_7_PROPORTION | SEGMENT_7_PROPORTION represents the fraction of total cells in the 7th angular segment, offering a detailed quantification of cell distribution in that specific region relative to the entire tumor area. |
| fwmuaexqb5bu | Tc,Treg,F,Ff | mean_infiltration_ratio | mean_infiltration_ratio is the average value of the computed infiltration ratio across all valid tumor clusters. The infiltration ratio is a normalized metric that reflects the balance of cytotoxic T cells and FSP1+ fibroblasts relative to regulatory T cells and fibroblasts FSP1- within a specified neighborhood around tumor clusters. This normalization enables comparison across different patient cases. |
| fwmuaexqb5bu | Tc,Treg,F,Ff | median_infiltration_ratio | median_infiltration_ratio represents the middle value of the infiltration ratios from all tumor clusters when sorted. Like the mean infiltration ratio, it offers a normalized measure of local cell interactions in the tumor microenvironment, facilitating effective comparisons across different samples. |
| fwmuaexqb5bu | Tc,Treg,F,Ff | max_infiltration_ratio | max_infiltration_ratio is the highest value of the infiltration ratio among all tumor clusters in a given patch. This parameter highlights the extreme cases of local cellular interactions in terms of immune and fibroblast infiltration, and its normalized nature allows for consistent comparisons between different patient cases. |
| fyyse1b272ey | F,M,E | FSP1_NEG_FIBROBLAST_PROPORTION | FSP1_NEG_FIBROBLAST_PROPORTION measures the normalized fraction of FSP1-negative fibroblasts among the combined set of FSP1-negative fibroblasts, macrophages, and endothelial cells located at the epithelial-stromal boundary. This ratio allows comparison across different patient cases as it represents a relative measurement of cell populations. |
| fyyse1b272ey | F,M,E | FIBROBLAST_TO_MACROPHAGE_RATIO | FIBROBLAST_TO_MACROPHAGE_RATIO represents the normalized ratio between the number of FSP1-negative fibroblasts and the number of macrophages at the epithelial-stromal boundary, with a small constant added to the denominator to avoid division by zero. This parameter facilitates an inter-case comparison of the balance between these two cell types. |
| fyyse1b272ey | F,M,E | FIBROBLAST_TO_ENDOTHELIAL_RATIO | FIBROBLAST_TO_ENDOTHELIAL_RATIO represents the normalized ratio between the number of FSP1-negative fibroblasts and the number of endothelial cells at the epithelial-stromal boundary, with a minor constant in the denominator added to handle cases of zero counts. This parameter is used to compare the relative abundance of fibroblasts to endothelial cells across different cases. |
| g6r5zbffzwar | TU,A | median_distance_tumor_to_apc_near_vessel | This parameter measures the median distance from tumor cells to the nearest antigen-presenting cell (APC) for those tumor cells that are located near a vessel (within a threshold of 50 pixels/micrometers). It provides a normalized spatial measurement that allows for comparison across different tumor patches or patient cases, capturing the closeness of tumor-APC interactions in regions adjacent to blood vessels. |
| g6r5zbffzwar | TU,A | median_distance_tumor_to_apc_far_from_vessel | This parameter measures the median distance from tumor cells to the nearest antigen-presenting cell (APC) for tumor cells that are located far from vessels (greater than 50 pixels/micrometers). Being a median value, it is normalized to the patch or patient case and can be used to compare spatial relationships between cell types in regions that are not immediately adjacent to vessels. |
| g6r5zbffzwar | TU,A | vessel_adjacency_threshold | This parameter is a constant numeric threshold (50 pixels/micrometers) used to classify tumor cells as either 'near' or 'far from' a vessel. It standardizes the criteria for vessel adjacency across different patches and patient cases, ensuring consistent categorization of tumor regions. |
| g7gj0hubhuc5 | TU,Tc,Th,Treg,B,P,M,MFp,MF,Ff,A | PROB_IMMUNE_STROMAL_INTERACTION_20UM | This parameter calculates the probability (a normalized fraction) that any pair of cells among a specific set of 11 cell types, which include tumor cells, various immune cells, and stromal cells, are located within a 20µm distance. For each tumor patch from whole-slide images, cell objects are first filtered to include only those of the designated types. Then, by computing the Euclidean distances between the centroids of every unique pair of filtered cells, the parameter is determined by dividing the number of pairs with distances less than or equal to 20µm by the total number of potential unique cell pairs. This metric is numeric and normalized, enabling meaningful comparisons across different patient cases or tumor regions. |
| g8i4o2nvga9t | E | proportion_endothelial_high_eccentricity | This parameter measures the fraction of endothelial cells within a tumor patch that exhibit a nucleus eccentricity above 0.8. It is calculated by dividing the number of endothelial cells with high eccentricity by the total number of endothelial cells (with a small epsilon added for numerical stability). The resulting proportion is a normalized value, allowing for meaningful comparisons across different patient cases. |
| g9uk9ah45eto | MFp | CV_PDPN_MF_NUCLEUS_ORIENTATION | CV_PDPN_MF_NUCLEUS_ORIENTATION represents the coefficient of variation of the nucleus orientation angles of PDPN+ myofibroblasts in stromal compartments. It is computed by taking the standard deviation of the orientation angles and dividing it by the mean (with an adjustment to prevent division by zero). This normalized measure allows for comparison across different patient cases by accounting for the variability in the orientation distribution. |
| g9uk9ah45eto | MFp | MEAN_PDPN_MF_NUCLEUS_ORIENTATION | MEAN_PDPN_MF_NUCLEUS_ORIENTATION represents the average nucleus orientation angle (in degrees, standardized between 0 and 180) of PDPN+ myofibroblast nuclei within the stroma. This average value is derived from measurements across multiple cells and provides a normalized basis for comparing orientation trends across different tissue patches and patients. |
| g9uk9ah45eto | MFp | STD_PDPN_MF_NUCLEUS_ORIENTATION | STD_PDPN_MF_NUCLEUS_ORIENTATION represents the standard deviation of the orientation angles of PDPN+ myofibroblast nuclei, quantifying the variability in nucleus orientation within the stromal compartments. It is a numeric metric that is computed from the orientation values, thereby allowing comparisons between different patient cases. |
| gh3yskj5ifia | Th,Treg,M,MF,Ff | Th_density_per_mm2 | Th_density_per_mm2 measures the density of Helper T cells (CD4+) in the stroma. These cells are first filtered from a set of cell objects based on their location in the stromal region and specific cell type classification. The number of helper T cells is then normalized by the stromal area, which is determined by counting relevant pixels in a tissue mask. This process produces a normalized metric (cells per square millimeter) that is suitable for comparing different patient cases. |
| gh3yskj5ifia | Th,Treg,M,MF,Ff | Treg_density_per_mm2 | Treg_density_per_mm2 measures the density of Regulatory T cells in the stroma. The parameter is derived by filtering cells located in the stroma by their specific Treg classification, counting them, and then normalizing this count by the calculated stromal area. The resulting value, expressed as cells per square millimeter, ensures that differences in patch areas across patient cases are taken into account. |
| gh3yskj5ifia | Th,Treg,M,MF,Ff | M_density_per_mm2 | M_density_per_mm2 assesses the density of macrophages in the stromal compartment. Macrophages are first isolated from the overall cell population by checking for both their location in the stroma and their unique cell classification. Their count is then divided by the stromal area computed from the tissue mask, yielding a standardized value in cells per square millimeter which facilitates direct comparison across samples. |
| gh3yskj5ifia | Th,Treg,M,MF,Ff | MF_density_per_mm2 | MF_density_per_mm2 represents the density of PDPN- myofibroblasts in the stroma. These cells are identified based on their specific cell type and location information. The count is normalized by the stromal area, calculated by evaluating the tissue mask, resulting in a metric that quantifies the number of myofibroblasts per square millimeter and supports analysis across different fields of view. |
| gh3yskj5ifia | Th,Treg,M,MF,Ff | Ff_density_per_mm2 | Ff_density_per_mm2 indicates the density of FSP1+ fibroblasts in the stromal area. The parameter is calculated by first filtering and counting the fibroblast cells that express FSP1 in the stromal region, followed by normalizing the counts using the area of the stroma as measured from a tissue mask. The final measure, given in cells per square millimeter, produces a normalized and comparable metric across various patient cases. |
| giz7jvsj00md | G,P | AVG_GRANULOCYTE_VESSEL_DISTANCE | AVG_GRANULOCYTE_VESSEL_DISTANCE represents the average of the minimum distances measured from the centroids of granulocytes located in the stroma to the nearest vessel. This metric provides a normalized spatial measurement that can be used to compare the positioning of granulocytes relative to vessels across different patient cases. |
| giz7jvsj00md | G,P | AVG_PLASMA_CELL_VESSEL_DISTANCE | AVG_PLASMA_CELL_VESSEL_DISTANCE represents the average of the minimum distances from the centroids of plasma cells in the stroma to the closest vessel. It quantifies the typical distance of plasma cells from vessels and is calculated per patch, allowing for comparisons across samples. |
| giz7jvsj00md | G,P | GRANULOCYTE_PLASMA_DISTANCE_DIFF | GRANULOCYTE_PLASMA_DISTANCE_DIFF is the computed difference between the average distances of granulocytes and plasma cells to vessels. A positive value indicates that, on average, granulocytes are positioned farther away from vessels than plasma cells, providing a comparative measure of their spatial distribution. |
| giz7jvsj00md | G,P | GRANULOCYTE_DISTANCE_STD | GRANULOCYTE_DISTANCE_STD is the standard deviation of the minimum distances from granulocytes to the nearest vessel. This metric quantifies the variability in the spatial distribution of granulocytes, reflecting how consistent their proximity to vessels is within a tissue patch. |
| giz7jvsj00md | G,P | PLASMA_CELL_DISTANCE_STD | PLASMA_CELL_DISTANCE_STD is the standard deviation of the minimum distances from plasma cells to vessels. It measures the dispersion in distances among plasma cells, indicating the consistency of their spatial positioning relative to vascular structures. |
| giz7jvsj00md | G,P | PLASMA_CELL_MIN_DISTANCE | PLASMA_CELL_MIN_DISTANCE is the smallest measured distance from any plasma cell to a vessel. This parameter identifies the point of closest proximity of plasma cells to vessels, highlighting areas where plasma cells are especially near vascular structures. |
| giz7jvsj00md | G,P | GRANULOCYTE_MAX_DISTANCE | GRANULOCYTE_MAX_DISTANCE is the largest measured minimum distance from any granulocyte to a vessel. It captures the most extreme case of granulocyte positioning by identifying the furthest distance encountered between a granulocyte and a vessel within the tissue patch. |
| giz7jvsj00md | G,P | PLASMA_CELL_MAX_DISTANCE | PLASMA_CELL_MAX_DISTANCE is the maximum measured minimum distance from any plasma cell to a vessel. This metric highlights the furthest distance plasma cells are from any vessel, reflecting the extent of their spatial dispersion within the analyzed patch. |
| gl4j4u7o1gxv | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | NUCLEUS_ORIENTATION_STD_ALL_CELLTYPES | The NUCLEUS_ORIENTATION_STD_ALL_CELLTYPES parameter represents the standard deviation of nucleus major axis orientation angles (in degrees) computed across 14 specified cell types. This numeric value quantifies the variability in the orientation of the cell nuclei, reflecting the heterogeneity of tissue architecture. A higher standard deviation indicates greater inconsistency in nucleus orientations, which may be linked to disorganized growth patterns and aggressive tumor behavior. The parameter is derived by calculating the major axis (through identifying the longest edge from the minimum rotated rectangle of each nucleus) and then computing the aggregated standard deviation across all valid cells. |
| gps643fkfslq | B,Ff,M,MFp,TU | mean_distance_b_to_mfPDPN | mean_distance_b_to_mfPDPN measures the average Euclidean distance (in μm) from B lymphocytes identified at the stromal-epithelial boundary to the nearest PDPN+ myofibroblast. The value is computed by first filtering B cells positioned within a defined boundary threshold, then determining for each the minimal distance to a PDPN+ myofibroblast, and finally calculating the mean of these distances across all selected B cells, thus providing a normalized metric that is comparable across patient cases. |
| gps643fkfslq | B,Ff,M,MFp,TU | mean_distance_b_to_fFSP1 | mean_distance_b_to_fFSP1 measures the average Euclidean distance (in μm) from B lymphocytes at the stromal-epithelial boundary to the nearest FSP1+ fibroblast. This parameter is derived by computing the minimal distance from each boundary-located B cell to the closest FSP1+ fibroblast and averaging these distances to yield a normalized spatial metric. |
| gps643fkfslq | B,Ff,M,MFp,TU | mean_distance_b_to_macrophage | mean_distance_b_to_macrophage measures the average Euclidean distance (in μm) from B lymphocytes at the stromal-epithelial boundary to the nearest macrophage. It is calculated by identifying the minimum distance for each eligible B cell to a macrophage and then averaging these distances, resulting in a normalized metric for comparing spatial relationships across samples. |
| gps643fkfslq | B,Ff,M,MFp,TU | mean_distance_b_to_tumor | mean_distance_b_to_tumor measures the average Euclidean distance (in μm) from B lymphocytes at the stromal-epithelial boundary to the nearest tumor cell. This parameter is obtained by computing the minimum distance from each B cell (that meets the boundary criterion) to a tumor cell and averaging these distances, yielding a normalized value that facilitates comparison across different patient cases. |
| grrj9spm5eyu | B,E,Ff,M,MFp,P,Th,Treg,TU | DIAS_SCORE | DIAS_SCORE is the Dormant Immune Activation Score that quantifies the relative abundance of immune cells (T helper, T regulatory, B cells, and plasma cells) compared to the cells within the local microenvironment (fibroblasts, myofibroblasts, endothelial cells, macrophages, and tumor cells). This ratio, being normalized by the local cell composition, allows for a consistent comparison across different patient cases. |
| grrj9spm5eyu | B,E,Ff,M,MFp,P,Th,Treg,TU | T_HELPER_PROP | T_HELPER_PROP represents the proportion of T helper cells among the total immune cell population in a tumor patch. By expressing the count of T helper cells as a fraction of the sum of T helper, T regulatory, B cells, and plasma cells, the metric is normalized, making it suitable for comparing across different regions and patient cases. |
| grrj9spm5eyu | B,E,Ff,M,MFp,P,Th,Treg,TU | TREG_PROP | TREG_PROP measures the normalized fraction of T regulatory cells within the total immune cell population. This parameter is derived by dividing the count of T regulatory cells by the total immune cells, providing a standardized metric for comparison. |
| grrj9spm5eyu | B,E,Ff,M,MFp,P,Th,Treg,TU | B_CELL_PROP | B_CELL_PROP indicates the proportion of B lymphocytes among all immune cells in a given tumor patch. It normalizes the count of B cells by the total immune cell count, which allows for direct comparison across different patient samples. |
| grrj9spm5eyu | B,E,Ff,M,MFp,P,Th,Treg,TU | PLASMA_CELL_PROP | PLASMA_CELL_PROP quantifies the fraction of plasma cells relative to the overall immune cell count. This normalized measure facilitates the analysis of plasma cell distribution in relation to the broader immune context across various patient cases. |
| gslkr0hocta3 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_distance_cells_to_vessel | This parameter represents the average of the minimum Euclidean distances from each cell (of the specified 14 cell types) to the nearest vessel polygon within a tumor patch. It quantifies the spatial proximity between the cells and blood vessels, providing an indication of the tumor microenvironment’s angiogenic activity. The measure is numeric and normalized by averaging over all considered cells per patch, ensuring comparability across different patient cases. |
| gw0mh1g4x92k | Th | CV_TH_NUCLEUS_MAJOR_AXIS_LENGTH | CV_TH_NUCLEUS_MAJOR_AXIS_LENGTH represents the coefficient of variation of the major axis length of the helper T lymphocyte nucleus in stromal compartments. It is computed as the standard deviation divided by the mean (with a small epsilon added to avoid division by zero), making it a normalized, dimensionless measure that can be used for comparing variability across different patient cases. |
| gw0mh1g4x92k | Th | MEAN_TH_NUCLEUS_MAJOR_AXIS_LENGTH | MEAN_TH_NUCLEUS_MAJOR_AXIS_LENGTH captures the average major axis length of the helper T lymphocyte nucleus in the stromal areas. This average is derived from individual measurements of the maximum distances between pairs of points on the nuclear boundary, reflecting the central tendency of nuclear size. |
| gw0mh1g4x92k | Th | STD_TH_NUCLEUS_MAJOR_AXIS_LENGTH | STD_TH_NUCLEUS_MAJOR_AXIS_LENGTH measures the spread or dispersion in the nucleus major axis lengths of helper T lymphocytes within stromal compartments. It quantifies how much variation there is around the average value, providing insight into the heterogeneity of the nuclear sizes. |
| gw0mh1g4x92k | Th | MIN_TH_NUCLEUS_MAJOR_AXIS_LENGTH | MIN_TH_NUCLEUS_MAJOR_AXIS_LENGTH identifies the smallest measured major axis length among the evaluated helper T lymphocyte nuclei in the stroma, indicating the lower boundary of the size distribution in that compartment. |
| gw0mh1g4x92k | Th | MAX_TH_NUCLEUS_MAJOR_AXIS_LENGTH | MAX_TH_NUCLEUS_MAJOR_AXIS_LENGTH identifies the largest measured major axis length among the evaluated helper T lymphocyte nuclei in the stroma, indicating the upper boundary of the size distribution in that compartment. |
| gw0mh1g4x92k | Th | MEDIAN_TH_NUCLEUS_MAJOR_AXIS_LENGTH | MEDIAN_TH_NUCLEUS_MAJOR_AXIS_LENGTH provides the median of the nuclear major axis lengths of helper T lymphocytes in the stromal regions. It offers a robust central measure less sensitive to outliers compared to the mean. |
| gzmexdcb1rl7 | Ff,B,Th | FSP1_B_TO_TH_RATIO | FSP1_B_TO_TH_RATIO: This parameter measures the ratio of the combined count of FSP1+ fibroblasts and B cells to the count of T helper cells within the stromal region. It is a normalized metric that allows for cross-sample comparisons by balancing the proportions of these immune and stromal components without being affected by the total cell counts. |
| gzmexdcb1rl7 | Ff,B,Th | FSP1_TO_TH_RATIO | FSP1_TO_TH_RATIO: This parameter calculates the ratio of FSP1+ fibroblasts to T helper cells in the stroma. As a normalized measure, it helps assess the relative abundance of pro-inflammatory fibroblasts compared to T helper cells, facilitating comparisons across different tissue patches. |
| gzmexdcb1rl7 | Ff,B,Th | B_TO_TH_RATIO | B_TO_TH_RATIO: This parameter quantifies the ratio of B cells to T helper cells within the stromal area. It provides a normalized metric to evaluate the balance between B cell infiltration and T helper cell presence across various patient cases. |
| gzmexdcb1rl7 | Ff,B,Th | FSP1_DENSITY | FSP1_DENSITY: This parameter represents the density of FSP1+ fibroblasts per 1000 μm² in the stroma. By normalizing the cell count to the area, it allows for meaningful comparisons of fibroblast distribution between different tumor patches. |
| gzmexdcb1rl7 | Ff,B,Th | B_CELL_DENSITY | B_CELL_DENSITY: This parameter indicates the density of B cells per 1000 μm² in the stroma. It offers a normalized view of B cell presence, ensuring that variations in tissue area do not influence comparisons across patient samples. |
| gzmexdcb1rl7 | Ff,B,Th | T_HELPER_DENSITY | T_HELPER_DENSITY: This parameter measures the density of T helper cells per 1000 μm² in the stroma. It is a normalized metric that reflects the spatial distribution of T helper cells, making it suitable for comparative analysis across different patient groups. |
| gzmexdcb1rl7 | Ff,B,Th | COMBINED_DENSITY | COMBINED_DENSITY: This parameter calculates the combined density of FSP1+ fibroblasts and B cells per 1000 μm² in the stroma. As a normalized metric, it provides an overall assessment of the immune-stromal environment by accounting for the distribution of both cell types relative to the tissue area. |
| h1no0ehfaul9 | Tc | MEDIAN_DISTANCE_CYTOTOXIC_T_TO_TUMOR_BOUNDARY | This parameter represents the median distance, measured in micrometers, from cytotoxic T cells (CD8+ cells) located in the stromal compartment to the nearest tumor boundary within a tumor patch. It is calculated by first identifying the relevant cytotoxic T cells in the stroma, then measuring the distance from each cell’s position to the tumor boundary determined via contour extraction and geometric conversion, and finally computing the median of all these distances. Because the computation integrates spatial measurements in a way that allows comparison across different patient cases and patches, it qualifies as a normalized metric. |
| h3gjffs3f9y7 | TU,Tc,Th,Treg,B,G,MFp,F,E,A | T_TO_FIBROBLAST_RATIO | The T_TO_FIBROBLAST_RATIO is a normalized metric that quantifies the balance between T cells and fibroblasts in the tumor environment by dividing the total count of T-cell subsets by the total count of fibroblast subsets. This ratio enables comparison across different patient cases and tumor patches by providing a relative measure rather than relying on absolute cell counts. |
| h3usuxmrius4 | P | CV_PLASMA_VESSEL_DIST | CV_PLASMA_VESSEL_DIST represents the coefficient of variation of the distances from plasma cells to the nearest vessels in the stromal compartments. This metric is calculated as the ratio between the standard deviation and the mean of these distances, providing a normalized, unitless measure that allows for comparison across different patient cases. |
| h3usuxmrius4 | P | PLASMA_VESSEL_DIST_MEAN | PLASMA_VESSEL_DIST_MEAN gives the average distance from each plasma cell, within the stromal compartment, to its nearest vessel. This parameter provides a central tendency measurement of spatial distribution and is computed using the distances derived for each plasma cell, making it a numeric metric that can be compared across patient cases. |
| h3usuxmrius4 | P | PLASMA_VESSEL_DIST_STD | PLASMA_VESSEL_DIST_STD quantifies the variability among the distances from plasma cells to the nearest vessels in the stromal compartments by calculating their standard deviation. This normalized, numeric parameter helps to understand the dispersion in plasma cell spatial distribution, thus facilitating comparison between different tumor cases. |
| h6ximf1gzd1u | A,B,G,M,P,Tc,Th,Treg,TU | TU_eccentricity_weighted_by_Tc | TU_eccentricity_weighted_by_Tc represents the normalized weighted average of tumor cell nucleus eccentricity, where the weighting is determined by the number of nearby CD8+ T cells (cytotoxic T cells). This parameter quantifies the morphological deformation of tumor nuclei in the context of CD8+ immune cell infiltration. |
| h6ximf1gzd1u | A,B,G,M,P,Tc,Th,Treg,TU | TU_eccentricity_weighted_by_Th | TU_eccentricity_weighted_by_Th represents the normalized weighted average of tumor cell nucleus eccentricity, with weighting based on nearby CD4+ T helper cells. It captures the relationship between tumor nuclear shape and the presence of helper T cells in the microenvironment. |
| h6ximf1gzd1u | A,B,G,M,P,Tc,Th,Treg,TU | TU_eccentricity_weighted_by_Treg | TU_eccentricity_weighted_by_Treg represents the normalized weighted average of tumor cell nucleus eccentricity, where the eccentricity is weighted by the number of neighboring regulatory T cells. This parameter indicates how tumor nuclear morphology may be influenced by the local immunosuppressive environment. |
| h6ximf1gzd1u | A,B,G,M,P,Tc,Th,Treg,TU | TU_eccentricity_weighted_by_B | TU_eccentricity_weighted_by_B represents the normalized weighted average of tumor cell nucleus eccentricity calculated by weighting with the count of nearby B cells. It reflects the association between tumor nuclear deformation and B cell infiltration. |
| h6ximf1gzd1u | A,B,G,M,P,Tc,Th,Treg,TU | TU_eccentricity_weighted_by_P | TU_eccentricity_weighted_by_P represents the normalized weighted average of tumor cell nucleus eccentricity, using plasma cell counts in the local neighborhood as weights. It measures the influence of plasma cells on the morphological aberration of tumor nuclei. |
| h6ximf1gzd1u | A,B,G,M,P,Tc,Th,Treg,TU | TU_eccentricity_weighted_by_M | TU_eccentricity_weighted_by_M represents the normalized weighted average of tumor cell nucleus eccentricity determined by weighting with the count of adjacent macrophages. This parameter highlights the relationship between tumor nuclear shape and macrophage presence. |
| h6ximf1gzd1u | A,B,G,M,P,Tc,Th,Treg,TU | TU_eccentricity_weighted_by_G | TU_eccentricity_weighted_by_G represents the normalized weighted average of tumor cell nucleus eccentricity with weighting provided by the count of nearby granulocytes. It quantifies how the granulocyte-rich microenvironment correlates with tumor nuclear deformation. |
| h6ximf1gzd1u | A,B,G,M,P,Tc,Th,Treg,TU | TU_eccentricity_weighted_by_A | TU_eccentricity_weighted_by_A represents the normalized weighted average of tumor cell nucleus eccentricity calculated by taking into account the number of antigen presenting cells in the tumor vicinity. This measurement reflects the impact of antigen presenting cells on the eccentricity of tumor nuclei. |
| h6ximf1gzd1u | A,B,G,M,P,Tc,Th,Treg,TU | TU_eccentricity_with_immune_neighbors | TU_eccentricity_with_immune_neighbors represents the average tumor cell nucleus eccentricity calculated only for those tumor cells that have at least one immune cell neighbor. This parameter is normalized and provides a comparative measure of tumor nuclear deformation in immune-infiltrated regions. |
| h74k6ead6n6m | Th,Ff | T_HELPER_DENSITY | T_HELPER_DENSITY represents the normalized density of T helper cells within the defined buffered boundary region around the epithelial-stromal interface. It is calculated by dividing the number of T helper cells found within that region by the total area of the boundary, thus allowing for comparison across different patient cases or patches. |
| h74k6ead6n6m | Th,Ff | FSP1_FIBROBLAST_DENSITY | FSP1_FIBROBLAST_DENSITY represents the normalized density of FSP1+ fibroblasts within the same buffered boundary region. It is computed by dividing the count of FSP1+ fibroblasts by the area of the boundary, ensuring that the measure is comparable across different tumor patches. |
| h74k6ead6n6m | Th,Ff | DENSITY_RATIO | DENSITY_RATIO is the normalized metric calculated as the ratio between the T helper cell density and the FSP1+ fibroblast density. This parameter provides a comparative measure of the immune response relative to the fibroblast presence, adjusted for the area, and can be effectively used to compare different patient cases. |
| hdo6lyn9mvr0 | TU,A,E,MFp,G,Th,Treg | mean_alignment_angle_TU | mean_alignment_angle_TU represents the average orientation difference, measured in degrees, between the major axis of tumor cells and the principal axis of the main blood vessel in the patch. The angle is normalized to a range from 0 to 90 degrees, where 0 indicates perfect alignment with the vessel and 90 indicates a perpendicular orientation. |
| hdo6lyn9mvr0 | TU,A,E,MFp,G,Th,Treg | mean_alignment_angle_A | mean_alignment_angle_A represents the average orientation difference, measured in degrees, between antigen presenting cells and the main vessel's axis. It quantifies how these cells are aligned with respect to the vessel’s orientation by calculating the mean difference in orientation angles, normalized to a range of 0 to 90 degrees. |
| hdo6lyn9mvr0 | TU,A,E,MFp,G,Th,Treg | mean_alignment_angle_E | mean_alignment_angle_E represents the average orientation difference, measured in degrees, between endothelial cells and the main vessel’s principal axis. This parameter provides a normalized measure of alignment, where lower values indicate alignment with the vessel axis and higher values indicate a more perpendicular orientation. |
| hdo6lyn9mvr0 | TU,A,E,MFp,G,Th,Treg | mean_alignment_angle_MFp | mean_alignment_angle_MFp represents the average orientation difference, measured in degrees, between PDPN+ myofibroblasts and the main vessel’s principal axis. The parameter is normalized between 0 and 90 degrees, and it measures the directional alignment of the cells relative to the vessel, with lower values suggesting parallel orientation. |
| hdo6lyn9mvr0 | TU,A,E,MFp,G,Th,Treg | mean_alignment_angle_G | mean_alignment_angle_G represents the average orientation difference, measured in degrees, between granulocytes and the main vessel’s orientation axis. By providing a normalized value between 0 and 90 degrees, it indicates whether the cells tend to be aligned parallel or perpendicular to the blood vessel. |
| hdo6lyn9mvr0 | TU,A,E,MFp,G,Th,Treg | mean_alignment_angle_Th | mean_alignment_angle_Th represents the average orientation difference, measured in degrees, between helper T cells and the principal axis of the main vessel. The normalization of the angle to the range of 0 to 90 degrees ensures that the parameter can be compared across different patches, reflecting the degree of alignment relative to the vessel. |
| hdo6lyn9mvr0 | TU,A,E,MFp,G,Th,Treg | mean_alignment_angle_Treg | mean_alignment_angle_Treg represents the average orientation difference, measured in degrees, between regulatory T cells and the main vessel’s principal axis. This parameter is normalized to a range from 0 to 90 degrees and quantifies how these cells align relative to the blood vessel, indicating the extent of parallel or perpendicular orientation. |
| hebvyp67sjmo | MF | PDPN_NEG_MYOFIBROBLAST_NUCLEUS_IQR | The parameter 'PDPN_NEG_MYOFIBROBLAST_NUCLEUS_IQR' measures the spread or heterogeneity of the nucleus areas of PDPN-negative myofibroblasts located in the stromal compartment. It is computed by first identifying the appropriate cell population based on cell type and tissue region, then measuring the nucleus area of each cell. The interquartile range is calculated as the difference between the 75th and 25th percentiles of these area measurements. This numeric metric, reported in square micrometers, is designed for comparative analysis across different patient cases as it is derived using a standardized, consistent methodology applied to tumor patches. |
| hfsie37s5awr | TU,P,G,MFp | TU_orientation_variance | TU_orientation_variance: This parameter quantifies the variance in nuclear orientation angles of tumor cells (epithelial_cell) near vessel structures. It is derived by calculating the orientation angle from the minimum rotated rectangle of each tumor cell's polygon, and then computing the statistical variance of these angles across cells in a given patch. The measure is normalized across patches, allowing for comparison between different patient cases. |
| hfsie37s5awr | TU,P,G,MFp | P_orientation_variance | P_orientation_variance: This parameter measures the variance in nuclear orientation angles of plasma cells near vessels. The orientation is determined from the geometric properties of each plasma cell's polygon, with the variance providing an estimate of heterogeneity in nuclear alignment relative to vessel proximity. Its normalized nature makes it suitable for cross-case comparisons. |
| hfsie37s5awr | TU,P,G,MFp | G_orientation_variance | G_orientation_variance: This parameter represents the variance in nuclear orientation angles of granulocytes identified near vessel structures. The orientation angles, computed from the cells’ shape properties, are used to calculate a statistical variance that reflects the diversity in cellular alignment. It is designed to be comparable among different patient cases. |
| hfsie37s5awr | TU,P,G,MFp | MFp_orientation_variance | MFp_orientation_variance: This parameter assesses the variance in nuclear orientation angles of PDPN+ myofibroblasts near vessels. The approach involves computing the cell's orientation based on its minimum rotated rectangle and then determining the variance among these angles. This normalized metric aids in comparing the cellular orientation variability across different tumor patches. |
| hfsie37s5awr | TU,P,G,MFp | combined_orientation_variance | combined_orientation_variance: This parameter provides an aggregated variance of nuclear orientation angles across all four cell types (tumor cells, plasma cells, granulocytes, and PDPN+ myofibroblasts) near vessel structures. By combining the individual orientation angle measurements and computing their overall variance, it offers a comprehensive metric for the heterogeneity in nuclear orientation across the tumor microenvironment. |
| hjqetj7bt7ep | B,Ff,MFp,TU,G | Eccentricity_Mean | Eccentricity_Mean: The overall average nuclear elliptical eccentricity computed from all analyzed cell types in a tumor patch. This metric quantifies how much, on average, the nuclear shape deviates from a perfect circle, making it comparable across different patient cases. |
| hjqetj7bt7ep | B,Ff,MFp,TU,G | Eccentricity_Variance | Eccentricity_Variance: The variance of the nuclear elliptical eccentricity across all cells in the analyzed patch. It measures the degree of variability in nuclear shapes, reflecting heterogeneity in cell morphology across different tumor regions. |
| hjqetj7bt7ep | B,Ff,MFp,TU,G | Eccentricity_StdDev | Eccentricity_StdDev: The standard deviation of nuclear elliptical eccentricity over all cells in the patch. As a normalized metric, it indicates the typical deviation from the mean eccentricity and allows for comparison across patient samples. |
| hjqetj7bt7ep | B,Ff,MFp,TU,G | Eccentricity_Mean_B_cells | Eccentricity_Mean_B_cells: The average nuclear eccentricity calculated specifically for B cells. This parameter isolates the nuclear shape deviation within the B cell population, enabling comparisons within and between patient cases. |
| hjqetj7bt7ep | B,Ff,MFp,TU,G | Eccentricity_StdDev_B_cells | Eccentricity_StdDev_B_cells: The standard deviation of nuclear eccentricity measurements among B cells, reflecting the spread of nuclear shape alterations within this immune cell subset. |
| hjqetj7bt7ep | B,Ff,MFp,TU,G | Eccentricity_Mean_FSP1+_fibroblasts | Eccentricity_Mean_FSP1+_fibroblasts: The mean value of nuclear eccentricity for FSP1+ fibroblasts, providing insight into the average nuclear morphology of these specialized fibroblasts relative to other cells. |
| hjqetj7bt7ep | B,Ff,MFp,TU,G | Eccentricity_StdDev_FSP1+_fibroblasts | Eccentricity_StdDev_FSP1+_fibroblasts: The standard deviation of nuclear eccentricity in FSP1+ fibroblasts, illustrating the variation in nuclear shape within this group and allowing for normalized comparisons. |
| hjqetj7bt7ep | B,Ff,MFp,TU,G | Eccentricity_Mean_PDPN+_myofibroblasts | Eccentricity_Mean_PDPN+_myofibroblasts: The computed average nuclear eccentricity for PDPN+ myofibroblasts, serving as a normalized measure of nuclear deformation specific to these stromal cells. |
| hjqetj7bt7ep | B,Ff,MFp,TU,G | Eccentricity_StdDev_PDPN+_myofibroblasts | Eccentricity_StdDev_PDPN+_myofibroblasts: The standard deviation of the nuclear eccentricity among PDPN+ myofibroblasts, indicating the variability in their nuclear morphology and supporting inter-patient comparison. |
| hjqetj7bt7ep | B,Ff,MFp,TU,G | Eccentricity_Mean_Tumor_cells | Eccentricity_Mean_Tumor_cells: The overall mean nuclear eccentricity calculated solely for tumor cells, reflecting the average nuclear shape alterations within the cancerous cell population in a patch. |
| hjqetj7bt7ep | B,Ff,MFp,TU,G | Eccentricity_StdDev_Tumor_cells | Eccentricity_StdDev_Tumor_cells: The standard deviation of nuclear eccentricity measurements for tumor cells, which quantifies the spread of nuclear morphological characteristics within this group in a normalized way. |
| hjqetj7bt7ep | B,Ff,MFp,TU,G | Eccentricity_Mean_Granulocytes | Eccentricity_Mean_Granulocytes: The average nuclear eccentricity for granulocytes, providing a normalized about the nuclear shape deviation in these immune cells, useful for cross-case comparison. |
| hjqetj7bt7ep | B,Ff,MFp,TU,G | Eccentricity_StdDev_Granulocytes | Eccentricity_StdDev_Granulocytes: The standard deviation of the nuclear eccentricity among granulocytes, capturing the extent of variability in their nuclear shapes and supporting comparative analysis. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_DIVERSITY_INDEX | TRIPLET_DIVERSITY_INDEX: This parameter quantifies the diversity of valid cell triplet interactions within a tumor patch. Calculated using the Shannon entropy formula based on the relative frequencies of each triplet type, it provides a normalized metric to compare the heterogeneity of cell interactions across different patient cases. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_Tc-Th-Th_FREQ | TRIPLET_Tc-Th-Th_FREQ: This parameter represents the normalized relative frequency of triplet interactions composed of one Tc cell and two Th cells. It is computed as the ratio of occurrences of this specific interaction to the total valid interactions in the patch, allowing cross-case comparisons. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-Tc-Th_FREQ | TRIPLET_B-Tc-Th_FREQ: This parameter measures the relative frequency, in a normalized form, of interactions involving a B cell, a Tc cell, and a Th cell. It facilitates the assessment of the prevalence of this particular triad across tumor samples. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_M-Tc-Th_FREQ | TRIPLET_M-Tc-Th_FREQ: This parameter indicates the proportion of triplet interactions consisting of a macrophage (M), a Tc cell, and a Th cell. Being a normalized frequency, it enables comparisons across different patches and patients. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_MFp-Tc-Th_FREQ | TRIPLET_MFp-Tc-Th_FREQ: This parameter provides the normalized frequency of interactions among myofibroblast (MFp), Tc, and Th cells. It reflects the relative occurrence of this specific triad pattern within the tumor microenvironment. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-M-Tc_FREQ | TRIPLET_B-M-Tc_FREQ: This parameter quantifies the normalized relative frequency of interactions among B, M, and Tc cells. It is a proportion that facilitates comparative analysis between different patient cases. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-B-Tc_FREQ | TRIPLET_B-B-Tc_FREQ: This parameter captures the normalized frequency of interactions consisting of two B cells and one Tc cell. It represents the proportion of these interactions relative to all triplet interactions in a patch. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-MFp-Tc_FREQ | TRIPLET_B-MFp-Tc_FREQ: This parameter represents the normalized relative frequency of a triplet composed of B, MFp, and Tc cells. It allows for standardized comparisons across different tumor regions. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_M-M-Tc_FREQ | TRIPLET_M-M-Tc_FREQ: This parameter measures the proportion of interactions with two macrophages (M) and one Tc cell, normalized relative to the total interactions. It serves as a comparative metric across patients. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_M-MFp-Tc_FREQ | TRIPLET_M-MFp-Tc_FREQ: This parameter indicates the normalized relative frequency of triplet interactions combining one macrophage (M), one myofibroblast (MFp), and one Tc cell. It is designed for cross-sample comparisons. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-M-M_FREQ | TRIPLET_B-M-M_FREQ: This parameter provides the normalized frequency of interactions composed of a B cell and two macrophages (M). As a proportional measure, it can be compared between different patient cases. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_M-M-M_FREQ | TRIPLET_M-M-M_FREQ: This parameter quantifies the normalized relative frequency of interactions where all three cells are macrophages (M). It standardizes the measurement for comparisons across patches. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_M-M-Th_FREQ | TRIPLET_M-M-Th_FREQ: This parameter captures the normalized frequency of triplets made up of two macrophages (M) and one Th cell. It reflects the relative prevalence of these interactions across tumor samples. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-B-M_FREQ | TRIPLET_B-B-M_FREQ: This parameter measures the normalized relative frequency of interactions involving two B cells and one macrophage (M). It is expressed as a proportion to allow direct comparisons. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-M-Th_FREQ | TRIPLET_B-M-Th_FREQ: This parameter quantifies the normalized frequency of interactions among B, M, and Th cells, facilitating assessments of interaction patterns across different patients. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_M-Th-Th_FREQ | TRIPLET_M-Th-Th_FREQ: This parameter represents the normalized relative frequency of triplet interactions that include one macrophage (M) and two Th cells. It is useful for comparing interaction prevalences. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_M-Tc-Tc_FREQ | TRIPLET_M-Tc-Tc_FREQ: This parameter indicates the normalized frequency of interactions where one macrophage (M) interacts with two Tc cells. The value, as a proportion, enables cross-case analysis. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-B-B_FREQ | TRIPLET_B-B-B_FREQ: This parameter captures the normalized relative frequency of interactions among three B cells. Being ratio‐based, it is suitable for comparing across patient samples. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-B-Th_FREQ | TRIPLET_B-B-Th_FREQ: This parameter quantifies the normalized frequency of interactions that involve two B cells and one Th cell, serving as a standardized measure for comparative studies. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-Th-Th_FREQ | TRIPLET_B-Th-Th_FREQ: This parameter represents the relative frequency, in normalized form, of triplet interactions consisting of one B cell and two Th cells across tumor patches. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-Tc-Tc_FREQ | TRIPLET_B-Tc-Tc_FREQ: This parameter measures the normalized relative frequency of interactions with one B cell and two Tc cells. The normalization allows for consistent comparisons across cases. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_MFp-Tc-Tc_FREQ | TRIPLET_MFp-Tc-Tc_FREQ: This parameter provides the normalized frequency of interactions involving one myofibroblast (MFp) and two Tc cells, facilitating comparative analysis. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_Tc-Tc-Th_FREQ | TRIPLET_Tc-Tc-Th_FREQ: This parameter indicates the normalized frequency of interactions comprising two Tc cells and one Th cell, serving as a cross-case comparative metric. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_Tc-Tc-Tc_FREQ | TRIPLET_Tc-Tc-Tc_FREQ: This parameter quantifies the normalized relative frequency of interactions where all three cells are Tc cells. It standardizes the measure for inter-patient comparisons. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-B-MFp_FREQ | TRIPLET_B-B-MFp_FREQ: This parameter captures the normalized frequency of interactions among two B cells and one myofibroblast (MFp), expressed as a proportion of total interactions. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-B-E_FREQ | TRIPLET_B-B-E_FREQ: This parameter measures the normalized relative frequency of interactions among two B cells and one endothelial (E) cell, allowing for standardized comparisons. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-E-Tc_FREQ | TRIPLET_B-E-Tc_FREQ: This parameter represents the normalized frequency of interactions involving a B cell, an endothelial (E) cell, and a Tc cell, expressed as a relative measure. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-M-MFp_FREQ | TRIPLET_B-M-MFp_FREQ: This parameter quantifies the normalized relative frequency of interactions among B, macrophage (M), and myofibroblast (MFp) cells, enabling comparison across patches. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-E-MFp_FREQ | TRIPLET_B-E-MFp_FREQ: This parameter captures the normalized frequency of interactions involving a B cell, an endothelial cell (E), and a myofibroblast (MFp), facilitating cross-sample analysis. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-MFp-Th_FREQ | TRIPLET_B-MFp-Th_FREQ: This parameter represents the normalized relative frequency of interactions among B, myofibroblast (MFp), and Th cells, standardized for comparative studies. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-E-M_FREQ | TRIPLET_B-E-M_FREQ: This parameter measures the normalized frequency of interactions involving a B cell, an endothelial (E) cell, and a macrophage (M), allowing normalized comparisons. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-E-Th_FREQ | TRIPLET_B-E-Th_FREQ: This parameter indicates the normalized relative frequency of interactions consisting of B, endothelial (E), and Th cells, enabling cross-sample evaluation. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-E-E_FREQ | TRIPLET_B-E-E_FREQ: This parameter quantifies the normalized frequency of interactions among a B cell and two endothelial (E) cells, expressed as a ratio for comparability. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-MFp-Tc_FREQ | TRIPLET_E-MFp-Tc_FREQ: This parameter provides the normalized relative frequency of interactions among an endothelial (E) cell, a myofibroblast (MFp), and a Tc cell, suitable for inter-patient comparison. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-M-Tc_FREQ | TRIPLET_E-M-Tc_FREQ: This parameter represents the normalized frequency of interactions involving an endothelial (E) cell, a macrophage (M), and a Tc cell, expressed as a proportion. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-Tc-Th_FREQ | TRIPLET_E-Tc-Th_FREQ: This parameter measures the normalized relative frequency of interactions among an endothelial (E) cell, a Tc cell, and a Th cell, allowing standardized comparisons. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-Tc-Tc_FREQ | TRIPLET_E-Tc-Tc_FREQ: This parameter indicates the normalized frequency of interactions involving an endothelial (E) cell and two Tc cells, presented as a proportion. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-E-Tc_FREQ | TRIPLET_E-E-Tc_FREQ: This parameter quantifies the normalized relative frequency of interactions among two endothelial (E) cells and one Tc cell, facilitating comparison across cases. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_MFp-Th-Th_FREQ | TRIPLET_MFp-Th-Th_FREQ: This parameter captures the normalized frequency of interactions consisting of one myofibroblast (MFp) and two Th cells, thereby standardizing the measure. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_Th-Th-Th_FREQ | TRIPLET_Th-Th-Th_FREQ: This parameter represents the normalized relative frequency of interactions where all three cells are Th cells, allowing for cross-patient comparisons. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_M-MFp-Th_FREQ | TRIPLET_M-MFp-Th_FREQ: This parameter quantifies the normalized frequency of interactions among a macrophage (M), a myofibroblast (MFp), and a Th cell, expressed as a comparative ratio. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_M-M-MFp_FREQ | TRIPLET_M-M-MFp_FREQ: This parameter measures the normalized relative frequency of interactions among two macrophages (M) and one myofibroblast (MFp), providing a normalized interaction metric. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-M-MFp_FREQ | TRIPLET_E-M-MFp_FREQ: This parameter indicates the normalized frequency of interactions involving an endothelial (E) cell, a macrophage (M), and a myofibroblast (MFp), expressed as a proportion. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-M-M_FREQ | TRIPLET_E-M-M_FREQ: This parameter captures the normalized relative frequency of interactions among an endothelial (E) cell and two macrophages (M), standardized for comparison. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-MFp-Th_FREQ | TRIPLET_E-MFp-Th_FREQ: This parameter represents the normalized frequency of interactions consisting of an endothelial (E) cell, a myofibroblast (MFp), and a Th cell, expressed as a ratio. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-E-MFp_FREQ | TRIPLET_E-E-MFp_FREQ: This parameter quantifies the normalized relative frequency of interactions among two endothelial (E) cells and one myofibroblast (MFp), providing a standardized measure. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-M-Th_FREQ | TRIPLET_E-M-Th_FREQ: This parameter measures the normalized frequency of interactions involving an endothelial (E) cell, a macrophage (M), and a Th cell, expressed as a relative proportion. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-E-M_FREQ | TRIPLET_E-E-M_FREQ: This parameter indicates the normalized relative frequency of interactions among two endothelial (E) cells and one macrophage (M), suitable for cross-case evaluation. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_M-MFp-MFp_FREQ | TRIPLET_M-MFp-MFp_FREQ: This parameter captures the normalized frequency of interactions among one macrophage (M) and two myofibroblasts (MFp), expressed as a ratio relative to all interactions. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-MFp-MFp_FREQ | TRIPLET_B-MFp-MFp_FREQ: This parameter represents the normalized relative frequency of interactions involving one B cell and two myofibroblasts (MFp), allowing standardized comparisons. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-Th-Th_FREQ | TRIPLET_E-Th-Th_FREQ: This parameter quantifies the normalized frequency of interactions among one endothelial (E) cell and two Th cells, presented as a proportion for comparative analysis. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-E-Th_FREQ | TRIPLET_E-E-Th_FREQ: This parameter measures the normalized relative frequency of interactions among two endothelial (E) cells and one Th cell, enabling cross-sample comparison. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-E-E_FREQ | TRIPLET_E-E-E_FREQ: This parameter indicates the normalized frequency of interactions where all three cells are endothelial (E) cells, expressed as a normalized ratio. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_MFp-MFp-Tc_FREQ | TRIPLET_MFp-MFp-Tc_FREQ: This parameter captures the normalized relative frequency of interactions with two myofibroblasts (MFp) and one Tc cell, facilitating standardized comparisons. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_MFp-MFp-Th_FREQ | TRIPLET_MFp-MFp-Th_FREQ: This parameter represents the normalized frequency of interactions among two myofibroblasts (MFp) and one Th cell, allowing for inter-patient comparisons. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-MFp-MFp_FREQ | TRIPLET_E-MFp-MFp_FREQ: This parameter quantifies the normalized relative frequency of interactions involving an endothelial (E) cell and two myofibroblasts (MFp), expressed as a proportion. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_MFp-MFp-MFp_FREQ | TRIPLET_MFp-MFp-MFp_FREQ: This parameter measures the normalized frequency of interactions where all three cells are myofibroblasts (MFp), providing a standardized metric. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_Ff-MFp-Th_FREQ | TRIPLET_Ff-MFp-Th_FREQ: This parameter indicates the normalized relative frequency of interactions among a fibroblast (Ff), a myofibroblast (MFp), and a Th cell, expressed as a proportion. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_Ff-M-Th_FREQ | TRIPLET_Ff-M-Th_FREQ: This parameter captures the normalized frequency of interactions involving a fibroblast (Ff), a macrophage (M), and a Th cell, facilitating cross-case comparisons. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_Ff-Tc-Th_FREQ | TRIPLET_Ff-Tc-Th_FREQ: This parameter represents the normalized relative frequency of interactions among a fibroblast (Ff), a Tc cell, and a Th cell, standardized for comparison. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_Ff-MFp-MFp_FREQ | TRIPLET_Ff-MFp-MFp_FREQ: This parameter quantifies the normalized frequency of interactions involving a fibroblast (Ff) and two myofibroblasts (MFp), expressed as a proportion. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_Ff-MFp-Tc_FREQ | TRIPLET_Ff-MFp-Tc_FREQ: This parameter measures the normalized relative frequency of interactions among a fibroblast (Ff), a myofibroblast (MFp), and a Tc cell, allowing standardized analyses. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_Ff-M-MFp_FREQ | TRIPLET_Ff-M-MFp_FREQ: This parameter indicates the normalized frequency of interactions with a fibroblast (Ff), a macrophage (M), and a myofibroblast (MFp), expressed as a relative measure. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_Ff-M-Tc_FREQ | TRIPLET_Ff-M-Tc_FREQ: This parameter captures the normalized relative frequency of interactions among a fibroblast (Ff), a macrophage (M), and a Tc cell, enabling cross-sample comparisons. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_Ff-M-M_FREQ | TRIPLET_Ff-M-M_FREQ: This parameter represents the normalized frequency of interactions involving a fibroblast (Ff) and two macrophages (M), standardized for inter-case comparison. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_Ff-Tc-Tc_FREQ | TRIPLET_Ff-Tc-Tc_FREQ: This parameter quantifies the normalized relative frequency of interactions where a fibroblast (Ff) interacts with two Tc cells, expressed as a normalized proportion. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_M-Th-Treg_FREQ | TRIPLET_M-Th-Treg_FREQ: This parameter measures the normalized frequency of interactions among a macrophage (M), a Th cell, and a Treg cell, providing a comparative metric across cases. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_M-Tc-Treg_FREQ | TRIPLET_M-Tc-Treg_FREQ: This parameter indicates the normalized relative frequency of interactions among a macrophage (M), a Tc cell, and a Treg cell, expressed as a proportion. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_Tc-Tc-Treg_FREQ | TRIPLET_Tc-Tc-Treg_FREQ: This parameter captures the normalized frequency of interactions consisting of two Tc cells and one Treg cell, allowing standardized comparison across patient samples. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_Tc-Th-Treg_FREQ | TRIPLET_Tc-Th-Treg_FREQ: This parameter represents the normalized relative frequency of interactions among a Tc cell, a Th cell, and a Treg cell, measured as a proportion of all interactions. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_Ff-Th-Th_FREQ | TRIPLET_Ff-Th-Th_FREQ: This parameter quantifies the normalized frequency of interactions where a fibroblast (Ff) interacts with two Th cells, providing a normalized measure. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_MFp-Th-Treg_FREQ | TRIPLET_MFp-Th-Treg_FREQ: This parameter indicates the normalized relative frequency of interactions among a myofibroblast (MFp), a Th cell, and a Treg cell, enabling cross-case comparisons. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-Ff-Th_FREQ | TRIPLET_E-Ff-Th_FREQ: This parameter measures the normalized frequency of interactions comprising an endothelial (E) cell, a fibroblast (Ff), and a Th cell, standardized for inter-sample analysis. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_MFp-Tc-Treg_FREQ | TRIPLET_MFp-Tc-Treg_FREQ: This parameter represents the normalized relative frequency of interactions among a myofibroblast (MFp), a Tc cell, and a Treg cell, expressed as a proportion for comparison. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-Tc-Treg_FREQ | TRIPLET_B-Tc-Treg_FREQ: This parameter captures the normalized frequency of interactions among a B cell, a Tc cell, and a Treg cell, providing a normalized measure across samples. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-Tc-Treg_FREQ | TRIPLET_E-Tc-Treg_FREQ: This parameter quantifies the normalized relative frequency of interactions among an endothelial (E) cell, a Tc cell, and a Treg cell, facilitating standardized comparisons. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_M-MFp-Treg_FREQ | TRIPLET_M-MFp-Treg_FREQ: This parameter indicates the normalized frequency of interactions involving a macrophage (M), a myofibroblast (MFp), and a Treg cell, expressed as a proportion. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-M-Treg_FREQ | TRIPLET_E-M-Treg_FREQ: This parameter represents the normalized relative frequency of interactions among an endothelial (E) cell, a macrophage (M), and a Treg cell, enabling cross-sample comparison. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_M-M-Treg_FREQ | TRIPLET_M-M-Treg_FREQ: This parameter captures the normalized frequency of interactions among two macrophages (M) and one Treg cell, expressed as a normalized ratio. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-MFp-Treg_FREQ | TRIPLET_E-MFp-Treg_FREQ: This parameter quantifies the normalized relative frequency of interactions involving an endothelial (E) cell, a myofibroblast (MFp), and a Treg cell, standardized for comparison. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-E-Treg_FREQ | TRIPLET_E-E-Treg_FREQ: This parameter measures the normalized frequency of interactions among two endothelial (E) cells and one Treg cell, expressed as a proportion. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-Ff-Tc_FREQ | TRIPLET_E-Ff-Tc_FREQ: This parameter indicates the normalized relative frequency of interactions among an endothelial (E) cell, a fibroblast (Ff), and a Tc cell, allowing direct comparison. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-Ff-M_FREQ | TRIPLET_E-Ff-M_FREQ: This parameter represents the normalized frequency of interactions among an endothelial (E) cell, a fibroblast (Ff), and a macrophage (M), expressed as a relative measure. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-Ff-MFp_FREQ | TRIPLET_E-Ff-MFp_FREQ: This parameter quantifies the normalized relative frequency of interactions among an endothelial (E) cell, a fibroblast (Ff), and a myofibroblast (MFp), enabling comparative analysis. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-E-Ff_FREQ | TRIPLET_E-E-Ff_FREQ: This parameter captures the normalized frequency of interactions involving two endothelial (E) cells and a fibroblast (Ff), presented as a proportion. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-P-Th_FREQ | TRIPLET_E-P-Th_FREQ: This parameter measures the normalized relative frequency of interactions among an endothelial (E) cell, a plasma (P) cell, and a Th cell, providing a standardized metric. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_MFp-P-Th_FREQ | TRIPLET_MFp-P-Th_FREQ: This parameter represents the normalized frequency of interactions among a myofibroblast (MFp), a plasma (P) cell, and a Th cell, expressed as a proportion. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_P-Tc-Th_FREQ | TRIPLET_P-Tc-Th_FREQ: This parameter quantifies the normalized relative frequency of interactions among a plasma (P) cell, a Tc cell, and a Th cell, allowing standardized comparisons. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-MFp-P_FREQ | TRIPLET_E-MFp-P_FREQ: This parameter indicates the normalized frequency of interactions among an endothelial (E) cell, a myofibroblast (MFp), and a plasma (P) cell, expressed as a normalized ratio. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-E-P_FREQ | TRIPLET_E-E-P_FREQ: This parameter measures the normalized relative frequency of interactions among two endothelial (E) cells and a plasma (P) cell, facilitating cross-sample analysis. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-P-Tc_FREQ | TRIPLET_E-P-Tc_FREQ: This parameter represents the normalized frequency of interactions among an endothelial (E) cell, a plasma (P) cell, and a Tc cell, expressed as a proportion. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_MFp-P-Tc_FREQ | TRIPLET_MFp-P-Tc_FREQ: This parameter captures the normalized relative frequency of interactions among a myofibroblast (MFp), a plasma (P) cell, and a Tc cell, providing a standardized measure. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-M-P_FREQ | TRIPLET_B-M-P_FREQ: This parameter quantifies the normalized frequency of interactions among a B cell, a macrophage (M), and a plasma (P) cell, expressed as a ratio. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_M-P-Th_FREQ | TRIPLET_M-P-Th_FREQ: This parameter indicates the normalized relative frequency of interactions among a macrophage (M), a plasma (P) cell, and a Th cell, enabling cross-case comparison. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-P-P_FREQ | TRIPLET_E-P-P_FREQ: This parameter measures the normalized frequency of interactions involving an endothelial (E) cell and two plasma (P) cells, expressed as a proportion. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-P-Th_FREQ | TRIPLET_B-P-Th_FREQ: This parameter represents the normalized relative frequency of interactions among a B cell, a plasma (P) cell, and a Th cell, standardized for comparison. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_P-Tc-Tc_FREQ | TRIPLET_P-Tc-Tc_FREQ: This parameter captures the normalized frequency of interactions among one plasma (P) cell and two Tc cells, facilitating standardized analyses. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_M-P-Tc_FREQ | TRIPLET_M-P-Tc_FREQ: This parameter quantifies the normalized relative frequency of interactions among a macrophage (M), a plasma (P) cell, and a Tc cell, expressed as a proportion. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_E-M-P_FREQ | TRIPLET_E-M-P_FREQ: This parameter indicates the normalized frequency of interactions among an endothelial (E) cell, a macrophage (M), and a plasma (P) cell, enabling comparison. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_P-P-Tc_FREQ | TRIPLET_P-P-Tc_FREQ: This parameter measures the normalized relative frequency of interactions among two plasma (P) cells and a Tc cell, expressed as a normalized ratio. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_M-M-P_FREQ | TRIPLET_M-M-P_FREQ: This parameter represents the normalized frequency of interactions involving two macrophages (M) and a plasma (P) cell, standardized for inter-patient comparison. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_M-P-P_FREQ | TRIPLET_M-P-P_FREQ: This parameter captures the normalized relative frequency of interactions among a macrophage (M) and two plasma (P) cells, expressed in proportion. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_P-P-Th_FREQ | TRIPLET_P-P-Th_FREQ: This parameter quantifies the normalized frequency of interactions among two plasma (P) cells and a Th cell, allowing for standardized comparisons. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-E-P_FREQ | TRIPLET_B-E-P_FREQ: This parameter indicates the normalized relative frequency of interactions among a B cell, an endothelial (E) cell, and a plasma (P) cell, expressed as a proportion. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_M-MFp-P_FREQ | TRIPLET_M-MFp-P_FREQ: This parameter measures the normalized frequency of interactions among a macrophage (M), a myofibroblast (MFp), and a plasma (P) cell, standardized for comparison. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_P-Th-Th_FREQ | TRIPLET_P-Th-Th_FREQ: This parameter represents the normalized relative frequency of interactions among one plasma (P) cell and two Th cells, expressed as a ratio. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_MFp-MFp-P_FREQ | TRIPLET_MFp-MFp-P_FREQ: This parameter captures the normalized frequency of interactions among two myofibroblasts (MFp) and a plasma (P) cell, facilitating cross-sample comparison. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_MFp-P-P_FREQ | TRIPLET_MFp-P-P_FREQ: This parameter quantifies the normalized relative frequency of interactions among a myofibroblast (MFp) and two plasma (P) cells, expressed as a proportion. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_MFp-MFp-Treg_FREQ | TRIPLET_MFp-MFp-Treg_FREQ: This parameter indicates the normalized frequency of interactions involving two myofibroblasts (MFp) and a Treg cell, allowing standardized comparisons. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-P-Tc_FREQ | TRIPLET_B-P-Tc_FREQ: This parameter measures the normalized relative frequency of interactions among a B cell, a plasma (P) cell, and a Tc cell, expressed as a proportion. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-MFp-P_FREQ | TRIPLET_B-MFp-P_FREQ: This parameter represents the normalized frequency of interactions among a B cell, a myofibroblast (MFp), and a plasma (P) cell, enabling comparison across samples. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-Ff-M_FREQ | TRIPLET_B-Ff-M_FREQ: This parameter captures the normalized relative frequency of interactions among a B cell, a fibroblast (Ff), and a macrophage (M), expressed as a normalized ratio. |
| hpbm5qpwotvf | Treg,Th,Tc,MFp,B,P,Ff,M,E | TRIPLET_B-Ff-Tc_FREQ | TRIPLET_B-Ff-Tc_FREQ: This parameter quantifies the normalized frequency of interactions among a B cell, a fibroblast (Ff), and a Tc cell, standardizing the comparison across tumor patches. |
| hqfi0e36sebz | Tc,MFp,Ff | TC_TO_FIBROBLAST_RATIO | TC_TO_FIBROBLAST_RATIO measures the proportion of cytotoxic T cells relative to the combined count of PDPN+ myofibroblasts and FSP1+ fibroblasts in the stromal compartment. This ratio is normalized, enabling comparison across different patient cases by quantifying the balance between immune surveillance and stromal remodeling. |
| hrt8wcgki7w2 | TU,Tc,Th,Treg,B,M,MFp,MF | IMMUNE_DENSITY | IMMUNE_DENSITY quantifies the relative presence of immune cells compared to tumor cells by dividing the immune cell count by the tumor cell count. This normalized metric allows for the comparison of immune infiltration across different patient samples. |
| hrt8wcgki7w2 | TU,Tc,Th,Treg,B,M,MFp,MF | MYOFIBROBLAST_DENSITY | MYOFIBROBLAST_DENSITY represents the proportion of myofibroblasts relative to tumor cells, calculated by dividing the myofibroblast count by the tumor cell count. This normalized value enables standardized assessment of stromal activation across various tumor cases. |
| hrt8wcgki7w2 | TU,Tc,Th,Treg,B,M,MFp,MF | IMMUNE_MYOFIBROBLAST_RATIO | IMMUNE_MYOFIBROBLAST_RATIO measures the balance between immune response and stromal activation by taking the ratio of immune cell count to myofibroblast count. As a normalized parameter, it facilitates comparisons of the interplay between these two cell types across different patient samples. |
| hsrvt90qrw0e | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | Coverage_Ratio | Coverage_Ratio represents the normalized measure of the spatial coverage of the selected cell populations within the epithelial compartment. It is calculated by dividing the area of the minimum convex polygon (which encloses all designated cell types) by the total epithelial area. This unitless ratio enables comparison between different patient cases by accounting for variations in epithelial area across samples. |
| hwbirjjmahtr | Tc,M,F,P | MAX_DIST_TO_VESSEL_STROMA_IMMUNE_CELLS | This parameter measures the maximum Euclidean distance from any immune cell (specifically cytotoxic T cells, macrophages, fibroblasts excluding those marked as FSP1+, and plasma cells) located in the stromal region to the nearest vessel. It is computed by first determining, for each qualifying immune cell, the minimum distance to any vessel and then taking the highest value among these distances. This normalized numerical measurement, provided in micrometers, facilitates direct comparison across different patient cases and tumor patches. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_median_distance | weighted_median_distance: A spatial metric representing the overall median distance of cell centroids from the epithelial‐stromal boundary, computed by weighting each cell’s distance by the proportion of its cell type among the 14 defined types. This parameter enables comparison across patient cases by accounting for cell type distribution. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | TU_median_distance | TU_median_distance: The median distance from the epithelial‐stromal boundary for epithelial (tumor) cells. It summarizes the central tendency of their spatial distribution relative to the boundary. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | TU_mean_distance | TU_mean_distance: The average distance calculated for epithelial (tumor) cells from the epithelial‐stromal boundary, offering an overall measure of their proximity. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | TU_min_distance | TU_min_distance: The smallest observed distance from the epithelial‐stromal boundary among epithelial (tumor) cells, indicating the closest cellular proximity in the tumor compartment. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | TU_max_distance | TU_max_distance: The largest distance from the epithelial‐stromal boundary among epithelial (tumor) cells, reflecting the extent of spatial dispersion within this cell type. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | TU_proportion | TU_proportion: The normalized fraction of epithelial (tumor) cells among all 14 cell types present in the analyzed patch, enabling relative comparison across cases. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Tc_median_distance | Tc_median_distance: The median distance from the epithelial‐stromal boundary for cytotoxic T cells (Tc). It represents the middle value of their distance distribution. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Tc_mean_distance | Tc_mean_distance: The mean distance of cytotoxic T cells from the epithelial‐stromal boundary, providing an averaged spatial metric for this cell type. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Tc_min_distance | Tc_min_distance: The minimum distance observed among cytotoxic T cells to the epithelial‐stromal boundary, showing the nearest occurrence for these cells. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Tc_max_distance | Tc_max_distance: The maximum distance recorded for cytotoxic T cells from the epithelial‐stromal boundary, indicating the furthest position reached. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Tc_proportion | Tc_proportion: The normalized proportion of cytotoxic T cells (Tc) relative to the total count of cells from all defined types, used to compare their prevalence between patches. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Th_median_distance | Th_median_distance: The median distance from the epithelial‐stromal boundary for helper T cells (Th), reflecting the central position of their spatial distribution. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Th_mean_distance | Th_mean_distance: The average distance from the epithelial‐stromal boundary calculated for helper T cells, capturing overall spatial positioning. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Th_min_distance | Th_min_distance: The smallest distance from the epithelial‐stromal boundary among helper T cells, indicating the closest proximity among these cells. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Th_max_distance | Th_max_distance: The largest distance measured from the epithelial‐stromal boundary for helper T cells, representing the range of their spatial dispersion. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Th_proportion | Th_proportion: The normalized fraction of helper T cells (Th) within the analyzed patch, allowing comparisons of their relative abundance across patient cases. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Treg_median_distance | Treg_median_distance: The median distance from the epithelial‐stromal boundary for regulatory T cells (Treg), summarizing the midpoint of their distance values. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Treg_mean_distance | Treg_mean_distance: The average distance of regulatory T cells from the epithelial‐stromal boundary, providing a summary measure of their spatial location. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Treg_min_distance | Treg_min_distance: The minimum distance among regulatory T cells to the epithelial‐stromal boundary, showing the closest these cells reach to the boundary. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Treg_max_distance | Treg_max_distance: The maximum distance for regulatory T cells from the epithelial‐stromal boundary, reflecting the furthest location within this cell subset. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Treg_proportion | Treg_proportion: The normalized proportion of regulatory T cells (Treg) relative to all cells of the 14 types, ensuring comparability between samples. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | B_median_distance | B_median_distance: The median distance from the epithelial‐stromal boundary for B cells, indicating the central tendency of their spatial positioning. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | B_mean_distance | B_mean_distance: The mean distance from the epithelial‐stromal boundary for B cells, serving as an overall indicator of their location relative to the boundary. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | B_min_distance | B_min_distance: The smallest distance recorded for B cells from the epithelial‐stromal boundary, demonstrating the closest occurrence among them. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | B_max_distance | B_max_distance: The largest distance measured for B cells from the epithelial‐stromal boundary, highlighting the extent of their spread. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | B_proportion | B_proportion: The normalized fraction of B cells within the total cellular composition of the patch, used to compare their relative density across cases. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | P_median_distance | P_median_distance: The median distance from the epithelial‐stromal boundary for plasma cells, summarizing their typical distance value. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | P_mean_distance | P_mean_distance: The average distance for plasma cells relative to the epithelial‐stromal boundary, offering an overall measure of their spatial distribution. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | P_min_distance | P_min_distance: The minimum distance among plasma cells to the epithelial‐stromal boundary, indicating the closest proximity observed. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | P_max_distance | P_max_distance: The maximum distance from the epithelial‐stromal boundary for plasma cells, reflecting the upper bound of their spatial range. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | P_proportion | P_proportion: The normalized proportion of plasma cells in the patch, allowing for direct comparisons of their prevalence among patient cases. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | M_median_distance | M_median_distance: The median distance from the epithelial‐stromal boundary for macrophages, representing the midpoint of their spatial distance distribution. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | M_mean_distance | M_mean_distance: The average distance calculated for macrophages from the epithelial‐stromal boundary, summarizing their overall spatial placement. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | M_min_distance | M_min_distance: The smallest distance recorded for macrophages to the epithelial‐stromal boundary, reflecting the minimum proximity in this cell type. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | M_max_distance | M_max_distance: The largest distance measured for macrophages from the epithelial‐stromal boundary, indicating the maximum extent of their spatial dispersion. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | M_proportion | M_proportion: The normalized fraction of macrophages among all measured cells, providing insight into their relative abundance across different patches. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | G_median_distance | G_median_distance: The median distance from the epithelial‐stromal boundary for granulocytes, reflecting the central value of their distance measurements. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | G_mean_distance | G_mean_distance: The average distance of granulocytes from the epithelial‐stromal boundary, serving as an overall spatial indicator. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | G_min_distance | G_min_distance: The minimum distance observed for granulocytes to the epithelial‐stromal boundary, indicating the closest cell occurrence. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | G_max_distance | G_max_distance: The maximum distance for granulocytes from the epithelial‐stromal boundary, illustrating the furthest extent reached. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | G_proportion | G_proportion: The normalized proportion of granulocytes relative to the total cell count in the patch, enabling comparison across samples. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MFp_median_distance | MFp_median_distance: The median distance from the epithelial‐stromal boundary for PDPN+ myofibroblasts (MFp), representing the middle value of their spatial distances. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MFp_mean_distance | MFp_mean_distance: The average distance for PDPN+ myofibroblasts from the epithelial‐stromal boundary, summarizing their general spatial trend. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MFp_min_distance | MFp_min_distance: The smallest distance recorded for PDPN+ myofibroblasts to the epithelial‐stromal boundary, showing their point of closest approach. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MFp_max_distance | MFp_max_distance: The largest distance measured for PDPN+ myofibroblasts from the epithelial‐stromal boundary, indicating the extent of their dispersion. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MFp_proportion | MFp_proportion: The normalized proportion of PDPN+ myofibroblasts in the patch, providing a relative measure of their abundance. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MF_median_distance | MF_median_distance: The median distance from the epithelial‐stromal boundary for myofibroblasts, representing the central tendency within this cell type. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MF_mean_distance | MF_mean_distance: The average distance for myofibroblasts relative to the epithelial‐stromal boundary, reflecting an overall spatial metric. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MF_min_distance | MF_min_distance: The minimum distance among myofibroblasts to the epithelial‐stromal boundary, indicating the closest measured position. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MF_max_distance | MF_max_distance: The maximum distance recorded for myofibroblasts from the epithelial‐stromal boundary, showing the furthest spatial extent. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MF_proportion | MF_proportion: The normalized fraction of myofibroblasts in relation to the full set of cell types, used for comparative analysis. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Ff_median_distance | Ff_median_distance: The median distance from the epithelial‐stromal boundary for FSP1+ fibroblasts (Ff), capturing the midpoint of their distance distribution. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Ff_mean_distance | Ff_mean_distance: The average distance for FSP1+ fibroblasts from the epithelial‐stromal boundary, summarizing their central spatial tendency. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Ff_min_distance | Ff_min_distance: The smallest distance observed for FSP1+ fibroblasts from the epithelial‐stromal boundary, reflecting the nearest occurrence. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Ff_max_distance | Ff_max_distance: The largest distance measured for FSP1+ fibroblasts from the epithelial‐stromal boundary, demonstrating the maximum spread. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Ff_proportion | Ff_proportion: The normalized proportion of FSP1+ fibroblasts in the analyzed patch, allowing for comparisons of their relative representation. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | F_median_distance | F_median_distance: The median distance from the epithelial‐stromal boundary for fibroblasts, indicating the central value of their spatial distribution. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | F_mean_distance | F_mean_distance: The average distance for fibroblasts from the epithelial‐stromal boundary, providing an overall measure of their location. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | F_min_distance | F_min_distance: The minimum distance recorded for fibroblasts to the epithelial‐stromal boundary, marking the closest approach among these cells. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | F_max_distance | F_max_distance: The maximum distance measured for fibroblasts from the epithelial‐stromal boundary, representing the furthest spatial extent. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | F_proportion | F_proportion: The normalized fraction of fibroblasts among all cells from the patch, reflecting their prevalence in a standardized manner. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | E_median_distance | E_median_distance: The median distance from the epithelial‐stromal boundary for endothelial cells, summarizing the central tendency of their spatial distribution. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | E_mean_distance | E_mean_distance: The average distance for endothelial cells from the epithelial‐stromal boundary, offering an overall spatial metric. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | E_min_distance | E_min_distance: The minimum distance observed for endothelial cells to the epithelial‐stromal boundary, indicating the point of closest proximity. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | E_max_distance | E_max_distance: The maximum distance recorded for endothelial cells from the epithelial‐stromal boundary, reflecting the highest measured distance. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | E_proportion | E_proportion: The normalized proportion of endothelial cells in the patch relative to the total cell population, enabling standardized comparisons. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | A_median_distance | A_median_distance: The median distance from the epithelial‐stromal boundary for antigen presenting cells, depicting the midpoint of their spatial distribution. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | A_mean_distance | A_mean_distance: The average distance for antigen presenting cells from the epithelial‐stromal boundary, summarizing their overall spatial position. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | A_min_distance | A_min_distance: The smallest distance observed for antigen presenting cells to the epithelial‐stromal boundary, indicating their closest proximity. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | A_max_distance | A_max_distance: The maximum distance for antigen presenting cells from the epithelial‐stromal boundary, demonstrating the furthest extent encountered. |
| i3ew4evg5a4d | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | A_proportion | A_proportion: The normalized fraction of antigen presenting cells within the patch, facilitating comparisons of their relative abundance across samples. |
| i40fz17riwqc | Tc | MEAN_DISTANCE_TC_TO_VESSEL | MEAN_DISTANCE_TC_TO_VESSEL represents the average Euclidean distance in micrometers from the centroid of each cytotoxic T cell, located within the tumor epithelial compartment, to the nearest blood vessel. This normalized metric provides insight into the typical spatial proximity of immune cells to vascular structures across different tumor patches. |
| i40fz17riwqc | Tc | MIN_DISTANCE_TC_TO_VESSEL | MIN_DISTANCE_TC_TO_VESSEL captures the smallest Euclidean distance in micrometers observed between any cytotoxic T cell in the tumor region and its closest blood vessel. It highlights the nearest instance of immune cell proximity to vasculature, serving as an indicator of potential localized immune infiltration. |
| i40fz17riwqc | Tc | MAX_DISTANCE_TC_TO_VESSEL | MAX_DISTANCE_TC_TO_VESSEL denotes the largest Euclidean distance in micrometers between a cytotoxic T cell and the nearest vessel within a given tumor patch. This measure reflects the furthest distance, which may indicate regions of the tumor with less direct vascular influence. |
| i40fz17riwqc | Tc | MEDIAN_DISTANCE_TC_TO_VESSEL | MEDIAN_DISTANCE_TC_TO_VESSEL indicates the middle value in the distribution of Euclidean distances (in micrometers) from cytotoxic T cells to their nearest vessels. This robust statistic is less affected by outliers and provides a balanced summary of the overall spatial relationship. |
| i5akwm0xbjyn | Th | PROPORTION_ADJACENT_TH_CELLS | The parameter 'PROPORTION_ADJACENT_TH_CELLS' measures the ratio of helper T lymphocytes in the stromal compartment that are directly adjacent to blood vessels (within a 5 µm radius) relative to the total number of helper T cells in the stroma. This normalized value enables comparison across different patient cases by accounting for variations in cell counts. |
| i7iw39qcjcbs | Tc | TC_STROMA_ECCENTRICITY_MEAN | TC_STROMA_ECCENTRICITY_MEAN represents the average nuclear eccentricity of cytotoxic T lymphocytes (CD8+ T cells) in the stroma. It is derived from shape analysis that measures how much the cell nucleus deviates from a circular shape, making it a normalized metric useful for comparing different tumor patches. |
| i7iw39qcjcbs | Tc | TC_STROMA_ECCENTRICITY_STD | TC_STROMA_ECCENTRICITY_STD is the standard deviation of the nuclear eccentricity values of CD8+ T cells in the stromal compartment. It quantifies the variability or dispersion of the eccentricity measurements around the mean, reflecting heterogeneity in nuclear shape. |
| i7iw39qcjcbs | Tc | TC_STROMA_ECCENTRICITY_CV | TC_STROMA_ECCENTRICITY_CV is the coefficient of variation of the nuclear eccentricity. Calculated as the standard deviation divided by the mean (with an added small constant for numerical stability), it provides a normalized measure of variability, allowing for comparison across different patient cases. |
| i7iw39qcjcbs | Tc | TC_STROMA_ECCENTRICITY_MIN | TC_STROMA_ECCENTRICITY_MIN indicates the minimum observed nuclear eccentricity among stromal CD8+ T cells, identifying the cell with the most circular nucleus within the assessed region. |
| i7iw39qcjcbs | Tc | TC_STROMA_ECCENTRICITY_MAX | TC_STROMA_ECCENTRICITY_MAX captures the maximum nuclear eccentricity value among the stromal cytotoxic T lymphocytes, highlighting the cell with the most elongated nucleus in the analysis. |
| i7iw39qcjcbs | Tc | TC_STROMA_ECCENTRICITY_MEDIAN | TC_STROMA_ECCENTRICITY_MEDIAN represents the median value of the nuclear eccentricity distribution for CD8+ T cells in the stroma, serving as a central tendency measure that is less affected by outliers. |
| i7iw39qcjcbs | Tc | TC_STROMA_ECCENTRICITY_Q1 | TC_STROMA_ECCENTRICITY_Q1 is the first quartile (25th percentile) of the nuclear eccentricity values, showing the lower range of the distribution of nuclear shapes in the stromal compartment. |
| i7iw39qcjcbs | Tc | TC_STROMA_ECCENTRICITY_Q3 | TC_STROMA_ECCENTRICITY_Q3 is the third quartile (75th percentile) of the eccentricity measurements, reflecting the upper end of the distribution of stromal cytotoxic T cell nuclear shapes. |
| i7iw39qcjcbs | Tc | TC_STROMA_ECCENTRICITY_IQR | TC_STROMA_ECCENTRICITY_IQR is the interquartile range of the nuclear eccentricity values, computed as the difference between the third and first quartiles. It provides insight into the spread of the middle 50% of the eccentricity data, indicating the extent of variability in nuclear shape. |
| igq39hf3xz2c | P,M,Treg,Ff,MFp,TU | PLASMA_MEAN_NUCLEUS_AREA | PLASMA_MEAN_NUCLEUS_AREA represents the average nucleus area for plasma cells. It is calculated by measuring the nucleus area for each plasma cell in a tumor patch and then computing the mean, allowing for the assessment of typical nuclear size in this cell type. |
| igq39hf3xz2c | P,M,Treg,Ff,MFp,TU | MACROPHAGE_MEAN_NUCLEUS_AREA | MACROPHAGE_MEAN_NUCLEUS_AREA indicates the average nucleus area for macrophages. It is derived by averaging the nucleus areas of all macrophages identified in a tumor region, which can be used to compare cell characteristics between patient cases. |
| igq39hf3xz2c | P,M,Treg,Ff,MFp,TU | TREG_MEAN_NUCLEUS_AREA | TREG_MEAN_NUCLEUS_AREA measures the average nucleus area for T regulatory cells. This parameter is obtained by averaging the measured nucleus areas for these cells, providing a normalized metric for comparing immune cell states. |
| igq39hf3xz2c | P,M,Treg,Ff,MFp,TU | FSP1_FIBROBLAST_MEAN_NUCLEUS_AREA | FSP1_FIBROBLAST_MEAN_NUCLEUS_AREA represents the average nucleus area for FSP1-positive fibroblasts. The value is computed as the mean of the nucleus areas from the relevant cells within a tumor patch, reflecting typical nuclear size. |
| igq39hf3xz2c | P,M,Treg,Ff,MFp,TU | PDPN_MYOFIBROBLAST_MEAN_NUCLEUS_AREA | PDPN_MYOFIBROBLAST_MEAN_NUCLEUS_AREA captures the average nucleus area for PDPN-positive myofibroblasts. It is calculated by determining the mean nucleus area for these cells, serving as a normalized indicator of nuclear size in this cell type. |
| igq39hf3xz2c | P,M,Treg,Ff,MFp,TU | TUMOR_MEAN_NUCLEUS_AREA | TUMOR_MEAN_NUCLEUS_AREA represents the mean nucleus area for tumor cells (epithelial cells). This parameter provides a normalized measurement of the typical nucleus size among tumor cells across different patches. |
| igq39hf3xz2c | P,M,Treg,Ff,MFp,TU | COMPOSITE_NUCLEUS_SIZE_VARIATION_INDEX | COMPOSITE_NUCLEUS_SIZE_VARIATION_INDEX is a normalized index that quantifies the variation in nucleus sizes across different cell types. It is calculated by taking the difference between the maximum and minimum mean nucleus areas among the cell types and dividing this value by the overall mean. This composite metric facilitates comparison of nucleus size heterogeneity between different tumor patches. |
| ikxnxd6yqd1j | Tc,MF | MEDIAN_TC_TO_MF_DISTANCE | MEDIAN_TC_TO_MF_DISTANCE represents the median of the shortest Euclidean distances measured from non-vessel-adjacent cytotoxic T cells to their nearest PDPN- myofibroblast within the stromal compartment. This metric is normalized across patches, allowing for direct comparisons between different patient cases and tumor regions. |
| ikxnxd6yqd1j | Tc,MF | PERCENT_NON_VESSEL_TC | PERCENT_NON_VESSEL_TC indicates the proportion of cytotoxic T cells that are not adjacent to vessels (i.e., those with a vessel distance greater than the specified threshold) as a percentage of the total number of cytotoxic T cells in the stroma. Being a ratio, it is normalized and suitable for inter-case comparisons. |
| il97k6kale5j | B | MEAN_NUCLEUS_CURVATURE_B_CELLS_STROMA | This parameter quantifies the average curvature along the nuclear boundaries of B lymphocytes located in the stromal compartments of breast cancer tissues. It is computed by first isolating B cells in the stroma, then extracting the boundary coordinates of each B cell nucleus. For each nucleus, a discrete curvature is calculated at each boundary point based on the angles between consecutive segments along the polygon, and an average curvature is derived for the cell. Finally, these cell-level curvature values are aggregated across all B cells to yield a single normalized metric that facilitates comparison across different patient cases and tumor patches. |
| iq1c3dwg7fcm | TU,MFp,Ff,G | TU_dominant_freq_x | TU_dominant_freq_x: This parameter measures the x-component of the dominant spatial frequency for tumor cells. It is derived from the Fourier analysis of a 2D cell density grid, quantifying the periodicity of tumor cell clustering along the x-axis in a normalized manner. |
| iq1c3dwg7fcm | TU,MFp,Ff,G | TU_dominant_freq_y | TU_dominant_freq_y: This parameter captures the y-component of the dominant spatial frequency for tumor cells, indicating the periodic pattern of cell organization along the y-axis based on a normalized Fourier transformation. |
| iq1c3dwg7fcm | TU,MFp,Ff,G | TU_dominant_amplitude | TU_dominant_amplitude: This numeric value represents the strength (amplitude) of the dominant frequency component in the tumor cell spatial distribution, reflecting the intensity of the periodic clustering pattern. |
| iq1c3dwg7fcm | TU,MFp,Ff,G | TU_secondary_freq_x | TU_secondary_freq_x: This parameter represents the x-component of the secondary (second highest) spatial frequency identified in the tumor cell distribution, providing additional insight into periodic patterns beyond the primary clustering. |
| iq1c3dwg7fcm | TU,MFp,Ff,G | TU_secondary_freq_y | TU_secondary_freq_y: This parameter quantifies the y-component of the secondary spatial frequency for tumor cells, offering a normalized measure of alternative periodic organization along the y-axis. |
| iq1c3dwg7fcm | TU,MFp,Ff,G | TU_secondary_amplitude | TU_secondary_amplitude: This measure denotes the amplitude corresponding to the secondary frequency component in the tumor cell clustering, indicating the relative strength of this secondary periodic pattern. |
| iq1c3dwg7fcm | TU,MFp,Ff,G | TU_spatial_periodicity | TU_spatial_periodicity: This parameter estimates the characteristic spatial periodicity (or distance) between tumor cell clusters. It converts the frequency domain measurements into a spatial metric, normalized by the image dimensions. |
| iq1c3dwg7fcm | TU,MFp,Ff,G | MFp_dominant_freq_x | MFp_dominant_freq_x: This parameter measures the x-component of the dominant spatial frequency for PDPN+ myofibroblasts, derived from Fourier analysis of the corresponding cell density distribution on a normalized grid. |
| iq1c3dwg7fcm | TU,MFp,Ff,G | MFp_dominant_freq_y | MFp_dominant_freq_y: This parameter captures the y-component of the dominant spatial frequency for PDPN+ myofibroblasts, indicating the direction and extent of their periodic clustering. |
| iq1c3dwg7fcm | TU,MFp,Ff,G | MFp_dominant_amplitude | MFp_dominant_amplitude: This numeric value reflects the intensity or strength of the dominant frequency pattern in the distribution of PDPN+ myofibroblasts, normalized across samples. |
| iq1c3dwg7fcm | TU,MFp,Ff,G | MFp_secondary_freq_x | MFp_secondary_freq_x: This measurement captures the x-component of the secondary spatial frequency for PDPN+ myofibroblasts, revealing additional periodic grouping patterns apart from the primary cluster. |
| iq1c3dwg7fcm | TU,MFp,Ff,G | MFp_secondary_freq_y | MFp_secondary_freq_y: This parameter represents the y-component of the secondary spatial frequency for PDPN+ myofibroblasts based on normalized Fourier spectrum analysis. |
| iq1c3dwg7fcm | TU,MFp,Ff,G | MFp_secondary_amplitude | MFp_secondary_amplitude: This value indicates the amplitude of the secondary frequency component in the spatial analysis of PDPN+ myofibroblast clustering, serving as a normalized measure of secondary periodicity. |
| iq1c3dwg7fcm | TU,MFp,Ff,G | MFp_spatial_periodicity | MFp_spatial_periodicity: This parameter estimates the distance metric (in micrometers) between clusters of PDPN+ myofibroblasts by converting frequency domain information into spatial periodicity, normalized by image dimensions. |
| iq1c3dwg7fcm | TU,MFp,Ff,G | Ff_dominant_freq_x | Ff_dominant_freq_x: This parameter represents the x-component of the dominant spatial frequency for fibroblasts FSP1+, derived from analysis of the cell density histogram using Fourier transformation to quantify periodic clustering along the x-axis. |
| iq1c3dwg7fcm | TU,MFp,Ff,G | Ff_dominant_freq_y | Ff_dominant_freq_y: This parameter measures the y-component of the dominant spatial frequency for fibroblasts FSP1+, reflecting the periodic spatial organization along the y-axis in a normalized manner. |
| iq1c3dwg7fcm | TU,MFp,Ff,G | Ff_dominant_amplitude | Ff_dominant_amplitude: This numeric parameter denotes the strength of the dominant frequency component for fibroblasts FSP1+, providing a measure of the intensity of their periodic clustering. |
| iq1c3dwg7fcm | TU,MFp,Ff,G | Ff_secondary_freq_x | Ff_secondary_freq_x: This parameter quantifies the x-component of the secondary spatial frequency for fibroblasts FSP1+, indicating an alternative periodic pattern in their spatial distribution. |
| iq1c3dwg7fcm | TU,MFp,Ff,G | Ff_secondary_freq_y | Ff_secondary_freq_y: This parameter captures the y-component of the secondary spatial frequency for fibroblasts FSP1+, offering complementary information to the primary clustering frequency along the y-axis. |
| iq1c3dwg7fcm | TU,MFp,Ff,G | Ff_secondary_amplitude | Ff_secondary_amplitude: This value represents the amplitude associated with the secondary frequency component for fibroblasts FSP1+, which serves as a normalized indicator of secondary pattern strength in their spatial organization. |
| iq1c3dwg7fcm | TU,MFp,Ff,G | Ff_spatial_periodicity | Ff_spatial_periodicity: This parameter estimates the characteristic distance between clusters of fibroblasts FSP1+ by converting the relative frequency measures into a spatial periodicity metric, normalized based on the imaging dimensions. |
| ix3ty67c12g6 | TU,F,M,P | CELL_ADJACENCY_RATIO | CELL_ADJACENCY_RATIO represents the proportion of cell adjacency events where a tumor cell is adjacent to a fibroblast, macrophage, or plasma cell relative to the total number of adjacency events observed among the four selected cell types. This normalized metric allows for comparisons across different tumor patches or patient samples by removing the influence of absolute cell counts. |
| ix3ty67c12g6 | TU,F,M,P | TUMOR_FIBROBLAST_RATIO | TUMOR_FIBROBLAST_RATIO measures the fraction of tumor-fibroblast adjacency events relative to the overall cell adjacency events among tumor cells, fibroblasts, macrophages, and plasma cells. By providing a ratio, it normalizes the interaction between tumor cells and fibroblasts, ensuring that comparisons across different cases reflect relative differences rather than raw event counts. |
| ix3ty67c12g6 | TU,F,M,P | TUMOR_MACROPHAGE_RATIO | TUMOR_MACROPHAGE_RATIO quantifies the proportion of tumor-macrophage adjacency events relative to the total cell adjacency events among the selected cell types. As a normalized parameter, it allows for the effective comparison of the extent of tumor-macrophage interactions across various patches or patient cases. |
| iy7w7eacconi | TU,Treg,F,MFp,G | mean_directionality_index | mean_directionality_index: This parameter represents the overall average of directional correlation indices calculated per vessel. It is derived by computing the cosine similarities between normalized infiltration vectors of selected cell types and then averaging these values over all regions, yielding a unitless index that reflects the degree of directional alignment among the cell types. |
| iy7w7eacconi | TU,Treg,F,MFp,G | mean_TU_Treg_correlation | mean_TU_Treg_correlation: This parameter is the average cosine similarity between the normalized infiltration vectors of tumor cells (TU) and regulatory T cells (Treg) computed across all vessels, quantifying the extent of directional agreement between these two cell types. |
| iy7w7eacconi | TU,Treg,F,MFp,G | mean_TU_F_correlation | mean_TU_F_correlation: This parameter measures the mean pairwise cosine similarity between the normalized infiltration vectors of tumor cells (TU) and fibroblasts (F). It reflects how consistently these cell types infiltrate in similar directions in the tissue microenvironment. |
| iy7w7eacconi | TU,Treg,F,MFp,G | mean_TU_MFp_correlation | mean_TU_MFp_correlation: This parameter represents the average cosine similarity between the normalized infiltration vectors of tumor cells (TU) and PDPN+ myofibroblasts (MFp) over all regions, indicating the degree of directional concordance between their infiltration patterns. |
| iy7w7eacconi | TU,Treg,F,MFp,G | mean_TU_G_correlation | mean_TU_G_correlation: This parameter calculates the mean cosine similarity between the normalized infiltration vectors of tumor cells (TU) and granulocytes (G). It provides a normalized measure of the directional alignment between these cell types across all analyzed regions. |
| iy7w7eacconi | TU,Treg,F,MFp,G | mean_Treg_F_correlation | mean_Treg_F_correlation: This parameter reflects the average pairwise cosine similarity between the normalized infiltration vectors of regulatory T cells (Treg) and fibroblasts (F) computed across all vessels, indicating the consistency of their directional infiltration. |
| iy7w7eacconi | TU,Treg,F,MFp,G | mean_Treg_MFp_correlation | mean_Treg_MFp_correlation: This parameter is the mean cosine similarity between the normalized infiltration vectors of regulatory T cells (Treg) and PDPN+ myofibroblasts (MFp). It serves as a normalized metric to assess the directional correlation between these two cell types. |
| iy7w7eacconi | TU,Treg,F,MFp,G | mean_F_MFp_correlation | mean_F_MFp_correlation: This parameter represents the averaged cosine similarity between the normalized infiltration vectors of fibroblasts (F) and PDPN+ myofibroblasts (MFp) across all regions, quantifying the degree of directional coordination between them. |
| iy7w7eacconi | TU,Treg,F,MFp,G | mean_F_G_correlation | mean_F_G_correlation: This parameter quantifies the average cosine similarity between the normalized infiltration vectors of fibroblasts (F) and granulocytes (G) computed over all vessels. It acts as a normalized measure of their directional relationship. |
| iy7w7eacconi | TU,Treg,F,MFp,G | mean_MFp_G_correlation | mean_MFp_G_correlation: This parameter provides the mean cosine similarity between the normalized infiltration vectors of PDPN+ myofibroblasts (MFp) and granulocytes (G) across all analyzed regions, reflecting the degree of directional alignment between these cell types. |
| j8nej8q32pvt | M | PROPORTION_MACROPHAGES_NEAR_VESSELS | PROPORTION_MACROPHAGES_NEAR_VESSELS represents the fraction of macrophages located within a 50 µm radius of any vessel polygon relative to the total number of macrophages. This parameter is normalized, meaning it offers a comparative metric across different tumor patches and patient cases by expressing the value as a ratio between 0 and 1. |
| jfbp5inj5mid | Tc,Th,Ff,MFp | CYTOTOXIC_TO_HELPER_RATIO | This parameter represents the normalized ratio of cytotoxic T cells (CD8+) to helper T cells (CD4+) within regions of interest surrounding fibroblast FSP1+ and myofibroblast PDPN+ areas. It is calculated by dividing the count of cytotoxic T cells by the count of helper T cells present within these ROIs, providing a comparative metric that normalizes differences between patient cases. The ratio is set to 0 if no helper T cells are detected, ensuring robustness against division by zero. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | TU_weighted_deformation_score | TU_weighted_deformation_score: Numeric value representing the tumor cell weighted deformation score, calculated as the product of the mean cell deformation (aggregate deviation) for tumor cells and their prevalence within the analyzed tissue patch, thereby normalizing the deformation measure across different cases. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Tc_weighted_deformation_score | Tc_weighted_deformation_score: Numeric value representing the weighted deformation score for CD8+ T cells. This score is derived from the average deviation of the cell positions relative to an ideal hexagonal packing arrangement, multiplied by the fraction of CD8+ T cells in the tissue patch, ensuring normalization for comparative analysis. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Th_weighted_deformation_score | Th_weighted_deformation_score: Numeric parameter measuring the weighted deformation for CD4+ T cells. It is computed by multiplying the aggregate deformation score for these cells by their prevalence in the analyzed region, providing a normalized measure of tissue disruption. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Treg_weighted_deformation_score | Treg_weighted_deformation_score: This parameter is a numeric score representing the weighted deformation for T regulatory cells. It is obtained by combining the mean angular and spacing deviations specific to T regulatory cells with their relative abundance in the sample, allowing for normalized comparison across patient cases. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | B_weighted_deformation_score | B_weighted_deformation_score: Numeric value measuring the weighted deformation for B cells. It results from the product of the average deviation score for B cells and their proportion in the tissue, ensuring a normalized metric for tissue analysis. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | P_weighted_deformation_score | P_weighted_deformation_score: A numeric parameter that represents the weighted deformation score for plasma cells. It is calculated by multiplying the mean deformation (aggregate deviation) of plasma cells by their prevalence in the tissue patch, offering a normalized assessment. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | M_weighted_deformation_score | M_weighted_deformation_score: Numeric score for macrophages that quantifies the weighted tissue deformation. It is determined as the product of the macrophage aggregate deformation score and their normalized prevalence within the region. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | G_weighted_deformation_score | G_weighted_deformation_score: This is a numeric value that reflects the weighted deformation for granulocytes. It is computed by multiplying the average deformation score for granulocytes by their fraction among all cells, ensuring the measure is normalized. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MFp_weighted_deformation_score | MFp_weighted_deformation_score: Numeric score representing the weighted deformation for PDPN+ myofibroblasts. Calculated by combining the aggregate (mean) deformation score of these cells with their prevalence, this parameter is normalized for inter-case comparisons. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MF_weighted_deformation_score | MF_weighted_deformation_score: A normalized numeric parameter that measures the weighted deformation for myofibroblasts. It is derived by multiplying the average deviation score of myofibroblasts by their proportion in the tissue sample. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Ff_weighted_deformation_score | Ff_weighted_deformation_score: Numeric value that measures the weighted deformation for FSP1+ fibroblasts. It is computed as the product of the aggregate deformation score and the prevalence of these specific fibroblasts within the tissue patch. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | F_weighted_deformation_score | F_weighted_deformation_score: This numeric parameter represents the weighted deformation score for fibroblasts. It is calculated by multiplying the mean deformation score of fibroblasts by their normalized prevalence, providing a standardized metric. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | E_weighted_deformation_score | E_weighted_deformation_score: A numeric metric that reflects the weighted tissue deformation for endothelial cells. It is obtained by multiplying the aggregate deviation score for these cells by their fraction of the total cells, ensuring normalization. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | A_weighted_deformation_score | A_weighted_deformation_score: Numeric parameter representing the weighted deformation for antigen presenting cells. It is computed as the product of the average cell deformation score for these cells and their prevalence in the region, resulting in a normalized measurement. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | composite_deformation_score | composite_deformation_score: Overall numeric score for the entire tissue patch that represents the sum of all weighted deformation scores computed across the 14 cell types. It provides a consolidated, normalized measure of tissue disruption relative to an ideal cell packing model. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | TU_aggregate_deformation_score | TU_aggregate_deformation_score: Numeric and normalized mean deviation score for tumor cells, calculated as the average of the combined angular and spacing deviations each cell exhibits from the ideal hexagonal arrangement. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Tc_aggregate_deformation_score | Tc_aggregate_deformation_score: This parameter is a numeric value representing the mean deformation score for CD8+ T cells. It is derived by averaging the deviation measures (from both angular and spacing differences) for cells of this type, ensuring normalization. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Th_aggregate_deformation_score | Th_aggregate_deformation_score: A numeric measure of the average deformation score for CD4+ T cells, computed by taking the mean of the combined deviation values, which allows for normalized assessment across samples. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Treg_aggregate_deformation_score | Treg_aggregate_deformation_score: Numeric parameter representing the mean deviation score for T regulatory cells. It is calculated by averaging the measured deviations from an ideal packing configuration, yielding a normalized metric. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | B_aggregate_deformation_score | B_aggregate_deformation_score: This numeric parameter reflects the average deformation score for B cells, which is obtained by computing the mean of the deviation scores regarding angular and spacing differences from an ideal pattern. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | P_aggregate_deformation_score | P_aggregate_deformation_score: Numeric measure of the mean deformation for plasma cells calculated by averaging combined deviations in angular orientation and spacing relative to an ideal hexagonal configuration. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | M_aggregate_deformation_score | M_aggregate_deformation_score: Numeric parameter representing the mean deviation score for macrophages, derived by averaging the individual cell deformation scores, thus providing a normalized aggregate measure. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | G_aggregate_deformation_score | G_aggregate_deformation_score: A numeric value indicating the average deformation score for granulocytes, calculated as the mean of all individual cell deviation scores from the ideal arrangement. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MFp_aggregate_deformation_score | MFp_aggregate_deformation_score: Numeric parameter for the mean deformation score of PDPN+ myofibroblasts, derived by averaging the combined deviations of these cells relative to an ideal hexagonal packing model. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MF_aggregate_deformation_score | MF_aggregate_deformation_score: This numeric value represents the mean deformation score for myofibroblasts, computed as the average of the deviation scores reflecting differences in angular and spacing parameters. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Ff_aggregate_deformation_score | Ff_aggregate_deformation_score: Numeric measure of the average deformation score for FSP1+ fibroblasts, calculated as the mean of their individual cell deviations from an ideal cell-organizing pattern. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | F_aggregate_deformation_score | F_aggregate_deformation_score: Numeric parameter reflecting the mean deviation score for fibroblasts, obtained by computing the average of their combined angular and spacing deviations. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | E_aggregate_deformation_score | E_aggregate_deformation_score: This normalized numeric value indicates the mean deformation score for endothelial cells, derived from averaging the computed deviations of individual cells. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | A_aggregate_deformation_score | A_aggregate_deformation_score: Numeric parameter representing the average deformation score for antigen presenting cells, calculated as the mean of the combined deviation measurements relative to an ideal configuration. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | TU_prevalence | TU_prevalence: A numeric fraction that represents the proportion of tumor cells relative to the total cell count in a tissue patch, allowing for normalized comparison between different patient cases. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Tc_prevalence | Tc_prevalence: Numeric value indicating the fraction of CD8+ T cells in the tissue, computed as the ratio of these cells to the total number of cells in the analyzed patch. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Th_prevalence | Th_prevalence: Numeric parameter that reflects the proportion of CD4+ T cells within the tissue patch, expressed as a fraction of the overall cell population. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Treg_prevalence | Treg_prevalence: A numeric ratio indicating the prevalence of T regulatory cells, measured as the fraction of T regulatory cells relative to the total cell count in the tissue region. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | B_prevalence | B_prevalence: Numeric value representing the proportion of B cells in the tissue patch, calculated as the ratio of B cells to the total number of cells. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | P_prevalence | P_prevalence: This numeric parameter reflects the fraction of plasma cells within the tissue patch, normalized by the total cell count. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | M_prevalence | M_prevalence: A normalized numeric value indicating the proportion of macrophages in the tissue, computed as the ratio of macrophages to the total number of cells. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | G_prevalence | G_prevalence: Numeric parameter representing the fraction of granulocytes, indicating their prevalence in the tissue sample as a proportion of all cells. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MFp_prevalence | MFp_prevalence: Numeric value showing the proportion of PDPN+ myofibroblasts in the tissue patch, calculated as a fraction of the overall cell count. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MF_prevalence | MF_prevalence: This numeric parameter represents the fraction of myofibroblasts relative to the total cells, normalized for cross-sample analysis. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Ff_prevalence | Ff_prevalence: Numeric parameter that reflects the proportion of FSP1+ fibroblasts in the tissue patch, expressed as a ratio of the total cell count. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | F_prevalence | F_prevalence: A numeric fraction indicating the prevalence of fibroblasts in the analyzed region, normalized by the overall cell count. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | E_prevalence | E_prevalence: Numeric parameter measuring the proportion of endothelial cells, calculated as the ratio of endothelial cells to the total cell population. |
| jl5tb6agvujt | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | A_prevalence | A_prevalence: This numeric value represents the fraction of antigen presenting cells within the tissue patch, ensuring normalization across different cases. |
| jonic111kekx | M,A,G,MFp,Tc,Treg | MF_T_RATIO | MF_T_RATIO is the normalized ratio obtained by dividing the count of myeloid cells and PDPN+ myofibroblasts in the stromal compartment by the count of cytotoxic and regulatory T cells in the tumor compartment. This metric reflects the balance between immunosuppressive cells and effector T cells, enabling comparisons across different patients or patches. |
| jonic111kekx | M,A,G,MFp,Tc,Treg | MF_T_WEIGHTED_RATIO | MF_T_WEIGHTED_RATIO represents a density-based normalized ratio that divides the density of myeloid cells and PDPN+ myofibroblasts in the stroma by the density of T cells in the tumor. By accounting for the area of each compartment, it provides a standardized measure that is comparable across different patient cases. |
| jonic111kekx | M,A,G,MFp,Tc,Treg | MYELOID_FIBROBLAST_DENSITY | MYELOID_FIBROBLAST_DENSITY measures the density of myeloid cells and PDPN+ myofibroblasts in the stromal compartment. Calculated as the cell count divided by the stroma area, this parameter is normalized for patch size, facilitating reliable comparisons across different samples. |
| jonic111kekx | M,A,G,MFp,Tc,Treg | T_CELL_DENSITY | T_CELL_DENSITY quantifies the density of cytotoxic and regulatory T cells in the tumor compartment by dividing the T cell count by the tumor area. This normalized measure allows for consistent comparison of T cell presence across various patient cases and tissue patches. |
| jwpurc1xc2xt | TU,Tc,Th,Treg,B,P,M,MFp,MF,A | MEAN_COMPACTNESS_TU | MEAN_COMPACTNESS_TU: Represents the average compactness of epithelial (tumor) cells. Compactness is calculated as the square of the cell perimeter divided by its area. This metric is derived from the nuclear outline of each tumor cell and averaged across cells in a patch, providing a normalized numeric measure for comparing different patient cases. |
| jwpurc1xc2xt | TU,Tc,Th,Treg,B,P,M,MFp,MF,A | MEAN_COMPACTNESS_Tc | MEAN_COMPACTNESS_Tc: Represents the average compactness of CD8+ T cells. The measurement is computed using the perimeter squared divided by the area of each cell’s nucleus and subsequently averaged over all CD8+ T cells in a tumor patch. This yields a normalized, numeric value suitable for further analysis. |
| jwpurc1xc2xt | TU,Tc,Th,Treg,B,P,M,MFp,MF,A | MEAN_COMPACTNESS_Th | MEAN_COMPACTNESS_Th: Represents the average compactness of CD4+ T helper cells. It is calculated by taking the square of the perimeter of the cell’s nucleus and dividing it by the area, with the resulting values averaged over the patch, resulting in a normalized and numeric metric. |
| jwpurc1xc2xt | TU,Tc,Th,Treg,B,P,M,MFp,MF,A | MEAN_COMPACTNESS_Treg | MEAN_COMPACTNESS_Treg: Represents the average compactness of regulatory T cells. It is computed by dividing the square of the nucleus perimeter by its area for each cell, and then averaging these values across all T regulatory cells in a specific region to provide a normalized, numeric parameter. |
| jwpurc1xc2xt | TU,Tc,Th,Treg,B,P,M,MFp,MF,A | MEAN_COMPACTNESS_B | MEAN_COMPACTNESS_B: Represents the average compactness of B cells. The compactness metric is derived from the nuclear outline using the perimeter squared divided by the area and is averaged for all B cells in a patch, resulting in a normalized numeric measure. |
| jwpurc1xc2xt | TU,Tc,Th,Treg,B,P,M,MFp,MF,A | MEAN_COMPACTNESS_P | MEAN_COMPACTNESS_P: Represents the average compactness of plasma cells. It is calculated by the same geometric measure (perimeter squared divided by area) for each cell and then averaged over the patch, creating a normalized, numeric parameter for analysis. |
| jwpurc1xc2xt | TU,Tc,Th,Treg,B,P,M,MFp,MF,A | MEAN_COMPACTNESS_M | MEAN_COMPACTNESS_M: Represents the average compactness of macrophages. This parameter is computed by measuring each cell's nuclear compactness (the square of the cell perimeter divided by its area) and averaging these values across the patch, which provides a normalized numeric value. |
| jwpurc1xc2xt | TU,Tc,Th,Treg,B,P,M,MFp,MF,A | MEAN_COMPACTNESS_MFp | MEAN_COMPACTNESS_MFp: Represents the average compactness of PDPN+ myofibroblasts. It is calculated using the geometric formula (perimeter squared divided by area) for each cell and averaged over a patch, yielding a normalized numeric measure for comparative analysis. |
| jwpurc1xc2xt | TU,Tc,Th,Treg,B,P,M,MFp,MF,A | MEAN_COMPACTNESS_MF | MEAN_COMPACTNESS_MF: Represents the average compactness of myofibroblasts. Calculated by dividing the square of the cell perimeter by its area for each cell and averaging these values across a tumor patch, it provides a normalized, numeric parameter. |
| jwpurc1xc2xt | TU,Tc,Th,Treg,B,P,M,MFp,MF,A | MEAN_COMPACTNESS_A | MEAN_COMPACTNESS_A: Represents the average compactness of antigen-presenting cells. This metric is derived by calculating each cell’s nuclear compactness (perimeter squared divided by area) and then averaging these values across the patch, resulting in a normalized numeric measurement. |
| jwt5r6r71f87 | G,Treg,Th,Ff,F,E,TU | G_infiltration_stroma | G_infiltration_stroma measures the density of granulocyte infiltration in the stromal compartment. It is normalized by dividing the granulocyte count in stroma by the tumor cell count, yielding a unitless numeric value that allows comparison across different patient patches. |
| jwt5r6r71f87 | G,Treg,Th,Ff,F,E,TU | Treg_infiltration_stroma | Treg_infiltration_stroma quantifies the level of regulatory T cell infiltration in the stroma. This normalized metric is obtained by dividing the count of regulatory T cells in the stroma by the number of tumor cells, enabling cross-case comparisons. |
| jwt5r6r71f87 | G,Treg,Th,Ff,F,E,TU | Th_infiltration_stroma | Th_infiltration_stroma measures the infiltration of helper T cells in the stromal compartment. It is normalized against the tumor cell count to produce a unitless metric for assessing immune cell density. |
| jwt5r6r71f87 | G,Treg,Th,Ff,F,E,TU | Ff_infiltration_stroma | Ff_infiltration_stroma represents the normalized infiltration of FSP1+ fibroblasts in the stromal region. By dividing their count by the tumor cell count, it provides a comparative measure of fibroblast presence in the stroma. |
| jwt5r6r71f87 | G,Treg,Th,Ff,F,E,TU | F_infiltration_stroma | F_infiltration_stroma quantifies the infiltration of FSP1- fibroblasts in the stroma. This parameter is normalized by the tumor cell count, offering a unitless value that facilitates comparisons across different samples. |
| jwt5r6r71f87 | G,Treg,Th,Ff,F,E,TU | E_infiltration_stroma | E_infiltration_stroma measures the density of endothelial cell infiltration in the stromal compartment. This normalized metric is calculated by dividing the endothelial cell count in stroma by the tumor cell count. |
| jwt5r6r71f87 | G,Treg,Th,Ff,F,E,TU | F_infiltration_epithelium | F_infiltration_epithelium calculates the normalized infiltration of FSP1- fibroblasts in the epithelial (tumor) compartment. It is obtained by dividing the corresponding cell count by the tumor cell count, ensuring comparability between samples. |
| jwt5r6r71f87 | G,Treg,Th,Ff,F,E,TU | F_stroma_to_epithelial_ratio | F_stroma_to_epithelial_ratio provides the ratio of FSP1- fibroblast infiltration between the stromal and epithelial compartments. It is derived by first normalizing the counts of FSP1- fibroblasts in both stroma and epithelium by the tumor cell count, and then computing the ratio of the stromal value to the epithelial value, which reflects the relative distribution of these cells. |
| jzztuucqtke6 | TU,M | AVERAGE_TU_M_DISTANCE_STROMA | AVERAGE_TU_M_DISTANCE_STROMA measures the average Euclidean distance between the centroids of tumor cells and macrophages specifically located in the stromal region of a tumor patch, providing a normalized metric that allows for comparison across different patient cases. It is calculated by identifying the relevant cells in the stroma, computing pairwise distances, and summarizing them using the mean value. |
| jzztuucqtke6 | TU,M | MEDIAN_TU_M_DISTANCE_STROMA | MEDIAN_TU_M_DISTANCE_STROMA measures the median Euclidean distance between the centroids of tumor cells and macrophages in the tumor stroma, offering another normalized spatial metric for comparison across cases. It is determined by computing all pairwise distances between the two cell types within the stromal region and then extracting the median value to represent a robust central tendency of the spatial association. |
| k0qnwr2b90nc | G,A | G_to_APC_Ratio_Perivascular | G_to_APC_Ratio_Perivascular: This parameter represents the normalized ratio of granulocytes to antigen-presenting cells within the perivascular regions. It is computed by dividing the number of granulocytes present by the number of antigen-presenting cells (with an adjustment to prevent division by zero), making it a dimensionless metric that can be compared across different patient cases. |
| k20wipdalr7j | G,M,B,P,E,Treg,Ff | mean_synergy_index | mean_synergy_index represents the average morphological synergy index across all analyzed neighborhoods. The synergy index is calculated as the inverse of the sum of the normalized standard deviations of nuclear area and shape metric, providing a measure of homogeneity in cell morphology. |
| k20wipdalr7j | G,M,B,P,E,Treg,Ff | median_synergy_index | median_synergy_index is the median value of the synergy indices across neighborhoods, offering a robust central tendency that is less influenced by outliers and reflects typical morphological synergy. |
| k20wipdalr7j | G,M,B,P,E,Treg,Ff | max_synergy_index | max_synergy_index reflects the highest observed synergy index among the neighborhoods, denoting the region with the highest degree of morphological homogeneity. |
| k20wipdalr7j | G,M,B,P,E,Treg,Ff | std_synergy_index | std_synergy_index is the standard deviation of the synergy indices across the tissue region, quantifying the variability in morphological synergy from one neighborhood to another. |
| k20wipdalr7j | G,M,B,P,E,Treg,Ff | p25_synergy_index | p25_synergy_index is the 25th percentile of the synergy index distribution, representing the lower bound of typical morphological homogeneity measurements within the patch. |
| k20wipdalr7j | G,M,B,P,E,Treg,Ff | p75_synergy_index | p75_synergy_index is the 75th percentile of the synergy index distribution, capturing the upper range of the typical morphological homogeneity values. |
| k20wipdalr7j | G,M,B,P,E,Treg,Ff | iqr_synergy_index | iqr_synergy_index, the interquartile range (p75 minus p25) of the synergy indices, measures the spread of the middle 50% of values, indicating the variability in local morphological homogeneity across neighborhoods. |
| k6muvcfq17ao | TU,Tc,Th,F,Ff,E,B,P,M,A | simpson_diversity_index | The simpson_diversity_index parameter quantifies the diversity of 10 specific cell types (epithelial cell, t_cell_cd8, t_cell_cd4, fibroblast, fibroblast_fsp1, endothelial cell, b_cell, plasma cell, macrophage, and ap_cell) present in the stromal compartment of tumor patches. It is a normalized metric, taking values between 0 and 1, where a value of 0 indicates no diversity (i.e., one cell type dominating) and a value of 1 indicates a highly balanced distribution of the cell types. This index is computed by first filtering for cells in the stroma, counting occurrences of each cell type, and then applying the Simpson diversity formula. The use of a normalized index allows comparison across different patient cases, as it adjusts for the overall number of cells counted in each patch. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | TU_tumor_roundness | TU_tumor_roundness: This parameter represents the average nuclear roundness for TU cells (epithelial cells) within the tumor compartment. Nuclear roundness is derived from a dimensionless formula based on the cell's area and perimeter, indicating how circular the nucleus is with a perfect circle scoring 1. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | TU_stroma_roundness | TU_stroma_roundness: This parameter indicates the average nuclear roundness for TU cells located in the stroma compartment, calculated using the standardized roundness formula to assess deviations from an ideal circle. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | TU_roundness_gradient | TU_roundness_gradient: This parameter measures the difference between the average nuclear roundness of TU cells in the tumor and stroma compartments. It provides insight into how the nuclear shape transitions across the tumor-stroma boundary. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | TU_tumor_aspect_ratio | TU_tumor_aspect_ratio: This parameter provides the average nuclear aspect ratio for TU cells in the tumor compartment. The aspect ratio, defined as the ratio of the longest side to the shortest side of the nucleus, reflects deviations from a perfect circular shape. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | TU_stroma_aspect_ratio | TU_stroma_aspect_ratio: This parameter captures the average nuclear aspect ratio for TU cells in the stroma compartment, facilitating comparisons of nuclear elongation between compartments. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | TU_aspect_ratio_gradient | TU_aspect_ratio_gradient: This parameter is the difference between the average nuclear aspect ratios of TU cells in the tumor and stroma compartments, highlighting the relative change in nuclear shape. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | Tc_tumor_roundness | Tc_tumor_roundness: This parameter represents the average nuclear roundness for Tc cells (CD8+ T cells) in the tumor compartment, computed using the normalized roundness metric. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | Tc_stroma_roundness | Tc_stroma_roundness: This parameter indicates the average nuclear roundness for Tc cells in the stroma compartment, reflecting cellular shape in a context outside the tumor region. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | Tc_roundness_gradient | Tc_roundness_gradient: This parameter measures the difference in average nuclear roundness for Tc cells between the tumor and stroma compartments, helping to capture compartment-specific morphological changes. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | Tc_tumor_aspect_ratio | Tc_tumor_aspect_ratio: This parameter provides the average nuclear aspect ratio for Tc cells in the tumor compartment, indicating how elongated the nuclei are relative to a circular shape. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | Tc_stroma_aspect_ratio | Tc_stroma_aspect_ratio: This parameter captures the average nuclear aspect ratio for Tc cells in the stroma compartment, using a dimensionless metric for comparative analysis. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | Tc_aspect_ratio_gradient | Tc_aspect_ratio_gradient: This parameter is the difference between the average nuclear aspect ratios for Tc cells in the tumor versus the stroma compartment, quantifying shape shifts across compartments. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | Th_stroma_roundness | Th_stroma_roundness: This parameter indicates the average nuclear roundness for Th cells (CD4+ T cells) in the stroma compartment, computed through a normalized evaluation of nuclear shape. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | Th_stroma_aspect_ratio | Th_stroma_aspect_ratio: This parameter represents the average nuclear aspect ratio for Th cells in the stroma compartment, reflecting the relative elongation of the nuclei. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | Treg_stroma_roundness | Treg_stroma_roundness: This parameter provides the average nuclear roundness for regulatory T cells (Treg) in the stroma compartment, offering insight into their nuclear morphology outside the tumor region. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | Treg_stroma_aspect_ratio | Treg_stroma_aspect_ratio: This parameter captures the average nuclear aspect ratio for Treg cells in the stroma compartment, serving as a comparison metric relative to a perfectly circular nucleus. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | B_stroma_roundness | B_stroma_roundness: This parameter represents the average nuclear roundness for B cells in the stroma compartment, calculated using a dimensionless formula that enables cross-case comparisons. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | B_stroma_aspect_ratio | B_stroma_aspect_ratio: This parameter indicates the average nuclear aspect ratio for B cells in the stroma compartment, reflecting the balance between the longest and shortest dimensions of the nucleus. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | P_stroma_roundness | P_stroma_roundness: This parameter represents the average nuclear roundness for plasma cells in the stroma compartment, providing a normalized measurement of nuclear circularity. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | P_stroma_aspect_ratio | P_stroma_aspect_ratio: This parameter provides the average nuclear aspect ratio for plasma cells in the stroma compartment, which helps in identifying shape variations relative to a circle. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | M_tumor_roundness | M_tumor_roundness: This parameter captures the average nuclear roundness for macrophages (M) in the tumor compartment, derived from a standardized formula to assess nuclear shape. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | M_stroma_roundness | M_stroma_roundness: This parameter represents the average nuclear roundness for macrophages in the stroma compartment, offering a normalized value for morphological assessment. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | M_roundness_gradient | M_roundness_gradient: This parameter quantifies the difference in average nuclear roundness for macrophages between the tumor and stroma compartments, highlighting compartment-specific morphological changes. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | M_tumor_aspect_ratio | M_tumor_aspect_ratio: This parameter provides the average nuclear aspect ratio for macrophages in the tumor compartment, indicating how the nuclei deviate from a circle. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | M_stroma_aspect_ratio | M_stroma_aspect_ratio: This parameter captures the average nuclear aspect ratio for macrophages in the stroma compartment, facilitating comparisons across tissue regions. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | M_aspect_ratio_gradient | M_aspect_ratio_gradient: This parameter is the difference between the average nuclear aspect ratios of macrophages in the tumor and stroma compartments, measuring the variation in nuclear shape between regions. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | MFp_tumor_roundness | MFp_tumor_roundness: This parameter represents the average nuclear roundness for myofibroblast cells (MFp) in the tumor compartment, computed as a normalized measure of nuclear shape. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | MFp_stroma_roundness | MFp_stroma_roundness: This parameter indicates the average nuclear roundness for myofibroblast cells in the stroma compartment, allowing assessment of spatial shape differences. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | MFp_roundness_gradient | MFp_roundness_gradient: This parameter measures the difference in nuclear roundness for myofibroblast cells between the tumor and stroma compartments, capturing the change in shape across boundaries. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | MFp_tumor_aspect_ratio | MFp_tumor_aspect_ratio: This parameter provides the average nuclear aspect ratio for myofibroblast cells in the tumor compartment, reflecting the deviation from an ideal circular shape. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | MFp_stroma_aspect_ratio | MFp_stroma_aspect_ratio: This parameter offers the average nuclear aspect ratio for myofibroblast cells in the stroma compartment, calculated to facilitate inter-compartment comparisons. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | MFp_aspect_ratio_gradient | MFp_aspect_ratio_gradient: This parameter is the difference between the average nuclear aspect ratios for myofibroblast cells in the tumor and stroma compartments, summarizing the morphological gradient. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | Ff_stroma_roundness | Ff_stroma_roundness: This parameter represents the average nuclear roundness for fibroblasts (Ff) in the stroma compartment, derived from a normalized calculation of the cell’s nuclear shape. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | Ff_stroma_aspect_ratio | Ff_stroma_aspect_ratio: This parameter provides the average nuclear aspect ratio for fibroblasts in the stroma compartment, indicating how the nucleus deviates from a perfect circle. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | E_stroma_roundness | E_stroma_roundness: This parameter indicates the average nuclear roundness for endothelial cells (E) in the stroma compartment, measuring how closely the nuclear shape approximates a circle. |
| kdfufu9x63yr | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | E_stroma_aspect_ratio | E_stroma_aspect_ratio: This parameter captures the average nuclear aspect ratio for endothelial cells in the stroma compartment, reflecting the elongation of the nucleus relative to its minimal dimensions. |
| kfe9dxrs3vlk | TU,Tc,Th,Treg,B,G,E,A | TU_fraction | TU_fraction: This parameter represents the normalized average fraction of tumor cells (coded as 'TU') within vessel buffer regions, calculated by dividing the count of tumor cells by the total number of cells identified in those regions and then averaging over all vessels in the patch. |
| kfe9dxrs3vlk | TU,Tc,Th,Treg,B,G,E,A | Tc_fraction | Tc_fraction: This parameter reflects the normalized average fraction of cytotoxic T cells (coded as 'Tc') that fall within vessel-associated regions, providing a measure of CD8+ T cell infiltration normalized to the total number of cells. |
| kfe9dxrs3vlk | TU,Tc,Th,Treg,B,G,E,A | Th_fraction | Th_fraction: This parameter captures the normalized average fraction of CD4+ T helper cells (coded as 'Th') within the vessel buffer regions, offering a quantitative insight into the helper T cell infiltration relative to the overall cellular composition. |
| kfe9dxrs3vlk | TU,Tc,Th,Treg,B,G,E,A | Treg_fraction | Treg_fraction: This parameter indicates the normalized average fraction of regulatory T cells (coded as 'Treg') present in the vessel-associated regions, calculated by the proportion of regulatory T cells among the total cells for each vessel and aggregated across the patch. |
| kfe9dxrs3vlk | TU,Tc,Th,Treg,B,G,E,A | B_fraction | B_fraction: This parameter denotes the normalized average fraction of B cells (coded as 'B') within the vessel buffer regions, computed as the ratio of B cells to the total number of cells and averaged over vessels in the analyzed patch. |
| kfe9dxrs3vlk | TU,Tc,Th,Treg,B,G,E,A | G_fraction | G_fraction: This parameter represents the normalized average fraction of granulocytes (coded as 'G') within vessel-centered analysis regions, providing a measure of granulocyte presence relative to total cell count across vessels. |
| kfe9dxrs3vlk | TU,Tc,Th,Treg,B,G,E,A | E_fraction | E_fraction: This parameter reflects the normalized average fraction of endothelial cells (coded as 'E') within the vessel buffer regions, offering insights into the vascular component by evaluating the proportion of endothelial cells. |
| kfe9dxrs3vlk | TU,Tc,Th,Treg,B,G,E,A | A_fraction | A_fraction: This parameter captures the normalized average fraction of antigen-presenting cells (coded as 'A') within the vessel-associated regions, expressing the activity of antigen presentation in a manner normalized against total cell counts. |
| kfe9dxrs3vlk | TU,Tc,Th,Treg,B,G,E,A | infiltration_score_mean | infiltration_score_mean: This parameter is the average vessel-associated infiltration score computed across all vessels in the patch. The score itself is derived by summing the fractions of immune-promoting cell types and subtracting the sum of suppressive cell types, providing an overall normalized measure of immune infiltration. |
| kfe9dxrs3vlk | TU,Tc,Th,Treg,B,G,E,A | infiltration_score_min | infiltration_score_min: This parameter indicates the minimum vessel-associated infiltration score among all analyzed vessels. It represents the lowest normalized infiltration value observed, highlighting the minimal immune activation or suppression within a vessel region in the patch. |
| kfe9dxrs3vlk | TU,Tc,Th,Treg,B,G,E,A | infiltration_score_max | infiltration_score_max: This parameter denotes the maximum vessel-associated infiltration score observed among all vessels. It serves as a normalized measure of the highest immune infiltration potential in any vessel-containing region within a patch. |
| kfe9dxrs3vlk | TU,Tc,Th,Treg,B,G,E,A | infiltration_score_std | infiltration_score_std: This parameter is the standard deviation of the vessel-associated infiltration scores among vessels. It captures the variability or dispersion of normalized infiltration measurements across the analyzed vessel regions. |
| kgzneu80dcx2 | B,A | MEDIAN_B_APC_DISTANCE_STROMA | MEDIAN_B_APC_DISTANCE_STROMA measures the median Euclidean distance between B cells and antigen-presenting cells (APCs) located in the stromal compartment of tumor tissue patches. It is computed by first identifying B cells and APCs within the stroma, extracting their centroid coordinates, and then calculating all pairwise distances between these cells. The median of these distances is taken as the representative value. This parameter reflects the typical spatial proximity between B cells and APCs, with lower values indicating closer interactions that may enhance effective antigen presentation and immune response. The metric is numeric and normalized to allow for comparison across different patient cases. |
| khecireri5zy | TU,MFp,MF,Tc,Th,Treg | fibroblast_to_tcell_ratio | fibroblast_to_tcell_ratio: A dimensionless ratio representing the relative number of direct contacts between tumor boundary cells and fibroblasts compared to those with T cells. This metric inherently normalizes the raw counts to yield a comparative measure between different patient cases. |
| khecireri5zy | TU,MFp,MF,Tc,Th,Treg | fibroblast_contacts_per_boundary | fibroblast_contacts_per_boundary: A normalized metric obtained by dividing the raw count of fibroblast contacts by the total length of the tumor boundary. This parameter reflects the density of fibroblast interactions per unit boundary length, suitable for cross-patient comparisons. |
| khecireri5zy | TU,MFp,MF,Tc,Th,Treg | t_cell_contacts_per_boundary | t_cell_contacts_per_boundary: A normalized measure calculated by dividing the T cell contact count by the tumor boundary length, providing an assessment of T cell interaction density per unit boundary and allowing normalization across different tumor patches. |
| khecireri5zy | TU,MFp,MF,Tc,Th,Treg | fibroblast_to_tcell_ratio_normalized | fibroblast_to_tcell_ratio_normalized: A normalized ratio that adjusts the fibroblast-to-T cell contact ratio by the total tumor boundary length, offering a measure that compensates for differences in patch sizes and tumor boundaries between patients. |
| khecireri5zy | TU,MFp,MF,Tc,Th,Treg | pdpn_pos_to_tcell_ratio | pdpn_pos_to_tcell_ratio: A ratio comparing the direct contacts between tumor cells and PDPN-positive fibroblasts to those between tumor cells and T cells. As a dimensionless measure, it normalizes the cell-cell interaction counts to reveal the relative prevalence of PDPN-positive fibroblast contacts. |
| khecireri5zy | TU,MFp,MF,Tc,Th,Treg | pdpn_neg_to_tcell_ratio | pdpn_neg_to_tcell_ratio: A dimensionless ratio that evaluates the contacts between tumor cells and PDPN-negative fibroblasts relative to T cell contacts, providing a normalized metric to compare PDPN-negative fibroblast interactions across patient cases. |
| khecireri5zy | TU,MFp,MF,Tc,Th,Treg | fibroblast_to_cytotoxic_ratio | fibroblast_to_cytotoxic_ratio: A normalized ratio that compares the number of tumor cell-to-fibroblast contacts with the tumor cell-to-cytotoxic T cell contacts, offering insight into the balance between fibroblast and cytotoxic immune cell interactions at the tumor interface. |
| khecireri5zy | TU,MFp,MF,Tc,Th,Treg | fibroblast_to_helper_ratio | fibroblast_to_helper_ratio: A ratio measuring the balance between fibroblast contacts and helper T cell contacts on tumor cells, presented as a normalized, dimensionless value that facilitates comparisons between different tumor cases. |
| khecireri5zy | TU,MFp,MF,Tc,Th,Treg | fibroblast_to_reg_ratio | fibroblast_to_reg_ratio: A normalized ratio that contrasts tumor cell-to-fibroblast contacts with tumor cell-to-regulatory T cell contacts, providing a measure of the relative frequency of these interactions independent of raw event counts. |
| knlu4pgoinj1 | TU,Tc,Th,Treg,B,P,M,G,MFp,E | GINI_COEF_NUCLEAR_AREA | GINI_COEF_NUCLEAR_AREA measures the inequality in the distribution of nuclear areas across selected cell types within a tumor region. This parameter is computed using the Gini coefficient formula, resulting in a normalized numeric value ranging from 0 (indicating perfect equality) to 1 (indicating complete inequality). It reflects the extent of heterogeneity in cell nucleus sizes, which has been associated with cellular diversity and potentially with worsened patient outcomes. |
| kpbtyinksyii | P | PROPORTION_PLASMA_CELLS_NEAR_VESSELS | This parameter quantifies the normalized proportion of plasma cells in the stromal compartments that are in close proximity to blood vessels, specifically within 20 µm. It is calculated by first isolating plasma cells located in the stromal regions, then determining the minimum Euclidean distance between the centroid of each plasma cell and any blood vessel represented as a polygon. Finally, the parameter is computed as the ratio of plasma cells meeting the proximity criterion (≤20 µm) to the total number of plasma cells in the stroma, ensuring it is a normalized metric and numerically comparable across different patient cases. |
| kuk3cj3g86e1 | B,G | B_CELL_MEAN_ORIENTATION_ANGLE | B_CELL_MEAN_ORIENTATION_ANGLE is a numeric measure representing the average orientation angle of B cell nuclei located in the stromal regions adjacent to vessels. The angle is calculated by determining the primary orientation of each B cell’s nucleus and then averaging these values, resulting in a normalized metric that can be compared across different patient cases. |
| kuk3cj3g86e1 | B,G | GRANULOCYTE_MEAN_ORIENTATION_ANGLE | GRANULOCYTE_MEAN_ORIENTATION_ANGLE is a numeric metric indicating the average primary orientation angle of granulocyte nuclei found in the stroma near vessels. This parameter is derived by computing the orientation of each granulocyte’s nucleus and averaging these values, yielding a normalized measurement suitable for cross-case comparisons. |
| kuk3cj3g86e1 | B,G | ANGLE_DIFFERENCE | ANGLE_DIFFERENCE is a numeric measure that quantifies the absolute difference between the mean orientation angles of B cells and granulocytes. The calculation takes into account the circular nature of angles to determine the smallest difference. This metric provides insight into the relative orientation disparity between the two cell types and is normalized for comparison across different samples. |
| l6qyq3tr9qpc | TU,Tc,Th,Treg,B,P,M,G,MFp,E | HETEROTYPIC_CONTACT_FRACTION | HETEROTYPIC_CONTACT_FRACTION is a normalized metric that quantifies the proportion of cell-cell contacts within the epithelial compartment that occur between different cell types. This parameter is derived by dividing the count of heterotypic contacts (contacts between cells of different types) by the total number of cell-cell contacts within the compartment. Because it represents a fraction, it is comparable across different patient cases and tissue patches. |
| l8yq7hsk5s6a | Treg | TREG_NUCLEUS_ORIENTATION_VARIANCE | TREG_NUCLEUS_ORIENTATION_VARIANCE represents the statistical variance of the orientation angles of regulatory T cell nuclei in stromal regions. It is calculated by measuring the angles obtained from the minimum rotated rectangle of each cell's nucleus and then computing the variance across these angles. This provides a measure of the heterogeneity in nucleus orientation, which can be compared between different patient cases. |
| l8yq7hsk5s6a | Treg | TREG_NUCLEUS_ORIENTATION_MEAN | TREG_NUCLEUS_ORIENTATION_MEAN represents the average orientation angle of regulatory T cell nuclei in stroma. It is computed by averaging the normalized angles (confined within a 0 to 180 degree range) derived from each cell’s nucleus orientation. This metric offers an overall summary of nuclear alignment among the regulatory T cells. |
| l8yq7hsk5s6a | Treg | TREG_NUCLEUS_ORIENTATION_MAX | TREG_NUCLEUS_ORIENTATION_MAX represents the maximum observed orientation angle among regulatory T cell nuclei in stromal regions. It is obtained by identifying the highest angle value from the set of normalized orientation angles, thereby reflecting the extreme alignment within the measured cells. |
| lfpqp7drqm33 | Treg,A | perivascular_treg_density | perivascular_treg_density: This parameter represents the normalized density of regulatory T cells in perivascular regions, expressed as the number of Treg cells per 1000 μm². It allows for comparison between patient cases by accounting for differences in perivascular area. |
| lfpqp7drqm33 | Treg,A | perivascular_apc_density | perivascular_apc_density: This parameter quantifies the normalized density of antigen presenting cells in perivascular regions in units of cells per 1000 μm², enabling standardized comparisons across different tumor cases. |
| lfpqp7drqm33 | Treg,A | perivascular_total_density | perivascular_total_density: This parameter measures the combined density of both Treg and APC cells in perivascular regions, normalized per 1000 μm², and provides an overall assessment of immune cell infiltration that is comparable across samples. |
| lfpqp7drqm33 | Treg,A | treg_to_apc_ratio | treg_to_apc_ratio: This is a normalized ratio of Treg cells to APC cells in the perivascular region, offering insight into the relative abundance of these two cell types and allowing for direct comparisons between different cases. |
| lfpqp7drqm33 | Treg,A | apc_clustering_index | apc_clustering_index: Derived from Ripley’s K function analysis, this normalized parameter indicates the spatial clustering of APC cells in perivascular areas. Values greater than 1 suggest that the cells are more clustered than would be expected under randomness. |
| lfpqp7drqm33 | Treg,A | overall_clustering_index | overall_clustering_index: Calculated using Ripley’s K function for all considered cell types (Treg and APC combined), this parameter provides a normalized measure of overall cell clustering in the perivascular region, facilitating comparison across different patient cases. |
| lv5r87pl7xym | Th | median_nucleus_circularity_helper_t_stroma | This parameter represents the median nucleus circularity of helper T lymphocytes (CD4+ cells) located within the stromal compartment of breast cancer tissue. Circularity is calculated as (4π × area) divided by the square of the nucleus perimeter, where a value of 1 indicates a perfect circle and values less than 1 indicate more irregular shapes. The measurement is derived by first selecting the appropriate helper T cells in the stroma, computing the area and perimeter of each cell's nucleus, calculating the circularity for each cell, and finally determining the median value for a given patch. This normalization enables the comparison of morphological features across different patient cases. |
| lz64wi0jm9xc | TU,Tc,Th,Treg,B,P,M,G,E | t_cell_cd8_radial_gradient_slope | t_cell_cd8_radial_gradient_slope: This parameter quantifies the rate at which the density of CD8+ T cells changes with increasing distance from tumor cell aggregates. The density is normalized by area (cells per unit area), enabling comparisons across different patient cases. A positive slope suggests an increasing CD8+ T cell density away from the tumor, indicative of an immune-active microenvironment, while a negative slope reflects decreasing density and may suggest an immunosuppressive region. |
| lz64wi0jm9xc | TU,Tc,Th,Treg,B,P,M,G,E | t_cell_cd8_radial_gradient_r2 | t_cell_cd8_radial_gradient_r2: This parameter represents the coefficient of determination (R-squared) for the linear regression model that fits CD8+ T cell density versus distance. It measures how well the linear model explains the variance in the normalized cell density data, with values closer to 1 indicating a strong linear relationship. |
| lz64wi0jm9xc | TU,Tc,Th,Treg,B,P,M,G,E | t_cell_cd4_radial_gradient_slope | t_cell_cd4_radial_gradient_slope: This parameter measures the gradient of density change for CD4+ T cells as a function of distance from tumor aggregates. By using normalized density values (cells per unit area) across defined radial bins, the computed slope reflects the spatial distribution pattern of CD4+ cells in the tumor microenvironment. |
| lz64wi0jm9xc | TU,Tc,Th,Treg,B,P,M,G,E | t_cell_cd4_radial_gradient_r2 | t_cell_cd4_radial_gradient_r2: This parameter indicates the goodness-of-fit of the linear regression model applied to CD4+ T cell density versus radial distance. A higher R-squared value points to a more reliable measurement of the relationship between the distance from the tumor and the observed normalized cell density. |
| lz64wi0jm9xc | TU,Tc,Th,Treg,B,P,M,G,E | t_cell_reg_radial_gradient_slope | t_cell_reg_radial_gradient_slope: This parameter captures the rate of change in regulatory T cell (Treg) density with increasing distance from tumor aggregates. It employs normalized density measurements, thereby providing a standardized gradient that enables comparisons across different tumor regions or patient cases. |
| lz64wi0jm9xc | TU,Tc,Th,Treg,B,P,M,G,E | t_cell_reg_radial_gradient_r2 | t_cell_reg_radial_gradient_r2: This parameter reports the R-squared value for the regression model used to compute the Treg cell density gradient. It reflects how well the linear model fits the spatial distribution data of regulatory T cells, enhancing the interpretability of the gradient slope. |
| lz64wi0jm9xc | TU,Tc,Th,Treg,B,P,M,G,E | b_cell_radial_gradient_slope | b_cell_radial_gradient_slope: This parameter quantifies the change in B cell density relative to the distance from tumor aggregates. The cell density is normalized by area, ensuring that the slope represents a standardized measurement that facilitates comparison across samples. |
| lz64wi0jm9xc | TU,Tc,Th,Treg,B,P,M,G,E | b_cell_radial_gradient_r2 | b_cell_radial_gradient_r2: This parameter provides the R-squared value for the linear regression on B cell density versus distance. It indicates the strength and reliability of the fitted model in explaining the variability in the normalized density data. |
| lz64wi0jm9xc | TU,Tc,Th,Treg,B,P,M,G,E | plasma_cell_radial_gradient_slope | plasma_cell_radial_gradient_slope: This parameter measures the rate at which plasma cell density changes with increasing radial distance from tumor aggregates. The normalization of cell density by area ensures that the slope is comparable across different patient cases, reflecting the spatial infiltration pattern of plasma cells. |
| lz64wi0jm9xc | TU,Tc,Th,Treg,B,P,M,G,E | plasma_cell_radial_gradient_r2 | plasma_cell_radial_gradient_r2: This parameter presents the R-squared value for the linear regression model applied to plasma cell density data. It assesses the fit of the model, thereby providing insight into the consistency of the plasma cell distribution pattern relative to distance. |
| lz64wi0jm9xc | TU,Tc,Th,Treg,B,P,M,G,E | macrophage_radial_gradient_slope | macrophage_radial_gradient_slope: This parameter assesses the gradient of macrophage density as a function of distance from tumor aggregates. Using normalized densities (cells per unit area) across defined radial bins, the slope indicates how macrophage infiltration varies spatially within the tumor microenvironment. |
| lz64wi0jm9xc | TU,Tc,Th,Treg,B,P,M,G,E | macrophage_radial_gradient_r2 | macrophage_radial_gradient_r2: This parameter reflects the goodness-of-fit (R-squared) for the regression model that correlates macrophage density with radial distance. A higher value suggests that the linear model is a good descriptor of the spatial distribution of macrophages. |
| lz64wi0jm9xc | TU,Tc,Th,Treg,B,P,M,G,E | granulocyte_radial_gradient_slope | granulocyte_radial_gradient_slope: This parameter captures the rate of change in granulocyte density with increasing distance from tumor aggregates. It is derived from normalized density values, allowing standardized comparisons, and indicates whether granulocyte presence increases or decreases with distance. |
| lz64wi0jm9xc | TU,Tc,Th,Treg,B,P,M,G,E | granulocyte_radial_gradient_r2 | granulocyte_radial_gradient_r2: This parameter provides the R-squared value of the linear regression model used for granulocyte density distribution. It measures the accuracy of the fit between the observed normalized densities and the predicted linear relationship. |
| lz64wi0jm9xc | TU,Tc,Th,Treg,B,P,M,G,E | endothelial_cell_radial_gradient_slope | endothelial_cell_radial_gradient_slope: This parameter measures the gradient of endothelial cell density relative to distance from tumor aggregates. Based on normalized density calculations, the slope offers a standardized metric to assess spatial variations in endothelial cell distribution across different tumor regions. |
| lz64wi0jm9xc | TU,Tc,Th,Treg,B,P,M,G,E | endothelial_cell_radial_gradient_r2 | endothelial_cell_radial_gradient_r2: This parameter signifies the R-squared value of the regression model that fits endothelial cell density versus radial distance. It evaluates the degree to which the linear model accurately represents the normalized spatial distribution of endothelial cells. |
| m3srmpywauh0 | TU,Ff,MF,Treg,G | TU_fractal | TU_fractal: This parameter measures the mean fractal dimension of tumor cell nuclei (epithelial cells). It is calculated by assessing the complexity of the nuclear polygon boundaries using a box-counting method and is averaged over the tumor cell population within each patch, providing a normalized metric for comparing different patient cases. |
| m3srmpywauh0 | TU,Ff,MF,Treg,G | Ff_fractal | Ff_fractal: This parameter represents the mean fractal dimension of FSP1+ fibroblast nuclei. The complexity of each fibroblast nucleus is quantified through a box-counting approach on its polygon boundary, and the resulting values are averaged to yield a normalized parameter suitable for comparative analysis. |
| m3srmpywauh0 | TU,Ff,MF,Treg,G | MF_fractal | MF_fractal: This parameter denotes the mean fractal dimension of PDPN- myofibroblast nuclei. By evaluating the boundary complexity of the nucleus via the box-counting method and then computing the arithmetic mean across the cell group, this numeric, normalized metric reflects nuclear structural intricacy in the myofibroblast population. |
| m3srmpywauh0 | TU,Ff,MF,Treg,G | Treg_fractal | Treg_fractal: This parameter captures the mean fractal dimension of regulatory T cell nuclei. It is computed by measuring the fractal dimension of each T cell nucleus and averaging these values, yielding a normalized, numeric metric that indicates the nuclear complexity of regulatory T cells across tumor regions. |
| m3srmpywauh0 | TU,Ff,MF,Treg,G | G_fractal | G_fractal: This parameter quantifies the mean fractal dimension of granulocyte nuclei. The box-counting method is employed to determine the complexity of each granulocyte nucleus, and the mean of these measurements provides a normalized parameter for evaluating nuclear structure. |
| m3srmpywauh0 | TU,Ff,MF,Treg,G | aggregated_fractal | aggregated_fractal: This parameter provides an aggregated measure of overall nuclear complexity by taking the arithmetic mean of the fractal dimensions calculated for tumor cells, FSP1+ fibroblasts, myofibroblasts, regulatory T cells, and granulocytes. It normalizes data across different cell types and serves as a comprehensive, numeric metric for correlating nuclear complexity with clinical outcomes. |
| m57fk7ddpt9u | M,Tc,G,MFp,B,P | CV_IMMUNE_NUCLEI_PERIMETER_NEAR_TUMOR | CV_IMMUNE_NUCLEI_PERIMETER_NEAR_TUMOR is a numeric, normalized metric that quantifies the morphological heterogeneity of immune cell nuclei at the tumor invasive margin. Specifically, it measures the coefficient of variation (calculated as the standard deviation divided by the mean) of the nuclear perimeters of selected immune cells (including macrophages, CD8+ T cells, granulocytes, PDPN+ myofibroblasts, B cells, and plasma cells) located within 50 micrometers of the tumor boundary. The metric is derived by first filtering immune cells and tumor cells, forming a single tumor boundary through the union of tumor cell nuclei, and then calculating the nuclear perimeters of immune cells that meet the proximity criterion. It provides a normalized measure for comparing different patient cases. |
| m8693e5z9j3h | TU,Th,Treg,B,P,M,G,F,Ff,E,A | Fraction_TU_within_50um_of_TU | Fraction_TU_within_50um_of_TU measures the average fraction of tumor cells (excluding the tumor cell that defines the neighborhood) among all cells located within a 50µm radius of each tumor cell, computed across tumor cell neighborhoods in a patch. |
| m8693e5z9j3h | TU,Th,Treg,B,P,M,G,F,Ff,E,A | Fraction_Th_within_50um_of_TU | Fraction_Th_within_50um_of_TU represents the average fraction of T helper cells found within the 50µm proximity of tumor cells. It is calculated as the ratio of T helper cell counts to the total number of cells in each tumor cell neighborhood and then averaged over the tumor cells in a patch. |
| m8693e5z9j3h | TU,Th,Treg,B,P,M,G,F,Ff,E,A | Fraction_Treg_within_50um_of_TU | Fraction_Treg_within_50um_of_TU indicates the average fraction of regulatory T cells present within the 50µm boundary surrounding tumor cells. This parameter normalizes the count of regulatory T cells by the total number of cells in the neighborhood and averages the fractions over all tumor cells. |
| m8693e5z9j3h | TU,Th,Treg,B,P,M,G,F,Ff,E,A | Fraction_B_within_50um_of_TU | Fraction_B_within_50um_of_TU quantifies the average fraction of B cells within the 50µm radius around tumor cells. It is derived from the ratio of B cell counts to the total neighboring cell counts in each tumor cell neighborhood, then averaged across all tumor cells. |
| m8693e5z9j3h | TU,Th,Treg,B,P,M,G,F,Ff,E,A | Fraction_P_within_50um_of_TU | Fraction_P_within_50um_of_TU measures the average fraction of plasma cells located within 50µm of tumor cells. The value is computed by dividing the number of plasma cells by the total number of cells in each tumor cell’s vicinity, and then averaging these proportions over the tumor cells. |
| m8693e5z9j3h | TU,Th,Treg,B,P,M,G,F,Ff,E,A | Fraction_M_within_50um_of_TU | Fraction_M_within_50um_of_TU calculates the average fraction of macrophages in the neighborhood of tumor cells within a 50µm radius. This fraction is normalized by the total cell count in the region and represents an averaged metric over all tumor cell neighborhoods in a patch. |
| m8693e5z9j3h | TU,Th,Treg,B,P,M,G,F,Ff,E,A | Fraction_G_within_50um_of_TU | Fraction_G_within_50um_of_TU represents the average fraction of granulocytes found within 50µm of tumor cells. It is computed as the ratio of granulocyte counts to the total count of neighboring cells and then averaged across all tumor cell neighborhoods. |
| m8693e5z9j3h | TU,Th,Treg,B,P,M,G,F,Ff,E,A | Fraction_F_within_50um_of_TU | Fraction_F_within_50um_of_TU measures the average fraction of fibroblasts present within the 50µm proximity of tumor cells. It is determined by calculating the ratio of fibroblast counts to the overall number of cells in the neighborhood and averaging these ratios over tumor cells. |
| m8693e5z9j3h | TU,Th,Treg,B,P,M,G,F,Ff,E,A | Fraction_Ff_within_50um_of_TU | Fraction_Ff_within_50um_of_TU captures the average fraction of FSP1-positive fibroblasts within the 50µm radius around tumor cells. The parameter is derived by normalizing the count of FSP1-positive fibroblasts by the total number of cells found in the vicinity and then averaging the result across tumor cells. |
| m8693e5z9j3h | TU,Th,Treg,B,P,M,G,F,Ff,E,A | Fraction_E_within_50um_of_TU | Fraction_E_within_50um_of_TU quantifies the average fraction of endothelial cells within a 50µm neighborhood of tumor cells. It is calculated as the ratio of endothelial cell counts to the total number of cells within this zone, averaged over all tumor cell neighborhoods. |
| m8693e5z9j3h | TU,Th,Treg,B,P,M,G,F,Ff,E,A | Fraction_A_within_50um_of_TU | Fraction_A_within_50um_of_TU indicates the average fraction of antigen presenting cells within the 50µm area surrounding tumor cells. This normalized measure is computed by dividing the count of antigen presenting cells by the total cell count in each tumor cell neighborhood and then averaged across all tumor cells. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | DENSITY_TU_LAYER_1 | DENSITY_TU_LAYER_1 measures the density of tumor cells (TU) in the first spatial layer (0-50 μm) surrounding the vessels. It is calculated by dividing the count of tumor cells in that layer by the area of the annular region, providing a normalized measure that allows comparison across different patient patches. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | DENSITY_Treg_LAYER_1 | DENSITY_Treg_LAYER_1 measures the density of T regulatory cells (Treg) in the first layer (0-50 μm) from the vessels. This parameter is the number of T regulatory cells per unit area of the defined layer, making it suitable for comparisons between patients. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | DENSITY_Th_LAYER_1 | DENSITY_Th_LAYER_1 represents the density of T helper cells (Th) in the first spatial layer (0-50 μm) around the vessels. It is derived by normalizing the cell count by the area of the annular region, thus allowing for cross-case comparison. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | DENSITY_B_LAYER_1 | DENSITY_B_LAYER_1 quantifies the density of B cells in the first layer (0-50 μm) surrounding vessels. The density is computed as the cell count divided by the area of the layer, making it a normalized parameter. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | DENSITY_P_LAYER_1 | DENSITY_P_LAYER_1 represents the density of plasma cells (P) in the first spatial layer (0-50 μm) adjacent to vessels, computed as the number of plasma cells normalized by the layer’s area. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | DENSITY_Ff_LAYER_1 | DENSITY_Ff_LAYER_1 measures the density of FSP1+ fibroblasts (Ff) in the first layer (0-50 μm) from vessels, determined by dividing the cell count by the computed area of the annular region. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | DENSITY_F_LAYER_1 | DENSITY_F_LAYER_1 indicates the density of FSP1- fibroblasts (F) in the first spatial layer (0-50 μm) surrounding vessels. It is normalized by calculating the number of fibroblasts per unit area of the layer. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | DENSITY_TU_LAYER_2 | DENSITY_TU_LAYER_2 measures the density of tumor cells (TU) in the second spatial layer (50-100 μm) from vessels. The density is normalized by the area of the annulus corresponding to this layer, allowing comparison across tumor patches. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | DENSITY_Th_LAYER_2 | DENSITY_Th_LAYER_2 represents the density of T helper cells (Th) in the second layer (50-100 μm) around vessels, computed as a normalized value by dividing the cell count by the layer’s area. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | DENSITY_B_LAYER_2 | DENSITY_B_LAYER_2 quantifies the density of B cells in the second spatial layer (50-100 μm) from vessels with normalization by the annular area, making it comparable across different patient samples. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | DENSITY_Ff_LAYER_2 | DENSITY_Ff_LAYER_2 measures the density of FSP1+ fibroblasts (Ff) in the second layer (50-100 μm) surrounding vessels, with the value normalized by the area of the corresponding annular region. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | DENSITY_F_LAYER_2 | DENSITY_F_LAYER_2 indicates the density of FSP1- fibroblasts (F) in the second spatial layer (50-100 μm) from vessels. It is calculated by normalizing the cell count by the area of that layer. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | DENSITY_TU_LAYER_3 | DENSITY_TU_LAYER_3 measures the density of tumor cells (TU) in the third spatial layer (100-150 μm) from the vessels, computed as the number of tumor cells per unit area of the corresponding annulus to yield a normalized metric. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | DENSITY_F_LAYER_3 | DENSITY_F_LAYER_3 quantifies the density of FSP1- fibroblasts (F) in the third layer (100-150 μm) surrounding vessels by normalizing the cell count with the area of the annular region. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | MEAN_DIST_TU_LAYER_1 | MEAN_DIST_TU_LAYER_1 represents the average (mean) distance of tumor cells (TU) from the nearest vessel within the first spatial layer (0-50 μm). This metric provides a normalized measure of spatial distribution by averaging the computed distances. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | MEAN_DIST_Treg_LAYER_1 | MEAN_DIST_Treg_LAYER_1 indicates the mean distance of T regulatory cells (Treg) from vessels in the first layer (0-50 μm), offering a normalized statistic based on the average distance of these cells to the vessels. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | MEAN_DIST_Th_LAYER_1 | MEAN_DIST_Th_LAYER_1 measures the average distance of T helper cells (Th) from the nearest vessel within the first layer (0-50 μm), providing a normalized metric that reflects cell spatial distribution. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | MEAN_DIST_B_LAYER_1 | MEAN_DIST_B_LAYER_1 quantifies the mean distance of B cells from vessels in the first spatial layer (0-50 μm), computed as the average of cell-to-vessel distances for that cell type in the layer. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | MEAN_DIST_P_LAYER_1 | MEAN_DIST_P_LAYER_1 represents the average distance of plasma cells (P) to the nearest vessel within the first layer (0-50 μm), yielding a normalized measure of spatial proximity. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | MEAN_DIST_Ff_LAYER_1 | MEAN_DIST_Ff_LAYER_1 indicates the mean distance of FSP1+ fibroblasts (Ff) from vessels in the first layer (0-50 μm), calculated as the average of the distances and thus normalized for cross-sample comparisons. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | MEAN_DIST_F_LAYER_1 | MEAN_DIST_F_LAYER_1 measures the average distance of FSP1- fibroblasts (F) from the closest vessel within the first spatial layer (0-50 μm), providing a normalized metric of cell distribution. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | MEAN_DIST_TU_LAYER_2 | MEAN_DIST_TU_LAYER_2 represents the mean distance of tumor cells (TU) from vessels in the second spatial layer (50-100 μm), calculated as an average of cell-to-vessel distances and normalized for comparative analysis. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | MEAN_DIST_Th_LAYER_2 | MEAN_DIST_Th_LAYER_2 quantifies the average distance of T helper cells (Th) from the nearest vessel within the second layer (50-100 μm), offering a normalized statistic of spatial distribution. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | MEAN_DIST_B_LAYER_2 | MEAN_DIST_B_LAYER_2 measures the mean distance of B cells from vessels in the second spatial layer (50-100 μm), computed as the average distance for those cells, serving as a normalized metric. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | MEAN_DIST_Ff_LAYER_2 | MEAN_DIST_Ff_LAYER_2 indicates the average distance of FSP1+ fibroblasts (Ff) from the closest vessel in the second layer (50-100 μm), providing a normalized measure based on the computed distances. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | MEAN_DIST_F_LAYER_2 | MEAN_DIST_F_LAYER_2 represents the mean distance of FSP1- fibroblasts (F) to vessels in the second spatial layer (50-100 μm), calculated as the average of the distances in this layer. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | MEAN_DIST_TU_LAYER_3 | MEAN_DIST_TU_LAYER_3 measures the average (mean) distance of tumor cells (TU) from vessels within the third spatial layer (100-150 μm), yielding a normalized metric for spatial comparison. |
| ma247h9d462z | TU,Treg,Th,B,P,Ff,F | MEAN_DIST_F_LAYER_3 | MEAN_DIST_F_LAYER_3 quantifies the mean distance of FSP1- fibroblasts (F) from the nearest vessel in the third layer (100-150 μm), offering a normalized statistic of cell distribution relative to vessels. |
| mc5dli1azo3k | TU,M,Ff,MF | TU_area_velocity | TU_area_velocity: For tumor cells, this parameter measures the infiltration velocity based on cell area. It is derived as the slope from a linear regression of average cell area versus a normalized position along the vessel-to-tumor axis, indicating how the cell area changes as tumor cells advance from vessel regions towards the tumor boundary. |
| mc5dli1azo3k | TU,M,Ff,MF | TU_area_r_value | TU_area_r_value: For tumor cells, this parameter represents the correlation coefficient between cell area and the normalized positional value, reflecting the strength and direction of the linear relationship in the regression analysis. |
| mc5dli1azo3k | TU,M,Ff,MF | TU_area_p_value | TU_area_p_value: For tumor cells, this parameter represents the statistical significance (p-value) of the correlation in the regression of cell area versus normalized position, indicating the reliability of the observed relationship. |
| mc5dli1azo3k | TU,M,Ff,MF | TU_perimeter_velocity | TU_perimeter_velocity: For tumor cells, this parameter measures the rate of change (velocity) in cell perimeter along the vessel-to-tumor axis. It is calculated as the slope from the linear regression of the average cell perimeter versus the normalized position. |
| mc5dli1azo3k | TU,M,Ff,MF | TU_perimeter_r_value | TU_perimeter_r_value: For tumor cells, this parameter quantifies the correlation coefficient from the linear regression of cell perimeter against the normalized spatial position, showing the strength and direction of the relationship. |
| mc5dli1azo3k | TU,M,Ff,MF | TU_perimeter_p_value | TU_perimeter_p_value: For tumor cells, this parameter indicates the p-value associated with the regression of cell perimeter versus normalized position, assessing the statistical significance of the trend observed. |
| mc5dli1azo3k | TU,M,Ff,MF | TU_circularity_velocity | TU_circularity_velocity: For tumor cells, this parameter measures the infiltration velocity based on cell circularity. It is derived as the slope of the linear regression of average cell circularity versus normalized position, reflecting changes in cell shape uniformity from vessels towards the tumor boundary. |
| mc5dli1azo3k | TU,M,Ff,MF | TU_circularity_r_value | TU_circularity_r_value: For tumor cells, this parameter represents the correlation coefficient associated with the regression between cell circularity and normalized position, indicating how strongly circularity is related to spatial positioning. |
| mc5dli1azo3k | TU,M,Ff,MF | TU_circularity_p_value | TU_circularity_p_value: For tumor cells, this parameter reflects the p-value for the regression analysis of cell circularity versus normalized position, demonstrating the statistical significance of the relationship. |
| mc5dli1azo3k | TU,M,Ff,MF | TU_aspect_ratio_velocity | TU_aspect_ratio_velocity: For tumor cells, this parameter quantifies the infiltration velocity based on cell aspect ratio. It is computed as the slope from the linear regression of average cell aspect ratio against the normalized vessel-to-tumor position, delineating changes in cell elongation along the axis. |
| mc5dli1azo3k | TU,M,Ff,MF | TU_aspect_ratio_r_value | TU_aspect_ratio_r_value: For tumor cells, this parameter indicates the correlation coefficient from the regression of cell aspect ratio versus normalized position, capturing the strength and direction of this relationship. |
| mc5dli1azo3k | TU,M,Ff,MF | TU_aspect_ratio_p_value | TU_aspect_ratio_p_value: For tumor cells, this parameter gives the p-value for the regression of cell aspect ratio versus normalized position, assessing the statistical significance of the observed trend. |
| mc5dli1azo3k | TU,M,Ff,MF | M_area_velocity | M_area_velocity: For macrophages, this parameter measures the infiltration velocity based on cell area, computed as the slope from a linear regression of average area against normalized position along the vessel-to-tumor axis, indicating how the cell area changes during infiltration. |
| mc5dli1azo3k | TU,M,Ff,MF | M_area_r_value | M_area_r_value: For macrophages, this parameter represents the correlation coefficient between the cell area and normalized position, conveying the strength and directional relationship in the regression analysis. |
| mc5dli1azo3k | TU,M,Ff,MF | M_area_p_value | M_area_p_value: For macrophages, this parameter represents the statistical significance (p-value) of the regression between cell area and normalized position, indicating the reliability of the observed correlation. |
| mc5dli1azo3k | TU,M,Ff,MF | M_perimeter_velocity | M_perimeter_velocity: For macrophages, this parameter quantifies the rate of change (velocity) in cell perimeter along the vessel-to-tumor axis, derived as the slope from a linear regression of average perimeter versus normalized position. |
| mc5dli1azo3k | TU,M,Ff,MF | M_perimeter_r_value | M_perimeter_r_value: For macrophages, this parameter measures the correlation coefficient for the regression of cell perimeter versus normalized position, indicating the strength and direction of the relationship. |
| mc5dli1azo3k | TU,M,Ff,MF | M_perimeter_p_value | M_perimeter_p_value: For macrophages, this parameter indicates the p-value from the regression analysis of cell perimeter against normalized position, assessing the significance of the trend. |
| mc5dli1azo3k | TU,M,Ff,MF | M_circularity_velocity | M_circularity_velocity: For macrophages, this parameter measures the infiltration velocity based on cell circularity. It is determined as the slope of the regression of average circularity versus normalized position, reflecting changes in shape uniformity along the infiltration path. |
| mc5dli1azo3k | TU,M,Ff,MF | M_circularity_r_value | M_circularity_r_value: For macrophages, this parameter represents the correlation coefficient of the regression between cell circularity and normalized position, indicating the degree of linear association. |
| mc5dli1azo3k | TU,M,Ff,MF | M_circularity_p_value | M_circularity_p_value: For macrophages, this parameter reflects the p-value associated with the regression of cell circularity versus normalized position, demonstrating the statistical significance of the relationship. |
| mc5dli1azo3k | TU,M,Ff,MF | M_aspect_ratio_velocity | M_aspect_ratio_velocity: For macrophages, this parameter quantifies the infiltration velocity based on cell aspect ratio, calculated as the slope from the regression of average aspect ratio against normalized position, indicating how cell elongation changes during infiltration. |
| mc5dli1azo3k | TU,M,Ff,MF | M_aspect_ratio_r_value | M_aspect_ratio_r_value: For macrophages, this parameter represents the correlation coefficient from the regression between cell aspect ratio and normalized position, reflecting the strength and direction of the association. |
| mc5dli1azo3k | TU,M,Ff,MF | M_aspect_ratio_p_value | M_aspect_ratio_p_value: For macrophages, this parameter represents the p-value for the regression of cell aspect ratio versus normalized position, assessing the statistical significance of the observed trend. |
| mc5dli1azo3k | TU,M,Ff,MF | Ff_area_velocity | Ff_area_velocity: For fibroblasts FSP1+, this parameter measures the infiltration velocity based on cell area. It is computed as the slope from a linear regression of the average cell area against normalized position along the vessel-to-tumor axis, indicating how the cell area changes during tissue infiltration. |
| mc5dli1azo3k | TU,M,Ff,MF | Ff_area_r_value | Ff_area_r_value: For fibroblasts FSP1+, this parameter indicates the correlation coefficient between cell area and normalized position, showing the strength and direction of the relationship in the regression analysis. |
| mc5dli1azo3k | TU,M,Ff,MF | Ff_area_p_value | Ff_area_p_value: For fibroblasts FSP1+, this parameter represents the p-value for the regression of cell area versus normalized position, determining the statistical significance of the trend. |
| mc5dli1azo3k | TU,M,Ff,MF | Ff_perimeter_velocity | Ff_perimeter_velocity: For fibroblasts FSP1+, this parameter quantifies the rate of change in cell perimeter along the vessel-to-tumor axis, determined as the slope from the linear regression of average perimeter versus normalized position. |
| mc5dli1azo3k | TU,M,Ff,MF | Ff_perimeter_r_value | Ff_perimeter_r_value: For fibroblasts FSP1+, this parameter measures the correlation coefficient from the regression of cell perimeter against normalized position, indicating the strength and direction of the association. |
| mc5dli1azo3k | TU,M,Ff,MF | Ff_perimeter_p_value | Ff_perimeter_p_value: For fibroblasts FSP1+, this parameter indicates the p-value of the regression between cell perimeter and normalized position, assessing the significance of the observed relationship. |
| mc5dli1azo3k | TU,M,Ff,MF | Ff_circularity_velocity | Ff_circularity_velocity: For fibroblasts FSP1+, this parameter measures the infiltration velocity based on cell circularity, calculated from the slope of the regression of average circularity against normalized position, highlighting changes in cell shape uniformity during infiltration. |
| mc5dli1azo3k | TU,M,Ff,MF | Ff_circularity_r_value | Ff_circularity_r_value: For fibroblasts FSP1+, this parameter represents the correlation coefficient for the regression of cell circularity versus normalized position, demonstrating the strength and direction of the relationship. |
| mc5dli1azo3k | TU,M,Ff,MF | Ff_circularity_p_value | Ff_circularity_p_value: For fibroblasts FSP1+, this parameter provides the p-value for the regression analysis of cell circularity versus normalized position, indicating the statistical significance of the trend. |
| mc5dli1azo3k | TU,M,Ff,MF | Ff_aspect_ratio_velocity | Ff_aspect_ratio_velocity: For fibroblasts FSP1+, this parameter quantifies the infiltration velocity based on cell aspect ratio by deriving the slope from the regression of average aspect ratio against normalized position, reflecting changes in cell elongation as they traverse from vessels to the tumor boundary. |
| mc5dli1azo3k | TU,M,Ff,MF | Ff_aspect_ratio_r_value | Ff_aspect_ratio_r_value: For fibroblasts FSP1+, this parameter measures the correlation coefficient between cell aspect ratio and normalized position, indicating the strength and consistency of the linear trend. |
| mc5dli1azo3k | TU,M,Ff,MF | Ff_aspect_ratio_p_value | Ff_aspect_ratio_p_value: For fibroblasts FSP1+, this parameter reflects the p-value of the regression analysis for cell aspect ratio versus normalized position, assessing the significance of the observed relationship. |
| mc5dli1azo3k | TU,M,Ff,MF | MF_area_velocity | MF_area_velocity: For PDPN- myofibroblasts, this parameter measures the infiltration velocity based on cell area. It is obtained as the slope from a regression of average cell area versus normalized position along the vessel-to-tumor axis, signifying how cell area changes across this spatial gradient. |
| mc5dli1azo3k | TU,M,Ff,MF | MF_area_r_value | MF_area_r_value: For PDPN- myofibroblasts, this parameter represents the correlation coefficient from the regression between cell area and normalized position, capturing the strength and direction of the association. |
| mc5dli1azo3k | TU,M,Ff,MF | MF_area_p_value | MF_area_p_value: For PDPN- myofibroblasts, this parameter provides the p-value for the regression of cell area versus normalized position, indicating the statistical significance of the relationship. |
| mc5dli1azo3k | TU,M,Ff,MF | MF_perimeter_velocity | MF_perimeter_velocity: For PDPN- myofibroblasts, this parameter quantifies the infiltration velocity based on cell perimeter, determined as the slope from the linear regression of average perimeter versus normalized position along the vessel-to-tumor axis. |
| mc5dli1azo3k | TU,M,Ff,MF | MF_perimeter_r_value | MF_perimeter_r_value: For PDPN- myofibroblasts, this parameter measures the correlation coefficient from the regression of cell perimeter against normalized position, reflecting the strength and directional nature of the relationship. |
| mc5dli1azo3k | TU,M,Ff,MF | MF_perimeter_p_value | MF_perimeter_p_value: For PDPN- myofibroblasts, this parameter indicates the statistical significance (p-value) of the regression relating cell perimeter to normalized position. |
| mc5dli1azo3k | TU,M,Ff,MF | MF_circularity_velocity | MF_circularity_velocity: For PDPN- myofibroblasts, this parameter measures the infiltration velocity based on cell circularity. It is computed as the slope from a regression of average circularity versus normalized position, outlining how cell shape uniformity changes along the axis. |
| mc5dli1azo3k | TU,M,Ff,MF | MF_circularity_r_value | MF_circularity_r_value: For PDPN- myofibroblasts, this parameter represents the correlation coefficient for the regression of cell circularity versus normalized position, indicating the strength and direction of the linear association. |
| mc5dli1azo3k | TU,M,Ff,MF | MF_circularity_p_value | MF_circularity_p_value: For PDPN- myofibroblasts, this parameter provides the p-value assessing the statistical significance of the regression between cell circularity and normalized position. |
| mc5dli1azo3k | TU,M,Ff,MF | MF_aspect_ratio_velocity | MF_aspect_ratio_velocity: For PDPN- myofibroblasts, this parameter quantifies the infiltration velocity based on cell aspect ratio, derived as the slope from the regression of average aspect ratio against normalized position, which reflects changes in cell elongation along the infiltration path. |
| mc5dli1azo3k | TU,M,Ff,MF | MF_aspect_ratio_r_value | MF_aspect_ratio_r_value: For PDPN- myofibroblasts, this parameter measures the correlation coefficient from the regression of cell aspect ratio versus normalized position, capturing the strength of the relationship. |
| mc5dli1azo3k | TU,M,Ff,MF | MF_aspect_ratio_p_value | MF_aspect_ratio_p_value: For PDPN- myofibroblasts, this parameter indicates the p-value for the regression of cell aspect ratio versus normalized position, assessing the statistical significance of the observed trend. |
| mhys2hlmkbj7 | Th,MF | Th_0-50_distance_concavity | Th_0-50_distance_concavity measures the average nucleus concavity of T helper cells located within 0 to 50 pixels of a blood vessel. Nucleus concavity is determined by the difference between the area of the convex hull and the actual nucleus area, providing a normalized, numeric metric for cell shape complexity. |
| mhys2hlmkbj7 | Th,MF | Th_50-100_distance_concavity | Th_50-100_distance_concavity measures the average nucleus concavity of T helper cells located within 50 to 100 pixels from a vessel. It represents a normalized numeric value enabling comparisons across different tumor regions based on cell morphology. |
| mhys2hlmkbj7 | Th,MF | MF_0-50_distance_concavity | MF_0-50_distance_concavity measures the average nucleus concavity of PDPN- fibroblasts (myofibroblasts) within 0 to 50 pixels of a vessel. This value is derived from the computed difference between the convex hull area and the actual nucleus area of each cell, subsequently averaged, thus serving as a normalized and numeric parameter. |
| mhys2hlmkbj7 | Th,MF | MF_50-100_distance_concavity | MF_50-100_distance_concavity measures the average nucleus concavity of myofibroblasts within 50 to 100 pixels from vessels. It is calculated by averaging the differences between the convex hull area and the actual nucleus area for the cells in this spatial bucket, providing a normalized, numeric metric. |
| mhys2hlmkbj7 | Th,MF | MF_>100_distance_concavity | MF_>100_distance_concavity measures the average nucleus concavity of myofibroblasts located more than 100 pixels away from blood vessels. As an average value of the concavity metric calculated per cell, it provides a normalized numeric measure for cross-case comparisons. |
| mhys2hlmkbj7 | Th,MF | diff_Th_MF_0-50_distance_concavity | diff_Th_MF_0-50_distance_concavity quantifies the difference in average nucleus concavity between T helper cells and PDPN- fibroblasts within 0 to 50 pixels from vessels. It is computed by subtracting the mean concavity value of myofibroblasts from that of T helper cells, yielding a normalized, numeric measure that reflects potential differences in cell states or behavior. |
| mhys2hlmkbj7 | Th,MF | diff_Th_MF_50-100_distance_concavity | diff_Th_MF_50-100_distance_concavity quantifies the difference in average nucleus concavity between T helper cells and PDPN- fibroblasts within the 50 to 100 pixels range from vessels. This normalized, numeric parameter is derived by calculating the difference between the corresponding mean concavity metrics, highlighting contrasts in nuclear morphology between the two cell types. |
| mj96dyoeaprv | TU | AVG_MIN_DIST_TUMOR_TO_VESSEL | AVG_MIN_DIST_TUMOR_TO_VESSEL represents the average of the minimum distances calculated from each tumor cell to its nearest vessel. It reflects the overall spatial proximity between tumor cells and the closest vessel within a given patch, providing a measure that can be compared across different patient cases. |
| mj96dyoeaprv | TU | MIN_DIST_TUMOR_TO_VESSEL | MIN_DIST_TUMOR_TO_VESSEL is the smallest distance measured from any single tumor cell to the nearest vessel polygon. This parameter highlights the point of closest interaction between a tumor cell and a vessel, which may be indicative of areas with potential intravascular invasion. |
| mj96dyoeaprv | TU | MAX_DIST_TUMOR_TO_VESSEL | MAX_DIST_TUMOR_TO_VESSEL denotes the largest minimal distance from tumor cells to their nearest vessel. It provides insight into the range of tumor cell distribution relative to vessels, showing the extent to which some tumor cells are isolated from vascular structures. |
| mj96dyoeaprv | TU | STD_DIST_TUMOR_TO_VESSEL | STD_DIST_TUMOR_TO_VESSEL is the standard deviation of the minimal distances between tumor cells and vessels. This parameter measures the variability in the distances and helps assess the heterogeneity in the tumor-vessel spatial relationships across the analyzed region. |
| mj96dyoeaprv | TU | MEDIAN_DIST_TUMOR_TO_VESSEL | MEDIAN_DIST_TUMOR_TO_VESSEL represents the median value of the minimal distances from tumor cells to their nearest vessel. Offering a central tendency measure that is less sensitive to outliers than the mean, it robustly summarizes the typical spatial separation in the examined patch. |
| mkt97saxydfo | MFp | Mean_Nucleus_Convexity_MFp | Mean_Nucleus_Convexity_MFp represents the average convexity of PDPN+ myofibroblast nuclei within stromal compartments. Convexity is calculated as the ratio of the nucleus area to the convex hull area, yielding values between 0 and 1, with 1 indicating a perfectly convex shape. This parameter reflects the overall nuclear shape regularity in a normalized manner. |
| mkt97saxydfo | MFp | Std_Nucleus_Convexity_MFp | Std_Nucleus_Convexity_MFp quantifies the variability in nucleus convexity among PDPN+ myofibroblasts in stromal regions. It is computed as the standard deviation of the convexity values, providing insight into the consistency of nuclear shapes across different cells, based on a normalized ratio. |
| mkt97saxydfo | MFp | Min_Nucleus_Convexity_MFp | Min_Nucleus_Convexity_MFp indicates the lowest convexity value observed among the analyzed PDPN+ myofibroblast nuclei in stroma. This value identifies the cells with the most irregular nuclear shape in the normalized measurement framework. |
| mkt97saxydfo | MFp | Max_Nucleus_Convexity_MFp | Max_Nucleus_Convexity_MFp reflects the highest convexity value of PDPN+ myofibroblast nuclei in the stromal compartments. A high value, approaching 1, signifies that the nucleus is nearly perfectly convex, representing the upper bound of the normalized convexity ratio. |
| mr5cb83893qn | Th | helper_T_cell_RipleyK | This parameter represents a normalized spatial metric that quantifies the clustering of helper T cells (CD4+ cells) in the vicinity of the tumor epithelial compartment. It is calculated using Ripley’s K function, which counts the number of cell pairs that lie within a fixed radius (100 pixels) and then normalizes the count by the total area of the patch and the square of the number of cells. The normalization ensures that the metric is comparable across different patient samples and image patches, with higher values indicating stronger clustering within a defined proximity (50 pixels) to the epithelium. |
| mw4jtbzc140r | MFp,MF,P,M | PDPN_RATIO | PDPN_RATIO represents the computed ratio of PDPN-positive myofibroblasts to PDPN-negative myofibroblasts within tumor patches that exhibit significant plasma cell and macrophage infiltration. This ratio is normalized as it compares two related cell measurement values, making it suitable for comparing different patient cases. |
| mw4jtbzc140r | MFp,MF,P,M | SIGNIFICANT_INFILTRATION | SIGNIFICANT_INFILTRATION is a binary indicator (1 or 0) that signals whether a tumor patch has notable infiltration by both plasma cells and macrophages. This normalized flag allows for comparisons across patient cases by standardizing the criterion for significant cell co-localization. |
| mwdob6g4j83h | TU,Treg,Th,M,Ff,E | MST_average_node_degree | MST_average_node_degree: A normalized metric representing the average number of connections per cell in the Minimum Spanning Tree (MST). This parameter is computed as the mean degree of all nodes in the MST, making it comparable across different patient cases regardless of differences in absolute cell counts. |
| mwdob6g4j83h | TU,Treg,Th,M,Ff,E | MST_avg_degree_TU | MST_avg_degree_TU: A normalized measure of the average connectivity specific to tumor cells (epithelial cells) within the MST. By averaging the degree (number of connections) for these cells, it provides a standardized insight into their interaction patterns, suitable for comparisons across cases. |
| mwdob6g4j83h | TU,Treg,Th,M,Ff,E | MST_avg_degree_Treg | MST_avg_degree_Treg: A normalized metric that reflects the average number of connections per regulatory T cell (Treg) within the MST. This value captures the spatial interactivity of Treg cells in a way that is independent of total cell counts, allowing for meaningful comparison across different patches. |
| mwdob6g4j83h | TU,Treg,Th,M,Ff,E | MST_avg_degree_Th | MST_avg_degree_Th: A normalized indicator representing the average connectivity of helper T cells (Th) in the MST. The parameter is calculated by averaging the node degree across all Th cells, ensuring that comparisons across different patient cases remain valid. |
| mwdob6g4j83h | TU,Treg,Th,M,Ff,E | MST_avg_degree_M | MST_avg_degree_M: A normalized metric showing the average number of connections per macrophage in the MST. Averaging the connectivity for macrophages provides insight into their spatial relationship and interaction within the tissue in a manner that is comparable between patients. |
| mwdob6g4j83h | TU,Treg,Th,M,Ff,E | MST_avg_degree_Ff | MST_avg_degree_Ff: A normalized measure of the average connectivity for FSP1+ fibroblasts in the MST. This parameter offers a standardized view of fibroblast interactions across samples, as it is derived from the mean degree of these cells in the network. |
| mwdob6g4j83h | TU,Treg,Th,M,Ff,E | MST_avg_degree_E | MST_avg_degree_E: A normalized metric representing the average number of connections per endothelial cell in the MST. By calculating the mean degree for endothelial cells, this parameter provides a comparative measure of their spatial connectivity across distinct patient tumor regions. |
| n147y2aw34cf | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | morans_i | morans_i is a normalized numeric parameter that represents the global Moran’s I statistic. It quantifies spatial autocorrelation by measuring the degree to which similar cell abundance values are clustered or dispersed across a patch. The statistic is calculated by comparing the weighted deviations of individual cell abundances from the mean within a spatially defined neighborhood, making it comparable across different tumor regions. Values typically range from -1 to 1 with 0 indicating a random spatial pattern. |
| n147y2aw34cf | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | p_value | p_value is a normalized numeric parameter that represents the statistical significance of the spatial autocorrelation measured by Moran’s I. It is derived from a permutation test where the observed pattern is compared against randomly shuffled distributions of cell weight values. A low p_value (typically less than 0.05) indicates that the observed spatial autocorrelation is unlikely to be due to chance, thereby validating the significance of the Moran’s I index for that patch. |
| n19xip1rv0xi | Treg,Th | overall_Th_mean_perimeter | overall_Th_mean_perimeter: This parameter represents the average nuclear perimeter of T helper cells calculated over all patches in the stromal compartment. It provides a normalized metric that can be used to compare different patient cases by summarizing cell nuclear size in that specific region. |
| n19xip1rv0xi | Treg,Th | overall_Treg_mean_perimeter | overall_Treg_mean_perimeter: This parameter represents the average nuclear perimeter of regulatory T cells within the stromal compartment. It offers a normalized value, which facilitates inter-case comparisons of nuclear dimensions between different patient samples. |
| n19xip1rv0xi | Treg,Th | overall_pvalue | overall_pvalue: This parameter is the p-value resulting from a t-test that compares the nuclear perimeter distributions between T helper and regulatory T cells across the entire stromal compartment. Being a probability value between 0 and 1, it is inherently normalized for comparing significance across patient cases. |
| n19xip1rv0xi | Treg,Th | bin_0_50_Th_mean_perimeter | bin_0_50_Th_mean_perimeter: This parameter indicates the mean nuclear perimeter of T helper cells that are located within 0-50 pixels of the epithelial boundary. It provides a normalized comparison of cell morphology in regions immediately adjacent to the epithelium. |
| n19xip1rv0xi | Treg,Th | bin_0_50_Treg_mean_perimeter | bin_0_50_Treg_mean_perimeter: This parameter indicates the mean nuclear perimeter of regulatory T cells within 0-50 pixels of the epithelial boundary. It enables a normalized comparison of nuclear dimensions near the epithelial margin between different cell types. |
| n19xip1rv0xi | Treg,Th | bin_0_50_Th_std_perimeter | bin_0_50_Th_std_perimeter: This parameter represents the standard deviation of the nuclear perimeter measurements for T helper cells in the 0-50 pixel distance bin. It quantifies the variability in cell size within this specific region and is normalized for inter-patient comparisons. |
| n19xip1rv0xi | Treg,Th | bin_0_50_Treg_std_perimeter | bin_0_50_Treg_std_perimeter: This parameter represents the standard deviation of nuclear perimeter measurements for regulatory T cells within 0-50 pixels of the epithelial boundary. It provides insight into the dispersion of cell size measurements in a controlled proximity area, allowing normalized comparisons. |
| n19xip1rv0xi | Treg,Th | bin_0_50_pvalue | bin_0_50_pvalue: This parameter is the p-value from a t-test comparing the nuclear perimeters of T helper and regulatory T cells confined to the 0-50 pixel bin. It quantifies the statistical significance of the difference in cell morphology in this region and is normalized for direct comparison. |
| n19xip1rv0xi | Treg,Th | bin_51_100_Th_mean_perimeter | bin_51_100_Th_mean_perimeter: This parameter calculates the mean nuclear perimeter of T helper cells that are situated between 51-100 pixels away from the epithelial boundary. This normalized metric allows the assessment of cell size in a region that is moderately distal from the epithelium. |
| n19xip1rv0xi | Treg,Th | bin_51_100_Th_std_perimeter | bin_51_100_Th_std_perimeter: This parameter measures the standard deviation of the nuclear perimeter for T helper cells in the 51-100 pixel distance range, reflecting the variability in cell nuclear perimeters in that stratified region and supporting standardized comparisons. |
| n83j0yrd2lsx | TU,Th,Treg,B,P,M,MFp,Ff,E,A | median_nucleus_area | This parameter represents the median area in square micrometers of cell nuclei derived from a set of ten specified cell types (including tumor cells, T helper cells, T regulatory cells, B cells, plasma cells, macrophages, PDPN+ myofibroblasts, FSP1+ fibroblasts, endothelial cells, and antigen presenting cells). The measurement is obtained by calculating the area of the nucleus polygons for each relevant cell in a tumor region (patch) and then computing the median value across these measurements. As a continuous numeric metric computed per patch, it serves as a normalized feature that can be applied for comparative analysis across different patient cases, reflecting potential variations in tumor aggressiveness. |
| n8zopzcfia3q | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,F | MEDIAN_ORIENTATION_ALL | MEDIAN_ORIENTATION_ALL represents the median orientation angle (in degrees) of the fitted bounding ellipses across all specified cell types in a tumor patch. It is computed using circular statistics to capture the central tendency of cell nucleus orientations, making it normalized and directly comparable between different patient cases. |
| n8zopzcfia3q | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,F | ALIGNMENT_CONSISTENCY | ALIGNMENT_CONSISTENCY quantifies the overall consistency in cell alignment by measuring the median absolute difference between each individual cell’s orientation angle and the aggregated median orientation. A lower value indicates higher uniformity in cellular alignment within the tumor region. |
| n8zopzcfia3q | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,F | MEDIAN_ORIENTATION_TU | MEDIAN_ORIENTATION_TU measures the median orientation angle for tumor cells (designated as epithelial cells) based on the fitted ellipse for each cell nucleus. This parameter reflects the common alignment characteristic of the tumor cell population. |
| n8zopzcfia3q | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,F | MEDIAN_ORIENTATION_Tc | MEDIAN_ORIENTATION_Tc captures the median orientation angle for cytotoxic T cells. It is determined by calculating the orientation from the cell nucleus ellipse, yielding a normalized and numeric measure for the immune cell alignment. |
| n8zopzcfia3q | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,F | MEDIAN_ORIENTATION_Th | MEDIAN_ORIENTATION_Th provides the median orientation angle for helper T cells as derived from their nucleus ellipse fitting. This measure enables comparison of cell alignment across different samples due to its normalized nature. |
| n8zopzcfia3q | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,F | MEDIAN_ORIENTATION_Treg | MEDIAN_ORIENTATION_Treg is the median orientation angle calculated for regulatory T cells. It is obtained by fitting an ellipse to the cell nucleus and measuring its orientation, thereby offering a normalized indicator for comparing patient cases. |
| n8zopzcfia3q | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,F | MEDIAN_ORIENTATION_B | MEDIAN_ORIENTATION_B is determined as the median orientation angle for B cells based on the computed ellipse parameters from their nucleus shape. The measure is numeric and normalized to allow cross-case comparisons. |
| n8zopzcfia3q | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,F | MEDIAN_ORIENTATION_P | MEDIAN_ORIENTATION_P represents the median orientation angle for plasma cells extracted from ellipse fitting of the nucleus. This parameter provides a normalized numerical value to assess cell alignment. |
| n8zopzcfia3q | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,F | MEDIAN_ORIENTATION_M | MEDIAN_ORIENTATION_M reflects the median orientation angle for macrophages, computed from the bounding ellipse of each cell nucleus. Its normalized, numeric nature makes it suitable to compare across different tumor patches. |
| n8zopzcfia3q | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,F | MEDIAN_ORIENTATION_G | MEDIAN_ORIENTATION_G denotes the median orientation angle for granulocytes derived from the cell nucleus ellipse, serving as a normalized metric for cellular alignment in these cells. |
| n8zopzcfia3q | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,F | MEDIAN_ORIENTATION_MFp | MEDIAN_ORIENTATION_MFp indicates the median orientation angle for PDPN+ myofibroblasts (MFp), calculated from the ellipse fitting of the cell nucleus. This normalized numeric parameter provides insight into the alignment characteristics of this cell type. |
| n8zopzcfia3q | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,F | MEDIAN_ORIENTATION_Ff | MEDIAN_ORIENTATION_Ff is the median orientation angle for FSP1+ fibroblasts, obtained by fitting ellipses to the cell nuclei. It offers a normalized, numeric measure suited for comparing cellular orientation across cases. |
| n8zopzcfia3q | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,F | MEDIAN_ORIENTATION_F | MEDIAN_ORIENTATION_F represents the median orientation angle for fibroblasts, determined from the ellipse-fitted nucleus orientations. Being normalized and numeric, it effectively reflects the central tendency of fibroblast alignment in tumor regions. |
| nczx2s6l4bhr | B,Treg,P | proportion_B_cells_perivascular | This parameter represents the normalized proportion of B cells among the immune cells (B cells, regulatory T cells, and plasma cells) located in the perivascular region. It is computed by dividing the count of B cells by the total count of these three cell types, thus providing a value between 0 and 1. This normalized measure allows for comparison across different patient cases by controlling for differences in overall cell density within the tumor patches. |
| nhyg06a5lpxf | B,MF | B_TO_MF_RATIO | B_TO_MF_RATIO is a normalized metric that represents the ratio of B cells to PDPN- myofibroblasts in the stromal compartment of tumor patches. It is derived by dividing the number of B cells by the number of PDPN- myofibroblasts with an added small constant to avoid division by zero. This ratio provides a comparable measure across different patient cases by adjusting for variations in raw cell counts, facilitating the assessment of anti-tumor immune response based on the relative cellular composition within the tumor microenvironment. |
| nn5t6xps09uy | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | average_crypt_void_area | average_crypt_void_area represents the average area of the inner void spaces within the ring-like, crypt formations detected in a given tumor patch. It is determined by computing the area of the void in each valid crypt formation and then averaging these values. This parameter is numeric and normalized by functioning as an average measure, enabling direct comparisons between tumor patches from different patient cases. |
| noz315rfzwe7 | E,F,Ff,G,M,MF,MFp,Th,Treg | STROMAL_IMMUNE_RATIO | STROMAL_IMMUNE_RATIO is a normalized numeric metric that represents the ratio of stromal cells to immune cells in a tumor patch. This parameter is computed by first counting specific stromal cell types (including endothelial cells, fibroblasts, and myofibroblasts) and then counting specific immune cell types (such as granulocytes, macrophages, and certain T-cell subsets). The ratio provides a standardized measure that can be compared across different patient cases, indicating the balance between supportive stromal elements and immune presence, which may be associated with immune exclusion and prognosis. |
| nuiuo9wpxjtx | MF | max_nucleus_eccentricity | Parameter 'max_nucleus_eccentricity' represents the highest nucleus eccentricity derived from PDPN- myofibroblasts within the stromal compartment. This parameter is obtained by first filtering the cells to include only those myofibroblasts in the stromal region, then determining the shape of each cell nucleus by fitting an ellipse to its polygon representation. From the fitted ellipse, the major and minor axes are extracted to compute the eccentricity using the formula sqrt(1 - (minor_axis / major_axis)^2). The resulting eccentricity is a normalized numeric value between 0 and 1, where 0 indicates a perfect circle and 1 indicates a highly elongated form. As a normalized measure, it is directly comparable across different patient cases and patch regions. |
| nusu5r3jp586 | G | GRANULOCYTE_ORIENTATION_CV | GRANULOCYTE_ORIENTATION_CV represents the coefficient of variation of nucleus orientation angles of granulocytes within the tumor (epithelial) compartment. It is obtained by dividing the standard deviation by the mean (with a small constant added to avoid division by zero), yielding a normalized and dimensionless measure of variability that allows comparison across different cases. |
| nusu5r3jp586 | G | GRANULOCYTE_ORIENTATION_MEAN | GRANULOCYTE_ORIENTATION_MEAN indicates the average orientation angle of granulocyte nuclei (measured in degrees) within the tumor region. This metric summarizes the central tendency of the orientation angles calculated from the longest edge of each nucleus's minimal rotated rectangle. |
| nusu5r3jp586 | G | GRANULOCYTE_ORIENTATION_STD | GRANULOCYTE_ORIENTATION_STD denotes the standard deviation of the granulocyte nucleus orientation angles in the epithelial compartment. It measures the dispersion of the orientation angles around the mean, offering insight into how variable the orientations are across different granulocytes. |
| nusu5r3jp586 | G | GRANULOCYTE_ORIENTATION_MIN | GRANULOCYTE_ORIENTATION_MIN records the minimum observed orientation angle (in degrees) among granulocyte nuclei within the epithelial region, providing a lower boundary of the range of orientations. |
| nusu5r3jp586 | G | GRANULOCYTE_ORIENTATION_MAX | GRANULOCYTE_ORIENTATION_MAX captures the maximum observed orientation angle (in degrees) among granulocyte nuclei in the tumor compartment, defining the upper boundary of the orientation distribution. |
| nusu5r3jp586 | G | GRANULOCYTE_ORIENTATION_RANGE | GRANULOCYTE_ORIENTATION_RANGE is calculated as the difference between the maximum and minimum orientation angles, quantifying the overall span or range of nuclear orientation variations among granulocytes within the epithelial compartment. |
| nvhy5aall1is | TU,Tc,Th,Treg,B,MFp,MF,E,M | TUMOR_PDPN_MFB_MEAN_WEIGHTED_PERIMETER | TUMOR_PDPN_MFB_MEAN_WEIGHTED_PERIMETER: Represents the average perimeter of PDPN+ myofibroblast cells in the tumor compartment, with each cell’s perimeter weighted by its local tumor-to-immune cell ratio. This provides a normalized measure that allows comparisons across different patient cases and patches by taking into account both cell morphology and local microenvironment context. |
| nvhy5aall1is | TU,Tc,Th,Treg,B,MFp,MF,E,M | TUMOR_PDPN_MFB_STD_WEIGHTED_PERIMETER | TUMOR_PDPN_MFB_STD_WEIGHTED_PERIMETER: Quantifies the standard deviation of the weighted perimeters of PDPN+ myofibroblast cells in the tumor region. This metric indicates the variability in the adjusted cell perimeter measurements, helping to assess the degree of dispersion relative to the mean. |
| nvhy5aall1is | TU,Tc,Th,Treg,B,MFp,MF,E,M | TUMOR_PDPN_MFB_CV_WEIGHTED_PERIMETER | TUMOR_PDPN_MFB_CV_WEIGHTED_PERIMETER: The coefficient of variation for the weighted perimeters in the tumor compartment, computed as the standard deviation divided by the mean and expressed as a percentage. This normalized metric facilitates comparison of variability across different patches or patient samples. |
| nvhy5aall1is | TU,Tc,Th,Treg,B,MFp,MF,E,M | TUMOR_PDPN_MFB_MIN_WEIGHTED_PERIMETER | TUMOR_PDPN_MFB_MIN_WEIGHTED_PERIMETER: Denotes the minimum weighted perimeter value among the PDPN+ myofibroblast cells in the tumor compartment, reflecting the smallest adjusted cell perimeter after accounting for the local tumor-to-immune ratio. |
| nvhy5aall1is | TU,Tc,Th,Treg,B,MFp,MF,E,M | TUMOR_PDPN_MFB_MAX_WEIGHTED_PERIMETER | TUMOR_PDPN_MFB_MAX_WEIGHTED_PERIMETER: Represents the maximum weighted perimeter observed in the tumor compartment among PDPN+ myofibroblast cells, capturing the highest adjusted cell perimeter value after incorporating local cellular context. |
| nvhy5aall1is | TU,Tc,Th,Treg,B,MFp,MF,E,M | TUMOR_PDPN_MFB_SKEW_WEIGHTED_PERIMETER | TUMOR_PDPN_MFB_SKEW_WEIGHTED_PERIMETER: Measures the skewness in the distribution of weighted perimeters in the tumor compartment. This parameter assesses the asymmetry of the distribution, indicating whether there is a tendency toward higher or lower values, and highlighting potential outliers. |
| nvhy5aall1is | TU,Tc,Th,Treg,B,MFp,MF,E,M | STROMA_PDPN_MFB_MEAN_WEIGHTED_PERIMETER | STROMA_PDPN_MFB_MEAN_WEIGHTED_PERIMETER: Indicates the average weighted perimeter of PDPN+ myofibroblast cells in the stroma compartment, where the cell perimeter is adjusted by the local tumor-to-immune ratio. It provides a normalized metric that is comparable across different patient cases. |
| nvhy5aall1is | TU,Tc,Th,Treg,B,MFp,MF,E,M | STROMA_PDPN_MFB_STD_WEIGHTED_PERIMETER | STROMA_PDPN_MFB_STD_WEIGHTED_PERIMETER: Reflects the standard deviation of the weighted perimeters for PDPN+ myofibroblast cells in the stroma, offering insight into the variability of cell morphology adjusted for the microenvironment. |
| nvhy5aall1is | TU,Tc,Th,Treg,B,MFp,MF,E,M | STROMA_PDPN_MFB_CV_WEIGHTED_PERIMETER | STROMA_PDPN_MFB_CV_WEIGHTED_PERIMETER: The coefficient of variation in the stroma compartment, expressed as a percentage, compares the extent of variability in the weighted perimeters relative to their mean, aiding in normalized comparisons across samples. |
| nvhy5aall1is | TU,Tc,Th,Treg,B,MFp,MF,E,M | STROMA_PDPN_MFB_MIN_WEIGHTED_PERIMETER | STROMA_PDPN_MFB_MIN_WEIGHTED_PERIMETER: Denotes the minimum adjusted perimeter of PDPN+ myofibroblast cells in the stroma, capturing the lowest value after weighting by the local cellular context. |
| nvhy5aall1is | TU,Tc,Th,Treg,B,MFp,MF,E,M | STROMA_PDPN_MFB_MAX_WEIGHTED_PERIMETER | STROMA_PDPN_MFB_MAX_WEIGHTED_PERIMETER: Represents the maximum weighted perimeter for PDPN+ myofibroblast cells within the stroma, indicating the highest adjusted measure in that compartment. |
| nvhy5aall1is | TU,Tc,Th,Treg,B,MFp,MF,E,M | STROMA_PDPN_MFB_IQR_WEIGHTED_PERIMETER | STROMA_PDPN_MFB_IQR_WEIGHTED_PERIMETER: Measures the interquartile range (IQR) of weighted perimeters in the stroma compartment, which is the difference between the 75th and 25th percentile values. This provides a robust indicator of the spread of the middle 50% of the data. |
| nvhy5aall1is | TU,Tc,Th,Treg,B,MFp,MF,E,M | STROMA_PDPN_MFB_SKEW_WEIGHTED_PERIMETER | STROMA_PDPN_MFB_SKEW_WEIGHTED_PERIMETER: Assesses the skewness of the distribution of weighted perimeters among PDPN+ myofibroblast cells in the stroma, signaling the asymmetry and potential presence of outlier values in the adjusted data. |
| nvhy5aall1is | TU,Tc,Th,Treg,B,MFp,MF,E,M | STROMA_PDPN_MFB_KURTOSIS_WEIGHTED_PERIMETER | STROMA_PDPN_MFB_KURTOSIS_WEIGHTED_PERIMETER: Quantifies the kurtosis of the distribution of weighted perimeters in the stroma compartment. This metric describes the 'tailedness' of the distribution, indicating the presence of extreme values and the overall shape of the data distribution. |
| nvjtkyjy2cjz | Th,B,P | Th_proportion | Th_proportion: This parameter represents the normalized proportion of T helper cells among the total of T helper, B, and plasma cells located in the epithelial/tumor compartment of breast cancer tissue. It is calculated by dividing the count of T helper cells by the sum of counts of T helper, B, and plasma cells (with an adjustment to prevent division by zero), making it suitable for comparison across different patient cases. |
| nyy1hgc3j2gw | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | vessel_immunomodulation_index | vessel_immunomodulation_index measures the composite ratio of immunostimulatory cells to immunosuppressive cells near vessels. It is computed by taking the sum of counts for cytotoxic T cells, B lymphocytes, plasma cells, macrophages, myofibroblasts, and fibroblasts, and dividing this sum by the count of regulatory T cells. This normalized index enables comparison across patient cases by accounting for variations in cell density. |
| nyy1hgc3j2gw | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | tc_treg_ratio_near_vessels | tc_treg_ratio_near_vessels represents the ratio of cytotoxic T cells to regulatory T cells within the vessel buffer region. By normalizing the relative frequencies of these two cell types, it provides an insight into the local immune balance and can be compared across different cases. |
| nyy1hgc3j2gw | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | t_cell_cd8_percent | t_cell_cd8_percent indicates the percentage of cytotoxic T cells among all cells counted in the vicinity of vessels. It is calculated by dividing the count of cytotoxic T cells by the total cell count and multiplying by 100, offering a normalized metric for inter-patient comparison. |
| nyy1hgc3j2gw | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | t_cell_reg_percent | t_cell_reg_percent is the percentage of regulatory T cells in the vascular region. It is derived by dividing the regulatory T cell count by the total cell count in the region and then converting it into a percentage, providing a normalized measure of immunosuppressive cell presence. |
| nyy1hgc3j2gw | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | t_cell_cd4_percent | t_cell_cd4_percent represents the percentage of helper T cells in the area surrounding vessels. This value is obtained by relating the helper T cell count to the total cell count, thus normalizing the measure for comparison across different samples. |
| nyy1hgc3j2gw | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | b_cell_percent | b_cell_percent denotes the percentage of B lymphocytes near vessels. It is a normalized metric computed by dividing the B cell count by the total number of cells and multiplying by 100, reflecting the relative presence of B cells. |
| nyy1hgc3j2gw | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | plasma_cell_percent | plasma_cell_percent shows the percentage of plasma cells in the vascular vicinity. It is calculated as the proportion of plasma cells relative to the total cell count, making it a normalized parameter for assessing immune cell composition. |
| nyy1hgc3j2gw | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | macrophage_percent | macrophage_percent indicates the percentage of macrophages among the cells near vessels. This percentage is calculated by dividing the macrophage count by the total cell count in the region, offering a normalized measure of their presence. |
| nyy1hgc3j2gw | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | myofibroblast_pdpn_percent | myofibroblast_pdpn_percent reflects the percentage of myofibroblasts expressing PDPN found in the vessel-proximal region. It is computed as the ratio of these cells to the total count, providing a normalized value for comparison across different patient cases. |
| nyy1hgc3j2gw | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | fibroblast_fsp1_percent | fibroblast_fsp1_percent denotes the percentage of fibroblasts expressing FSP1 near vessels. This normalized parameter is determined by dividing the fibroblast count by the total cell count in the region, thus supporting inter-patient comparisons. |
| nyy1hgc3j2gw | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | epithelial_cell_percent | epithelial_cell_percent represents the percentage of epithelial cells, typically tumor cells, in the vascular region. This is calculated by comparing the epithelial cell count with the total cell count, producing a normalized metric. |
| nyy1hgc3j2gw | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | endothelial_cell_percent | endothelial_cell_percent indicates the percentage of endothelial cells within the area near vessels. It is derived by dividing the endothelial cell count by the overall cell count, offering a normalized value for comparison among patients. |
| nz5uowd4cgq5 | MFp | PDPN_MF_NUCLEUS_CIRC_VARIANCE | PDPN_MF_NUCLEUS_CIRC_VARIANCE quantifies the variability in nuclear circularity among PDPN-positive myofibroblasts within each patch. It is computed using the formula for circularity (4π*area divided by the square of the perimeter) for each cell, and the variance of these values is calculated. This parameter reflects the heterogeneity in nuclear shape and can be compared across patient cases due to its independent, descriptive nature. |
| nz5uowd4cgq5 | MFp | PDPN_MF_NUCLEUS_CIRC_MEAN | PDPN_MF_NUCLEUS_CIRC_MEAN represents the average nuclear circularity of PDPN-positive myofibroblasts in a patch. By averaging the values obtained from each cell's circularity calculation, this parameter provides a central measure of nuclear shape, which supports cross-case comparisons. |
| nz5uowd4cgq5 | MFp | PDPN_MF_NUCLEUS_CIRC_MIN | PDPN_MF_NUCLEUS_CIRC_MIN identifies the lowest observed nuclear circularity value among PDPN-positive myofibroblasts within a patch. This minimal value offers insight into the range of nuclear shape variability and is normalized for comparative analysis. |
| nz5uowd4cgq5 | MFp | PDPN_MF_NUCLEUS_CIRC_MAX | PDPN_MF_NUCLEUS_CIRC_MAX indicates the highest nuclear circularity value among PDPN-positive myofibroblasts in a patch. It highlights the extreme of nuclear shape measurements and, as a normalized metric, facilitates comparisons across different patient cases. |
| nzweu2cgqwhi | M,F,MFp,TU,Th | mean_max_chord_length | mean_max_chord_length represents the average of the maximum chord lengths measured across all macrophage-containing clusters. Each maximum chord length is determined as the largest Euclidean distance between any two cell centroids within a cluster, providing insight into the spatial span of these clusters. |
| nzweu2cgqwhi | M,F,MFp,TU,Th | median_max_chord_length | median_max_chord_length is the median value of the maximum chord lengths across the macrophage-laden clusters. This statistic gives a robust measure of central tendency, mitigating the effect of extreme values. |
| nzweu2cgqwhi | M,F,MFp,TU,Th | max_max_chord_length | max_max_chord_length denotes the highest value among the maximum chord lengths computed from all the clusters, highlighting the largest spatial extent observed in any macrophage-containing aggregation. |
| nzweu2cgqwhi | M,F,MFp,TU,Th | min_max_chord_length | min_max_chord_length indicates the smallest maximum chord length recorded among the clusters, representing the lower bound of cluster spans within the analyzed regions. |
| nzweu2cgqwhi | M,F,MFp,TU,Th | std_max_chord_length | std_max_chord_length captures the standard deviation of the maximum chord lengths across clusters, reflecting the variability and heterogeneity in the spatial dimensions of the clusters. |
| nzweu2cgqwhi | M,F,MFp,TU,Th | macrophage_density_in_clusters | macrophage_density_in_clusters is the ratio of the total number of macrophages to the total number of cells within all macrophage-containing clusters. This normalized measure facilitates comparison across different patient cases by accounting for variations in overall cell counts. |
| o0660d0c0obd | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | normalized_void_area | normalized_void_area: This parameter represents the total void area within the tissue divided by the overall tissue area, ensuring that the measurement is normalized and comparable across different patient cases by adjusting for variations in tissue size. |
| o0660d0c0obd | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | max_void_normalized_area | max_void_normalized_area: This metric reflects the area of the largest void region normalized by the total tissue area, allowing for direct comparison between different tumor patches by accounting for tissue area differences. |
| o0660d0c0obd | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | composite_void_score | composite_void_score: This is an aggregated score computed as the sum of cell-type weighted void scores, where each void’s area is weighted by the proportion of surrounding cells of specific types and then normalized by the tissue area. It provides an overall measure of tissue void characteristics that is comparable between cases. |
| o0660d0c0obd | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_void_score_TU | weighted_void_score_TU: For the cell type 'TU', this parameter measures the void area weighted by the proportion of epithelial cells in the buffer zone around each void and normalized by tissue area, allowing comparison across different patient samples. |
| o0660d0c0obd | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_void_score_Tc | weighted_void_score_Tc: This metric reflects the void area contribution weighted by the local proportion of CD8+ T cells in the vicinity of voids, normalized by tissue area for cross-case comparability. |
| o0660d0c0obd | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_void_score_Th | weighted_void_score_Th: This parameter quantifies the void area weighted by the relative abundance of CD4+ T cells around the voids, with normalization ensuring comparability between samples. |
| o0660d0c0obd | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_void_score_Treg | weighted_void_score_Treg: This score represents the void area weighted by the proportion of regulatory T cells in the surrounding buffer regions, adjusted for tissue area to allow comparisons. |
| o0660d0c0obd | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_void_score_B | weighted_void_score_B: For B cells, this parameter captures the void area weighted by the relative count of B cells in the vicinity of the voids, normalized by the tissue area. |
| o0660d0c0obd | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_void_score_P | weighted_void_score_P: This metric measures the void area weighted by the proportion of plasma cells found around the void regions, normalized by tissue area to facilitate comparison. |
| o0660d0c0obd | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_void_score_M | weighted_void_score_M: This parameter reflects the void area weighted by the relative abundance of macrophages in the surrounding buffer area, with normalization applied to account for differences in tissue size. |
| o0660d0c0obd | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_void_score_G | weighted_void_score_G: For granulocytes, this parameter evaluates the void area weighted by their local proportion in the void vicinity, ensuring comparability by normalizing with tissue area. |
| o0660d0c0obd | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_void_score_MFp | weighted_void_score_MFp: This metric represents the void area weighted by the proportion of myofibroblast_pdpn cells in the buffer zone, normalized by tissue area for consistent comparison. |
| o0660d0c0obd | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_void_score_MF | weighted_void_score_MF: This parameter quantifies the void area weighted by the local proportion of myofibroblast cells, normalized by tissue area to allow comparisons across cases. |
| o0660d0c0obd | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_void_score_Ff | weighted_void_score_Ff: This score measures the void area weighted by the relative presence of fibroblast_fsp1 cells in the neighborhood of voids, normalized to facilitate cross-sample comparisons. |
| o0660d0c0obd | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_void_score_F | weighted_void_score_F: For fibroblast cells, this parameter evaluates the void area weighted by the local cell proportion, with normalization ensuring that the metric is comparable between different tissue samples. |
| o0660d0c0obd | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_void_score_E | weighted_void_score_E: This metric reflects the void area weighted by the proportion of endothelial cells around void regions, normalized by tissue area for effective inter-case analysis. |
| o0660d0c0obd | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_void_score_A | weighted_void_score_A: For ap cells, this parameter measures the void area weighted by the local abundance of these cells in the surrounding buffer, normalized by tissue area to allow direct comparisons. |
| o37ukl0ly6vh | G,Th | G_TH_RATIO | G_TH_RATIO is a normalized numerical parameter that represents the ratio of granulocytes to T helper cells within a specific tissue patch. It is computed by dividing the count of granulocytes by the count of T helper cells, ensuring that comparisons can be made across different patient cases and tumor regions. This ratio provides insight into the inflammatory environment of the tissue, with a higher value potentially indicating a pro-tumor inflammatory milieu. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | TU_MAX_CHORD_LENGTH_MEAN | TU_MAX_CHORD_LENGTH_MEAN measures the average of the maximum chord lengths across tumor (epithelial) cell nuclei. The maximum chord length for each cell represents the greatest distance between any two points along the nucleus boundary, reflecting the characteristic nuclear size. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | TU_MAX_CHORD_LENGTH_MEDIAN | TU_MAX_CHORD_LENGTH_MEDIAN provides the median value of the maximum chord lengths for tumor cell nuclei, offering a robust central tendency of this morphological measurement. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | TU_MAX_CHORD_LENGTH_MIN | TU_MAX_CHORD_LENGTH_MIN captures the smallest value of the maximum chord length among tumor cell nuclei, indicating the lower boundary of nuclear dimension variability within this cell population. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | TU_MAX_CHORD_LENGTH_MAX | TU_MAX_CHORD_LENGTH_MAX represents the largest maximum chord length observed among tumor cell nuclei, highlighting the upper limit of nuclear size in this group. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | TU_MAX_CHORD_LENGTH_STD | TU_MAX_CHORD_LENGTH_STD quantifies the standard deviation of the maximum chord lengths for tumor cell nuclei, reflecting the variability or dispersion in nuclear sizes. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | Th_MAX_CHORD_LENGTH_MEAN | Th_MAX_CHORD_LENGTH_MEAN measures the average maximum chord length of T helper cell nuclei, summarizing their overall nuclear dimension based on the longest distance across each nucleus. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | Th_MAX_CHORD_LENGTH_MEDIAN | Th_MAX_CHORD_LENGTH_MEDIAN provides the median of maximum chord lengths for T helper cells, offering a central value that is less sensitive to outliers. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | Th_MAX_CHORD_LENGTH_MIN | Th_MAX_CHORD_LENGTH_MIN captures the minimum maximum chord length among T helper cell nuclei, indicating the smallest nuclear dimension found in this subpopulation. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | Th_MAX_CHORD_LENGTH_MAX | Th_MAX_CHORD_LENGTH_MAX represents the maximum value of the maximum chord length for T helper cell nuclei, highlighting the greatest nuclear extension in this group. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | Th_MAX_CHORD_LENGTH_STD | Th_MAX_CHORD_LENGTH_STD quantifies the variation in the maximum chord lengths of T helper cell nuclei, providing insight into the consistency of nuclear sizes. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | Treg_MAX_CHORD_LENGTH_MEAN | Treg_MAX_CHORD_LENGTH_MEAN measures the average maximum chord length of T regulatory cell nuclei, summarizing the characteristic maximal nuclear distance for this cell type. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | Treg_MAX_CHORD_LENGTH_MEDIAN | Treg_MAX_CHORD_LENGTH_MEDIAN provides the median of the maximum chord lengths for T regulatory cells, reflecting the typical nuclear size within this group. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | Treg_MAX_CHORD_LENGTH_MIN | Treg_MAX_CHORD_LENGTH_MIN captures the minimum of the maximum chord lengths in T regulatory cell nuclei, indicating the lower extreme of nuclear dimensions. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | Treg_MAX_CHORD_LENGTH_MAX | Treg_MAX_CHORD_LENGTH_MAX represents the highest maximum chord length observed in T regulatory cell nuclei, marking the upper extreme of nuclear size. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | Treg_MAX_CHORD_LENGTH_STD | Treg_MAX_CHORD_LENGTH_STD quantifies the standard deviation of the maximum chord lengths in T regulatory cell nuclei, showing the degree of variation in nuclear sizes. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | B_MAX_CHORD_LENGTH_MEAN | B_MAX_CHORD_LENGTH_MEAN measures the average maximum chord length of B cell nuclei, indicating the typical maximal nuclear distance within this immune cell population. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | B_MAX_CHORD_LENGTH_MEDIAN | B_MAX_CHORD_LENGTH_MEDIAN provides the median of maximum chord lengths for B cells, capturing the central tendency of nuclear size measurements. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | B_MAX_CHORD_LENGTH_MIN | B_MAX_CHORD_LENGTH_MIN captures the smallest maximum chord length observed among B cell nuclei, representing the lower boundary of their nuclear dimension distribution. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | B_MAX_CHORD_LENGTH_MAX | B_MAX_CHORD_LENGTH_MAX represents the largest maximum chord length among B cell nuclei, highlighting the upper limit of nuclear sizes in this group. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | B_MAX_CHORD_LENGTH_STD | B_MAX_CHORD_LENGTH_STD quantifies the variability in maximum chord lengths for B cell nuclei, reflecting the spread in nuclear size measurements. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | P_MAX_CHORD_LENGTH_MEAN | P_MAX_CHORD_LENGTH_MEAN measures the average maximum chord length of plasma cell nuclei, summarizing their characteristic largest nuclear diameter. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | P_MAX_CHORD_LENGTH_MEDIAN | P_MAX_CHORD_LENGTH_MEDIAN provides the median value of maximum chord lengths for plasma cells, representing a robust central measurement of nuclear size. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | P_MAX_CHORD_LENGTH_MIN | P_MAX_CHORD_LENGTH_MIN captures the minimum maximum chord length among plasma cell nuclei, indicating the smallest nuclear dimension within this group. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | P_MAX_CHORD_LENGTH_MAX | P_MAX_CHORD_LENGTH_MAX represents the highest maximum chord length observed in plasma cell nuclei, marking the upper extreme of nuclear size. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | P_MAX_CHORD_LENGTH_STD | P_MAX_CHORD_LENGTH_STD quantifies the standard deviation of maximum chord lengths in plasma cell nuclei, highlighting the variability in their nuclear dimensions. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | M_MAX_CHORD_LENGTH_MEAN | M_MAX_CHORD_LENGTH_MEAN measures the average maximum chord length of macrophage nuclei, summarizing the typical maximal nuclear distance for these cells. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | M_MAX_CHORD_LENGTH_MEDIAN | M_MAX_CHORD_LENGTH_MEDIAN provides the median of the maximum chord lengths for macrophages, offering a central value for nuclear size. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | M_MAX_CHORD_LENGTH_MIN | M_MAX_CHORD_LENGTH_MIN captures the minimum maximum chord length among macrophage nuclei, indicating the smallest observed nuclear extension. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | M_MAX_CHORD_LENGTH_MAX | M_MAX_CHORD_LENGTH_MAX represents the highest maximum chord length among macrophage nuclei, showing the largest nuclear size in this population. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | M_MAX_CHORD_LENGTH_STD | M_MAX_CHORD_LENGTH_STD quantifies the dispersion of the maximum chord lengths in macrophage nuclei, reflecting the variability in their nuclear morphology. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | MFp_MAX_CHORD_LENGTH_MEAN | MFp_MAX_CHORD_LENGTH_MEAN measures the average maximum chord length of myofibroblasts with high PDPN expression, summarizing their typical maximal nuclear size. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | MFp_MAX_CHORD_LENGTH_MEDIAN | MFp_MAX_CHORD_LENGTH_MEDIAN provides the median of the maximum chord lengths for MFp cells, indicating the central tendency of their nuclear dimensions. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | MFp_MAX_CHORD_LENGTH_MIN | MFp_MAX_CHORD_LENGTH_MIN captures the minimum maximum chord length observed in MFp cell nuclei, representing the lower extreme of nuclear sizes. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | MFp_MAX_CHORD_LENGTH_MAX | MFp_MAX_CHORD_LENGTH_MAX represents the highest maximum chord length among MFp cell nuclei, highlighting the upper limit of nuclear dimensions in this subset. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | MFp_MAX_CHORD_LENGTH_STD | MFp_MAX_CHORD_LENGTH_STD quantifies the standard deviation of the maximum chord lengths for MFp cells, reflecting variability in their nuclear sizes. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | MF_MAX_CHORD_LENGTH_MEAN | MF_MAX_CHORD_LENGTH_MEAN measures the average maximum chord length of myofibroblast nuclei, providing a summary of their typical maximal nuclear distance. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | MF_MAX_CHORD_LENGTH_MEDIAN | MF_MAX_CHORD_LENGTH_MEDIAN provides the median maximum chord length for myofibroblasts, representing the central value of nuclear size measurements in this group. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | MF_MAX_CHORD_LENGTH_MIN | MF_MAX_CHORD_LENGTH_MIN captures the minimum maximum chord length among myofibroblast nuclei, indicating the smallest nuclear size observed. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | MF_MAX_CHORD_LENGTH_MAX | MF_MAX_CHORD_LENGTH_MAX represents the largest maximum chord length among myofibroblast nuclei, highlighting the upper limit of nuclear dimension. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | MF_MAX_CHORD_LENGTH_STD | MF_MAX_CHORD_LENGTH_STD quantifies the variability in the maximum chord lengths for myofibroblasts, reflecting differences in nuclear morphology within this cell type. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | Ff_MAX_CHORD_LENGTH_MEAN | Ff_MAX_CHORD_LENGTH_MEAN measures the average maximum chord length of FSP1-positive fibroblast nuclei, summarizing the characteristic maximal nuclear distance for this cell population. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | Ff_MAX_CHORD_LENGTH_MEDIAN | Ff_MAX_CHORD_LENGTH_MEDIAN provides the median value of maximum chord lengths for FSP1-positive fibroblasts, offering a robust central measure of nuclear size. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | Ff_MAX_CHORD_LENGTH_MIN | Ff_MAX_CHORD_LENGTH_MIN captures the smallest maximum chord length among FSP1-positive fibroblast nuclei, indicating the lower boundary of nuclear dimensions. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | Ff_MAX_CHORD_LENGTH_MAX | Ff_MAX_CHORD_LENGTH_MAX represents the highest maximum chord length observed among FSP1-positive fibroblast nuclei, marking the upper extreme of nuclear size. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | Ff_MAX_CHORD_LENGTH_STD | Ff_MAX_CHORD_LENGTH_STD quantifies the standard deviation of maximum chord lengths for FSP1-positive fibroblasts, indicating the variability in their nuclear morphology. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | E_MAX_CHORD_LENGTH_MEAN | E_MAX_CHORD_LENGTH_MEAN measures the average maximum chord length of endothelial cell nuclei, summarizing the typical maximal distance within these cells’ nuclear boundaries. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | E_MAX_CHORD_LENGTH_MEDIAN | E_MAX_CHORD_LENGTH_MEDIAN provides the median maximum chord length for endothelial cells, reflecting the central tendency of their nuclear size measurements. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | E_MAX_CHORD_LENGTH_MIN | E_MAX_CHORD_LENGTH_MIN captures the minimum maximum chord length among endothelial cell nuclei, representing the smallest nuclear dimension observed. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | E_MAX_CHORD_LENGTH_MAX | E_MAX_CHORD_LENGTH_MAX represents the highest maximum chord length among endothelial cell nuclei, highlighting the largest nuclear extent in this population. |
| o5e7loe72rdf | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | E_MAX_CHORD_LENGTH_STD | E_MAX_CHORD_LENGTH_STD quantifies the variability in maximum chord lengths for endothelial cells, indicating the dispersion of nuclear size measurements. |
| o6m2bv7yxt7m | TU,P,Ff,F,MFp,MF,M,G | core_plasma_fibroblast_ratio | core_plasma_fibroblast_ratio: A normalized metric representing the ratio of plasma cells to fibroblasts in the tumor core region. This parameter adjusts for differences in fibroblast counts using a small constant to avoid division errors and provides a comparative measure across patients. |
| o6m2bv7yxt7m | TU,P,Ff,F,MFp,MF,M,G | periphery_plasma_fibroblast_ratio | periphery_plasma_fibroblast_ratio: A normalized ratio indicating the balance between plasma cells and fibroblasts in the tumor periphery region. It is calculated by dividing plasma cell counts by fibroblast counts, thus enabling comparison across different tumor samples. |
| o6m2bv7yxt7m | TU,P,Ff,F,MFp,MF,M,G | core_periphery_ratio_difference | core_periphery_ratio_difference: A normalized differential measure showing the difference between the plasma-to-fibroblast ratios in the tumor core and periphery. It highlights spatial variations in the tumor microenvironment relative to cell type proportions. |
| o6m2bv7yxt7m | TU,P,Ff,F,MFp,MF,M,G | total_plasma_fibroblast_ratio | total_plasma_fibroblast_ratio: A globally normalized ratio assessing the overall balance of plasma cells to fibroblasts across the entire tumor region (core and periphery combined). This metric facilitates inter-patient comparisons by providing a standard relative measure. |
| o6m2bv7yxt7m | TU,P,Ff,F,MFp,MF,M,G | core_plasma_density_per_mm2 | core_plasma_density_per_mm2: A normalized density measure representing the number of plasma cells per square millimeter in the tumor core region. It accounts for the area of the core, making it suitable for comparisons between cases. |
| o6m2bv7yxt7m | TU,P,Ff,F,MFp,MF,M,G | core_fibroblast_density_per_mm2 | core_fibroblast_density_per_mm2: A normalized density estimate of fibroblasts in the tumor core, calculated as cells per square millimeter. This parameter corrects for the core area differences, enabling cross-patient analysis. |
| o6m2bv7yxt7m | TU,P,Ff,F,MFp,MF,M,G | periphery_plasma_density_per_mm2 | periphery_plasma_density_per_mm2: A normalized measure of plasma cell density in the tumor periphery, expressed in cells per square millimeter. It uses the area of the periphery to yield a comparative metric among different patient samples. |
| o6m2bv7yxt7m | TU,P,Ff,F,MFp,MF,M,G | periphery_fibroblast_density_per_mm2 | periphery_fibroblast_density_per_mm2: A normalized density metric for fibroblasts in the tumor periphery, quantified as cells per square millimeter. By considering the periphery area, this parameter allows for standardized inter-case comparisons. |
| o9isby80amno | Treg,B,Th,M,MFp,TU | Proportion_Elongated_Th | Proportion_Elongated_Th measures the fraction of T helper cells located in the stromal compartment that have an elongated nuclear shape. The elongation is determined by comparing the major and minor axes of the cell nucleus, and a cell is classified as elongated if this ratio exceeds a fixed threshold (2.0). This ratio provides a normalized metric to compare the activation state or invasive properties of these cells across different patient cases. |
| o9isby80amno | Treg,B,Th,M,MFp,TU | Proportion_Elongated_M | Proportion_Elongated_M measures the fraction of macrophages in the stromal compartment whose nuclei exhibit elongation. The parameter is calculated by determining the elongation ratio of each macrophage (by calculating the major and minor axes of the nuclear shape) and then computing the proportion that exceed the fixed threshold. This resulting value is normalized, allowing comparisons across patients. |
| o9isby80amno | Treg,B,Th,M,MFp,TU | Proportion_Elongated_MFp | Proportion_Elongated_MFp measures the fraction of PDPN+ myofibroblasts found in the stromal compartment that demonstrate an elongated nuclear shape. The elongation is computed based on the ratio of the nucleus's major to minor axis, with cells above the threshold being labeled as elongated. This normalized metric is useful for comparing tissue characteristics between cases. |
| o9isby80amno | Treg,B,Th,M,MFp,TU | Proportion_Elongated_TU | Proportion_Elongated_TU measures the fraction of tumor cells (epithelial cells within the stromal compartment) that have elongated nuclei. The measurement involves calculating the elongation ratio of each cell nucleus and classifying cells as elongated if the ratio exceeds the threshold. The resulting proportion provides a normalized value ideally suited for inter-patient comparative analysis. |
| ob2nfiv0cddt | M,G,B | macrophage_proportion | The 'macrophage_proportion' parameter quantifies the relative abundance of macrophage cells among three inflammatory cell types (macrophages, granulocytes, and B cells) within the stromal compartment. It is calculated by dividing the number of macrophage cells by the sum of macrophages, granulocytes, and B cells in each analyzed patch. This normalized, numeric value enables comparisons across different patient cases and tissue patches, which is essential for assessing the protumor environment hypothesis. |
| onzw9jn1l2lj | Tc,Th,Treg,B,MFp,F,M | Tc_epithelial_avg_distance | Tc_epithelial_avg_distance represents the average Euclidean distance from the centroids of Cytotoxic T cells located in the epithelial compartment to the nearest point on the epithelial-stromal interface, measured in micrometers. This metric enables comparison of the spatial infiltration characteristics of Cytotoxic T cells across different patient tumor patches. |
| onzw9jn1l2lj | Tc,Th,Treg,B,MFp,F,M | MFp_epithelial_avg_distance | MFp_epithelial_avg_distance represents the average Euclidean distance from the centroids of PDPN+ Myofibroblasts located in the epithelial compartment to the epithelial-stromal boundary, measured in micrometers. It provides insights into the spatial positioning of these stromal cells relative to the tumor boundary in different cases. |
| onzw9jn1l2lj | Tc,Th,Treg,B,MFp,F,M | F_epithelial_avg_distance | F_epithelial_avg_distance represents the average Euclidean distance from the centroids of Fibroblasts within the epithelial compartment to the epithelial-stromal interface, measured in micrometers. It reflects the localization of fibroblasts relative to the tumor-stroma border for inter-patient comparisons. |
| onzw9jn1l2lj | Tc,Th,Treg,B,MFp,F,M | M_epithelial_avg_distance | M_epithelial_avg_distance represents the average Euclidean distance from the centroids of Macrophages in the epithelial compartment to the nearest point on the epithelial-stromal boundary, measured in micrometers. It is used to evaluate the spatial behavior of macrophages in different tumor regions. |
| onzw9jn1l2lj | Tc,Th,Treg,B,MFp,F,M | Tc_stromal_avg_distance | Tc_stromal_avg_distance represents the average Euclidean distance from the centroids of Cytotoxic T cells located in the stromal compartment to the epithelial-stromal interface, measured in micrometers. This metric allows for standardized comparisons of immune cell infiltration within stromal areas across cases. |
| onzw9jn1l2lj | Tc,Th,Treg,B,MFp,F,M | Th_stromal_avg_distance | Th_stromal_avg_distance represents the average Euclidean distance from the centroids of Helper T cells within the stromal compartment to the epithelial-stromal boundary, measured in micrometers. It quantifies how Helper T cells are positioned in the stromal area relative to the tumor boundary. |
| onzw9jn1l2lj | Tc,Th,Treg,B,MFp,F,M | Treg_stromal_avg_distance | Treg_stromal_avg_distance represents the average Euclidean distance from the centroids of Regulatory T cells located in the stromal compartment to the epithelial-stromal boundary, measured in micrometers. This parameter helps in assessing spatial immune regulation in the tumor microenvironment. |
| onzw9jn1l2lj | Tc,Th,Treg,B,MFp,F,M | B_stromal_avg_distance | B_stromal_avg_distance represents the average Euclidean distance from the centroids of B cells in the stromal compartment to the nearest point on the epithelial-stromal interface, measured in micrometers. It is used to compare the infiltration patterns of B cells among different patient samples. |
| onzw9jn1l2lj | Tc,Th,Treg,B,MFp,F,M | MFp_stromal_avg_distance | MFp_stromal_avg_distance represents the average Euclidean distance from the centroids of PDPN+ Myofibroblasts located in the stromal compartment to the epithelial-stromal interface, measured in micrometers. This metric aids in evaluating the spatial arrangement of these cells in the tumor stroma. |
| onzw9jn1l2lj | Tc,Th,Treg,B,MFp,F,M | F_stromal_avg_distance | F_stromal_avg_distance represents the average Euclidean distance from the centroids of Fibroblasts in the stromal compartment to the nearest epithelial-stromal boundary, measured in micrometers. It provides standardized spatial metrics for fibroblast positioning in the stroma. |
| onzw9jn1l2lj | Tc,Th,Treg,B,MFp,F,M | M_stromal_avg_distance | M_stromal_avg_distance represents the average Euclidean distance from the centroids of Macrophages within the stromal compartment to the epithelial-stromal interface, measured in micrometers. This enables consistent comparisons of macrophage spatial distribution across tumor samples. |
| onzw9jn1l2lj | Tc,Th,Treg,B,MFp,F,M | Tc_differential | Tc_differential is defined as the difference between the average distance of Cytotoxic T cells to the epithelial-stromal interface in the epithelial compartment and in the stromal compartment. This differential metric, measured in micrometers, indicates the relative preference of these cells for either compartment. |
| onzw9jn1l2lj | Tc,Th,Treg,B,MFp,F,M | MFp_differential | MFp_differential is the difference between the average distances of PDPN+ Myofibroblasts to the epithelial-stromal boundary in the epithelial versus the stromal compartments. This parameter highlights compartment-specific spatial patterns for these cells. |
| onzw9jn1l2lj | Tc,Th,Treg,B,MFp,F,M | F_differential | F_differential is the difference between the average distances of Fibroblasts to the epithelial-stromal interface in the epithelial and stromal compartments, measured in micrometers. It offers a normalized view of fibroblast distribution relative to the tumor boundary. |
| onzw9jn1l2lj | Tc,Th,Treg,B,MFp,F,M | M_differential | M_differential is the difference between the average distances of Macrophages to the epithelial-stromal boundary in the epithelial and stromal compartments, measured in micrometers. This metric quantifies the spatial difference in macrophage localization between the two compartments. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | clustering_index | clustering_index: A normalized metric representing the overall tightness of spatial clustering among the selected cell types. It is calculated as the reciprocal of the average pairwise Euclidean distance between all cell centroids, where higher values indicate tighter clustering in the tumor microenvironment. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | myofibroblast_pdpn_to_myofibroblast_pdpn_clustering | myofibroblast_pdpn_to_myofibroblast_pdpn_clustering: A normalized metric measuring the degree of clustering among myofibroblast_pdpn cells. It is determined as the reciprocal of the mean distance between pairs of myofibroblast_pdpn cells, indicating how closely these cells are grouped together. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | myofibroblast_pdpn_to_b_cell_clustering | myofibroblast_pdpn_to_b_cell_clustering: A normalized parameter quantifying the spatial proximity between myofibroblast_pdpn cells and b cells. It uses the reciprocal of the average distance between their centroids, so higher values suggest a closer interaction between the two cell types. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | myofibroblast_pdpn_to_plasma_cell_clustering | myofibroblast_pdpn_to_plasma_cell_clustering: A normalized metric that assesses the clustering between myofibroblast_pdpn cells and plasma cells by computing the reciprocal of their average pairwise distance, reflecting tighter clustering with higher values. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | myofibroblast_pdpn_to_t_cell_reg_clustering | myofibroblast_pdpn_to_t_cell_reg_clustering: A normalized measure capturing the spatial co-localization between myofibroblast_pdpn cells and regulatory T cells (t_cell_reg). It is defined as the reciprocal of the mean distance between cells of these types, with higher values indicating closer proximity. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | myofibroblast_pdpn_to_t_cell_cd4_clustering | myofibroblast_pdpn_to_t_cell_cd4_clustering: A normalized metric that evaluates the spatial proximity between myofibroblast_pdpn cells and helper T cells (t_cell_cd4). It is calculated as the reciprocal of the average distance between their centroids, so higher values denote tighter clustering. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | myofibroblast_pdpn_to_macrophage_clustering | myofibroblast_pdpn_to_macrophage_clustering: A normalized parameter representing the degree of spatial clustering between myofibroblast_pdpn cells and macrophages. It uses the reciprocal of the mean distance between these cells, where increased values indicate stronger colocalization. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | myofibroblast_pdpn_to_epithelial_cell_clustering | myofibroblast_pdpn_to_epithelial_cell_clustering: A normalized metric that measures the closeness between myofibroblast_pdpn cells and epithelial cells by computing the reciprocal of their average pairwise distance, reflecting tighter spatial arrangement with higher values. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | b_cell_to_b_cell_clustering | b_cell_to_b_cell_clustering: A normalized metric that assesses how closely b cells are clustered together. It is derived as the reciprocal of the average distance between pairs of b cells, with higher values indicating more compact clustering. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | b_cell_to_plasma_cell_clustering | b_cell_to_plasma_cell_clustering: A normalized parameter that quantifies the spatial arrangement between b cells and plasma cells, determined by taking the reciprocal of the mean distance between their centroids. Higher values indicate a tighter spatial relationship. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | b_cell_to_t_cell_reg_clustering | b_cell_to_t_cell_reg_clustering: A normalized metric representing the degree of clustering between b cells and regulatory T cells (t_cell_reg). It is computed as the reciprocal of the average inter-cell distance, where higher values signify closer proximity. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | b_cell_to_t_cell_cd4_clustering | b_cell_to_t_cell_cd4_clustering: A normalized measure of the spatial proximity between b cells and helper T cells (t_cell_cd4). It is calculated as the reciprocal of the average distance between the two cell types, indicating tighter clustering with higher values. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | b_cell_to_macrophage_clustering | b_cell_to_macrophage_clustering: A normalized metric that evaluates the clustering between b cells and macrophages by taking the reciprocal of the mean distance between their centroids. Higher values denote a closer spatial relationship. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | b_cell_to_epithelial_cell_clustering | b_cell_to_epithelial_cell_clustering: A normalized parameter that quantifies the spatial relationship between b cells and epithelial cells, computed as the reciprocal of the average inter-cell distance. Higher values indicate that the cells are more tightly clustered. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | plasma_cell_to_plasma_cell_clustering | plasma_cell_to_plasma_cell_clustering: A normalized metric that measures the clustering among plasma cells. It is the reciprocal of the average distance between pairs of plasma cells, with higher values reflecting tighter grouping. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | plasma_cell_to_t_cell_reg_clustering | plasma_cell_to_t_cell_reg_clustering: A normalized parameter representing the spatial proximity between plasma cells and regulatory T cells (t_cell_reg). It uses the reciprocal of the mean distance between these cells, indicating greater clustering with higher values. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | plasma_cell_to_t_cell_cd4_clustering | plasma_cell_to_t_cell_cd4_clustering: A normalized metric assessing the spatial closeness between plasma cells and helper T cells (t_cell_cd4). It is defined as the reciprocal of the average pairwise distance, where higher values suggest nearer positioning. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | plasma_cell_to_macrophage_clustering | plasma_cell_to_macrophage_clustering: A normalized parameter quantifying the spatial clustering between plasma cells and macrophages by using the reciprocal of the mean inter-cell distance, with higher values indicative of tighter clustering. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | plasma_cell_to_epithelial_cell_clustering | plasma_cell_to_epithelial_cell_clustering: A normalized metric that measures the proximity between plasma cells and epithelial cells. It is calculated as the reciprocal of the average distance between the two cell types, so higher values denote stronger clustering. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | t_cell_reg_to_t_cell_reg_clustering | t_cell_reg_to_t_cell_reg_clustering: A normalized metric evaluating the degree of clustering among regulatory T cells (t_cell_reg). It is computed as the reciprocal of the average distance between these cells, with higher values indicating more compact clustering. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | t_cell_reg_to_t_cell_cd4_clustering | t_cell_reg_to_t_cell_cd4_clustering: A normalized parameter that captures the spatial proximity between regulatory T cells (t_cell_reg) and helper T cells (t_cell_cd4). It is derived as the reciprocal of the mean distance between them, where higher values mean closer clustering. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | t_cell_reg_to_macrophage_clustering | t_cell_reg_to_macrophage_clustering: A normalized metric that measures the spatial closeness between regulatory T cells (t_cell_reg) and macrophages. It is calculated as the reciprocal of the average distance, indicating that higher values reflect tighter clustering between these cell types. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | t_cell_reg_to_epithelial_cell_clustering | t_cell_reg_to_epithelial_cell_clustering: A normalized parameter quantifying the degree of spatial co-localization between regulatory T cells (t_cell_reg) and epithelial cells. It uses the reciprocal of the mean pairwise distance with higher values suggesting closer interactions. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | t_cell_cd4_to_t_cell_cd4_clustering | t_cell_cd4_to_t_cell_cd4_clustering: A normalized metric assessing the clustering among helper T cells (t_cell_cd4). It is defined as the reciprocal of the average distance between cell pairs, with higher values indicating more concentrated clustering. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | t_cell_cd4_to_macrophage_clustering | t_cell_cd4_to_macrophage_clustering: A normalized parameter that evaluates the spatial proximity between helper T cells (t_cell_cd4) and macrophages by taking the reciprocal of their mean inter-cell distance, where higher values denote tighter clustering. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | t_cell_cd4_to_epithelial_cell_clustering | t_cell_cd4_to_epithelial_cell_clustering: A normalized metric measuring the closeness between helper T cells (t_cell_cd4) and epithelial cells. It is computed as the reciprocal of the average distance, so higher values indicate a more compact spatial arrangement. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | macrophage_to_macrophage_clustering | macrophage_to_macrophage_clustering: A normalized metric representing the degree of clustering among macrophages, computed as the reciprocal of the mean distance between them, with higher values indicating closer grouping. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | macrophage_to_epithelial_cell_clustering | macrophage_to_epithelial_cell_clustering: A normalized parameter that quantifies the spatial proximity between macrophages and epithelial cells. It is calculated as the reciprocal of the average pairwise distance between them, where higher values reflect stronger clustering. |
| oo4b0saemdgm | MFp,B,P,Treg,Th,M,TU | epithelial_cell_to_epithelial_cell_clustering | epithelial_cell_to_epithelial_cell_clustering: A normalized metric measuring the spatial clustering among epithelial cells. It is determined as the reciprocal of the average distance between pairs of these cells, indicating tighter clustering with higher values. |
| oxtb07j8p6t0 | Tc,Treg,B,P,M,F | boundary_infiltration_diversity_index | The boundary infiltration diversity index measures the diversity of six specific cell types—cytotoxic T cells, T regulatory cells, B cells, plasma cells, macrophages, and FSP1- fibroblasts—within a defined 40μm buffer zone around the tumor boundary. This index is computed using the Shannon diversity formula, where individual cell counts are first normalized into relative proportions, allowing for direct comparisons across different patient cases. The parameter is numeric and represents a normalized metric reflecting the complexity of the tumor microenvironment at the tumor-stroma interface. |
| oyan3anr70zd | TU | MEDIAN_NUCLEUS_ELONGATION_FACTOR_BOUNDARY_TUMOR_CELLS | This parameter measures the median elongation factor of tumor cell nuclei located at the tumor-stromal interface. The elongation factor is defined as the ratio of the longer side to the shorter side of the minimum rotated rectangle that encloses each tumor cell nucleus. As a normalized, dimensionless ratio derived from geometric properties, it enables comparisons across different patient cases. |
| oz62k9a0fuvq | MFp,MF,Ff,B,Treg,Th,M | tumor_overlap_index | tumor_overlap_index is a normalized metric that quantifies the alignment between the nuclear polarity angles of fibroblast and immune cells within the tumor compartment. It is calculated by first determining the mean minimal angular difference between the cell types, then normalizing this difference by dividing by 90, and finally subtracting the result from 1. The resulting value ranges from 0 (no alignment) to 1 (perfect alignment), making it suitable for comparing different patient cases. |
| oz62k9a0fuvq | MFp,MF,Ff,B,Treg,Th,M | stroma_overlap_index | stroma_overlap_index operates similarly to tumor_overlap_index, but it is computed for the stroma compartment. This parameter measures the degree of alignment in nuclear polarity between fibroblast and immune cells in the stromal region, following the same normalization process and yielding values between 0 and 1 for effective cross-case comparison. |
| p14ux16zy2l3 | G,Ff,Treg,A | Ff_density_bin1 | Ff_density_bin1: This parameter represents the normalized cell density of FSP1+ fibroblasts within the first radial distance bin from the tumor boundary. It is computed by dividing the count of FSP1+ fibroblasts falling within the annular segment by the area of that segment, producing a rate (cells per unit area) that enables direct comparison between different regions or patients. |
| p14ux16zy2l3 | G,Ff,Treg,A | Ff_density_bin2 | Ff_density_bin2: This parameter represents the normalized cell density of FSP1+ fibroblasts in the second radial bin from the tumor margin. The value is calculated as the number of FSP1+ fibroblasts in this specific annular region divided by the area of that bin, yielding a comparable metric across samples. |
| p14ux16zy2l3 | G,Ff,Treg,A | Ff_density_bin3 | Ff_density_bin3: This parameter measures the normalized cell density of FSP1+ fibroblasts within the third radial distance range from the tumor boundary. It is obtained by standardizing cell counts by the area of the corresponding annular segment, ensuring comparison is based on density rather than raw numbers. |
| p14ux16zy2l3 | G,Ff,Treg,A | Ff_density_bin4 | Ff_density_bin4: This parameter indicates the normalized cell density of FSP1+ fibroblasts in the fourth distance bin from the tumor edge. The value results from dividing the cell count in this annular region by its area, providing a normalized metric for analysis. |
| p14ux16zy2l3 | G,Ff,Treg,A | Ff_density_bin5 | Ff_density_bin5: This parameter provides the normalized cell density of FSP1+ fibroblasts in the fifth radial bin measured from the tumor boundary. It is computed as the ratio of the cell count to the area of the annular segment, ensuring normalization across different samples. |
| p14ux16zy2l3 | G,Ff,Treg,A | A_density_bin1 | A_density_bin1: This parameter reflects the normalized cell density of antigen presenting cells within the first radial distance bin from the tumor boundary. The cell count in the annular region is normalized by the area, yielding a density measure useful for comparative analysis. |
| p14ux16zy2l3 | G,Ff,Treg,A | A_density_bin2 | A_density_bin2: This parameter represents the normalized cell density of antigen presenting cells in the second radial bin from the tumor margin. The density is calculated by dividing the number of cells in this bin by the area of the corresponding annular segment. |
| p14ux16zy2l3 | G,Ff,Treg,A | A_density_bin3 | A_density_bin3: This parameter captures the normalized density of antigen presenting cells in the third radial bin from the tumor interface. It is measured as the ratio of the cell count to the area of the annular region, enabling comparisons between cases. |
| p14ux16zy2l3 | G,Ff,Treg,A | A_density_bin4 | A_density_bin4: This parameter indicates the normalized cell density of antigen presenting cells in the fourth radial bin. The calculation normalizes the cell count by the area of the bin, providing a standardized measure across different tumor patches. |
| p14ux16zy2l3 | G,Ff,Treg,A | A_density_bin5 | A_density_bin5: This parameter measures the normalized cell density of antigen presenting cells within the fifth bin from the tumor boundary. The normalization by annular area ensures that the value represents a rate that can be compared across patient cases. |
| p14ux16zy2l3 | G,Ff,Treg,A | G_infiltration_gradient | G_infiltration_gradient: This parameter is the slope derived from a linear regression model that relates granulocyte density to the radial distance from the tumor boundary. It is a normalized measure that quantifies the rate of change in granulocyte density across the radial segments. |
| p14ux16zy2l3 | G,Ff,Treg,A | Ff_infiltration_gradient | Ff_infiltration_gradient: This parameter is the infiltration gradient for FSP1+ fibroblasts, calculated as the slope of the linear regression between the fibroblast density (across the defined bins) and distance from the tumor border. It normalizes the spatial distribution into a single comparative value. |
| p14ux16zy2l3 | G,Ff,Treg,A | Treg_infiltration_gradient | Treg_infiltration_gradient: This parameter represents the normalized infiltration gradient for regulatory T cells. The gradient is computed as the slope of a linear relationship between Treg density in the radial bins and the distance from the tumor boundary, allowing standardized comparisons. |
| p14ux16zy2l3 | G,Ff,Treg,A | A_infiltration_gradient | A_infiltration_gradient: This parameter is the slope obtained from linear regression of antigen presenting cell density versus distance from the tumor margin. It provides a normalized measure of how antigen presenting cell density shifts radially, enabling patient-to-patient comparisons. |
| p14ux16zy2l3 | G,Ff,Treg,A | composite_infiltration_score | composite_infiltration_score: This parameter is a composite score that combines the individual infiltration gradients of the various cell types (granulocytes, FSP1+ fibroblasts, regulatory T cells, and antigen presenting cells) by averaging them. It offers a single, normalized metric that encapsulates the overall spatial infiltration pattern from the tumor boundary. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | WEIGHTED_VAR_COEF | WEIGHTED_VAR_COEF: A weighted coefficient quantifying inter-type variation in Voronoi polygon areas across cell types. It is calculated by summing the squared deviations of each cell type's mean area from the global mean area (weighted by the number of cells in that type) and then dividing by the total cell count, thereby normalizing the variation for comparisons. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | TU_MEAN_AREA | TU_MEAN_AREA: The average area of Voronoi polygons for tumor epithelial cells (TU), representing the central tendency of the spatial distribution of these cells within a patch. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | TU_STD_AREA | TU_STD_AREA: The standard deviation of Voronoi polygon areas for tumor epithelial cells (TU), reflecting the variability in polygon sizes around the mean. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Tc_MEAN_AREA | Tc_MEAN_AREA: The average area of Voronoi polygons for cytotoxic T cells (Tc), indicating the typical size of the spatial territories occupied by these immune cells. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Tc_STD_AREA | Tc_STD_AREA: The standard deviation of Voronoi polygon areas for cytotoxic T cells (Tc), measuring the dispersion of their polygon sizes. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Th_MEAN_AREA | Th_MEAN_AREA: The average area of Voronoi polygons for helper T cells (Th), which provides a measure of central tendency in their spatial configuration. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Th_STD_AREA | Th_STD_AREA: The standard deviation of Voronoi polygon areas for helper T cells (Th), quantifying the variability of the polygon sizes within this cell type. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Treg_MEAN_AREA | Treg_MEAN_AREA: The average area of Voronoi polygons for regulatory T cells (Treg), reflecting the typical space occupied by these cells. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Treg_STD_AREA | Treg_STD_AREA: The standard deviation of Voronoi polygon areas for regulatory T cells (Treg), indicating the spread in their cell area distribution. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | B_MEAN_AREA | B_MEAN_AREA: The average area of Voronoi polygons for B cells, representing the mean spatial territory of these cells. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | B_STD_AREA | B_STD_AREA: The standard deviation of Voronoi polygon areas for B cells, which indicates how much the sizes vary around the mean. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | P_MEAN_AREA | P_MEAN_AREA: The average area of Voronoi polygons for plasma cells (P), indicating the typical area these cells cover in the analysis. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | P_STD_AREA | P_STD_AREA: The standard deviation of Voronoi polygon areas for plasma cells (P), reflecting the spread of polygon areas around the average. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | M_MEAN_AREA | M_MEAN_AREA: The average area of Voronoi polygons for macrophages (M), capturing the central tendency of their spatial regions. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | M_STD_AREA | M_STD_AREA: The standard deviation of Voronoi polygon areas for macrophages (M), measuring variation in the areas occupied by these cells. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | G_MEAN_AREA | G_MEAN_AREA: The average area of Voronoi polygons for granulocytes (G), signifying the typical size of their spatial segments. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | G_STD_AREA | G_STD_AREA: The standard deviation of Voronoi polygon areas for granulocytes (G), showing the variability in their polygon sizes. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MFp_MEAN_AREA | MFp_MEAN_AREA: The average area of Voronoi polygons for myofibroblasts identified with pdpn marker (MFp), indicating the normal extent of their spatial domains. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MFp_STD_AREA | MFp_STD_AREA: The standard deviation of Voronoi polygon areas for myofibroblasts (MFp), representing the dispersion of these area measurements. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MF_MEAN_AREA | MF_MEAN_AREA: The average area of Voronoi polygons for myofibroblasts (MF), which describes the central spatial tendency for these cells. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MF_STD_AREA | MF_STD_AREA: The standard deviation of Voronoi polygon areas for myofibroblasts (MF), reflecting the consistency of their polygon sizes. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Ff_MEAN_AREA | Ff_MEAN_AREA: The average area of Voronoi polygons for fibroblasts identified with FSP1 (Ff), indicating the mean area covered by these cells. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Ff_STD_AREA | Ff_STD_AREA: The standard deviation of Voronoi polygon areas for FSP1-positive fibroblasts (Ff), quantifying area variability. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | F_MEAN_AREA | F_MEAN_AREA: The average area of Voronoi polygons for fibroblasts (F), representing the typical spatial extent of these cells. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | F_STD_AREA | F_STD_AREA: The standard deviation of Voronoi polygon areas for fibroblasts (F), measuring how widely the polygon areas vary around the average. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | E_MEAN_AREA | E_MEAN_AREA: The average area of Voronoi polygons for endothelial cells (E), indicating the central tendency of their spatial allocation within a patch. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | E_STD_AREA | E_STD_AREA: The standard deviation of Voronoi polygon areas for endothelial cells (E), reflecting variability in their spatial metrics. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | A_MEAN_AREA | A_MEAN_AREA: The average area of Voronoi polygons for ap cells (A), capturing the mean size of the regions attributed to this cell type. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | A_STD_AREA | A_STD_AREA: The standard deviation of Voronoi polygon areas for ap cells (A), which shows the dispersion around the average area. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | GLOBAL_MEAN_AREA | GLOBAL_MEAN_AREA: The overall average Voronoi polygon area computed from cells of all types within a tumor patch, providing a baseline for comparison. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | GLOBAL_STD_AREA | GLOBAL_STD_AREA: The overall standard deviation of Voronoi polygon areas from all cell types, indicating the general variability of cell spatial distribution within the patch. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | TU_CV | TU_CV: The coefficient of variation for tumor epithelial cells (TU), calculated as the ratio of the standard deviation to the mean polygon area, offering a normalized measure of dispersion. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Tc_CV | Tc_CV: The coefficient of variation for cytotoxic T cells (Tc), which normalizes the spread of polygon areas relative to their mean. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Th_CV | Th_CV: The coefficient of variation for helper T cells (Th), providing a dimensionless measure of variability in their polygon sizes. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Treg_CV | Treg_CV: The coefficient of variation for regulatory T cells (Treg), representing the relative dispersion of their polygon area measurements. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | B_CV | B_CV: The coefficient of variation for B cells, offering a normalized indicator of variability in their spatial territories. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | P_CV | P_CV: The coefficient of variation for plasma cells (P), calculated to compare the spread of polygon areas in a normalized manner. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | M_CV | M_CV: The coefficient of variation for macrophages (M), which is the ratio of the standard deviation to the mean area, enabling comparisons across patches. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | G_CV | G_CV: The coefficient of variation for granulocytes (G), providing a dimensionless value for the relative variability in their polygon areas. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MFp_CV | MFp_CV: The coefficient of variation for myofibroblasts with pdpn marker (MFp), normalizing the dispersion in area measurements by their mean. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MF_CV | MF_CV: The coefficient of variation for myofibroblasts (MF), a normalized metric that reflects variability in their spatial distribution. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Ff_CV | Ff_CV: The coefficient of variation for FSP1-positive fibroblasts (Ff), calculated by dividing the standard deviation by the mean polygon area for this cell type. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | F_CV | F_CV: The coefficient of variation for fibroblasts (F), which provides a normalized measure of dispersion in their area measurements. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | E_CV | E_CV: The coefficient of variation for endothelial cells (E), representing the ratio of their standard deviation to the mean area for a normalized comparison. |
| p88xbgclxczq | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | A_CV | A_CV: The coefficient of variation for ap cells (A), offering a dimensionless indicator of variability in polygon areas relative to their mean. |
| pbyvmdvdrh87 | TU,Tc,Th,Treg,B,P,M,G,MF,MFp,E | mean_grid_spacing | mean_grid_spacing measures the average distance between cells in grid-like arrangements within each detected cluster. It is computed by determining the median nearest-neighbor distance in each cluster and then averaging these values across clusters. This parameter is normalized as it reflects a physical spacing (in micrometers) that can be compared across different patient cases. |
| pbyvmdvdrh87 | TU,Tc,Th,Treg,B,P,M,G,MF,MFp,E | mean_angle_consistency | mean_angle_consistency quantifies the average proportion of angular measurements that are consistent with grid-like patterns (i.e., angles close to 0°, 90°, 180°, or 270°) across all analyzed clusters. As a normalized ratio ranging from 0 to 1, it allows for meaningful comparisons between different patient cases, capturing the consistency of spatial grid arrangements. |
| pfe7eto1kzq4 | B,M | min_b_to_m_distance_perivascular | This parameter quantifies the minimum Euclidean distance (in micrometers) between any B cell and macrophage pair that is located within perivascular regions, defined by a 50µm buffer zone around vessel structures. It offers a normalized spatial metric that allows direct comparison across tumor patches by indicating the closest proximity between these two cell types, which may reflect localized immunological interactions influencing tumor progression. |
| piuke826pmye | TU,Th,Treg,B,P,F,E,M | GLOBAL_INHIBITORY_PROXIMITY_SCORE | GLOBAL_INHIBITORY_PROXIMITY_SCORE is a normalized spatial metric representing the overall inhibitory effect within a tumor patch. It is computed by summing the weighted contributions of all immunosuppressive cells based on their distance to neighboring immune or stromal cells, and then normalizing by the number of inhibitory cells considered. This score reflects the average proximity and potential for immunosuppression exerted by the cell population. |
| piuke826pmye | TU,Th,Treg,B,P,F,E,M | TREG_INHIBITORY_SCORE | TREG_INHIBITORY_SCORE quantifies the contribution of T regulatory cells to the inhibitory spatial landscape. It is calculated by evaluating the proximity of T regulatory cells to other relevant cells within a defined radius, with each contributing value weighted by the cell's immunosuppressive potential and normalized by the number of T regulatory cells. The score indicates the localized inhibitory impact of Tregs. |
| piuke826pmye | TU,Th,Treg,B,P,F,E,M | MACROPHAGE_INHIBITORY_SCORE | MACROPHAGE_INHIBITORY_SCORE represents the spatial influence of macrophages in the tumor microenvironment. It is derived from the proximity-based interactions between macrophages and surrounding cells using a weight that reflects their immunosuppressive capacity, and is normalized by the number of macrophages. A higher value signals a stronger inhibitory effect via macrophage presence. |
| piuke826pmye | TU,Th,Treg,B,P,F,E,M | FIBROBLAST_INHIBITORY_SCORE | FIBROBLAST_INHIBITORY_SCORE is the combined normalized metric for the inhibitory contributions of both standard fibroblasts and FSP1-positive fibroblasts. It averages the individual scores obtained for each fibroblast subtype, calculated based on their proximity to other cells and weighted by their immunosuppressive strength. This parameter provides insight into the stromal inhibitory influence. |
| piuke826pmye | TU,Th,Treg,B,P,F,E,M | ENDOTHELIAL_INHIBITORY_SCORE | ENDOTHELIAL_INHIBITORY_SCORE assesses the contribution of endothelial cells to the inhibitory proximity profile. It is computed by measuring the distance-weighted contributions of endothelial cells towards nearby immune and stromal cells, and then normalizing by the number of endothelial cells. It reflects the localized influence of endothelial structures on modulating immune responses. |
| piuke826pmye | TU,Th,Treg,B,P,F,E,M | THELPER_INHIBITORY_SCORE | THELPER_INHIBITORY_SCORE captures the spatial inhibitory impact of T helper cells. The score is calculated by considering the proximity of T helper cells to neighboring cells within a predetermined radius, applying a weight to reflect their lesser but significant immunosuppressive potential, and normalizing by their total count. This score aids in understanding T helper cell interactions. |
| piuke826pmye | TU,Th,Treg,B,P,F,E,M | BCELL_INHIBITORY_SCORE | BCELL_INHIBITORY_SCORE quantifies the influence of B cells through a proximity-based, normalized measurement. It evaluates the distance-dependent contributions of B cells to the inhibitory microenvironment, with contributions weighted based on the defined immunosuppressive potential. The normalization aspect ensures comparability across different patches. |
| piuke826pmye | TU,Th,Treg,B,P,F,E,M | PLASMA_INHIBITORY_SCORE | PLASMA_INHIBITORY_SCORE evaluates the contribution of plasma cells to the overall spatial inhibitory profile within a tissue patch. Derived by computing distance-weighted interactions between plasma cells and their neighboring cells, it is normalized by the number of plasma cells to provide a comparable measure of their inhibitory capacity. |
| pk83mb6m2aqo | TU,Th,Treg,B,P,M,MFp,MF,Ff,E | ANGLE_VARIANCE | ANGLE_VARIANCE measures the variance of angles formed between pairs of vectors that connect a central cell to two of its neighboring cells. This parameter is calculated by first filtering the cell population to include relevant cell types, computing the centroids of these cells, and then determining which cells are spatially adjacent based on a defined distance threshold. For each cell with at least two neighbors, each unique pair of neighboring cells constitutes a triplet, from which the angles between the vectors from the central cell to each neighbor are calculated. The variance of all these angles across a tumor section provides a quantitative indicator of the structural heterogeneity within the tumor microenvironment. Because this measure represents a statistical dispersion rather than a raw count, it is normalized and suitable for comparing different patient cases. |
| pkfe9b4ewcf5 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | MST_TOTAL_LENGTH | MST_TOTAL_LENGTH measures the total length of the minimum spanning tree connecting all cell centroids within a TMA spot. The parameter is obtained by extracting the centroids of all cells in a spot, computing the Euclidean distances between every pair of centroids, and then constructing the minimum spanning tree that connects all cells with the minimum cumulative distance. A smaller MST_TOTAL_LENGTH value indicates a denser arrangement of cells, which may suggest a more invasive tumor phenotype. Since the value is computed in a consistent manner across patches from all patient cases and is a continuous numeric measure, it can be used to compare different patient cases. |
| pkjykbx9n180 | B | B_Cell_Nucleus_Area_Skewness | B_Cell_Nucleus_Area_Skewness measures the asymmetry in the distribution of nucleus areas for B lymphocytes located within the stromal compartment of tumor samples. This statistic is computed by assessing how far the distribution deviates from a symmetrical (normal) distribution. A positive skewness indicates that the tail of the distribution is longer on the right side, meaning that there are relatively more B cells with larger nucleus areas, while a negative skew suggests a longer tail on the left side, indicating more B cells with smaller nucleus areas. This normalized measure allows for meaningful comparisons across different patient cases. |
| plu376b637yo | Th,Tc,Treg | FRACTION_TH | FRACTION_TH represents the proportion of T helper cells (CD4+) relative to the total number of T cells (including T helper, cytotoxic (CD8+), and regulatory T cells). This metric is calculated by dividing the count of T helper cells by the combined count of all T cell types, providing a normalized and comparable value across different tumor regions. |
| plvlc581r404 | E | ENDOTHELIAL_CELL_PROPORTION | This parameter quantifies the normalized proportion of endothelial cells in a tumor patch. It is determined by dividing the number of endothelial cells by the total number of cells (with a small correction to avoid division by zero), ensuring that the measure is comparable across different patient cases. The metric reflects the relative abundance of endothelial cells, which serve as an indicator of microvessel formation and angiogenesis activity within the tumor tissue. |
| pqbx7muopm1r | Treg,Th,MFp,Ff,E,P | Treg_infiltration_angle_variance | Treg_infiltration_angle_variance measures the variance of infiltration angles for regulatory T cells. It is computed by first determining the angular deviation of each Treg cell's directional infiltration vector relative to the local inward normal of the stroma-epithelium boundary. The resulting variance reflects how consistently these cells align when moving from the stromal compartment into the epithelial tumor area. This parameter is numeric and normalized, allowing for comparison across different patient cases and tumor regions. |
| pqbx7muopm1r | Treg,Th,MFp,Ff,E,P | Th_infiltration_angle_variance | Th_infiltration_angle_variance measures the variance of infiltration angles for helper T cells. The parameter is obtained by calculating the angular differences between the infiltration vectors of individual helper T cells and the inward normal of the tumor boundary. The variance represents the dispersion of these angles across a patch and is numerically computed, facilitating comparisons between different patient cases. |
| pqbx7muopm1r | Treg,Th,MFp,Ff,E,P | MFp_infiltration_angle_variance | MFp_infiltration_angle_variance quantifies the variance in infiltration angles for PDPN+ Myofibroblasts. The parameter is derived by measuring the angles between each myofibroblast's infiltration vector and the computed inward normal at the stroma-epithelium boundary, then computing the variance of these angles. Being a normalized numeric measure, it supports comparative analyses across different tumors. |
| pqbx7muopm1r | Treg,Th,MFp,Ff,E,P | Ff_infiltration_angle_variance | Ff_infiltration_angle_variance measures the variance in infiltration angles for FSP1+ Fibroblasts. It is calculated by assessing the angular difference between the fibroblast's infiltration vector and the defined normal vector at the boundary, and then computing the variance of these angles across the analyzed region. This numeric and normalized metric enables robust comparisons between cases. |
| pqbx7muopm1r | Treg,Th,MFp,Ff,E,P | E_infiltration_angle_variance | E_infiltration_angle_variance captures the variance of infiltration angles for endothelial cells. This parameter is obtained by determining each endothelial cell's angular deviation from the inward normal vector at the boundary and then computing the variance. Being a numeric value derived from normalized angles, it allows for meaningful comparisons across patient cases and tumor regions. |
| pqbx7muopm1r | Treg,Th,MFp,Ff,E,P | P_infiltration_angle_variance | P_infiltration_angle_variance quantifies the variance of infiltration angles for plasma cells. It is computed by measuring the infiltration angle for each plasma cell with respect to the inward normal at the stroma-epithelium interface, and then calculating the statistical variance. As a normalized and numeric parameter, it supports comparison across different cases and tumor patches. |
| pqed5r71uvec | TU,Tc,Th,Treg,B,P,M,G,MFp,MF | SHANNON_DIVERSITY_INDEX | SHANNON_DIVERSITY_INDEX measures the overall cell diversity within the tumor compartment using the Shannon diversity index formula. It is calculated based on the normalized proportions of ten specific cell types, reflecting the complexity of the tumor microenvironment. |
| pqed5r71uvec | TU,Tc,Th,Treg,B,P,M,G,MFp,MF | PROPORTION_TU | PROPORTION_TU represents the normalized proportion of epithelial (tumor) cells within the tumor compartment. This parameter is derived by dividing the count of tumor epithelial cells by the total count of the ten analyzed cell types, allowing comparisons across different patient cases. |
| pqed5r71uvec | TU,Tc,Th,Treg,B,P,M,G,MFp,MF | PROPORTION_Tc | PROPORTION_Tc represents the normalized proportion of CD8+ T cells within the tumor compartment. This parameter is calculated by dividing the count of CD8+ T cells by the total cell count of the selected cell types, supporting comparative analysis between tumor regions. |
| pqed5r71uvec | TU,Tc,Th,Treg,B,P,M,G,MFp,MF | PROPORTION_M | PROPORTION_M represents the normalized proportion of macrophages within the tumor compartment. It is computed by normalizing the number of macrophages against the total count of the ten cell types, ensuring that the metric is comparable across different cases. |
| pqed5r71uvec | TU,Tc,Th,Treg,B,P,M,G,MFp,MF | PROPORTION_MFp | PROPORTION_MFp represents the normalized proportion of PDPN+ myofibroblasts within the tumor compartment. This parameter is determined by calculating the fraction of PDPN+ myofibroblasts relative to the overall count of the ten cell types, allowing valid cross-case comparisons. |
| pqed5r71uvec | TU,Tc,Th,Treg,B,P,M,G,MFp,MF | PROPORTION_MF | PROPORTION_MF represents the normalized proportion of conventional myofibroblasts within the tumor compartment. It is determined by dividing the number of conventional myofibroblasts by the total count of the defined cell types, making it a normalized numeric measure suitable for comparative analysis. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | b_cell_stromal_mean_area | b_cell_stromal_mean_area: Represents the mean nuclear area (in square micrometers) calculated from B cells segmented in the stromal compartment. This parameter is derived by averaging individual nuclear area measurements obtained from the cell's polygon and is comparable across different patient cases. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | fibroblast_epithelial_mean_area | fibroblast_epithelial_mean_area: Represents the average nuclear area for fibroblast cells located in the epithelial (tumor) compartment. The value is computed by averaging all relevant polygon area measurements for these cells. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | fibroblast_stromal_mean_area | fibroblast_stromal_mean_area: Represents the average nuclear area for fibroblast cells in the stromal compartment, derived by averaging the nuclear area values computed from the cell polygon areas. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | fibroblast_nuclear_area_difference | fibroblast_nuclear_area_difference: Represents the difference between the epithelial and stromal mean nuclear areas for fibroblast cells. It is computed by subtracting the mean stromal area from the mean epithelial area to highlight the disparity between compartments. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | fibroblast_fsp1_stromal_mean_area | fibroblast_fsp1_stromal_mean_area: Represents the mean nuclear area for the fibroblast_fsp1 cell subtype measured in the stromal compartment. The value reflects the average polygon-derived area of nuclei for these cells. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | myofibroblast_epithelial_mean_area | myofibroblast_epithelial_mean_area: Represents the average nuclear area for myofibroblast cells found in the epithelial compartment. It is calculated by averaging individual nuclear area measurements from cells identified as myofibroblasts. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | myofibroblast_stromal_mean_area | myofibroblast_stromal_mean_area: Represents the mean nuclear area for myofibroblast cells in the stromal compartment. This parameter is derived from averaging the cell polygon areas specific to this compartment. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | myofibroblast_nuclear_area_difference | myofibroblast_nuclear_area_difference: Represents the difference between the mean nuclear areas of myofibroblasts in the epithelial compartment and those in the stromal compartment. This difference is calculated by subtracting the stromal mean from the epithelial mean. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | myofibroblast_pdpn_epithelial_mean_area | myofibroblast_pdpn_epithelial_mean_area: Represents the average nuclear area for myofibroblast cells expressing pdpn in the epithelial compartment, calculated from the polygon areas of individual cell nuclei. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | myofibroblast_pdpn_stromal_mean_area | myofibroblast_pdpn_stromal_mean_area: Represents the mean nuclear area for myofibroblast cells expressing pdpn located in the stromal compartment, derived through averaging their polygon area measurements. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | myofibroblast_pdpn_nuclear_area_difference | myofibroblast_pdpn_nuclear_area_difference: Represents the difference in average nuclear area for pdpn-expressing myofibroblast cells between the epithelial and stromal compartments. It highlights the contrast by subtracting the stromal mean from the epithelial mean. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | t_cell_cd8_epithelial_mean_area | t_cell_cd8_epithelial_mean_area: Represents the average nuclear area for CD8 T cells located in the epithelial compartment. It is computed by averaging the cell polygon areas and serves as a normalized measure for comparison across cases. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | t_cell_cd8_stromal_mean_area | t_cell_cd8_stromal_mean_area: Represents the mean nuclear area for CD8 T cells found in the stromal compartment, calculated by averaging the nuclear area values for cells in that group. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | t_cell_cd8_nuclear_area_difference | t_cell_cd8_nuclear_area_difference: Represents the difference in mean nuclear area between the epithelial and stromal compartments for CD8 T cells, obtained by subtracting the stromal mean from the epithelial mean. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | t_cell_cd4_stromal_mean_area | t_cell_cd4_stromal_mean_area: Represents the average nuclear area for CD4 T cells in the stromal compartment. It is derived from averaging individual nuclear area measurements from polygon geometries. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | t_cell_reg_stromal_mean_area | t_cell_reg_stromal_mean_area: Represents the mean nuclear area for regulatory T cells (T cell reg) measured in the stromal compartment. This average is computed from the polygon areas of the cell nuclei. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | granulocyte_stromal_mean_area | granulocyte_stromal_mean_area: Represents the average nuclear area for granulocytes located in the stromal compartment, reflecting the mean value calculated from their polygon-derived area measurements. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | macrophage_epithelial_mean_area | macrophage_epithelial_mean_area: Represents the mean nuclear area for macrophages in the epithelial compartment, calculated by averaging the nuclear areas as computed from the cell polygon. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | macrophage_stromal_mean_area | macrophage_stromal_mean_area: Represents the average nuclear area for macrophages found in the stromal compartment. This value is derived from averaging individual nuclear area measurements. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | macrophage_nuclear_area_difference | macrophage_nuclear_area_difference: Represents the difference between the epithelial and stromal mean nuclear areas for macrophages, calculated as the epithelial mean minus the stromal mean. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | endothelial_cell_stromal_mean_area | endothelial_cell_stromal_mean_area: Represents the average nuclear area for endothelial cells in the stromal compartment, computed by averaging the nucleus polygon area measurements. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | ap_cell_stromal_mean_area | ap_cell_stromal_mean_area: Represents the mean nuclear area for AP cells (antigen-presenting cells) located in the stromal compartment, derived by averaging their polygon area values. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | plasma_cell_stromal_mean_area | plasma_cell_stromal_mean_area: Represents the average nuclear area for plasma cells found in the stromal compartment, calculated by averaging the individual nuclear area measurements. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | epithelial_cell_epithelial_mean_area | epithelial_cell_epithelial_mean_area: Represents the mean nuclear area for epithelial cells in the epithelial (tumor) compartment, computed from averaging polygon-derived nuclear area measurements. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | epithelial_cell_stromal_mean_area | epithelial_cell_stromal_mean_area: Represents the average nuclear area for epithelial cells that are identified in the stromal compartment. This value is calculated by averaging the nuclear area values from cell polygon measurements when the cell is in the stromal area. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | epithelial_cell_nuclear_area_difference | epithelial_cell_nuclear_area_difference: Represents the difference between the mean nuclear areas of epithelial cells in the epithelial and stromal compartments, computed by subtracting the stromal mean from the epithelial mean. |
| pryzdm74e43w | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | overall_mean_nuclear_area_difference | overall_mean_nuclear_area_difference: Represents the overall average difference in nuclear area between the epithelial and stromal compartments across all valid cell types. This summary statistic is calculated by averaging the cell type-specific differences and is normalized to facilitate comparisons across patient cases. |
| pvush9sb1jbe | TU,Tc,Treg,M,MFp,Ff,B | MEAN_NUCLEAR_SOLIDITY_Tumor_Epithelial | MEAN_NUCLEAR_SOLIDITY_Tumor_Epithelial: Average value of nuclear solidity for tumor cells located in the epithelial compartment. Nuclear solidity is measured as the ratio of the actual nuclear area to the area of the nucleus's convex hull, providing a normalized metric of nuclear shape. |
| pvush9sb1jbe | TU,Tc,Treg,M,MFp,Ff,B | STD_NUCLEAR_SOLIDITY_Tumor_Epithelial | STD_NUCLEAR_SOLIDITY_Tumor_Epithelial: Standard deviation of nuclear solidity for tumor cells in the epithelial compartment, reflecting the variability in the solidity measurements among these cells. |
| pvush9sb1jbe | TU,Tc,Treg,M,MFp,Ff,B | MEAN_NUCLEAR_SOLIDITY_Tumor_Stromal | MEAN_NUCLEAR_SOLIDITY_Tumor_Stromal: Average nuclear solidity for tumor cells in the stromal compartment, computed as the mean ratio of the nuclear area to the convex hull area, allowing for comparisons across patient cases. |
| pvush9sb1jbe | TU,Tc,Treg,M,MFp,Ff,B | STD_NUCLEAR_SOLIDITY_Tumor_Stromal | STD_NUCLEAR_SOLIDITY_Tumor_Stromal: Standard deviation of nuclear solidity for tumor cells in the stromal compartment, indicating the spread or variability of these normalized solidity values. |
| pvush9sb1jbe | TU,Tc,Treg,M,MFp,Ff,B | MEAN_NUCLEAR_SOLIDITY_Cytotoxic T_Epithelial | MEAN_NUCLEAR_SOLIDITY_Cytotoxic T_Epithelial: Average nuclear solidity for cytotoxic T cells within the epithelial compartment, offering a normalized measure of nuclear shape that can be compared across patients. |
| pvush9sb1jbe | TU,Tc,Treg,M,MFp,Ff,B | MEAN_NUCLEAR_SOLIDITY_Cytotoxic T_Stromal | MEAN_NUCLEAR_SOLIDITY_Cytotoxic T_Stromal: Average nuclear solidity for cytotoxic T cells in the stromal compartment, calculated as the mean ratio of nuclear area to convex hull area. |
| pvush9sb1jbe | TU,Tc,Treg,M,MFp,Ff,B | STD_NUCLEAR_SOLIDITY_Cytotoxic T_Stromal | STD_NUCLEAR_SOLIDITY_Cytotoxic T_Stromal: Standard deviation of nuclear solidity for cytotoxic T cells in the stromal compartment, describing the variability around the mean solidity value for these cells. |
| pvush9sb1jbe | TU,Tc,Treg,M,MFp,Ff,B | MEAN_NUCLEAR_SOLIDITY_Treg_Stromal | MEAN_NUCLEAR_SOLIDITY_Treg_Stromal: Average nuclear solidity for regulatory T cells in the stromal compartment, representing the normalized average ratio of nuclear area to convex hull area. |
| pvush9sb1jbe | TU,Tc,Treg,M,MFp,Ff,B | STD_NUCLEAR_SOLIDITY_Treg_Stromal | STD_NUCLEAR_SOLIDITY_Treg_Stromal: Standard deviation of nuclear solidity for regulatory T cells in the stromal compartment, indicating the degree of variation in their normalized solidity measurements. |
| pvush9sb1jbe | TU,Tc,Treg,M,MFp,Ff,B | MEAN_NUCLEAR_SOLIDITY_Macrophage_Epithelial | MEAN_NUCLEAR_SOLIDITY_Macrophage_Epithelial: Average nuclear solidity for macrophages located in the epithelial compartment, computed as a normalized ratio of the nuclear area to its convex hull area. |
| pvush9sb1jbe | TU,Tc,Treg,M,MFp,Ff,B | MEAN_NUCLEAR_SOLIDITY_Macrophage_Stromal | MEAN_NUCLEAR_SOLIDITY_Macrophage_Stromal: Average nuclear solidity for macrophages in the stromal compartment, offering a normalized measure to compare nuclear shape characteristics. |
| pvush9sb1jbe | TU,Tc,Treg,M,MFp,Ff,B | STD_NUCLEAR_SOLIDITY_Macrophage_Stromal | STD_NUCLEAR_SOLIDITY_Macrophage_Stromal: Standard deviation of nuclear solidity for macrophages in the stromal compartment, reflecting the variability in these normalized metrics. |
| pvush9sb1jbe | TU,Tc,Treg,M,MFp,Ff,B | MEAN_NUCLEAR_SOLIDITY_PDPN+ Myofibroblast_Epithelial | MEAN_NUCLEAR_SOLIDITY_PDPN+ Myofibroblast_Epithelial: Average nuclear solidity for PDPN+ myofibroblasts found in the epithelial compartment, calculated as the mean ratio of the actual nuclear area to the convex hull area. |
| pvush9sb1jbe | TU,Tc,Treg,M,MFp,Ff,B | STD_NUCLEAR_SOLIDITY_PDPN+ Myofibroblast_Epithelial | STD_NUCLEAR_SOLIDITY_PDPN+ Myofibroblast_Epithelial: Standard deviation of nuclear solidity for PDPN+ myofibroblasts in the epithelial compartment, indicating the spread of the normalized solidity values. |
| pvush9sb1jbe | TU,Tc,Treg,M,MFp,Ff,B | MEAN_NUCLEAR_SOLIDITY_PDPN+ Myofibroblast_Stromal | MEAN_NUCLEAR_SOLIDITY_PDPN+ Myofibroblast_Stromal: Average nuclear solidity for PDPN+ myofibroblasts in the stromal compartment, providing a normalized measure of nuclear shape. |
| pvush9sb1jbe | TU,Tc,Treg,M,MFp,Ff,B | STD_NUCLEAR_SOLIDITY_PDPN+ Myofibroblast_Stromal | STD_NUCLEAR_SOLIDITY_PDPN+ Myofibroblast_Stromal: Standard deviation of nuclear solidity for PDPN+ myofibroblasts in the stromal compartment, reflecting the variability in solidity measurements. |
| pvush9sb1jbe | TU,Tc,Treg,M,MFp,Ff,B | MEAN_NUCLEAR_SOLIDITY_FSP1+ Fibroblast_Stromal | MEAN_NUCLEAR_SOLIDITY_FSP1+ Fibroblast_Stromal: Average nuclear solidity for FSP1+ fibroblasts in the stromal compartment, representing the normalized mean of the ratio between nuclear area and convex hull area. |
| pvush9sb1jbe | TU,Tc,Treg,M,MFp,Ff,B | STD_NUCLEAR_SOLIDITY_FSP1+ Fibroblast_Stromal | STD_NUCLEAR_SOLIDITY_FSP1+ Fibroblast_Stromal: Standard deviation of nuclear solidity for FSP1+ fibroblasts in the stromal compartment, indicating the dispersion in their normalized nuclear solidity values. |
| pvush9sb1jbe | TU,Tc,Treg,M,MFp,Ff,B | MEAN_NUCLEAR_SOLIDITY_B Cell_Stromal | MEAN_NUCLEAR_SOLIDITY_B Cell_Stromal: Average nuclear solidity for B cells in the stromal compartment, calculated as the mean ratio of nuclear area to the convex hull area, serving as a normalized metric for analysis. |
| pvush9sb1jbe | TU,Tc,Treg,M,MFp,Ff,B | STD_NUCLEAR_SOLIDITY_B Cell_Stromal | STD_NUCLEAR_SOLIDITY_B Cell_Stromal: Standard deviation of nuclear solidity for B cells in the stromal compartment, reflecting the variability in these normalized nuclear solidity measurements. |
| pvvr707bi8ay | TU,Ff,MFp,B | epithelial_cell_mean_roughness | epithelial_cell_mean_roughness: This parameter represents the average nuclear boundary roughness for tumor cells in breast cancer. The roughness metric is computed as the ratio between the raw perimeter of the nucleus and a corresponding smoothed perimeter where minor irregularities are removed. This normalization allows for cross-sample comparisons. |
| pvvr707bi8ay | TU,Ff,MFp,B | epithelial_cell_median_roughness | epithelial_cell_median_roughness: This parameter represents the median nuclear boundary roughness for tumor cells, reflecting the middle value of the roughness ratio distribution. It is a normalized measure that assists in comparing different patient cases. |
| pvvr707bi8ay | TU,Ff,MFp,B | epithelial_cell_std_roughness | epithelial_cell_std_roughness: This parameter indicates the standard deviation of the nuclear boundary roughness for tumor cells, quantifying the variability around the mean measurement. This normalized value adds insight into the consistency of the measured roughness across cells. |
| pvvr707bi8ay | TU,Ff,MFp,B | fibroblast_fsp1_mean_roughness | fibroblast_fsp1_mean_roughness: This parameter represents the average nuclear boundary roughness calculated for FSP1+ fibroblasts, using the normalized ratio of raw to smoothed cell boundary perimeters. This allows for comparison across different patches and patient cases. |
| pvvr707bi8ay | TU,Ff,MFp,B | fibroblast_fsp1_median_roughness | fibroblast_fsp1_median_roughness: This parameter is the median value of the nuclear boundary roughness for FSP1+ fibroblasts, offering a robust, normalized statistic that can mitigate the influence of outliers. |
| pvvr707bi8ay | TU,Ff,MFp,B | fibroblast_fsp1_std_roughness | fibroblast_fsp1_std_roughness: This parameter measures the standard deviation of the nuclear boundary roughness among FSP1+ fibroblasts, indicating how variable the normalized measurements are across individual cells. |
| pvvr707bi8ay | TU,Ff,MFp,B | myofibroblast_pdpn_mean_roughness | myofibroblast_pdpn_mean_roughness: This parameter reflects the average roughness of the nuclear boundary for PDPN+ myofibroblasts, derived from the ratio of the raw to smoothed perimeters. It is normalized to allow inter-patient and intra-patient comparisons. |
| pvvr707bi8ay | TU,Ff,MFp,B | myofibroblast_pdpn_median_roughness | myofibroblast_pdpn_median_roughness: This parameter provides the median value of the roughness metric for PDPN+ myofibroblasts, serving as a normalized statistic that can be reliably compared between patient cases. |
| pvvr707bi8ay | TU,Ff,MFp,B | myofibroblast_pdpn_std_roughness | myofibroblast_pdpn_std_roughness: This parameter quantifies the dispersion of the roughness values among PDPN+ myofibroblasts, offering insight into the variability of the normalized metric. |
| pvvr707bi8ay | TU,Ff,MFp,B | b_cell_mean_roughness | b_cell_mean_roughness: This parameter gives the average nuclear boundary roughness for B lymphocytes by calculating a normalized ratio of raw to smoothed perimeters. This normalization facilitates direct comparisons across different patient samples. |
| pvvr707bi8ay | TU,Ff,MFp,B | b_cell_median_roughness | b_cell_median_roughness: This parameter indicates the median nuclear boundary roughness for B lymphocytes, serving as a normalized robust measure of central tendency in the roughness data. |
| pvvr707bi8ay | TU,Ff,MFp,B | b_cell_std_roughness | b_cell_std_roughness: This parameter represents the standard deviation of the nuclear boundary roughness for B lymphocytes, providing a normalized measure of variability in the observed metric. |
| pw1uvidlyilf | MFp,F,G,A | anisotropy_coefficient | anisotropy_coefficient: This parameter represents the variance among the mean anisotropy ratios (where each ratio is the quotient of the major axis divided by the minor axis of the nucleus) calculated for PDPN+ myofibroblasts, fibroblasts, granulocytes, and antigen presenting cells in vessel-rich areas. It provides a normalized coefficient of morphological anisotropy, serving as an indicator of variations in nuclear shape across different cell types. |
| pw1uvidlyilf | MFp,F,G,A | mean_anisotropy_mfp | mean_anisotropy_mfp: This parameter is the mean anisotropy ratio for PDPN+ myofibroblasts in vessel-rich areas. It is computed by determining the ratio of the major axis to the minor axis of the minimum rotated rectangle that approximates the cell nucleus, yielding a normalized, dimensionless value that reflects nuclear elongation. |
| pw1uvidlyilf | MFp,F,G,A | mean_anisotropy_fibroblast | mean_anisotropy_fibroblast: This parameter represents the average anisotropy ratio for fibroblasts in vessel-rich areas. It is calculated by measuring the ratio of the longest to the shortest axis of the cell nucleus, normalizing the measurement for easier comparison across different tumor patches. |
| pw1uvidlyilf | MFp,F,G,A | mean_anisotropy_granulocyte | mean_anisotropy_granulocyte: This parameter indicates the average anisotropy ratio for granulocytes located in vessel-rich areas. The ratio is derived from the major and minor axes of the nucleus, providing a dimensionless measure of nuclear shape that facilitates comparative analysis across patient cases. |
| pw1uvidlyilf | MFp,F,G,A | mean_anisotropy_apc | mean_anisotropy_apc: This parameter is the mean anisotropy ratio for antigen presenting cells determined in vessel-rich regions. It is calculated as the quotient of the major axis length and the minor axis length of the nucleus, resulting in a normalized metric that can be compared across different tumor samples. |
| q0jk9psq5ssw | Th,Treg,B,P,M,G,MFp,Ff,E,A | nuclear_aspect_ratio_cv | nuclear_aspect_ratio_cv represents the coefficient of variation of the nuclear aspect ratios computed across different specified cell types. This parameter is calculated by first obtaining the mean aspect ratio for each cell type, and then evaluating the ratio of the standard deviation to the mean of these values. It provides a normalized measure that facilitates comparison across different patient cases. |
| q0jk9psq5ssw | Th,Treg,B,P,M,G,MFp,Ff,E,A | mean_aspect_ratio_Th | mean_aspect_ratio_Th is the average nuclear aspect ratio for T helper cells (CD4 positive). It quantifies the typical elongation of the nuclei of these cells, allowing for comparisons across different samples. |
| q0jk9psq5ssw | Th,Treg,B,P,M,G,MFp,Ff,E,A | mean_aspect_ratio_B | mean_aspect_ratio_B is the average nuclear aspect ratio for B cells. It reflects the mean elongation of the nucleus in B cells, providing a normalized value for histological comparison. |
| q0jk9psq5ssw | Th,Treg,B,P,M,G,MFp,Ff,E,A | mean_aspect_ratio_P | mean_aspect_ratio_P is the mean nuclear aspect ratio for plasma cells. This parameter summarizes the nuclear shape, computed as the ratio of the major to minor axis of the nucleus, and serves as a normalized metric for these cells. |
| q0jk9psq5ssw | Th,Treg,B,P,M,G,MFp,Ff,E,A | mean_aspect_ratio_M | mean_aspect_ratio_M is the average nuclear aspect ratio for macrophages. It measures the typical nuclear elongation of macrophages in the tumor microenvironment. |
| q0jk9psq5ssw | Th,Treg,B,P,M,G,MFp,Ff,E,A | mean_aspect_ratio_G | mean_aspect_ratio_G is the average nuclear aspect ratio for granulocytes. It quantifies the average shape elongation of granulocyte nuclei, contributing as a normalized measure for comparative studies. |
| q0jk9psq5ssw | Th,Treg,B,P,M,G,MFp,Ff,E,A | mean_aspect_ratio_MFp | mean_aspect_ratio_MFp is the average nuclear aspect ratio for PDPN-positive myofibroblasts. The parameter indicates the average elongation of the nuclear shape for these cells and is normalized for patient-level comparison. |
| q0jk9psq5ssw | Th,Treg,B,P,M,G,MFp,Ff,E,A | mean_aspect_ratio_Ff | mean_aspect_ratio_Ff is the mean nuclear aspect ratio for FSP1-positive fibroblasts. It measures the typical nuclear elongation in these fibroblasts using the ratio of the major to minor axes. |
| q0jk9psq5ssw | Th,Treg,B,P,M,G,MFp,Ff,E,A | mean_aspect_ratio_E | mean_aspect_ratio_E is the average nuclear aspect ratio for endothelial cells. It indicates the nuclear shape properties of these cells and is normalized to facilitate comparisons across patient samples. |
| q0jk9psq5ssw | Th,Treg,B,P,M,G,MFp,Ff,E,A | mean_aspect_ratio_A | mean_aspect_ratio_A is the average nuclear aspect ratio for antigen-presenting cells. This parameter captures the typical elongation of the nucleus in these cells, ensuring a normalized metric for inter-sample analysis. |
| q0jk9psq5ssw | Th,Treg,B,P,M,G,MFp,Ff,E,A | mean_aspect_ratio_Treg | mean_aspect_ratio_Treg is the mean nuclear aspect ratio for T regulatory cells. It reflects the average shape elongation of the nuclei of these cells and is a normalized measure suitable for comparisons among different patient cases. |
| q4nz3rpo84ih | Th,Ff,MF,TU | MF_IQR | MF_IQR represents the interquartile range of the maximal feret diameter measurements for PDPN- myofibroblasts found in the epithelial regions of the tumor. This value quantifies the spread or variability in nuclear size by calculating the difference between the 75th and 25th percentiles of the measured diameters. As a numeric parameter derived from direct image measurements and statistical computation, it is normalized and suitable for comparison across different patient cases. |
| q4nz3rpo84ih | Th,Ff,MF,TU | TU_IQR | TU_IQR represents the interquartile range of the maximal feret diameter measurements for tumor cells located in the epithelial regions. This parameter quantifies the variation in nuclear sizes by computing the difference between the 75th percentile and the 25th percentile of the diameter measurements. Being a numeric, statistically derived metric, it serves as a normalized measure for comparing tumor cell heterogeneity across patient samples. |
| qe5n72h1cvel | Treg,E | median_distance_treg | median_distance_treg measures the central tendency of the distances from the centroids of regulatory T cells to the epithelial-stromal boundary. It is computed as the median of the minimum Euclidean distances from individual cell centroids to any point along the identified boundary, allowing for comparison across different patient cases. |
| qe5n72h1cvel | Treg,E | median_distance_endothelial | median_distance_endothelial captures the central distance metric for endothelial cells by computing the median of the minimum Euclidean distances from each endothelial cell's centroid to the epithelial-stromal boundary. This parameter provides a robust numeric value that is comparable across analyses. |
| qe5n72h1cvel | Treg,E | distance_difference_treg_minus_endothelial | distance_difference_treg_minus_endothelial quantifies the spatial difference between the regulatory T cells’ and endothelial cells’ median distances from the epithelial-stromal boundary. It is derived by subtracting the median distance of endothelial cells from that of regulatory T cells, offering a normalized numeric metric that highlights relative positioning differences between these two cell types. |
| qewylya65fv9 | TU | tumor_cell_density_per_mm2 | tumor_cell_density_per_mm2 quantifies the average number of tumor cells per square millimeter within epithelial regions by dividing the tumor cell count by the total epithelial area. This normalized metric allows for meaningful comparisons across different patient cases or tissue patches, standardizing the measure despite variations in patch size. |
| qju7vfw9b5xz | Treg,B,MFp | Treg_to_B_MFp_Ratio | Treg_to_B_MFp_Ratio is a normalized metric that measures the ratio of regulatory T cells to the combined count of B cells and PDPN+ myofibroblasts within the stromal compartment of a tumor. This parameter is calculated as a density ratio, making it suitable for comparing different patient cases by normalizing for variations in absolute cell counts. A higher ratio may indicate an immunosuppressive microenvironment associated with aggressive tumor behavior in breast cancer. |
| qmmrck8lqr2v | TU,M,Th,Tc,Treg,B,P,G,E | Variance_Tumor | Variance_Tumor quantifies the variability in the nuclear compactness of tumor cells. It is computed as the variance of the compactness values (calculated using the ratio of area to perimeter squared) for cells identified as epithelial tumor cells, providing a normalized measure of morphological heterogeneity that can be compared across different patient cases. |
| qmmrck8lqr2v | TU,M,Th,Tc,Treg,B,P,G,E | Variance_Macrophage | Variance_Macrophage measures the variability in the nuclear compactness of macrophages. This parameter is the variance of compactness values for cells identified as macrophages, offering a normalized numeric indicator of morphological variability and heterogeneity in these cells across different patient patches. |
| qmmrck8lqr2v | TU,M,Th,Tc,Treg,B,P,G,E | Dispersion_Index | Dispersion_Index represents the absolute difference between the variance of macrophages and the variance of tumor cells. It is a normalized parameter that captures the disparity in the heterogeneity of nuclear compactness between these two cell types, making it suitable for inter-case comparisons. |
| qmmrck8lqr2v | TU,M,Th,Tc,Treg,B,P,G,E | Mean_Compactness_Tumor | Mean_Compactness_Tumor is the average value of nuclear compactness for tumor cells. This parameter summarizes the central tendency of the shape descriptor derived from cell area and perimeter, and because it is calculated on a normalized ratio, it allows for comparison across different patient samples. |
| qmmrck8lqr2v | TU,M,Th,Tc,Treg,B,P,G,E | Mean_Compactness_Macrophage | Mean_Compactness_Macrophage is the average nuclear compactness calculated for macrophages. It provides a numeric, normalized measure of the typical nuclear shape characteristic of these cells, supporting comparative analyses between patient cases. |
| qpqknkkc4lj0 | G | mean_granulocyte_nucleus_elongation_factor | This parameter calculates a normalized numeric value representing the average elongation of granulocyte nuclei in the stromal compartment of breast cancer tumors. It is computed by first identifying granulocytes located in the stroma, then measuring the nucleus shape by fitting a minimum rotated rectangle around each nucleus. Two principal side lengths are determined from this rectangle, representing the major and minor axes. The cut ratio of the major axis to the minor axis is calculated for each cell and these ratios are averaged across all eligible granulocytes. Higher values indicate more elongated nuclei, which may be associated with activated cell states influenced by tumor-derived factors. |
| qwpqk4soadjo | Tc,Th | mean_eccentricity_tc | mean_eccentricity_tc represents the average nuclear eccentricity of cytotoxic T cells within the epithelial region. The nucleus eccentricity is calculated using the covariance of the polygon coordinates that define the cell nucleus, resulting in a normalized value that reflects the shape attributes of the nucleus. |
| qwpqk4soadjo | Tc,Th | min_eccentricity_tc | min_eccentricity_tc captures the minimum nuclear eccentricity observed among the cytotoxic T cells in the epithelial region. This metric, being derived from the normalized eccentricity values, reflects the smallest deviation from a circular shape in the sampled cell population. |
| qwpqk4soadjo | Tc,Th | max_eccentricity_tc | max_eccentricity_tc indicates the maximum nuclear eccentricity among the cytotoxic T cells within the epithelial region. It is a normalized value that marks the cell with the most elongated or irregular nuclear shape in that specific patch. |
| qycarqk8shm4 | TU,Tc,Th,Treg,B,P,M,G,Ff,E | tumor_center_x | tumor_center_x represents the x-coordinate of the center of mass for tumor cells calculated by taking the average of the x-coordinates of all tumor cell centroids within a given patch. This allows comparison across different patient cases since it is based on spatial positioning rather than raw counts. |
| qycarqk8shm4 | TU,Tc,Th,Treg,B,P,M,G,Ff,E | tumor_center_y | tumor_center_y represents the y-coordinate of the center of mass for tumor cells calculated by averaging the y-coordinates of tumor cell centroids. It reflects the spatial distribution of tumor cells in a normalized manner, enabling cross-case comparisons. |
| qycarqk8shm4 | TU,Tc,Th,Treg,B,P,M,G,Ff,E | immune_center_x | immune_center_x represents the x-coordinate of the center of mass for immune cells, computed as the average x-coordinate of immune cell centroids present in the image patch. This metric is normalized as it is derived from spatial averaging rather than raw cell counts. |
| qycarqk8shm4 | TU,Tc,Th,Treg,B,P,M,G,Ff,E | immune_center_y | immune_center_y represents the y-coordinate of the center of mass for immune cells, determined by averaging the y-coordinates of immune cell centroids. This spatial metric is normalized, allowing for valid comparisons between different cases. |
| qycarqk8shm4 | TU,Tc,Th,Treg,B,P,M,G,Ff,E | weighted_shift_metric | weighted_shift_metric quantifies the spatial separation between tumor and immune cell centers by calculating the Euclidean distance between the computed centers and then weighting this distance by the proportion of immune cells relative to the total of tumor and immune cells. This weighting corrects for differences in cell abundance, making the result comparable across patient cases. |
| r0jbnto4a9xk | TU,M,Ff,F,E,A | infiltration_score | The infiltration_score parameter quantifies the density of selected immune and stromal cells (macrophages, fibroblasts, endothelial cells, and antigen-presenting cells) along the tumor-stroma interface. It is computed by delineating the tumor boundary from the tissue mask, generating a 50 µm buffer zone around this boundary, and counting the relevant cells within this zone. The count is then normalized by dividing by the length of the tumor boundary, ensuring that the score is comparable across different patient cases and patches. |
| r0mado6l679j | M,MFp,MF,Tc,Th,Treg | M_infiltration_ratio | M_infiltration_ratio quantifies the proportion of macrophages located within vessel-rich regions relative to the total number of macrophages present in tumor and stroma areas, offering a normalized metric to compare spatial infiltration across patient cases. |
| r0mado6l679j | M,MFp,MF,Tc,Th,Treg | MFp_infiltration_ratio | MFp_infiltration_ratio measures the fraction of PDPN+ myofibroblasts found in the vicinity of vessel-rich zones relative to the overall count in tumor and stroma regions, serving as a normalized indicator of vessel-associated infiltration. |
| r0mado6l679j | M,MFp,MF,Tc,Th,Treg | MF_infiltration_ratio | MF_infiltration_ratio represents the ratio of PDPN- myofibroblasts residing near vessel-rich regions compared to their total number in the tumor/stroma, providing a normalized assessment of spatial distribution related to vessel density. |
| r0mado6l679j | M,MFp,MF,Tc,Th,Treg | Tc_infiltration_ratio | Tc_infiltration_ratio assesses the proportion of cytotoxic T cells located in vessel-rich regions relative to the total cytotoxic T cells in tumor and stroma areas, resulting in a normalized measure for comparing immune infiltration across cases. |
| r0mado6l679j | M,MFp,MF,Tc,Th,Treg | Th_infiltration_ratio | Th_infiltration_ratio quantifies the fraction of helper T cells present in vessel-rich zones compared to the overall count in tumor and stroma regions, serving as a normalized parameter to evaluate cellular distribution in relation to vessels. |
| r0mado6l679j | M,MFp,MF,Tc,Th,Treg | Treg_infiltration_ratio | Treg_infiltration_ratio calculates the ratio of regulatory T cells found in vessel-rich regions to the total regulatory T cells in the tumor/stroma areas, offering a normalized index of vessel-associated regulatory immune cell infiltration. |
| r0rbaa975p5e | E | ENDOTHELIAL_NUCLEUS_CV | ENDOTHELIAL_NUCLEUS_CV measures the coefficient of variation of endothelial cell nucleus areas. It is computed by dividing the standard deviation by the mean of the nucleus areas, providing a normalized metric that reflects the relative heterogeneity in nucleus sizes across different patches in patient cases. |
| r0rbaa975p5e | E | ENDOTHELIAL_NUCLEUS_MEAN_AREA | ENDOTHELIAL_NUCLEUS_MEAN_AREA represents the average area of the nuclei of endothelial cells. This parameter is derived by computing the mean of all nucleus area measurements, offering insight into typical nuclear dimensions that can be compared across different tumor regions. |
| r0rbaa975p5e | E | ENDOTHELIAL_NUCLEUS_STD_AREA | ENDOTHELIAL_NUCLEUS_STD_AREA quantifies the variability in endothelial cell nucleus areas through the standard deviation. It captures the spread of the nucleus area values, indicating the degree of heterogeneity in nucleus size within each analyzed patch. |
| r3dvyud3akqn | Tc,P | t_cell_anisotropy_mean | t_cell_anisotropy_mean: The average ratio of the major axis to the minor axis of the nuclei of cytotoxic T cells in the stroma. This normalized measure captures the typical elongation or irregularity of T cell nuclei across different tumor patches. |
| r3dvyud3akqn | Tc,P | t_cell_anisotropy_std | t_cell_anisotropy_std: The standard deviation of the nuclear anisotropy ratios for cytotoxic T cells, reflecting the variability or spread of nuclear shape measurements among these cells in the analyzed regions. |
| r3dvyud3akqn | Tc,P | t_cell_near_anisotropy_mean | t_cell_near_anisotropy_mean: The mean nuclear anisotropy ratio computed for cytotoxic T cells that are located within 50 micrometers of the tumor boundary, providing insight into the cell morphology in areas immediately adjacent to the tumor edge. |
| r3dvyud3akqn | Tc,P | t_cell_mid_anisotropy_mean | t_cell_mid_anisotropy_mean: The average nuclear anisotropy ratio for cytotoxic T cells positioned between 50 and 100 micrometers from the tumor boundary, indicating the characteristic nuclear morphology in the intermediate zone. |
| r3dvyud3akqn | Tc,P | t_cell_far_anisotropy_mean | t_cell_far_anisotropy_mean: The mean nuclear anisotropy ratio for cytotoxic T cells found beyond 100 micrometers from the tumor boundary, serving as a normalized metric for cells in regions more distant from the tumor. |
| r3dvyud3akqn | Tc,P | plasma_cell_anisotropy_mean | plasma_cell_anisotropy_mean: The average ratio of the major to minor axis of plasma cell nuclei in the stroma, representing a normalized measure of plasma cell nuclear shape across different tumor patches. |
| r3dvyud3akqn | Tc,P | plasma_cell_anisotropy_std | plasma_cell_anisotropy_std: The standard deviation of the nuclear anisotropy ratio for plasma cells, quantifying the variability in plasma cell nuclear morphology among the evaluated regions. |
| r3dvyud3akqn | Tc,P | plasma_cell_near_anisotropy_mean | plasma_cell_near_anisotropy_mean: The mean nuclear anisotropy ratio for plasma cells located within 50 micrometers of the tumor boundary, used to assess the average shape characteristic of plasma cells in close proximity to the tumor. |
| r3dvyud3akqn | Tc,P | plasma_cell_mid_anisotropy_mean | plasma_cell_mid_anisotropy_mean: The average nuclear anisotropy ratio for plasma cells positioned between 50 and 100 micrometers from the tumor boundary, offering a normalized measure of nuclear morphology in the intermediate zone. |
| r3dvyud3akqn | Tc,P | plasma_cell_far_anisotropy_mean | plasma_cell_far_anisotropy_mean: The mean nuclear anisotropy ratio for plasma cells found beyond 100 micrometers from the tumor boundary, reflecting the average nuclear shape metrics of plasma cells in regions distant from the tumor edge. |
| r3dvyud3akqn | Tc,P | anisotropy_diff_t_vs_plasma | anisotropy_diff_t_vs_plasma: The difference between the overall mean nuclear anisotropy ratios of cytotoxic T cells and plasma cells. This parameter quantifies the disparity in nuclear shape between the two cell types in a normalized manner. |
| r3dvyud3akqn | Tc,P | anisotropy_near_diff_t_vs_plasma | anisotropy_near_diff_t_vs_plasma: The difference in mean nuclear anisotropy between cytotoxic T cells and plasma cells within the region that is within 50 micrometers of the tumor boundary, highlighting local cellular differences adjacent to the tumor. |
| r3dvyud3akqn | Tc,P | anisotropy_mid_diff_t_vs_plasma | anisotropy_mid_diff_t_vs_plasma: The difference between the mean nuclear anisotropy ratios of T cells and plasma cells in the mid-boundary region (50-100 micrometers from the tumor), providing a normalized comparative metric in this zone. |
| r3dvyud3akqn | Tc,P | anisotropy_far_diff_t_vs_plasma | anisotropy_far_diff_t_vs_plasma: The difference in mean nuclear anisotropy between T cells and plasma cells located beyond 100 micrometers from the tumor boundary, capturing normalized differences in nuclear morphology in distal regions. |
| r54p776u9b9n | TU,Tc | CTL_TUMOR_AVG_NEAREST_NEIGHBOR_DISTANCE | This parameter quantifies the infiltration index by calculating the average nearest-neighbor Euclidean distance, in micrometers, from cytotoxic T lymphocytes (CD8+ T cells) to tumor cells (epithelial cells). The computation involves finding the nearest tumor cell for each cytotoxic T lymphocyte based on their centroid positions and then averaging these minimum distances across all immune cells in a given patch. This metric is normalized for different patient cases and tissue patches, allowing for comparative analyses, with lower average distances suggesting a closer proximity of immune cells to tumor cells and potentially better immune-mediated tumor control. |
| r5xeh4kx553p | B,P,Ff,F,TU | mean_chain_length | mean_chain_length: This metric represents the average number of cells per continuous contact chain detected along the epithelial boundary in a tumor patch. It is computed by dividing the total sum of cells in all chains by the number of chains, thereby providing a normalized measure that allows for comparisons across different patient cases. |
| r5xeh4kx553p | B,P,Ff,F,TU | median_chain_length | median_chain_length: This metric indicates the middle value of the chain lengths when they are ordered from smallest to largest. It offers a robust estimation of typical chain length by reducing the effect of outliers, and is normalized by virtue of representing the central tendency of the chains measured. |
| r5xeh4kx553p | B,P,Ff,F,TU | mean_unique_cell_types | mean_unique_cell_types: This parameter calculates the average number of distinct cell types present within each continuous contact chain. By averaging the diversity in cell types across chains, this metric yields a normalized measure that reflects the heterogeneity of cell interactions along the epithelial boundary. |
| r7gmy55kz7q6 | P,TU,MF | plasma_cell_proportion | plasma_cell_proportion represents the normalized ratio of plasma cells relative to the combined count of plasma cells, tumor cells, and PDPN- myofibroblasts in the stromal region. This parameter allows for comparison across different patient cases because it conveys the relative abundance of plasma cells in the microenvironment rather than just raw cell counts. |
| re0ur1d001n5 | TU,Tc,Th,Treg,B,M,G,MFp,Ff,E | AVG_FILL_RATIO_TU | AVG_FILL_RATIO_TU: This parameter represents the average fill ratio for tumor cells. It is calculated as the ratio of the area of a tumor cell's nucleus polygon to the area of its minimum bounding box, providing a normalized measurement that allows for comparisons across different patient cases. |
| re0ur1d001n5 | TU,Tc,Th,Treg,B,M,G,MFp,Ff,E | AVG_FILL_RATIO_Tc | AVG_FILL_RATIO_Tc: This parameter represents the average fill ratio for cytotoxic T cells. It is computed as the ratio of the nucleus polygon area to the area of the minimum bounding box and serves as a normalized metric for cell shape regularity in these immune cells. |
| re0ur1d001n5 | TU,Tc,Th,Treg,B,M,G,MFp,Ff,E | AVG_FILL_RATIO_Th | AVG_FILL_RATIO_Th: This parameter represents the average fill ratio for T helper cells. It is derived from the ratio of the area of the cell's nucleus polygon to its bounding box area, offering a normalized measurement of nuclear fill for these cells. |
| re0ur1d001n5 | TU,Tc,Th,Treg,B,M,G,MFp,Ff,E | AVG_FILL_RATIO_Treg | AVG_FILL_RATIO_Treg: This parameter represents the average fill ratio for T regulatory cells. It is calculated by comparing the area of the cell's nucleus polygon with the area of its minimum bounding box, thus normalizing the measure to enable cross-case comparisons. |
| re0ur1d001n5 | TU,Tc,Th,Treg,B,M,G,MFp,Ff,E | AVG_FILL_RATIO_B | AVG_FILL_RATIO_B: This parameter represents the average fill ratio for B cells, calculated as the ratio of the B cell's nucleus polygon area to its minimum bounding box area. It provides a normalized metric useful in comparing cell morphology across samples. |
| re0ur1d001n5 | TU,Tc,Th,Treg,B,M,G,MFp,Ff,E | AVG_FILL_RATIO_M | AVG_FILL_RATIO_M: This parameter is the average fill ratio for macrophages. Derived from the ratio of the nucleus area to the bounding box area for each macrophage, it offers a normalized value that can be compared between different patient cases. |
| re0ur1d001n5 | TU,Tc,Th,Treg,B,M,G,MFp,Ff,E | AVG_FILL_RATIO_G | AVG_FILL_RATIO_G: This parameter represents the average fill ratio for granulocytes. It is computed as the ratio of the nucleus polygon area to its corresponding minimum bounding box area, allowing for normalized analysis of cell morphology. |
| re0ur1d001n5 | TU,Tc,Th,Treg,B,M,G,MFp,Ff,E | AVG_FILL_RATIO_MFp | AVG_FILL_RATIO_MFp: This parameter measures the average fill ratio for myofibroblasts (including variations labeled as myofibroblast and myofibroblast_pdpn). It is derived as the ratio of the area of the cell's nucleus polygon to the minimum bounding box area, providing a normalized metric for comparison. |
| re0ur1d001n5 | TU,Tc,Th,Treg,B,M,G,MFp,Ff,E | AVG_FILL_RATIO_Ff | AVG_FILL_RATIO_Ff: This parameter represents the average fill ratio for fibroblasts (including variants such as fibroblast and fibroblast_fsp1). It is calculated as the ratio between the nucleus polygon area and the area of its minimum bounding box, yielding a normalized measurement of cell structure. |
| re0ur1d001n5 | TU,Tc,Th,Treg,B,M,G,MFp,Ff,E | AVG_FILL_RATIO_E | AVG_FILL_RATIO_E: This parameter captures the average fill ratio for endothelial cells. It is computed by taking the ratio of the nucleus polygon area and its minimum bounding box area, resulting in a normalized metric that can be compared across patient cases. |
| re0ur1d001n5 | TU,Tc,Th,Treg,B,M,G,MFp,Ff,E | AVG_FILL_RATIO_OVERALL | AVG_FILL_RATIO_OVERALL: This parameter represents the overall average fill ratio across all analyzed cell types. It is calculated by combining the individual fill ratios from each eligible cell, thereby providing a normalized value suitable for comparative analysis across different patient cases. |
| rfsj5qx9stk0 | Tc,A | VESSEL_BUFFER_AREA | VESSEL_BUFFER_AREA quantifies the total area of the buffered vessel regions within the epithelial compartment. In this analysis, each vessel polygon is expanded by a fixed distance (50 units) to define a 'near vessel' area. The individual buffered regions are then merged into a single compound area whose total area is calculated. This measurement, expressed in square micrometers, is normalized relative to the standardized patch or tumor region, allowing meaningful comparisons across different patient cases. |
| rgf16xr862lm | M | MEDIAN_NUCLEUS_COMPACTNESS_MACROPHAGES_EPITHELIAL | MEDIAN_NUCLEUS_COMPACTNESS_MACROPHAGES_EPITHELIAL represents the median value of the compactness of macrophage nuclei located in epithelial (tumor) compartments. The compactness is calculated as (perimeter^2)/(4*pi*area) for each macrophage nucleus, providing a normalized measure of nuclear irregularity that is comparable across different patient cases and tumor regions. |
| rhzlank6q19i | A,B,E,G,M,Tc,Th,Treg,TU | T_CELL_POLARITY_SCORE | T_CELL_POLARITY_SCORE represents the ratio of the mean directional consistency of T cells to that of non-T cells. It is normalized by design, as it compares the T cell alignment relative to the tumor centroid to the reference alignment of other immune cells, allowing comparison across different patient cases. |
| rhzlank6q19i | A,B,E,G,M,Tc,Th,Treg,TU | T_CELL_DIRECTIONAL_CONSISTENCY | T_CELL_DIRECTIONAL_CONSISTENCY measures the average consistency of T cell orientation, calculated as the mean resultant vector length of T cell unit vectors. This value, which typically ranges between 0 and 1, reflects how tightly or uniformly the T cells align around the tumor centroid. |
| rhzlank6q19i | A,B,E,G,M,Tc,Th,Treg,TU | NON_T_CELL_DIRECTIONAL_CONSISTENCY | NON_T_CELL_DIRECTIONAL_CONSISTENCY is the mean resultant vector length calculated for non-T immune cells (including B cells, APCs, macrophages, granulocytes, and endothelial cells). It serves as a normalization reference by capturing the general directional consistency of these cells, ensuring the T cell metric is adjusted for overall spatial distributions. |
| rhzlank6q19i | A,B,E,G,M,Tc,Th,Treg,TU | MEAN_T_CELL_ANGLE_DEG | MEAN_T_CELL_ANGLE_DEG is the average angle (expressed in degrees) of T cells relative to the tumor centroid. This angular metric summarizes the overall orientation of T cells in a normalized and comparable manner across different tissue patches. |
| rhzlank6q19i | A,B,E,G,M,Tc,Th,Treg,TU | MEAN_NON_T_CELL_ANGLE_DEG | MEAN_NON_T_CELL_ANGLE_DEG is the average angular orientation (in degrees) of the non-T immune cells relative to the tumor centroid. Like the T cell angle, it provides a normalized measure of directionality that is useful when comparing different patient cases. |
| rt1vd4efajeb | Treg,Tc | Treg_Tc_ratio | Treg_Tc_ratio measures the proportion of regulatory T cells relative to cytotoxic T cells within a tumor patch. This normalized metric reflects the immunosuppressive state of the tumor microenvironment and allows for meaningful comparisons across different patient cases. |
| rxnm2a3j57a0 | TU,G,F,M | MEAN_PACKING_FACTOR | MEAN_PACKING_FACTOR: This parameter represents the average local packing factor calculated across all analyzed cells in the stromal microenvironment. It is a normalized metric that reflects the ratio of the total nucleus area (including neighboring cells within a fixed radius) to the area of a circle defined by that radius, allowing comparison between different patient cases. |
| rxnm2a3j57a0 | TU,G,F,M | MEDIAN_PACKING_FACTOR | MEDIAN_PACKING_FACTOR: This parameter is the median value of the local packing factors computed over all cells in the stroma, providing a robust central measure of cell density that is normalized and comparable across cases. |
| rxnm2a3j57a0 | TU,G,F,M | MIN_PACKING_FACTOR | MIN_PACKING_FACTOR: This metric indicates the smallest observed local packing factor among the analyzed cells. It represents the minimum degree of local cellular area accumulation relative to the reference circle area and is normalized to allow comparison between patient patches. |
| rxnm2a3j57a0 | TU,G,F,M | MAX_PACKING_FACTOR | MAX_PACKING_FACTOR: This parameter shows the highest local packing factor detected among cells in the stromal region. It reflects the densest region's cell area accumulation relative to the fixed analysis area, normalized for comparative studies. |
| rxnm2a3j57a0 | TU,G,F,M | STD_PACKING_FACTOR | STD_PACKING_FACTOR: The standard deviation of the local packing factor values across all cells in the stroma. This normalized metric quantifies variability in local cell packing density across different patches. |
| rxnm2a3j57a0 | TU,G,F,M | TU_MEAN_PACKING_FACTOR | TU_MEAN_PACKING_FACTOR: The average local packing factor calculated specifically for tumor cells (epithelial cells). This value estimates the typical density of tumor cell clusters relative to their surrounding defined area. |
| rxnm2a3j57a0 | TU,G,F,M | TU_MEDIAN_PACKING_FACTOR | TU_MEDIAN_PACKING_FACTOR: The median local packing factor among tumor cells, providing a robust measurement of tumor cell density that is normalized across different patient cases. |
| rxnm2a3j57a0 | TU,G,F,M | TU_MIN_PACKING_FACTOR | TU_MIN_PACKING_FACTOR: The lowest local packing factor observed in tumor cells within a patch, indicating the minimal tumor cell density relative to the cell’s effective neighborhood. |
| rxnm2a3j57a0 | TU,G,F,M | TU_MAX_PACKING_FACTOR | TU_MAX_PACKING_FACTOR: The highest local packing factor recorded among tumor cells, reflecting the maximum tumor cell density in the analyzed area and normalized with respect to the defined circular area. |
| rxnm2a3j57a0 | TU,G,F,M | TU_STD_PACKING_FACTOR | TU_STD_PACKING_FACTOR: The standard deviation of tumor cell packing factors, which measures the variability or heterogeneity in tumor cell density in the local microenvironment. |
| rxnm2a3j57a0 | TU,G,F,M | G_MEAN_PACKING_FACTOR | G_MEAN_PACKING_FACTOR: The average local packing factor computed for granulocytes, reflecting the typical density of granulocyte clusters relative to their neighborhood area. |
| rxnm2a3j57a0 | TU,G,F,M | G_MEDIAN_PACKING_FACTOR | G_MEDIAN_PACKING_FACTOR: The median value of the granulocyte-specific packing factors, providing a robust measure of granulocyte density that is normalized for cross-patient comparisons. |
| rxnm2a3j57a0 | TU,G,F,M | G_MIN_PACKING_FACTOR | G_MIN_PACKING_FACTOR: The minimum packing factor among granulocytes, indicating the lowest observed local density of granulocytes relative to a normalized analysis area. |
| rxnm2a3j57a0 | TU,G,F,M | G_MAX_PACKING_FACTOR | G_MAX_PACKING_FACTOR: The maximum packing factor found among granulocytes, representing the densest granulocyte clustering measured relative to the standard reference area. |
| rxnm2a3j57a0 | TU,G,F,M | G_STD_PACKING_FACTOR | G_STD_PACKING_FACTOR: The standard deviation of the granulocyte packing factors, quantifying the variability in granulocyte local density in a normalized manner. |
| rxnm2a3j57a0 | TU,G,F,M | F_MEAN_PACKING_FACTOR | F_MEAN_PACKING_FACTOR: The average local packing factor for fibroblasts, which quantifies the typical cell density of fibroblast populations relative to the area of influence. |
| rxnm2a3j57a0 | TU,G,F,M | F_MEDIAN_PACKING_FACTOR | F_MEDIAN_PACKING_FACTOR: The median local packing factor for fibroblasts, offering a robust, normalized measure of their typical local density. |
| rxnm2a3j57a0 | TU,G,F,M | F_MIN_PACKING_FACTOR | F_MIN_PACKING_FACTOR: The minimum observed local packing factor among fibroblasts, indicating the least dense fibroblast region in a patch with normalization. |
| rxnm2a3j57a0 | TU,G,F,M | F_MAX_PACKING_FACTOR | F_MAX_PACKING_FACTOR: The maximum local packing factor recorded for fibroblasts, reflecting the most densely packed fibroblast area relative to the defined circle area. |
| rxnm2a3j57a0 | TU,G,F,M | F_STD_PACKING_FACTOR | F_STD_PACKING_FACTOR: The standard deviation of fibroblast packing factors, indicating how much variation exists in fibroblast density across the analyzed area. |
| rxnm2a3j57a0 | TU,G,F,M | M_MEAN_PACKING_FACTOR | M_MEAN_PACKING_FACTOR: The average local packing factor calculated for macrophages, representing the typical local density of macrophages in the stroma in a normalized manner. |
| rxnm2a3j57a0 | TU,G,F,M | M_MEDIAN_PACKING_FACTOR | M_MEDIAN_PACKING_FACTOR: The median value of the macrophage packing factors, providing a robust measure of their typical normalized local density. |
| rxnm2a3j57a0 | TU,G,F,M | M_MIN_PACKING_FACTOR | M_MIN_PACKING_FACTOR: The smallest observed local packing factor among macrophages, indicating the minimal macrophage density within the neighborhood area. |
| rxnm2a3j57a0 | TU,G,F,M | M_MAX_PACKING_FACTOR | M_MAX_PACKING_FACTOR: The largest local packing factor measured for macrophages, reflecting the area where macrophages are most densely packed, normalized for comparative analysis. |
| rxnm2a3j57a0 | TU,G,F,M | M_STD_PACKING_FACTOR | M_STD_PACKING_FACTOR: The standard deviation for macrophage packing factors, quantifying the variability in local macrophage density using a normalized scale. |
| rxnm2a3j57a0 | TU,G,F,M | TU_TO_G_PACKING_RATIO | TU_TO_G_PACKING_RATIO: This ratio compares the mean packing factor of tumor cells to that of granulocytes. It is a normalized parameter that facilitates the comparative evaluation of tumor cell density relative to granulocyte density. |
| rxnm2a3j57a0 | TU,G,F,M | TU_TO_F_PACKING_RATIO | TU_TO_F_PACKING_RATIO: A normalized metric that expresses the ratio of the mean packing factor for tumor cells to that for fibroblasts, enabling direct comparison of local densities between these two cell types. |
| rxnm2a3j57a0 | TU,G,F,M | TU_TO_M_PACKING_RATIO | TU_TO_M_PACKING_RATIO: This parameter represents the ratio between the mean packing factor of tumor cells and that of macrophages, allowing assessment of their relative density in a normalized manner. |
| rxnm2a3j57a0 | TU,G,F,M | G_TO_TU_PACKING_RATIO | G_TO_TU_PACKING_RATIO: This ratio is the comparative measure of the mean packing factor of granulocytes with respect to tumor cells, providing normalized insights into cell density differences. |
| rxnm2a3j57a0 | TU,G,F,M | G_TO_F_PACKING_RATIO | G_TO_F_PACKING_RATIO: A normalized ratio comparing the granulocytes' mean packing factor to the fibroblasts' mean packing factor, facilitating cross-cell-type density analysis. |
| rxnm2a3j57a0 | TU,G,F,M | G_TO_M_PACKING_RATIO | G_TO_M_PACKING_RATIO: This parameter represents the ratio of mean packing factors between granulocytes and macrophages, yielding a normalized metric for cell density comparison between these types. |
| rxnm2a3j57a0 | TU,G,F,M | F_TO_TU_PACKING_RATIO | F_TO_TU_PACKING_RATIO: A normalized ratio that compares the mean packing factor of fibroblasts to that of tumor cells, offering a relative measure of their local densities. |
| rxnm2a3j57a0 | TU,G,F,M | F_TO_G_PACKING_RATIO | F_TO_G_PACKING_RATIO: This ratio compares the fibroblasts' mean packing factor with that of granulocytes and is normalized to enable consistent comparison between the cell types. |
| rxnm2a3j57a0 | TU,G,F,M | F_TO_M_PACKING_RATIO | F_TO_M_PACKING_RATIO: A comparative, normalized metric that reflects the ratio of mean packing factors between fibroblasts and macrophages. |
| rxnm2a3j57a0 | TU,G,F,M | M_TO_TU_PACKING_RATIO | M_TO_TU_PACKING_RATIO: This parameter is the normalized ratio of the mean packing factor of macrophages to that of tumor cells, allowing clear cross-comparison of local cellular densities. |
| rxnm2a3j57a0 | TU,G,F,M | M_TO_G_PACKING_RATIO | M_TO_G_PACKING_RATIO: A normalized ratio comparing the mean packing factor of macrophages to that of granulocytes, facilitating comparative analysis of their cell densities. |
| rxnm2a3j57a0 | TU,G,F,M | M_TO_F_PACKING_RATIO | M_TO_F_PACKING_RATIO: This parameter represents the ratio of macrophages' mean packing factor to fibroblasts' mean packing factor, providing a normalized measure for evaluating their relative cell density. |
| ry8tmgx2nt37 | Ff | MEDIAN_FRACTAL_DIM_FSP1_FIBROBLASTS | MEDIAN_FRACTAL_DIM_FSP1_FIBROBLASTS represents the median value of the fractal dimensions calculated for the nuclei of FSP1+ fibroblasts located in the stromal compartment. This metric is derived from applying a box-counting method to assess the complexity and irregularity of the nuclear shape and is used as a normalized, comparable measurement across different patient cases or tissue patches. |
| ry8tmgx2nt37 | Ff | MIN_FRACTAL_DIM_FSP1_FIBROBLASTS | MIN_FRACTAL_DIM_FSP1_FIBROBLASTS indicates the minimum fractal dimension measured among all FSP1+ fibroblast nuclei in the stromal region. It provides a lower bound of nuclear complexity in a given tissue patch, reflecting the simplest or least irregular nuclear outlines generated by the adopted method. |
| ry8tmgx2nt37 | Ff | MAX_FRACTAL_DIM_FSP1_FIBROBLASTS | MAX_FRACTAL_DIM_FSP1_FIBROBLASTS denotes the maximum fractal dimension observed among the FSP1+ fibroblast nuclei in the stromal area. This metric highlights the upper end of complexity in nuclear morphology, giving insight into cells with the most irregular or intricate outlines. |
| ry8tmgx2nt37 | Ff | MEAN_FRACTAL_DIM_FSP1_FIBROBLASTS | MEAN_FRACTAL_DIM_FSP1_FIBROBLASTS is the average fractal dimension computed over all selected FSP1+ fibroblast nuclei in the stroma. As a normalized numeric parameter, it provides an overall estimate of the nuclear structural complexity and serves as a comparative metric between different patches or patient cases. |
| ry8tmgx2nt37 | Ff | Q1_FRACTAL_DIM_FSP1_FIBROBLASTS | Q1_FRACTAL_DIM_FSP1_FIBROBLASTS represents the first quartile (25th percentile) of the fractal dimensions derived from FSP1+ fibroblast nuclei. It helps in understanding the lower spread of nuclear complexity values, offering additional context on data distribution within each analyzed tissue patch. |
| ry8tmgx2nt37 | Ff | Q3_FRACTAL_DIM_FSP1_FIBROBLASTS | Q3_FRACTAL_DIM_FSP1_FIBROBLASTS corresponds to the third quartile (75th percentile) of the fractal dimensions of FSP1+ fibroblast nuclei. It provides insights into the upper spread of the nuclear complexity measurements, complementing the understanding of variability within the tissue sample. |
| ryndxqzofphm | M | MEDIAN_MACROPHAGE_NUCLEUS_MAJOR_AXIS_EPITHELIAL | MEDIAN_MACROPHAGE_NUCLEUS_MAJOR_AXIS_EPITHELIAL represents the median value of the major axis lengths of macrophage nuclei measured in epithelial compartments. This metric is derived by initially extracting the geometric description of each macrophage nucleus, computing the appropriate major axis length through shape analysis techniques, and then summarizing these values using the median. The resulting value is numeric and normalized to support comparisons across different patient cases. |
| ryndxqzofphm | M | MIN_MACROPHAGE_NUCLEUS_MAJOR_AXIS_EPITHELIAL | MIN_MACROPHAGE_NUCLEUS_MAJOR_AXIS_EPITHELIAL indicates the smallest major axis length measured among the macrophage nuclei in epithelial compartments. It is determined by comparing the computed measurements for all qualifying cells and selecting the minimum value. This parameter is numeric and consistently scaled to allow for inter-case comparisons. |
| ryndxqzofphm | M | MAX_MACROPHAGE_NUCLEUS_MAJOR_AXIS_EPITHELIAL | MAX_MACROPHAGE_NUCLEUS_MAJOR_AXIS_EPITHELIAL indicates the largest major axis length measured among the macrophage nuclei in epithelial compartments. It is computed by determining the maximum value from the set of measured major axis lengths for the cells, providing a numeric metric that is normalized and comparable across different patient cases. |
| s0uo24a38tkf | TU,E,MFp | MEAN_MIN_DIST_PDPN_MF_TO_TUM_ENDO | MEAN_MIN_DIST_PDPN_MF_TO_TUM_ENDO represents the average of the minimum Euclidean distances computed from each PDPN-positive myofibroblast to the nearest tumor or endothelial cell. This normalized distance, expressed in micrometers, reflects how closely these myofibroblasts are associated with tumor or vascular structures across different tumor patches. |
| s0uo24a38tkf | TU,E,MFp | MEDIAN_MIN_DIST_PDPN_MF_TO_TUM_ENDO | MEDIAN_MIN_DIST_PDPN_MF_TO_TUM_ENDO represents the median value of the minimum distances from each PDPN-positive myofibroblast to the nearest candidate cell (either tumor or endothelial). This metric, provided in micrometers, conveys the central tendency of the distance distribution and is useful for comparing different tumor patches. |
| s0uo24a38tkf | TU,E,MFp | STD_MIN_DIST_PDPN_MF_TO_TUM_ENDO | STD_MIN_DIST_PDPN_MF_TO_TUM_ENDO represents the standard deviation of the minimum distances from PDPN-positive myofibroblasts to the nearest tumor or endothelial cell, expressed in micrometers. It quantifies the variability in proximity across the analyzed cells within a tumor patch, making it a normalized measure for inter-case comparisons. |
| s0uo24a38tkf | TU,E,MFp | MIN_MIN_DIST_PDPN_MF_TO_TUM_ENDO | MIN_MIN_DIST_PDPN_MF_TO_TUM_ENDO represents the smallest minimum distance detected among all PDPN-positive myofibroblasts to the nearest tumor or endothelial cell in a tumor patch. This value, in micrometers, highlights the closest association of any such cell with a tumor or vascular element and is normalized for comparative analysis. |
| s0uo24a38tkf | TU,E,MFp | MAX_MIN_DIST_PDPN_MF_TO_TUM_ENDO | MAX_MIN_DIST_PDPN_MF_TO_TUM_ENDO represents the largest minimum distance among all computed distances from PDPN-positive myofibroblasts to the nearest tumor or endothelial cell, measured in micrometers. It provides a normalized extreme value for understanding the range of cellular proximities across tumor patches. |
| s3gkpz5i725j | TU,G,MFp,Ff | tumor_cell_proportion | Tumor cell proportion represents the normalized fraction of tumor cells (identified as epithelial cells) within the stromal compartment. It is calculated by dividing the count of tumor cells by the total number of stromal cells, allowing for comparative analysis across different patient cases. |
| s3gkpz5i725j | TU,G,MFp,Ff | granulocyte_proportion | Granulocyte proportion denotes the normalized fraction of granulocytes present in the stroma. It is computed by dividing the count of granulocytes by the total stromal cell count, ensuring the parameter is comparable between different samples. |
| s3gkpz5i725j | TU,G,MFp,Ff | myofibroblast_pdpn_proportion | Myofibroblast PDPN proportion measures the normalized fraction of PDPN+ myofibroblasts within the stromal compartment. It is derived by dividing the count of PDPN+ myofibroblasts by the total stromal cell number, making it suitable for cross-patient comparisons. |
| s3gkpz5i725j | TU,G,MFp,Ff | fibroblast_fsp1_proportion | Fibroblast FSP1 proportion indicates the normalized fraction of FSP1+ fibroblasts in the stroma. It is calculated by dividing their count by the total number of stromal cells, thereby normalizing the measurement across different patient cases. |
| s3gkpz5i725j | TU,G,MFp,Ff | stromal_infiltration_score | Stromal infiltration score is a combined normalized metric that accounts for the infiltration of multiple cell types in the stroma. It is calculated by summing the counts of tumor cells, granulocytes, PDPN+ myofibroblasts, and FSP1+ fibroblasts, and then dividing by the total number of stromal cells. This score provides an integrated measure of stromal cellular infiltration. |
| s41oq31c38u5 | Th,M,Tc | TH_M_TO_TC_RATIO | TH_M_TO_TC_RATIO represents the infiltration ratio calculated by dividing the combined count of T helper cells (CD4+) and macrophages by the number of cytotoxic T cells (CD8+) in the stromal compartment. This parameter is normalized, allowing comparisons across different patient cases by providing a relative measure of cell composition balance in tumor patches rather than relying on raw cell counts. |
| s5aiwvqzyfdt | MFp,Tc | MIN_DIST_PDPN_MFB_TO_CD8_MEAN | MIN_DIST_PDPN_MFB_TO_CD8_MEAN represents the average of the minimum Euclidean distances calculated between each PDPN+ myofibroblast and its nearest cytotoxic T cell in the stromal compartment. It reflects the overall spatial closeness of these cells and allows comparison across different patient cases. |
| s5aiwvqzyfdt | MFp,Tc | MIN_DIST_PDPN_MFB_TO_CD8_MEDIAN | MIN_DIST_PDPN_MFB_TO_CD8_MEDIAN is the median of the minimum distances determined for each PDPN+ myofibroblast to the closest cytotoxic T cell. This statistic provides a robust measure of the typical spatial relationship between these cell types by reducing the influence of outliers, making it useful for inter-case comparisons. |
| s5aiwvqzyfdt | MFp,Tc | MIN_DIST_PDPN_MFB_TO_CD8_MIN | MIN_DIST_PDPN_MFB_TO_CD8_MIN captures the smallest value among all the computed minimum distances between PDPN+ myofibroblasts and their nearest cytotoxic T cells. It indicates the closest point of interaction observed within the stromal compartment, serving as a specific marker for extreme cell proximity. |
| s5aiwvqzyfdt | MFp,Tc | MIN_DIST_PDPN_MFB_TO_CD8_MAX | MIN_DIST_PDPN_MFB_TO_CD8_MAX reflects the maximum value among the computed minimum distances, representing the furthest minimal separation observed between any PDPN+ myofibroblast and a cytotoxic T cell. This parameter helps to define the range of spatial interactions in the tumor's stromal region. |
| s5aiwvqzyfdt | MFp,Tc | MIN_DIST_PDPN_MFB_TO_CD8_STD | MIN_DIST_PDPN_MFB_TO_CD8_STD measures the standard deviation of the minimum distances between PDPN+ myofibroblasts and their nearest cytotoxic T cells. It provides an indication of the variability in spatial relationships, indicating how consistent the proximity measurements are across different regions. |
| sbzy922rfm79 | Tc,F | TC_NUCLEUS_ASPECT_RATIO_AVG | TC_NUCLEUS_ASPECT_RATIO_AVG: This parameter represents the average aspect ratio of nuclei in the cytotoxic T cells found in the stromal compartment. The aspect ratio is determined by measuring the width and height of each nucleus's bounding box, ensuring consistency in measurements across different patches. |
| sbzy922rfm79 | Tc,F | TC_NUCLEUS_ASPECT_RATIO_MIN | TC_NUCLEUS_ASPECT_RATIO_MIN: This parameter denotes the minimum observed aspect ratio among the cytotoxic T cell nuclei in the stroma. It identifies the smallest aspect ratio value from the set of measured nuclei, allowing for comparisons across patient samples. |
| sbzy922rfm79 | Tc,F | TC_NUCLEUS_ASPECT_RATIO_MAX | TC_NUCLEUS_ASPECT_RATIO_MAX: This parameter indicates the maximum observed aspect ratio among the cytotoxic T cell nuclei in the stromal compartment. It provides the largest aspect ratio value, reflecting the range of morphological variation. |
| sbzy922rfm79 | Tc,F | TC_NUCLEUS_ASPECT_RATIO_STD | TC_NUCLEUS_ASPECT_RATIO_STD: This parameter calculates the standard deviation of the aspect ratio values of cytotoxic T cell nuclei in the stroma, quantifying the variability in nucleus shape within each analyzed patch. |
| sbzy922rfm79 | Tc,F | FIBROBLAST_NUCLEUS_ASPECT_RATIO_AVG | FIBROBLAST_NUCLEUS_ASPECT_RATIO_AVG: This parameter represents the average aspect ratio of FSP1- fibroblast nuclei in the stromal compartment. It is computed in the same manner as the T cell values, facilitating comparison across different patches. |
| sbzy922rfm79 | Tc,F | FIBROBLAST_NUCLEUS_ASPECT_RATIO_MIN | FIBROBLAST_NUCLEUS_ASPECT_RATIO_MIN: This parameter denotes the smallest aspect ratio value measured among FSP1- fibroblast nuclei, reflecting the lower bound of nucleus shape variation within the stromal region. |
| sbzy922rfm79 | Tc,F | FIBROBLAST_NUCLEUS_ASPECT_RATIO_MAX | FIBROBLAST_NUCLEUS_ASPECT_RATIO_MAX: This parameter indicates the largest aspect ratio value observed among FSP1- fibroblast nuclei, useful for understanding the upper limit of nucleus shape variation in a given tumor patch. |
| sbzy922rfm79 | Tc,F | FIBROBLAST_NUCLEUS_ASPECT_RATIO_STD | FIBROBLAST_NUCLEUS_ASPECT_RATIO_STD: This parameter computes the standard deviation of the aspect ratio values for FSP1- fibroblast nuclei, thereby quantifying the degree of variation in nuclear morphology. |
| sbzy922rfm79 | Tc,F | NUCLEUS_ASPECT_RATIO_DIFFERENCE | NUCLEUS_ASPECT_RATIO_DIFFERENCE: This parameter is the difference between the average nucleus aspect ratios of cytotoxic T cells and FSP1- fibroblasts within each analyzed patch. It provides a normalized metric that can be compared across different patient cases, highlighting the relative differences in nuclear morphology between the two cell types. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | OVERALL_MEAN_HOMOPHILY | OVERALL_MEAN_HOMOPHILY: This parameter represents the overall average morphological homophily score computed across all analyzed cells. It is calculated as the mean ratio of morphologically similar neighbors (based on nuclear area similarity within a defined tolerance) to the total number of neighbors, making it a normalized measure that allows for comparisons between different patient cases. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | OVERALL_MEDIAN_HOMOPHILY | OVERALL_MEDIAN_HOMOPHILY: This parameter captures the overall median morphological homophily score across all cells. It reflects the central tendency of the ratio of neighbors with similar nuclear areas, ensuring robustness against outliers and enabling standardized comparisons across patient samples. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | TU_MEAN_HOMOPHILY | TU_MEAN_HOMOPHILY: This parameter is the mean homophily score specifically for tumor (TU) cells. It quantifies the average normalized proportion of neighboring cells with a nuclear area similar to that of the tumor cell, providing a metric for assessing spatial clustering among tumor cells. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | TU_MEDIAN_HOMOPHILY | TU_MEDIAN_HOMOPHILY: This parameter represents the median homophily score for tumor (TU) cells. It provides a robust central measure of the proportion of morphologically similar neighbors for tumor cells, helping to eliminate the impact of extreme values. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | TU_STD_HOMOPHILY | TU_STD_HOMOPHILY: This parameter measures the variability in the homophily scores among tumor (TU) cells by calculating the standard deviation of the normalized ratios. It indicates the dispersion in neighbor similarity and supports comparative analysis across tumor regions. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | Th_MEAN_HOMOPHILY | Th_MEAN_HOMOPHILY: This parameter calculates the mean homophily score for T helper (Th) cells. It reflects the average normalized proportion of neighboring cells with similar nuclear areas, which is useful for comparing spatial patterns between different patient cases. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | Th_MEDIAN_HOMOPHILY | Th_MEDIAN_HOMOPHILY: This parameter represents the median homophily score for T helper (Th) cells, capturing the typical value of the normalized ratio of similar neighbors, thereby providing a robust statistic less influenced by outliers. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | Th_STD_HOMOPHILY | Th_STD_HOMOPHILY: This parameter indicates the standard deviation of the homophily scores for T helper (Th) cells. It measures the variability in the normalized proportions of similar neighbors, offering insights into the heterogeneity of local cell arrangements. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | Treg_MEAN_HOMOPHILY | Treg_MEAN_HOMOPHILY: This parameter is the mean morphological homophily score for regulatory T (Treg) cells. It quantifies the average normalized ratio of neighbors exhibiting similar nuclear areas among Treg cells, thus facilitating the assessment of their spatial clustering. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | Treg_MEDIAN_HOMOPHILY | Treg_MEDIAN_HOMOPHILY: This parameter represents the median homophily score for regulatory T (Treg) cells, offering a robust central measure of the normalized proportion of neighboring cells with similar nuclear morphology. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | Treg_STD_HOMOPHILY | Treg_STD_HOMOPHILY: This parameter computes the standard deviation of homophily scores for Treg cells, showcasing the variability in the normalized similarity measures among these cells. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | B_MEAN_HOMOPHILY | B_MEAN_HOMOPHILY: This parameter calculates the mean homophily score for B cells. It is determined by averaging the normalized ratios of neighboring cells with similar nuclear areas, providing a meaningful metric for inter-patient comparison. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | B_MEDIAN_HOMOPHILY | B_MEDIAN_HOMOPHILY: This parameter represents the median homophily score for B cells, reflecting the central tendency of the normalized proportion of similar neighbors in the B cell population. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | B_STD_HOMOPHILY | B_STD_HOMOPHILY: This parameter defines the standard deviation of the homophily scores for B cells, illustrating the variability in the normalized ratios of morphologically similar neighbor cells. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | P_MEAN_HOMOPHILY | P_MEAN_HOMOPHILY: This parameter is the mean homophily score for plasma (P) cells, computed as the average normalized proportion of neighboring cells with similar nuclear areas, ensuring that the metric is suitable for cross-patient analysis. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | P_MEDIAN_HOMOPHILY | P_MEDIAN_HOMOPHILY: This parameter represents the median homophily score for plasma (P) cells, capturing the central tendency of the normalized measure of neighbor similarity. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | P_STD_HOMOPHILY | P_STD_HOMOPHILY: This parameter measures the standard deviation of the homophily scores for plasma (P) cells, signifying the dispersion in the normalized ratios of similar neighboring cells. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | M_MEAN_HOMOPHILY | M_MEAN_HOMOPHILY: This parameter calculates the mean homophily score for macrophages (M) by averaging the normalized ratios of morphologically similar neighboring cells, providing a consistent metric for spatial analysis. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | M_MEDIAN_HOMOPHILY | M_MEDIAN_HOMOPHILY: This parameter represents the median homophily score for macrophages (M), offering a robust measure of the central value of the normalized neighbor similarity ratios among these cells. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | M_STD_HOMOPHILY | M_STD_HOMOPHILY: This parameter determines the standard deviation of the homophily scores for macrophages (M), indicating the variability in the normalized proportions of similar neighbors across macrophage cells. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | G_MEAN_HOMOPHILY | G_MEAN_HOMOPHILY: This parameter is the mean homophily score for granulocytes (G), computed as the average normalized ratio of neighboring cells with similar nuclear areas, aiding in the comparison of spatial patterns across different samples. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | G_MEDIAN_HOMOPHILY | G_MEDIAN_HOMOPHILY: This parameter represents the median homophily score for granulocytes (G), capturing the central tendency of the normalized proportion of similar neighbors in granulocyte populations. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | G_STD_HOMOPHILY | G_STD_HOMOPHILY: This parameter measures the standard deviation of granulocyte homophily scores, reflecting the variability in the normalized ratios of morphologically similar neighboring cells. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | MFp_MEAN_HOMOPHILY | MFp_MEAN_HOMOPHILY: This parameter calculates the mean homophily score for myofibroblasts (MFp) by averaging the normalized ratios of neighboring cells with similar nuclear areas, thereby providing a consistent metric for spatial heterogeneity. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | MFp_MEDIAN_HOMOPHILY | MFp_MEDIAN_HOMOPHILY: This parameter represents the median homophily score for myofibroblasts (MFp), offering a robust measure of the central value of the normalized neighbor similarity ratios. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | MFp_STD_HOMOPHILY | MFp_STD_HOMOPHILY: This parameter computes the standard deviation of the homophily scores for myofibroblasts (MFp), indicating the variability in the normalized proportion of similar neighboring cells. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | Ff_MEAN_HOMOPHILY | Ff_MEAN_HOMOPHILY: This parameter is the mean homophily score for fibroblasts (Ff), calculated as the average normalized ratio of neighboring cells with similar nuclear areas, which supports comparisons across different tumor patches. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | Ff_MEDIAN_HOMOPHILY | Ff_MEDIAN_HOMOPHILY: This parameter represents the median homophily score for fibroblasts (Ff), capturing the central tendency of the normalized similarity measure in the fibroblast population. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | Ff_STD_HOMOPHILY | Ff_STD_HOMOPHILY: This parameter measures the standard deviation of fibroblast homophily scores, reflecting the variability in the normalized ratios of similar neighboring cells among fibroblasts. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | E_MEAN_HOMOPHILY | E_MEAN_HOMOPHILY: This parameter calculates the mean homophily score for endothelial cells (E), quantifying the average normalized proportion of neighbors with similar nuclear areas and enabling standardized comparisons. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | E_MEDIAN_HOMOPHILY | E_MEDIAN_HOMOPHILY: This parameter represents the median homophily score for endothelial cells (E), reflecting the central tendency of the normalized proportion of similar neighbors in the endothelial population. |
| sht66kzb6tcz | TU,Th,Treg,B,P,M,G,MFp,Ff,E | E_STD_HOMOPHILY | E_STD_HOMOPHILY: This parameter computes the standard deviation of the homophily scores for endothelial cells (E), indicating the variability and dispersion in the normalized similarity measures among these cells. |
| sjsa26uoz3hg | MFp,TU | PROPORTION_ADJACENT_MFP | PROPORTION_ADJACENT_MFP represents the fraction of PDPN+ myofibroblasts that are in immediate adjacency to tumor cells. This parameter is calculated by identifying PDPN+ myofibroblasts from the cell population, determining the subset that lie within a defined distance threshold from any tumor cell, and then computing the ratio of these adjacent cells to the total number of PDPN+ myofibroblasts. Being a normalized ratio, it enables direct comparison across different patient cases and tumor patches. |
| sjsa26uoz3hg | MFp,TU | MIN_DISTANCE_MFP_TUMOR | MIN_DISTANCE_MFP_TUMOR measures the smallest Euclidean distance between any PDPN+ myofibroblast and any tumor cell within a given tissue patch. This distance, expressed in micrometers, provides insight into the closest proximity between these two cell types. As a continuous and standardized metric, it is suitable for comparing spatial relationships across different patient samples. |
| srftt66t079n | P | Median_Minor_Axis_Length | This parameter represents the median value of the minor axis lengths of plasma cell nuclei located in the stromal compartments. It is derived by identifying plasma cells within the stroma, extracting the nuclear shape from the polygon data, fitting an ellipse to this shape, and then extracting the minor axis length from the fitted ellipse. The median of these measured lengths provides a normalized, numeric metric that can be compared across different patient cases, aiding in the assessment of potential links between nuclear morphology, immunoglobulin production, and tumor control or progression. |
| svm3bq5whkzv | TU,Treg,P,M,Ff | Treg_mean_circularity | Treg_mean_circularity: This parameter represents the average nuclear circularity of tumor cells that are spatially close to T regulatory cells. The circularity, calculated using a standard formula based on cell area and perimeter, is normalized across tumor patches, enabling comparisons across different patient samples. |
| svm3bq5whkzv | TU,Treg,P,M,Ff | Treg_median_circularity | Treg_median_circularity: This parameter captures the median value of the nuclear circularity measured for tumor cells in proximity to T regulatory cells. The median, as a normalized metric, provides a robust statistic that can be reliably compared across different tumor regions and patient cases. |
| svm3bq5whkzv | TU,Treg,P,M,Ff | Plasma_mean_circularity | Plasma_mean_circularity: This parameter denotes the mean nuclear circularity of tumor cells that are near plasma cells. By deriving the circularity from individual tumor cell measurements and averaging them, the result is normalized, allowing for valid comparison across distinct patient patches. |
| svm3bq5whkzv | TU,Treg,P,M,Ff | Plasma_median_circularity | Plasma_median_circularity: This metric reflects the median nuclear circularity of tumor cells in the vicinity of plasma cells. It serves as a normalized statistic, summarizing the central tendency of the circularity distribution, and is useful for comparative analysis across different tumors. |
| svm3bq5whkzv | TU,Treg,P,M,Ff | Macrophage_mean_circularity | Macrophage_mean_circularity: This parameter calculates the average nuclear circularity of tumor cells neighboring macrophages. The tumor cell circularity is determined based on geometric properties, and the averaging produces a normalized metric suitable for inter-patient and inter-region comparisons. |
| svm3bq5whkzv | TU,Treg,P,M,Ff | Macrophage_median_circularity | Macrophage_median_circularity: This metric represents the median nuclear circularity of tumor cells that are adjacent to macrophages. As a normalized measure derived from individual cell calculations, it supports robust comparisons across different tumor regions and patient cases. |
| svm3bq5whkzv | TU,Treg,P,M,Ff | Fibroblast_FSP1_mean_circularity | Fibroblast_FSP1_mean_circularity: This parameter indicates the average nuclear circularity of tumor cells located near FSP1-positive fibroblasts. Normalized through an averaging process, it facilitates the comparison of tumor morphology across various patches and patients. |
| svm3bq5whkzv | TU,Treg,P,M,Ff | Fibroblast_FSP1_median_circularity | Fibroblast_FSP1_median_circularity: This parameter reflects the median nuclear circularity value of tumor cells in proximity to FSP1-positive fibroblasts. Being a normalized metric, it provides a reliable statistic for comparing cellular morphological characteristics across different tumor images. |
| swcsjdcwggrw | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | HIGH_DENSITY_REGION_SIZE_VARIATION | HIGH_DENSITY_REGION_SIZE_VARIATION represents the standard deviation of the aggregated high-density region areas computed for the 14 specified cell types in a given tumor patch. This metric captures the overall spatial variability in the sizes of dense cell clusters, thereby enabling comparisons across different patient cases. |
| swcsjdcwggrw | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | AREA_TU | AREA_TU represents the average area of high-density clusters specifically for tumor cells (epithelial cells). These areas are obtained by applying a density-based clustering method on cell centroid coordinates and computing the area of the resulting convex hulls, ensuring the measure is comparable across samples. |
| swcsjdcwggrw | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | AREA_Tc | AREA_Tc represents the average area of high-density clusters for cytotoxic T cells. The value is derived by clustering the spatial distribution of these cells and averaging the areas of the convex hulls from identified clusters, allowing for normalized comparison between patient cases. |
| swcsjdcwggrw | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | AREA_Th | AREA_Th represents the average area of high-density clusters for helper T cells. The measure is calculated by aggregating the areas of spatial clusters (ignoring noise) and serves as a comparable metric for assessing the spatial distribution of these cells. |
| swcsjdcwggrw | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | AREA_B | AREA_B represents the average area of high-density clusters for B cells. The metric is obtained through clustering the cell coordinates and evaluating the convex hull areas of the clusters, ensuring that variations across different tumor regions are meaningfully reflected. |
| swcsjdcwggrw | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | AREA_P | AREA_P represents the average area of high-density clusters for plasma cells. This parameter quantifies the typical size of spatial cell clusters, computed through an algorithmic approach that factors in only significant clusters, making it suitable for cross-case comparison. |
| swcsjdcwggrw | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | AREA_M | AREA_M represents the average area of high-density clusters for macrophages. Calculated using spatial clustering and averaging the convex hull areas, this measure acts as a normalized metric indicating the spatial extent of macrophage clusters in tumor patches. |
| swcsjdcwggrw | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | AREA_MFp | AREA_MFp represents the average area of high-density clusters for PDPN-positive myofibroblasts. It quantifies the typical cluster size by computing the convex hull area of detected clusters, which allows for standardized comparisons across samples. |
| swcsjdcwggrw | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | AREA_MF | AREA_MF represents the average area of high-density clusters for myofibroblasts. This parameter is derived from spatial clustering and subsequent averaging of cluster areas, ensuring that it serves as a comparable numerical value between different patient cases. |
| swcsjdcwggrw | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | AREA_F | AREA_F represents the average area of high-density clusters for fibroblasts. The measure results from the application of a clustering algorithm on spatial cell data and reflects the typical size of fibroblast clusters in a normalized manner across tumor patches. |
| swcsjdcwggrw | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | AREA_E | AREA_E represents the average area of high-density clusters for endothelial cells. It is computed by analyzing the spatial distribution of these cells, calculating convex hull areas for clusters, and averaging them to provide a normalized parameter for inter-case comparisons. |
| swcsjdcwggrw | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | AREA_A | AREA_A represents the average area of high-density clusters for antigen-presenting cells. This parameter is based on the clustering of cell coordinates and the evaluation of convex hull areas for each cluster, ensuring a meaningful and normalized spatial metric. |
| sx0umwebijcg | Treg,F,M,G | STD_MINOR_AXIS_LENGTH_IMMUNE_STROMAL | This parameter measures the variability in the shape of cell nuclei among regulatory T cells, fibroblasts (FSP1-), macrophages, and granulocytes within a tumor patch. It does so by calculating the standard deviation of the minor axis lengths of nuclear polygons, obtained via computing the minimum rotated rectangle for each cell. The resulting numerical value reflects the heterogeneity in nuclear dimensions, which may indicate localized tumor microenvironmental stress and potentially correlate with worse clinical outcomes. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | Th_MEAN_P2A_RATIO | Th_MEAN_P2A_RATIO: Represents the average ratio of nucleus perimeter to area for T helper cells. It quantifies the mean irregularity in nuclear shape, calculated from individual cell ratios that are aggregated across the analyzed region. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | Th_STD_P2A_RATIO | Th_STD_P2A_RATIO: Indicates the variability in the perimeter-to-area ratios among T helper cells, reflecting how much the nuclear shape irregularity differs from cell to cell. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | Th_MIN_P2A_RATIO | Th_MIN_P2A_RATIO: Records the minimum observed perimeter-to-area ratio for T helper cells within the analyzed region, highlighting the most circular or least irregular nucleus among them. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | Th_MAX_P2A_RATIO | Th_MAX_P2A_RATIO: Captures the maximum observed perimeter-to-area ratio for T helper cells, identifying the cell with the most irregular nuclear shape in the sample. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | Treg_MEAN_P2A_RATIO | Treg_MEAN_P2A_RATIO: Represents the average nucleus perimeter-to-area ratio for regulatory T cells, serving as a measure of the typical nuclear shape irregularity for this cell type. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | Treg_STD_P2A_RATIO | Treg_STD_P2A_RATIO: Measures the standard deviation of the nucleus perimeter-to-area ratios for regulatory T cells, indicating the degree of variability in their nuclear shapes. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | Treg_MIN_P2A_RATIO | Treg_MIN_P2A_RATIO: Provides the minimum value among the calculated nucleus perimeter-to-area ratios for regulatory T cells, corresponding to the least irregular nuclear structure observed. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | Treg_MAX_P2A_RATIO | Treg_MAX_P2A_RATIO: Provides the maximum value among the perimeter-to-area ratios for regulatory T cells, reflecting the highest degree of nuclear irregularity in the sample. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | B_MEAN_P2A_RATIO | B_MEAN_P2A_RATIO: Represents the mean perimeter-to-area ratio for B cells, quantifying the typical level of nuclear shape irregularity observed from individual cell measurements. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | B_STD_P2A_RATIO | B_STD_P2A_RATIO: Reflects the variability in nucleus perimeter-to-area ratios for B cells, indicating differences in nuclear shape irregularity across the cell population. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | B_MIN_P2A_RATIO | B_MIN_P2A_RATIO: Denotes the lowest measured perimeter-to-area ratio for B cells, highlighting the cell with the most regular (or least irregular) nuclear shape. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | B_MAX_P2A_RATIO | B_MAX_P2A_RATIO: Denotes the highest measured perimeter-to-area ratio for B cells, indicating the cell with the most pronounced nuclear shape irregularity. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | P_MEAN_P2A_RATIO | P_MEAN_P2A_RATIO: Captures the average nucleus perimeter-to-area ratio for plasma cells, where the ratio serves as a normalized measure allowing comparison across different patient cases. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | P_STD_P2A_RATIO | P_STD_P2A_RATIO: Reflects the standard deviation of the nucleus perimeter-to-area ratios for plasma cells, showing the spread or variability in nuclear irregularity measurements. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | P_MIN_P2A_RATIO | P_MIN_P2A_RATIO: Indicates the smallest nucleus perimeter-to-area ratio observed among plasma cells, representing the most regular nuclear shape in the group. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | P_MAX_P2A_RATIO | P_MAX_P2A_RATIO: Indicates the largest nucleus perimeter-to-area ratio among plasma cells, identifying the cell with the highest level of nuclear irregularity. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | M_MEAN_P2A_RATIO | M_MEAN_P2A_RATIO: Represents the average nucleus perimeter-to-area ratio for macrophages, providing a normalized mean measure of cellular nuclear shape irregularity. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | M_STD_P2A_RATIO | M_STD_P2A_RATIO: Quantifies the variability in the perimeter-to-area ratios of macrophages, reflecting how consistently the nuclear shape irregularities are distributed in the sample. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | M_MIN_P2A_RATIO | M_MIN_P2A_RATIO: Registers the lowest perimeter-to-area ratio for macrophages, denoting the instance of the most regular nuclear shape among these cells. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | M_MAX_P2A_RATIO | M_MAX_P2A_RATIO: Registers the highest perimeter-to-area ratio for macrophages, indicating the most irregular nuclear structure observed. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | G_MEAN_P2A_RATIO | G_MEAN_P2A_RATIO: Indicates the mean nucleus perimeter-to-area ratio for granulocytes, summarizing the average level of nuclear irregularity for this cell type. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | G_STD_P2A_RATIO | G_STD_P2A_RATIO: Measures the spread of the nucleus perimeter-to-area ratios among granulocytes, showing the degree of dispersion in nuclear shape irregularities. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | G_MIN_P2A_RATIO | G_MIN_P2A_RATIO: Reflects the minimum nucleus perimeter-to-area ratio found in granulocytes, pointing to the most regular nuclear shape within the group. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | G_MAX_P2A_RATIO | G_MAX_P2A_RATIO: Reflects the maximum nucleus perimeter-to-area ratio found in granulocytes, highlighting the cell with the most markedly irregular nucleus. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | F_MEAN_P2A_RATIO | F_MEAN_P2A_RATIO: Represents the average nucleus perimeter-to-area ratio for fibroblasts, offering a normalized measure of typical nuclear shape irregularity in the analyzed population. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | F_STD_P2A_RATIO | F_STD_P2A_RATIO: Illustrates the variability in nucleus perimeter-to-area ratios for fibroblasts, indicating how heterogeneous the nuclear shapes are within this cell type. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | F_MIN_P2A_RATIO | F_MIN_P2A_RATIO: Captures the minimum observed ratio in fibroblasts, identifying the most regular cell nucleus among the fibroblast population. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | F_MAX_P2A_RATIO | F_MAX_P2A_RATIO: Captures the maximum observed ratio in fibroblasts, pinpointing the cell with the most irregular nuclear shape in the group. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | MF_MEAN_P2A_RATIO | MF_MEAN_P2A_RATIO: Denotes the average nucleus perimeter-to-area ratio for myofibroblasts, providing a normalized indicator of nuclear shape irregularity. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | MF_STD_P2A_RATIO | MF_STD_P2A_RATIO: Denotes the standard deviation of nucleus perimeter-to-area ratios for myofibroblasts, reflecting the variability in nuclear shape irregularity across these cells. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | MF_MIN_P2A_RATIO | MF_MIN_P2A_RATIO: Denotes the minimum perimeter-to-area ratio observed in the myofibroblast population, marking the cell with the smoothest nuclear contour. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | MF_MAX_P2A_RATIO | MF_MAX_P2A_RATIO: Denotes the maximum perimeter-to-area ratio observed among myofibroblasts, highlighting the cell with the greatest irregularity in nuclear shape. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | TU_MEAN_P2A_RATIO | TU_MEAN_P2A_RATIO: Represents the average nucleus perimeter-to-area ratio for tumor (epithelial) cells, providing a normalized metric for comparing nuclear irregularity across cases. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | TU_STD_P2A_RATIO | TU_STD_P2A_RATIO: Represents the standard deviation of the nucleus perimeter-to-area ratios for tumor cells, illustrating the variability in the nuclear shapes of these cells. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | TU_MIN_P2A_RATIO | TU_MIN_P2A_RATIO: Represents the minimum nucleus perimeter-to-area ratio recorded for tumor cells, corresponding to the most regular nuclear shape observed. |
| t02w8qb3y4vv | Th,Treg,B,P,M,G,F,MF,TU | TU_MAX_P2A_RATIO | TU_MAX_P2A_RATIO: Represents the maximum nucleus perimeter-to-area ratio recorded for tumor cells, indicating the cell with the most irregular nucleus. |
| t13ronckd0ik | B | median_distance_Bcell_to_vessel | The parameter 'median_distance_Bcell_to_vessel' measures the median distance in micrometers from B lymphocytes located in the stromal compartment to their nearest vessel. It is computed by first filtering for B cells in stroma, then calculating the minimum distance from each cell's centroid to any vessel polygon, and finally determining the median of these distances for each patch. This numeric metric is normalized across tumor patches, allowing for direct comparison of spatial relationships between different patient cases. |
| t35hpsao1502 | TU,P | CLUSTERING_INDEX | CLUSTERING_INDEX represents the area under the curve of the difference between the observed and the expected values of Ripley’s K function. It measures the overall spatial clustering between tumor and plasma cells relative to a null model of complete spatial randomness, allowing for comparison across different patient cases. |
| t35hpsao1502 | TU,P | MAX_CLUSTERING_VALUE | MAX_CLUSTERING_VALUE is the highest value observed in the difference between the Ripley’s K function and its expected value under a random distribution. This parameter reflects the strongest local clustering effect detected at any scale, and is normalized to permit meaningful comparisons among cases. |
| t35hpsao1502 | TU,P | CLUSTERING_AT_50UM | CLUSTERING_AT_50UM represents the value of the difference between the observed and expected Ripley’s K function specifically at a biologically relevant distance of 50 micrometers. It quantifies the level of spatial clustering at that particular scale and is suitable for comparing distinct patient samples. |
| t35hpsao1502 | TU,P | TUMOR_PLASMA_RATIO_NEAR_VESSELS | TUMOR_PLASMA_RATIO_NEAR_VESSELS is the ratio of tumor cells to plasma cells found within a defined proximity to blood vessels. Being a ratio, it is normalized across different regions, providing an index of the relative abundance of these cell types in perivascular regions that is comparable between patient cases. |
| t4net1nvbyr4 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff | stromal_infiltration_ratio | The stromal infiltration ratio measures the proportion of cells within the stromal compartment that have a nearest neighbor of a different cell type. This ratio is computed by first identifying the nearest neighbor for each stromal cell and then determining whether the neighbor belongs to a different cell class. The resulting value is normalized, ranging from 0 to 1, making it suitable for comparing across different patient cases and patches. A higher ratio indicates an increased heterogeneity of cell types, which may be indicative of coordinated cellular infiltration associated with immune surveillance or evasion in the tumor microenvironment. |
| tawsllbo9fwe | F,MFp,E,G | MEAN_ORIENTATION_ANGLE | MEAN_ORIENTATION_ANGLE represents the average orientation angle (in degrees) of the major axis of ellipses fitted to the nuclei of fibroblasts and PDPN+ myofibroblasts that are in proximity to both endothelial cells and granulocytes. The measurement is normalized to the range [0, 180) degrees, which allows for consistent comparison across different patient cases and tumor patches. |
| tawsllbo9fwe | F,MFp,E,G | STD_ORIENTATION_ANGLE | STD_ORIENTATION_ANGLE quantifies the variability or spread in the orientation angles of the fitted ellipses. It is calculated as the standard deviation of the individual orientation angles, providing an assessment of the heterogeneity in cell alignment within a tissue patch, and is normalized across cases. |
| tawsllbo9fwe | F,MFp,E,G | MIN_ORIENTATION_ANGLE | MIN_ORIENTATION_ANGLE denotes the minimum observed orientation angle (in degrees) among all candidate cells that met the spatial criteria. This parameter, normalized within the 0 to 180-degree range, highlights the lowest measured alignment value in the analyzed region. |
| tawsllbo9fwe | F,MFp,E,G | MAX_ORIENTATION_ANGLE | MAX_ORIENTATION_ANGLE denotes the maximum observed orientation angle (in degrees) among the candidate cells that passed the filtering criteria. Normalized to the range [0, 180), it reflects the highest degree of alignment relative to the horizontal axis among cells in the tumor patch. |
| tb3wmtd8rofy | TU,Th,Treg,B,P,M,MFp,MF,F,E | STD_NUCLEAR_SOLIDITY | STD_NUCLEAR_SOLIDITY represents the variability in the compactness of nuclear shapes across selected cell types. This parameter is calculated by measuring the solidity of each nucleus (obtained by dividing the nucleus polygon area by its convex hull area) and then computing the standard deviation of these values over the cell populations of interest. The measure is normalized in the sense that it reflects variation relative to the mean behavior of the tumor and immune cells, enabling comparisons across different tumor cases or patches. |
| td29c04foc15 | TU,Tc,Ff,M | TU_mean_chord_length | TU_mean_chord_length represents the average chord length calculated from the nuclear polygon outlines of tumor cells (epithelial cells) located in the stromal regions of a tissue patch. This metric is computed by averaging chord lengths measured at fixed angles and serves as a normalized measure of nuclear dimensions across patient cases. |
| td29c04foc15 | TU,Tc,Ff,M | Tc_mean_chord_length | Tc_mean_chord_length is the average chord length derived from the nuclear measurements of cytotoxic T cells (t_cell_cd8) in the stroma. It reflects key geometric features of the nuclei and is calculated by averaging chord measurements, allowing for inter-case comparison. |
| td29c04foc15 | TU,Tc,Ff,M | Ff_mean_chord_length | Ff_mean_chord_length denotes the mean chord length computed for fibroblasts expressing FSP1 (fibroblast_fsp1) within the stromal compartment. The parameter quantifies nuclear dimensions based on multiple chord measurements per cell, and is normalized so it can be compared across different patient samples. |
| td29c04foc15 | TU,Tc,Ff,M | M_mean_chord_length | M_mean_chord_length is the average chord length computed for macrophages in the stroma based on their nuclear shape. It provides a normalized numeric measure of nuclear size and irregularity through averaging over chord measurements from fixed angles. |
| td29c04foc15 | TU,Tc,Ff,M | TU_to_Tc_ratio | TU_to_Tc_ratio is the computed ratio of the tumor cell mean chord length to that of cytotoxic T cells. This ratio provides a normalized comparative measure of nuclear dimensions between these two cell types, reflecting potential differences in nuclear irregularities. |
| td29c04foc15 | TU,Tc,Ff,M | TU_to_Ff_ratio | TU_to_Ff_ratio is the ratio of the mean chord length of tumor cells to that of fibroblasts FSP1+. It is designed to normalize and contrast the nuclear geometry between tumor cells and the stromal fibroblasts. |
| td29c04foc15 | TU,Tc,Ff,M | TU_to_M_ratio | TU_to_M_ratio is the ratio comparing the mean chord lengths of tumor cells to macrophages, providing a normalized metric for assessing relative differences in nuclear dimensions among these cell types in the stroma. |
| td29c04foc15 | TU,Tc,Ff,M | Tc_to_Ff_ratio | Tc_to_Ff_ratio is the ratio of the mean chord length of cytotoxic T cells to fibroblasts FSP1+. This normalized parameter compares the nuclear geometric features of two distinct cell types present in the stromal regions. |
| td29c04foc15 | TU,Tc,Ff,M | Tc_to_M_ratio | Tc_to_M_ratio is the ratio of the average chord length of cytotoxic T cells to that of macrophages, serving as a normalized metric that facilitates direct comparison of nuclear features between these immune cell types. |
| td29c04foc15 | TU,Tc,Ff,M | Ff_to_M_ratio | Ff_to_M_ratio is the ratio of fibroblasts FSP1+ mean chord length to macrophages’ mean chord length. It provides a normalized measure for comparing the nuclear geometrical measurements between these two cell populations. |
| tfpee8vh41yv | Treg,MF | bin_1_upper_bound | bin_1_upper_bound: The upper distance boundary (in micrometers) of the first concentric distance bin from the vessel polygons, used to define the spatial region for cell density measurement. |
| tfpee8vh41yv | Treg,MF | bin_1_treg_density | bin_1_treg_density: The density of regulatory T cells within the first distance bin, calculated as the number of Treg cells per square micrometer, ensuring normalization across different tissue regions. |
| tfpee8vh41yv | Treg,MF | bin_1_mf_density | bin_1_mf_density: The density of PDPN-myofibroblasts in the first bin, computed as the number of these cells per square micrometer, which supports normalized comparison across patches. |
| tfpee8vh41yv | Treg,MF | bin_1_density_diff | bin_1_density_diff: The difference between the density of regulatory T cells and PDPN-myofibroblasts in the first bin, providing a normalized metric of cell-type imbalance. |
| tfpee8vh41yv | Treg,MF | bin_2_lower_bound | bin_2_lower_bound: The lower distance boundary (in micrometers) that marks the beginning of the second concentric distance bin from the vessels. |
| tfpee8vh41yv | Treg,MF | bin_2_upper_bound | bin_2_upper_bound: The upper distance boundary (in micrometers) of the second distance bin, defining the spatial limits in which cell densities are calculated. |
| tfpee8vh41yv | Treg,MF | bin_2_mf_density | bin_2_mf_density: The normalized density (cells per square micrometer) of PDPN-myofibroblasts in the second bin, derived by dividing the cell count by the bin area. |
| tfpee8vh41yv | Treg,MF | bin_2_density_diff | bin_2_density_diff: The normalized difference in cell densities between regulatory T cells and PDPN-myofibroblasts in the second bin, used to assess spatial variations in cell infiltration. |
| tfpee8vh41yv | Treg,MF | treg_mf_density_diff_trend_slope | treg_mf_density_diff_trend_slope: The slope of the linear trend derived from density differences across multiple distance bins; this value quantifies how the Treg versus PDPN-myofibroblast density difference changes with increasing distance from vessels. |
| tfpee8vh41yv | Treg,MF | treg_mf_density_diff_trend_correlation | treg_mf_density_diff_trend_correlation: The correlation coefficient that measures the strength and direction of the relationship between the density differences and the distance from the vessels, providing insight into spatial trends. |
| tfpee8vh41yv | Treg,MF | treg_mf_density_diff_mean | treg_mf_density_diff_mean: The mean value of the density differences (Treg minus PDPN-myofibroblast) across all bins, summarizing the overall trend in cell density imbalances in a normalized manner. |
| tfpee8vh41yv | Treg,MF | treg_mf_density_diff_std | treg_mf_density_diff_std: The standard deviation of density differences across all distance bins, reflecting the variability in the cell-type differences normalized by area. |
| tfpee8vh41yv | Treg,MF | treg_mf_density_diff_min | treg_mf_density_diff_min: The minimum observed density difference (Treg minus PDPN-myofibroblast) across all concentric bins, providing the lower bound of cell imbalance. |
| tfpee8vh41yv | Treg,MF | treg_mf_density_diff_max | treg_mf_density_diff_max: The maximum observed density difference across all bins, indicating the upper bound of spatial cell-type imbalance in a normalized context. |
| tfpee8vh41yv | Treg,MF | bin_3_lower_bound | bin_3_lower_bound: The lower distance boundary (in micrometers) of the third concentric distance bin, used to segment the tissue region for analysis. |
| tfpee8vh41yv | Treg,MF | bin_3_upper_bound | bin_3_upper_bound: The upper distance boundary (in micrometers) of the third bin, delineating the spatial extent over which cell densities are measured. |
| tfpee8vh41yv | Treg,MF | bin_3_mf_density | bin_3_mf_density: The normalized density of PDPN-myofibroblasts in the third bin, computed as cells per square micrometer and enabling comparisons between different tissue patches. |
| tfpee8vh41yv | Treg,MF | bin_3_density_diff | bin_3_density_diff: The difference between the regulatory T cell density and PDPN-myofibroblast density in the third bin, representing the normalized cell composition balance within that specific spatial region. |
| tfpee8vh41yv | Treg,MF | bin_4_lower_bound | bin_4_lower_bound: The lower boundary (in micrometers) of the fourth concentric distance bin, marking the start of the measurement region for cell density analysis. |
| tfpee8vh41yv | Treg,MF | bin_4_upper_bound | bin_4_upper_bound: The upper boundary (in micrometers) of the fourth bin, which defines the extent of the spatial domain used for calculating normalized cell densities. |
| tiy2j5t49apu | A,M,E | APC_PROPORTION | APC_PROPORTION represents the normalized proportion of antigen presenting cells relative to the sum of antigen presenting cells, macrophages, and endothelial cells in the stromal compartment. It provides a relative metric that can be compared across different patient cases by indicating the fraction of APCs in the immune cell mix. |
| tiy2j5t49apu | A,M,E | APC_TO_MACROPHAGE_RATIO | APC_TO_MACROPHAGE_RATIO is a normalized ratio measuring the relative abundance of antigen presenting cells compared to macrophages within the stromal region. By using a small constant to avoid division by zero, this parameter offers a stable comparison between different tumor patches across various patient cases. |
| tiy2j5t49apu | A,M,E | APC_TO_ENDOTHELIAL_RATIO | APC_TO_ENDOTHELIAL_RATIO is a normalized ratio that quantifies the relationship between the number of antigen presenting cells and endothelial cells in the stromal compartment. The parameter, derived with a safeguard against zero denominators, is designed to allow direct comparison across different patient cases by reflecting the balance between these cell types. |
| tjsbu27c9ang | B,G,M,MF,MFp,P,Treg,TU | MEAN_MIN_DISTANCE_MACRO_MYOFIB | MEAN_MIN_DISTANCE_MACRO_MYOFIB measures the average minimum Euclidean distance from each macrophage to its nearest myofibroblast. This value indicates the spatial proximity between the two cell types, and being an average distance, it is normalized across patient patches, making it comparable between different patient cases. |
| tjsbu27c9ang | B,G,M,MF,MFp,P,Treg,TU | MM_CONGRUENCE_INDEX | MM_CONGRUENCE_INDEX is computed as the inverse of the mean minimum distance between macrophages and myofibroblasts, with a small constant added to avoid division by zero. This parameter reflects the degree of spatial congruence, where higher values indicate closer proximity between the two cell types. Its normalized nature allows for effective comparison across different samples. |
| tjsbu27c9ang | B,G,M,MF,MFp,P,Treg,TU | IMMUNE_DENSITY_NEAR_TUMOR | IMMUNE_DENSITY_NEAR_TUMOR quantifies the average number of immune cells (including regulatory T cells, B cells, plasma cells, and granulocytes) found within a 50 micrometer radius around each tumor cell. The count is normalized by dividing by the total number of tumor cells, ensuring that the metric is comparable across different patient cases and patch regions. |
| tjsbu27c9ang | B,G,M,MF,MFp,P,Treg,TU | FINAL_SPATIAL_CONGRUENCE_INDEX | FINAL_SPATIAL_CONGRUENCE_INDEX is the product of the MM_CONGRUENCE_INDEX and the IMMUNE_DENSITY_NEAR_TUMOR. This combined metric integrates the spatial co-localization of macrophages and myofibroblasts with the local immune context around tumor cells, yielding a comprehensive and normalized indicator of the spatial interactions within the tumor microenvironment. |
| tk4rsgoyofiy | F,Ff,M,Treg,TU | PERCENT_FSP1_PAIRS_WITH_MACROPHAGE | PERCENT_FSP1_PAIRS_WITH_MACROPHAGE measures the percentage of fibroblast pairs, composed of one FSP1 positive and one FSP1 negative cell, that are in direct spatial contact with macrophages. This metric is derived by identifying all valid fibroblast pairs based on their proximity, then determining how many of these pairs are directly adjacent to macrophages. The result is normalized as a percentage, which allows for comparative analysis across different tumor patches or patient cases. |
| tk4rsgoyofiy | F,Ff,M,Treg,TU | PERCENT_FSP1_PAIRS_WITH_TUMOR | PERCENT_FSP1_PAIRS_WITH_TUMOR quantifies the percentage of fibroblast pairs, formed by one FSP1 positive and one FSP1 negative fibroblast, which are in direct contact with tumor epithelial cells. The calculation involves assessing each pair to establish if either fibroblast is in immediate contact with a tumor cell. The outcome is expressed as a percentage, thereby providing a normalized metric suitable for comparative studies across various samples. |
| ttrkqph41kjb | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,E | FB_BC_MEAN | FB_BC_MEAN represents the average bridging centrality across all fibroblast cells within a tumor patch. It quantifies the typical strength with which fibroblasts function as communication hubs, reflecting the combined effect of their network betweenness and their local bridging role. This metric is normalized, allowing comparison across different patient cases. |
| ttrkqph41kjb | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,E | FB_BC_MEDIAN | FB_BC_MEDIAN is the median bridging centrality value for fibroblasts, providing a robust measure of the central tendency of the bridging capabilities in the network. It minimizes the influence of outliers, ensuring a consistent comparison between different tumor regions. |
| ttrkqph41kjb | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,E | FB_BC_MAX | FB_BC_MAX captures the highest bridging centrality value among fibroblasts, indicating the fibroblast that functions as the most influential communication bridge within the cellular network. This normalized maximum value highlights the peak network communication role in a given tumor patch. |
| ttrkqph41kjb | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,E | FB_BC_STD | FB_BC_STD reflects the standard deviation of bridging centrality values among fibroblasts, quantifying the variability or dispersion of their network roles. A higher standard deviation indicates a diverse range of bridging capabilities within the cellular population, while a lower value suggests uniformity. |
| ttrkqph41kjb | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,E | FB_BC_Q1 | FB_BC_Q1 represents the first quartile (25th percentile) of fibroblast bridging centrality, indicating that 25% of the values lie below this threshold. This helps in understanding the lower end of the distribution of fibroblast bridging roles. |
| ttrkqph41kjb | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,E | FB_BC_Q3 | FB_BC_Q3 denotes the third quartile (75th percentile) of bridging centrality, defining the upper boundary where 25% of the fibroblasts exhibit higher values. This metric is used as a threshold to identify fibroblasts with relatively higher bridging significance. |
| ttrkqph41kjb | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,E | FB_BC_TOP10_MEAN | FB_BC_TOP10_MEAN is the mean bridging centrality calculated for the top 10% of fibroblasts with the highest values. This parameter focuses on the most influential fibroblasts in terms of network communication, providing insight into the strength of the upper tail of the distribution in a normalized manner. |
| ttrkqph41kjb | TU,Tc,Th,Treg,B,P,M,G,MFp,Ff,E | FB_BC_HIGH_PROP | FB_BC_HIGH_PROP is the proportion of fibroblasts that have a bridging centrality above the third quartile. As a normalized metric, it reflects the relative frequency of fibroblasts that serve as significant communication hubs, enabling comparisons across different tumor patches. |
| tuehyjxe2ndv | Th,M | th_mean_distance | th_mean_distance: The average minimum distance from each T helper cell to its nearest vessel, allowing for standardized comparisons across different patient cases and patches. |
| tuehyjxe2ndv | Th,M | th_median_distance | th_median_distance: The median value of the minimum distances from T helper cells to the nearest vessel, providing a robust central measure that minimizes the effect of outliers. |
| tuehyjxe2ndv | Th,M | th_std_distance | th_std_distance: The standard deviation of the T helper cell distances to the nearest vessel, reflecting the variability in their spatial distribution relative to vascular structures. |
| tuehyjxe2ndv | Th,M | th_min_distance | th_min_distance: The smallest measured distance from a T helper cell to a vessel, indicating the closest proximity observed in the stromal compartment. |
| tuehyjxe2ndv | Th,M | th_max_distance | th_max_distance: The largest measured distance from a T helper cell to a vessel, representing the extreme end of infiltration distance within the analyzed tissue patch. |
| tuehyjxe2ndv | Th,M | th_q25_distance | th_q25_distance: The 25th percentile of T helper cell distances to the nearest vessel, showing that 25% of these distances fall below this threshold, and offering insight into the lower range of the distribution. |
| tuehyjxe2ndv | Th,M | th_q75_distance | th_q75_distance: The 75th percentile of T helper cell distances to the nearest vessel, indicating that 75% of the distances are below this value, thus outlining the upper quartile of the distribution. |
| tuehyjxe2ndv | Th,M | m_mean_distance | m_mean_distance: The average minimum distance from each macrophage to its nearest vessel, which normalizes the spatial relationship and enables comparative analysis across different cases. |
| tuehyjxe2ndv | Th,M | m_median_distance | m_median_distance: The median minimum distance from macrophages to the nearest vessel, providing a central measure that is less sensitive to extreme values. |
| tuehyjxe2ndv | Th,M | m_std_distance | m_std_distance: The standard deviation of macrophage distances to the nearest vessel, quantifying the spread and variability in their spatial positioning relative to vessels. |
| tuehyjxe2ndv | Th,M | m_min_distance | m_min_distance: The smallest distance recorded from a macrophage to a vessel, capturing the closest spatial association within the patch. |
| tuehyjxe2ndv | Th,M | m_max_distance | m_max_distance: The largest distance recorded from a macrophage to a vessel, denoting the most remote infiltration instance observed in the tissue sample. |
| tuehyjxe2ndv | Th,M | m_q25_distance | m_q25_distance: The 25th percentile of macrophage distances to the nearest vessel, offering insights into the lower end of the infiltration distance distribution for macrophages. |
| tuehyjxe2ndv | Th,M | m_q75_distance | m_q75_distance: The 75th percentile of macrophage distances to the nearest vessel, reflecting the upper range in the distribution of macrophage spatial relationships to vessels. |
| tuehyjxe2ndv | Th,M | mean_distance_difference | mean_distance_difference: The difference between the mean distances of T helper cells and macrophages to their nearest vessels, designed to capture comparative spatial behavior between the two cell types. |
| tuehyjxe2ndv | Th,M | median_distance_difference | median_distance_difference: The difference between the medians of the infiltration distances for T helper cells and macrophages, providing a robust comparison of their typical distance metrics. |
| tuehyjxe2ndv | Th,M | ttest_pvalue | ttest_pvalue: The p-value derived from Welch's t-test comparing T helper cell and macrophage distance distributions, used to assess whether the differences in their average distances are statistically significant. |
| tuehyjxe2ndv | Th,M | mannwhitney_pvalue | mannwhitney_pvalue: The p-value from the Mann-Whitney U test evaluating the difference in distance distributions between T helper cells and macrophages, offering a nonparametric measure of statistical significance. |
| tv2ux1s9cgae | MFp,F,TU,P | cluster_ratio | The parameter 'cluster_ratio' represents the normalized ratio calculated by dividing the number of PDPN+ myofibroblast clusters by the number of FSP1- fibroblast clusters within a 100µm radius of tumor and plasma cells. This ratio is derived from applying a clustering algorithm on cell centroids to identify spatial clusters within the defined region, and then computing the ratio by taking the count of PDPN+ clusters over the count of FSP1- clusters (with a small constant added to avoid division by zero). As a normalized measure, it allows for effective comparisons across different patient cases and patch regions. |
| tw5cs9gwrjds | Th | MEAN_MINOR_AXIS_LENGTH_TH_EPITHELIAL | MEAN_MINOR_AXIS_LENGTH_TH_EPITHELIAL represents the average minor axis length of the nuclei of helper T lymphocytes located in epithelial compartments (Tumor regions) of breast cancer tissue. This measurement is obtained by computing the minimal axis (from the minimum rotated rectangle) for each cell's nucleus and then calculating the average value across all relevant cells within a given patch. As an averaged value measured in micrometers, it is normalized for comparisons across different patient cases. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | TU_Tumor_mean_nuclear_area | TU_Tumor_mean_nuclear_area: Represents the average area of the nuclei for tumor cells (epithelial_cell) located in the Tumor compartment. It provides a normalized metric derived from averaging the polygonal areas of individual nuclei over a given patch. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | TU_Tumor_std_nuclear_area | TU_Tumor_std_nuclear_area: Denotes the standard deviation of nuclear areas for tumor cells in the Tumor compartment, capturing the variability in nuclear sizes across cells in the same region. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | TU_Tumor_min_nuclear_area | TU_Tumor_min_nuclear_area: Shows the smallest measured nuclear area among tumor cells in the Tumor compartment, serving as the lower bound of nuclear size distribution. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | TU_Tumor_max_nuclear_area | TU_Tumor_max_nuclear_area: Shows the largest measured nuclear area among tumor cells in the Tumor compartment, serving as the upper bound of nuclear size distribution. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | TU_Stroma_mean_nuclear_area | TU_Stroma_mean_nuclear_area: Represents the average nuclear area of tumor cells (epithelial_cell) found within the Stroma compartment, allowing for comparison with measurements from the Tumor compartment. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | TU_Stroma_std_nuclear_area | TU_Stroma_std_nuclear_area: Denotes the standard deviation of the nuclear areas for tumor cells in the Stroma compartment, indicating how variable the cell sizes are in that region. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | TU_Stroma_min_nuclear_area | TU_Stroma_min_nuclear_area: Indicates the minimum nuclear area observed for tumor cells within the Stroma compartment. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | TU_Stroma_max_nuclear_area | TU_Stroma_max_nuclear_area: Indicates the maximum nuclear area observed for tumor cells within the Stroma compartment. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | Tc_Tumor_mean_nuclear_area | Tc_Tumor_mean_nuclear_area: Represents the average nuclear area of cytotoxic T cells (t_cell_cd8) in the Tumor compartment, calculated as the mean of the nuclear polygon areas. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | Tc_Tumor_min_nuclear_area | Tc_Tumor_min_nuclear_area: Reflects the smallest nuclear area measured among cytotoxic T cells in the Tumor compartment. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | Tc_Tumor_max_nuclear_area | Tc_Tumor_max_nuclear_area: Reflects the largest nuclear area measured among cytotoxic T cells in the Tumor compartment. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | Tc_Stroma_mean_nuclear_area | Tc_Stroma_mean_nuclear_area: Represents the average nuclear area of cytotoxic T cells located in the Stroma compartment, offering a normalized value for inter-patient comparison. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | Tc_Stroma_std_nuclear_area | Tc_Stroma_std_nuclear_area: Denotes the standard deviation of nuclear areas for cytotoxic T cells in the Stroma compartment, highlighting the spread of nuclear sizes. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | Tc_Stroma_min_nuclear_area | Tc_Stroma_min_nuclear_area: Indicates the minimum nuclear area observed for cytotoxic T cells in the Stroma compartment. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | Tc_Stroma_max_nuclear_area | Tc_Stroma_max_nuclear_area: Indicates the maximum nuclear area observed for cytotoxic T cells in the Stroma compartment. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | Treg_Stroma_mean_nuclear_area | Treg_Stroma_mean_nuclear_area: Represents the average nuclear area for regulatory T cells (t_cell_reg) in the Stroma compartment, computed from the polygonal area measurements of individual nuclei. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | Treg_Stroma_std_nuclear_area | Treg_Stroma_std_nuclear_area: Denotes the standard deviation of nuclear areas for regulatory T cells in the Stroma compartment, reflecting the variability of the size measurements. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | Treg_Stroma_min_nuclear_area | Treg_Stroma_min_nuclear_area: Shows the minimum nuclear area recorded for regulatory T cells in the Stroma compartment. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | Treg_Stroma_max_nuclear_area | Treg_Stroma_max_nuclear_area: Shows the maximum nuclear area recorded for regulatory T cells in the Stroma compartment. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | MFp_Tumor_mean_nuclear_area | MFp_Tumor_mean_nuclear_area: Represents the average nuclear area for PDPN+ myofibroblasts (myofibroblast_pdpn) in the Tumor compartment, providing a normalized measure for analysis across patients. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | MFp_Tumor_std_nuclear_area | MFp_Tumor_std_nuclear_area: Indicates the standard deviation of nuclear areas for PDPN+ myofibroblasts in the Tumor compartment, describing the dispersion in nuclear size measurements. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | MFp_Tumor_min_nuclear_area | MFp_Tumor_min_nuclear_area: Reflects the smallest nuclear area determined among PDPN+ myofibroblasts in the Tumor compartment. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | MFp_Tumor_max_nuclear_area | MFp_Tumor_max_nuclear_area: Reflects the largest nuclear area determined among PDPN+ myofibroblasts in the Tumor compartment. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | MFp_Stroma_mean_nuclear_area | MFp_Stroma_mean_nuclear_area: Represents the average nuclear area for PDPN+ myofibroblasts within the Stroma compartment, derived from individual cell measurements. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | MFp_Stroma_std_nuclear_area | MFp_Stroma_std_nuclear_area: Denotes the standard deviation of nuclear areas for PDPN+ myofibroblasts in the Stroma compartment, indicating the variability among the cells. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | MFp_Stroma_min_nuclear_area | MFp_Stroma_min_nuclear_area: Shows the minimum nuclear area observed among PDPN+ myofibroblasts in the Stroma compartment. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | MFp_Stroma_max_nuclear_area | MFp_Stroma_max_nuclear_area: Shows the maximum nuclear area observed among PDPN+ myofibroblasts in the Stroma compartment. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | Ff_Stroma_mean_nuclear_area | Ff_Stroma_mean_nuclear_area: Represents the average nuclear area for FSP1+ fibroblasts (fibroblast_fsp1) in the Stroma compartment, enabling comparisons across different regions and patients based on normalized metrics. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | Ff_Stroma_std_nuclear_area | Ff_Stroma_std_nuclear_area: Denotes the standard deviation of nuclear areas for FSP1+ fibroblasts in the Stroma compartment, measuring dispersion in nuclear sizes. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | Ff_Stroma_min_nuclear_area | Ff_Stroma_min_nuclear_area: Indicates the minimum nuclear area measured among FSP1+ fibroblasts in the Stroma compartment. |
| tz3iv6y6iq11 | TU,Tc,Treg,MFp,Ff | Ff_Stroma_max_nuclear_area | Ff_Stroma_max_nuclear_area: Indicates the maximum nuclear area measured among FSP1+ fibroblasts in the Stroma compartment. |
| tzbt72e9u7fm | A,Ff,G,M,MFp,P,Tc,Th | median_inter_cell_gap | The 'median_inter_cell_gap' parameter measures the median gap distance between immune and fibroblast cells within a tissue patch. It is computed by determining the minimal pairwise distances between the boundaries of the target cells, which include various immune and fibroblast subtypes. This metric provides a quantitative indicator of cell packing density, allowing for comparisons across different patient cases due to its normalized nature as a spatial distance measure. The value is numeric and reflects the typical inter-cell gap in the analyzed tumor region. |
| ufzyu6bgr2wx | TU,Tc,F,MFp | TU_perivascular_ratio | TU_perivascular_ratio indicates the proportion of tumor cells, identified as epithelial cells, that are within a 50 µm perivascular zone relative to the total number of tumor cells in a tumor region patch. This normalized ratio facilitates comparison between different patient cases. |
| ufzyu6bgr2wx | TU,Tc,F,MFp | Tc_perivascular_ratio | Tc_perivascular_ratio represents the fraction of cytotoxic T lymphocytes (t_cell_cd8) that fall within the 50 µm perivascular boundary compared to the overall pool of cytotoxic T lymphocytes in the patch. As a normalized metric, it can be reliably compared across patient cases. |
| ufzyu6bgr2wx | TU,Tc,F,MFp | F_perivascular_ratio | F_perivascular_ratio measures the ratio of fibroblasts (specifically the FSP1- subtype) that are located within the designated 50 µm perivascular zone relative to the total number of fibroblasts in the tumor patch, ensuring normalized and comparable results. |
| ufzyu6bgr2wx | TU,Tc,F,MFp | MFp_perivascular_ratio | MFp_perivascular_ratio quantifies the normalized fraction of PDPN+ myofibroblasts that reside within the 50 µm perivascular area relative to the total PDPN+ myofibroblasts in the patch, thus enabling effective comparisons across patient samples. |
| um57vtzuz5sp | TU,B,P,Th,Treg,M,G,E | STROMAL_B_PLASMA_MEDIAN_DISTANCE | STROMAL_B_PLASMA_MEDIAN_DISTANCE measures the median distance between each stromal B cell and its closest plasma cell, providing a normalized metric that can be compared across different tumor patches. |
| um57vtzuz5sp | TU,B,P,Th,Treg,M,G,E | STROMAL_B_PLASMA_MIN_DISTANCE | STROMAL_B_PLASMA_MIN_DISTANCE represents the smallest distance observed between a B cell and its nearest plasma cell in the stromal compartment, capturing the most immediate spatial proximity in a normalized manner. |
| um57vtzuz5sp | TU,B,P,Th,Treg,M,G,E | STROMAL_B_PLASMA_MAX_DISTANCE | STROMAL_B_PLASMA_MAX_DISTANCE captures the largest value among the computed minimum distances between stromal B cells and plasma cells, indicating the upper limit of spatial separation within a patch. |
| um57vtzuz5sp | TU,B,P,Th,Treg,M,G,E | STROMAL_B_PLASMA_MEAN_DISTANCE | STROMAL_B_PLASMA_MEAN_DISTANCE calculates the average of the minimum distances from stromal B cells to plasma cells, offering a normalized measure of central tendency for spatial proximity. |
| um57vtzuz5sp | TU,B,P,Th,Treg,M,G,E | STROMAL_B_PLASMA_STD_DISTANCE | STROMAL_B_PLASMA_STD_DISTANCE quantifies the variability around the mean of the nearest-neighbor distances in the stromal compartment, reflecting the consistency of spatial relationships across patches. |
| ux2qevu8ioso | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | Cumulative_Centroid_Dispersion | Cumulative_Centroid_Dispersion represents a numeric index that quantifies the overall spatial dispersion of distinct cell type centroids within a tissue patch. It is computed by first determining the mean spatial (x, y) coordinates (centroids) for each cell type present in the region, and then summing the Euclidean distances between every unique pair of these centroids. This metric, being derived from spatial geometry and consistently measured across patches, is normalized in the sense that it allows for comparison between different patient cases. |
| v5hwq304721v | E,G,P | ENDOTHELIAL_FRACTION | The ENDOTHELIAL_FRACTION parameter measures the proportion of endothelial cells relative to the sum of endothelial cells, granulocytes, and plasma cells within the stromal compartment. It is computed by first filtering cells within the stroma, then counting the endothelial cells and the total cells of interest, and finally calculating the ratio of endothelial cells to the total. This normalized metric, ranging from 0 to 1, allows for comparative analysis across different patient cases and tissue patches. |
| v6xxmi1n0il2 | TU,B,P,M,Ff,F,A | B_TO_P_RATIO | B_TO_P_RATIO measures the ratio of B cells to plasma cells in the stromal compartment. This normalized metric allows comparison across different patient cases by expressing the relative abundance of B cells versus plasma cells without being influenced by absolute cell counts. |
| v6xxmi1n0il2 | TU,B,P,M,Ff,F,A | MODULATORY_CELL_DENSITY | MODULATORY_CELL_DENSITY represents the density of modulatory cells—specifically macrophages, fibroblasts (both FSP1+ and FSP1-), and antigen presenting cells—relative to the tumor area. This parameter normalizes the count of these cells by the tumor area, yielding a value that can be compared between different samples or patients. |
| v6xxmi1n0il2 | TU,B,P,M,Ff,F,A | MATURATION_RATIO | MATURATION_RATIO is a composite parameter that integrates the B_TO_P_RATIO with the MODULATORY_CELL_DENSITY. It reflects the overall effect of the stromal immune context on the maturation process from B cells to plasma cells, normalizing for differences in tumor area and cell abundances to facilitate cross-case comparisons. |
| vb58uh4u2y4v | M,G,F,Ff,MFp,Tc | MULTICELL_CONTACT_RATIO | The MULTICELL_CONTACT_RATIO metric quantifies the proportion of cells within a specified set (macrophages, granulocytes, fibroblasts, FSP1+ fibroblasts, PDPN+ myofibroblasts, and cytotoxic T cells) that are in direct contact with at least one cell of a different type. This ratio is determined by dividing the number of cells that have at least one heterotypic (different cell type) contact by the total number of cells in the specified set. As a normalized value, it allows for meaningful comparisons across different patient cases and tumor regions while reflecting the level of cellular crosstalk in the tumor microenvironment. |
| velf6vihx0yh | Treg,B,P,MFp | mean_distance_Treg | mean_distance_Treg: Represents the average distance (in micrometers) from the centroids of T regulatory cells to the nearest vessel. This metric quantifies the spatial proximity of Tregs to blood vessels, which may be indicative of processes such as tumor-associated angiogenesis or immunosuppression. |
| velf6vihx0yh | Treg,B,P,MFp | mean_distance_B | mean_distance_B: Represents the average distance (in micrometers) from the centroids of B cells to the nearest vessel. This normalized distance measure allows for comparisons of B cell spatial distribution across different tumor patches. |
| velf6vihx0yh | Treg,B,P,MFp | mean_distance_P | mean_distance_P: Represents the average distance (in micrometers) from the centroids of plasma cells to the nearest vessel. This parameter standardizes the relative positioning of plasma cells with respect to vessels, facilitating inter-patient comparisons. |
| velf6vihx0yh | Treg,B,P,MFp | mean_distance_MFp | mean_distance_MFp: Represents the average distance (in micrometers) from the centroids of PDPN+ myofibroblasts to the nearest vessel. This metric evaluates the spatial relationship of these myofibroblasts with the vasculature, contributing to the assessment of tumor stroma dynamics. |
| velf6vihx0yh | Treg,B,P,MFp | combined_mean_infiltration_metric | combined_mean_infiltration_metric: An aggregated measure computed by averaging the mean distances from Tregs, B cells, plasma cells, and PDPN+ myofibroblasts. This integrated metric provides an overall indicator of vessel infiltration by these cell types, which is useful for comparing different patient cases. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | tumor_myofibroblast_pdpn_percent | tumor_myofibroblast_pdpn_percent: Represents the percentage of myofibroblast cells expressing pdpn among all fibroblast subtypes in the tumor compartment, providing a normalized measure for comparing different patient patches. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_myofibroblast_pdpn_percent | stroma_myofibroblast_pdpn_percent: Represents the percentage of myofibroblast cells expressing pdpn among all fibroblast subtypes in the stroma compartment, allowing for normalized comparison across samples. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | tumor_myofibroblast_percent | tumor_myofibroblast_percent: Denotes the percentage of myofibroblast cells (excluding the pdpn subtype) within the total fibroblast population in the tumor region, yielding a normalized metric. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_myofibroblast_percent | stroma_myofibroblast_percent: Denotes the percentage of myofibroblast cells (excluding the pdpn subtype) among the fibroblasts in the stroma, facilitating normalized comparisons. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_fibroblast_fsp1_percent | stroma_fibroblast_fsp1_percent: Measures the percentage of fibroblasts marked by fsp1 in the stroma compartment relative to the total fibroblast count, ensuring normalization across analyses. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | tumor_fibroblast_percent | tumor_fibroblast_percent: Represents the percentage of fibroblast cells (of the generic subtype) in the tumor compartment relative to all fibroblasts in that region, offering a normalized parameter. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_fibroblast_percent | stroma_fibroblast_percent: Represents the percentage of generic fibroblast cells in the stroma compared to the overall fibroblast population in that compartment, normalized for patient case comparisons. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | myofibroblast_pdpn_percent_diff | myofibroblast_pdpn_percent_diff: Captures the absolute difference in the percentage of myofibroblast pdpn cells between the tumor and stroma compartments, providing a normalized differential metric. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | myofibroblast_percent_diff | myofibroblast_percent_diff: Captures the absolute difference in the percentage of myofibroblast cells (excluding pdpn) between tumor and stroma regions, serving as a normalized measure of variation. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | fibroblast_fsp1_percent_diff | fibroblast_fsp1_percent_diff: Represents the absolute difference in the percentage of fibroblast cells marked by fsp1 between the tumor and stroma compartments, ensuring a normalized comparison. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | fibroblast_percent_diff | fibroblast_percent_diff: Denotes the absolute percentage difference of generic fibroblast cells between tumor and stroma regions, allowing for normalization in cross-case analysis. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | tumor_myofibroblast_pdpn_to_epithelial_cell_ratio | tumor_myofibroblast_pdpn_to_epithelial_cell_ratio: Provides a normalized ratio comparing the count of myofibroblast pdpn cells to the count of epithelial cells in the tumor region, allowing inter-patient comparisons independent of absolute scales. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | tumor_myofibroblast_pdpn_to_macrophage_ratio | tumor_myofibroblast_pdpn_to_macrophage_ratio: Represents the normalized ratio of myofibroblast pdpn cells to macrophages in the tumor compartment, useful for evaluating cellular interactions in a comparable manner. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_myofibroblast_pdpn_to_epithelial_cell_ratio | stroma_myofibroblast_pdpn_to_epithelial_cell_ratio: Denotes the ratio of myofibroblast pdpn cells to epithelial cells in the stroma, normalized to mitigate differences in absolute cell counts between patches. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_myofibroblast_pdpn_to_t_cell_cd8_ratio | stroma_myofibroblast_pdpn_to_t_cell_cd8_ratio: Represents the normalized ratio of myofibroblast pdpn cells to CD8+ T cells in the stroma, facilitating comparison across different patient cases. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_myofibroblast_pdpn_to_t_cell_cd4_ratio | stroma_myofibroblast_pdpn_to_t_cell_cd4_ratio: Provides the ratio of myofibroblast pdpn cells to CD4+ T cells in the stroma, normalized for cross-case analysis. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_myofibroblast_pdpn_to_t_cell_reg_ratio | stroma_myofibroblast_pdpn_to_t_cell_reg_ratio: Indicates the normalized ratio of myofibroblast pdpn cells to regulatory T cells in the stroma, offering a comparative metric. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_myofibroblast_pdpn_to_macrophage_ratio | stroma_myofibroblast_pdpn_to_macrophage_ratio: Offers a normalized ratio of myofibroblast pdpn cells to macrophages in the stroma, aiding in comparing different tumor regions. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_myofibroblast_pdpn_to_b_cell_ratio | stroma_myofibroblast_pdpn_to_b_cell_ratio: Represents the normalized ratio comparing myofibroblast pdpn cells to B cells in the stroma, useful in inter-patient comparisons. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_myofibroblast_pdpn_to_plasma_cell_ratio | stroma_myofibroblast_pdpn_to_plasma_cell_ratio: Denotes the ratio of myofibroblast pdpn cells to plasma cells in the stroma, normalized to serve as a consistent metric across cases. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | tumor_myofibroblast_to_epithelial_cell_ratio | tumor_myofibroblast_to_epithelial_cell_ratio: Provides the normalized ratio of myofibroblast cells (excluding pdpn) to epithelial cells in the tumor region, facilitating comparison across samples. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | tumor_myofibroblast_to_macrophage_ratio | tumor_myofibroblast_to_macrophage_ratio: Represents the normalized ratio of myofibroblast cells to macrophages in the tumor compartment, allowing for standard comparisons between patches. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_myofibroblast_to_epithelial_cell_ratio | stroma_myofibroblast_to_epithelial_cell_ratio: Denotes the normalized ratio of myofibroblast cells to epithelial cells in the stroma, mitigating biases from absolute counts. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_myofibroblast_to_t_cell_cd8_ratio | stroma_myofibroblast_to_t_cell_cd8_ratio: Captures the ratio between myofibroblast cells and CD8+ T cells in the stroma, normalized for direct case-to-case comparison. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_myofibroblast_to_t_cell_cd4_ratio | stroma_myofibroblast_to_t_cell_cd4_ratio: Measures the normalized ratio of myofibroblast cells to CD4+ T cells in the stroma, ensuring comparability across different patient regions. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_myofibroblast_to_t_cell_reg_ratio | stroma_myofibroblast_to_t_cell_reg_ratio: Provides the normalized ratio of myofibroblast cells to regulatory T cells in the stroma, serving as a standardized metric. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_myofibroblast_to_macrophage_ratio | stroma_myofibroblast_to_macrophage_ratio: Offers a normalized measure comparing myofibroblast cells to macrophages in the stroma, useful in differential analyses. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_myofibroblast_to_b_cell_ratio | stroma_myofibroblast_to_b_cell_ratio: Represents the normalized ratio of myofibroblast cells to B cells in the stroma, facilitating reliable comparisons across datasets. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_myofibroblast_to_plasma_cell_ratio | stroma_myofibroblast_to_plasma_cell_ratio: Indicates the normalized ratio between myofibroblast cells and plasma cells in the stroma, allowing consistent inter-case analysis. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_fibroblast_fsp1_to_epithelial_cell_ratio | stroma_fibroblast_fsp1_to_epithelial_cell_ratio: Provides a normalized ratio of fibroblast fsp1 cells to epithelial cells in the stroma, thus allowing standardized comparisons. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_fibroblast_fsp1_to_t_cell_cd8_ratio | stroma_fibroblast_fsp1_to_t_cell_cd8_ratio: Denotes the normalized ratio of fibroblast fsp1 cells to CD8+ T cells in the stroma, ensuring comparability across different patches. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_fibroblast_fsp1_to_t_cell_cd4_ratio | stroma_fibroblast_fsp1_to_t_cell_cd4_ratio: Represents the normalized ratio of fibroblast fsp1 cells to CD4+ T cells in the stroma, serving as a comparable metric. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_fibroblast_fsp1_to_t_cell_reg_ratio | stroma_fibroblast_fsp1_to_t_cell_reg_ratio: Captures the normalized ratio between fibroblast fsp1 cells and regulatory T cells in the stroma, facilitating inter-patient comparisons. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_fibroblast_fsp1_to_macrophage_ratio | stroma_fibroblast_fsp1_to_macrophage_ratio: Measures the normalized ratio of fibroblast fsp1 cells to macrophages in the stroma, offering a standardized comparison metric. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_fibroblast_fsp1_to_b_cell_ratio | stroma_fibroblast_fsp1_to_b_cell_ratio: Denotes the normalized ratio of fibroblast fsp1 cells to B cells in the stroma, which is useful for cross-case analysis. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_fibroblast_fsp1_to_plasma_cell_ratio | stroma_fibroblast_fsp1_to_plasma_cell_ratio: Provides a normalized measure comparing fibroblast fsp1 cells to plasma cells in the stroma, ensuring consistency across analyses. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | tumor_fibroblast_to_epithelial_cell_ratio | tumor_fibroblast_to_epithelial_cell_ratio: Represents the normalized ratio of generic fibroblast cells to epithelial cells in the tumor compartment, supporting inter-sample comparison. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | tumor_fibroblast_to_t_cell_cd8_ratio | tumor_fibroblast_to_t_cell_cd8_ratio: Offers the normalized ratio of fibroblast cells to CD8+ T cells in the tumor region, useful for comparative analysis. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | tumor_fibroblast_to_macrophage_ratio | tumor_fibroblast_to_macrophage_ratio: Denotes the normalized ratio of fibroblast cells to macrophages in the tumor compartment, providing standardized data for comparison. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_fibroblast_to_epithelial_cell_ratio | stroma_fibroblast_to_epithelial_cell_ratio: Provides a normalized ratio of generic fibroblast cells to epithelial cells in the stroma, facilitating robust cross-case comparisons. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_fibroblast_to_t_cell_cd8_ratio | stroma_fibroblast_to_t_cell_cd8_ratio: Represents the normalized ratio of fibroblast cells to CD8+ T cells in the stroma, ensuring data comparability. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_fibroblast_to_t_cell_cd4_ratio | stroma_fibroblast_to_t_cell_cd4_ratio: Measures the normalized ratio of fibroblast cells to CD4+ T cells in the stroma, offering a consistent comparative metric. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_fibroblast_to_t_cell_reg_ratio | stroma_fibroblast_to_t_cell_reg_ratio: Captures the normalized ratio of fibroblast cells to regulatory T cells in the stroma, aiding in systematic analysis. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_fibroblast_to_macrophage_ratio | stroma_fibroblast_to_macrophage_ratio: Represents the normalized ratio of fibroblast cells to macrophages in the stroma, ensuring comparability across patient cases. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_fibroblast_to_b_cell_ratio | stroma_fibroblast_to_b_cell_ratio: Provides a normalized ratio between fibroblast cells and B cells in the stroma, useful for inter-case comparisons. |
| vkzlzyx082c4 | MFp,MF,Ff,F,TU,M,B,P | stroma_fibroblast_to_plasma_cell_ratio | stroma_fibroblast_to_plasma_cell_ratio: Denotes the normalized ratio of fibroblast cells to plasma cells in the stroma, allowing standardized analysis across samples. |
| vl3pk636hj62 | TU,Tc,Th,Treg,MFp,MF,Ff,F,M,B,P | overall_mean_alignment_angle | overall_mean_alignment_angle: The average alignment angle (in degrees ranging from 0 to 180) computed over all cells that are in proximity to vessels. It reflects how closely the cells' major axes align with the vessel directional axis, enabling normalized comparisons across different patient cases. |
| vl3pk636hj62 | TU,Tc,Th,Treg,MFp,MF,Ff,F,M,B,P | overall_circular_variance | overall_circular_variance: A normalized measure (ranging from 0 to 1) of the dispersion of alignment angles for all cells relative to their associated vessel orientation. Lower values indicate highly consistent alignment, while values closer to 1 suggest a random orientation. |
| vl3pk636hj62 | TU,Tc,Th,Treg,MFp,MF,Ff,F,M,B,P | TU_mean_alignment_angle | TU_mean_alignment_angle: The mean alignment angle (in degrees, 0-180) for tumor epithelial cells (coded as TU) relative to the nearest vessel’s orientation. It provides a normalized metric of directional alignment for this specific cell type. |
| vl3pk636hj62 | TU,Tc,Th,Treg,MFp,MF,Ff,F,M,B,P | TU_circular_variance | TU_circular_variance: The circular variance for tumor epithelial cells (TU), indicating the degree of dispersion in their alignment angles relative to vessel orientation. This normalized value ranges from 0 (perfect alignment) to 1 (complete randomness). |
| vl3pk636hj62 | TU,Tc,Th,Treg,MFp,MF,Ff,F,M,B,P | Tc_mean_alignment_angle | Tc_mean_alignment_angle: The average alignment angle (in degrees, 0-180) for cytotoxic T-cells (Tc) in relation to the vessel axis, representing how consistently these cells align relative to nearby vessel structures. |
| vl3pk636hj62 | TU,Tc,Th,Treg,MFp,MF,Ff,F,M,B,P | Tc_circular_variance | Tc_circular_variance: The circular variance for cytotoxic T-cells (Tc), providing a normalized scale (0 to 1) that quantifies the dispersion of alignment angles, with lower values indicating closer alignment. |
| vl3pk636hj62 | TU,Tc,Th,Treg,MFp,MF,Ff,F,M,B,P | Th_mean_alignment_angle | Th_mean_alignment_angle: The mean alignment angle (in degrees, 0-180) for helper T-cells (Th), describing the typical directional discrepancy between the cell’s orientation and the corresponding vessel’s directional axis. |
| vl3pk636hj62 | TU,Tc,Th,Treg,MFp,MF,Ff,F,M,B,P | Th_circular_variance | Th_circular_variance: The circular variance for helper T-cells (Th), a normalized measure of the variability in the alignment angles relative to vessel orientation, where values near 0 reflect uniform alignment. |
| vl3pk636hj62 | TU,Tc,Th,Treg,MFp,MF,Ff,F,M,B,P | Treg_mean_alignment_angle | Treg_mean_alignment_angle: The average alignment angle (in degrees, 0-180) calculated for regulatory T-cells (Treg) with respect to vessel orientation, ensuring normalization for comparing different tumor patches. |
| vl3pk636hj62 | TU,Tc,Th,Treg,MFp,MF,Ff,F,M,B,P | Treg_circular_variance | Treg_circular_variance: A normalized metric (0-1) representing the dispersion of the alignment angles for regulatory T-cells (Treg), where lower values indicate more uniform alignment with the vessels. |
| vl3pk636hj62 | TU,Tc,Th,Treg,MFp,MF,Ff,F,M,B,P | MFp_mean_alignment_angle | MFp_mean_alignment_angle: The mean alignment angle (in degrees, 0-180) for myofibroblast cells marked with pdpn (MFp) calculated relative to the vessel axis, serving as a normalized metric across patient cases. |
| vl3pk636hj62 | TU,Tc,Th,Treg,MFp,MF,Ff,F,M,B,P | MFp_circular_variance | MFp_circular_variance: The circular variance for myofibroblast pdpn-positive cells (MFp), given as a normalized value between 0 and 1 that reflects the consistency of cell orientation towards vessels. |
| vl3pk636hj62 | TU,Tc,Th,Treg,MFp,MF,Ff,F,M,B,P | MF_mean_alignment_angle | MF_mean_alignment_angle: The average alignment angle (in degrees, 0-180) for myofibroblast cells (MF) in relation to the vessel’s directional axis. This normalized parameter facilitates comparisons across different tumor regions. |
| vl3pk636hj62 | TU,Tc,Th,Treg,MFp,MF,Ff,F,M,B,P | MF_circular_variance | MF_circular_variance: A normalized measure (ranging from 0 to 1) of the dispersion of the alignment angles for myofibroblast cells (MF), indicating the degree of their alignment variation with nearby vessels. |
| vl3pk636hj62 | TU,Tc,Th,Treg,MFp,MF,Ff,F,M,B,P | Ff_mean_alignment_angle | Ff_mean_alignment_angle: The mean alignment angle (in degrees, 0-180) for fibroblast cells marked with FSP1 (Ff) relative to the associated vessel’s orientation, providing a normalized comparison of cell alignment. |
| vl3pk636hj62 | TU,Tc,Th,Treg,MFp,MF,Ff,F,M,B,P | Ff_circular_variance | Ff_circular_variance: The circular variance for FSP1-positive fibroblasts (Ff), expressed as a normalized measure (0-1) that indicates the consistency or randomness of the cells' directional alignment towards vessels. |
| vl3pk636hj62 | TU,Tc,Th,Treg,MFp,MF,Ff,F,M,B,P | F_mean_alignment_angle | F_mean_alignment_angle: The average alignment angle (in degrees, 0-180) for fibroblast cells (F) measured against the vessel axis, serving as a normalized metric to gauge directional alignment. |
| vl3pk636hj62 | TU,Tc,Th,Treg,MFp,MF,Ff,F,M,B,P | F_circular_variance | F_circular_variance: A normalized circular variance (ranging from 0 to 1) for fibroblast cells (F), quantifying the spread in the alignment angles relative to vessel orientation. |
| vl3pk636hj62 | TU,Tc,Th,Treg,MFp,MF,Ff,F,M,B,P | M_mean_alignment_angle | M_mean_alignment_angle: The mean alignment angle (in degrees, 0-180) for macrophages (M) with respect to the vessel’s directional axis, which is normalized and supports cross-case comparisons. |
| vl3pk636hj62 | TU,Tc,Th,Treg,MFp,MF,Ff,F,M,B,P | M_circular_variance | M_circular_variance: The circular variance for macrophages (M), given as a normalized value between 0 and 1 that measures the dispersion in the alignment angle distribution relative to vessels. |
| vl3pk636hj62 | TU,Tc,Th,Treg,MFp,MF,Ff,F,M,B,P | B_mean_alignment_angle | B_mean_alignment_angle: The average alignment angle (in degrees, 0-180) for B-cells (B) computed relative to the orientation of the nearest vessel, offering a normalized assessment of alignment. |
| vl3pk636hj62 | TU,Tc,Th,Treg,MFp,MF,Ff,F,M,B,P | B_circular_variance | B_circular_variance: A normalized metric (0-1) that represents the circular variance in the alignment angles of B-cells (B) with respect to the vessel axis, where lower values indicate uniform alignment. |
| vl3pk636hj62 | TU,Tc,Th,Treg,MFp,MF,Ff,F,M,B,P | P_mean_alignment_angle | P_mean_alignment_angle: The mean alignment angle (in degrees, 0-180) for plasma cells (P) relative to the nearest vessel’s directional axis, used as a normalized indicator of alignment. |
| vl3pk636hj62 | TU,Tc,Th,Treg,MFp,MF,Ff,F,M,B,P | P_circular_variance | P_circular_variance: The circular variance for plasma cells (P), expressed as a normalized value between 0 and 1, measuring the degree of angular dispersion around the vessel orientation. |
| vmfm23j9l4vp | TU,Tc,Th,Treg,B,P,M,G,MFp,F | symmetry_index_TU | symmetry_index_TU: This parameter quantifies the spatial symmetry of tumor cells (epithelial cells) around the aggregated tumor center. It is calculated by dividing the full circular angle into bins, comparing the cell counts in each pair of diametrically opposed bins, and normalizing the total difference against the total number of tumor cells. Values range from 0 (completely asymmetric) to 1 (perfectly symmetric), making it suitable for comparing different patient cases. |
| vmfm23j9l4vp | TU,Tc,Th,Treg,B,P,M,G,MFp,F | symmetry_index_Tc | symmetry_index_Tc: This metric measures the spatial symmetry of cytotoxic T cells (t_cell_cd8) with respect to the tumor center. The angular positions of these cells are binned and the differences between counts in opposing bins are normalized by the total cell count, resulting in a value between 0 and 1. |
| vmfm23j9l4vp | TU,Tc,Th,Treg,B,P,M,G,MFp,F | symmetry_index_Th | symmetry_index_Th: This parameter assesses the symmetry of helper T cells (t_cell_cd4) distribution. It is derived by calculating the cell counts in paired opposing angular bins relative to the tumor center, then normalizing the difference to yield a symmetry score that is directly comparable across different cases. |
| vmfm23j9l4vp | TU,Tc,Th,Treg,B,P,M,G,MFp,F | symmetry_index_B | symmetry_index_B: This metric evaluates the spatial symmetry of B cells. The calculation involves converting cell positions into polar coordinates, binning the angles, and comparing paired bins to obtain a normalized index from 0 to 1, indicating the degree of symmetry. |
| vmfm23j9l4vp | TU,Tc,Th,Treg,B,P,M,G,MFp,F | symmetry_index_M | symmetry_index_M: This parameter quantifies the symmetry of macrophage (macrophage) distribution around the tumor center using paired angular bins. The symmetry index is normalized to provide a measure between 0 (asymmetric) and 1 (symmetric), facilitating comparison between different tumor patches. |
| vmfm23j9l4vp | TU,Tc,Th,Treg,B,P,M,G,MFp,F | symmetry_index_MFp | symmetry_index_MFp: This metric measures the symmetry of PDPN+ myofibroblasts (myofibroblast_pdpn) in relation to the tumor center. It is obtained by comparing the counts in opposing angular sectors, then normalizing the difference to yield a value between 0 and 1. |
| vmfm23j9l4vp | TU,Tc,Th,Treg,B,P,M,G,MFp,F | symmetry_index_F | symmetry_index_F: This parameter represents the spatial symmetry of fibroblast distribution. It is calculated by assigning cells to angular bins based on their relative positions from the tumor center, comparing counts in opposite bins, and normalizing the result, thus providing a value in the range of 0 to 1. |
| vmfm23j9l4vp | TU,Tc,Th,Treg,B,P,M,G,MFp,F | overall_symmetry_index | overall_symmetry_index: This aggregate metric is computed as the average of the individual symmetry indices from the selected cell types. It provides a comprehensive measure of spatial symmetry in the tumor microenvironment, normalized for comparative analysis across different patient cases. |
| vnu2mx3x2rzq | Th,Treg,B,A,MFp,G | Helper T_level_1_directional_ratio | For a given cell type, the level 1 directional ratio represents the proportion of the maximum directional energy (obtained from the horizontal, vertical, or diagonal wavelet detail coefficients) relative to the total energy at the first wavelet decomposition level. This ratio is inherently scale-free and provides insight into the dominant spatial pattern orientation in the region of interest. |
| vnu2mx3x2rzq | Th,Treg,B,A,MFp,G | Helper T_level_2_directional_ratio | For a given cell type, the level 2 directional ratio measures the ratio of the highest among horizontal, vertical, or diagonal detail energies to the total energy at the second wavelet level. This normalized ratio allows comparison across different patient cases by focusing on the relative contribution of directional features. |
| vnu2mx3x2rzq | Th,Treg,B,A,MFp,G | Helper T_level_3_directional_ratio | For a given cell type, the level 3 directional ratio is the ratio of the maximum directional energy (horizontal, vertical, or diagonal) to the sum of all directional energies at the third wavelet decomposition level. Being a normalized metric, it is useful for comparing spatial infiltration patterns between different tumor patches. |
| vnu2mx3x2rzq | Th,Treg,B,A,MFp,G | Helper T_normalized_wavelet_energy | For a given cell type, the normalized wavelet energy is calculated by summing the wavelet energies obtained across all decomposition levels and then normalizing by the number of non-zero pixels in the density map. This normalization allows the metric to be used for comparing the overall spatial complexity of the infiltration pattern across patient cases, independent of ROI size. |
| vnu2mx3x2rzq | Th,Treg,B,A,MFp,G | Regulatory T_level_1_directional_ratio | For a given cell type, the level 1 directional ratio represents the proportion of the largest directional energy relative to the total energy extracted at the first wavelet level. It indicates the dominant spatial orientation in the cellular infiltration pattern around the epithelial boundary. |
| vnu2mx3x2rzq | Th,Treg,B,A,MFp,G | Regulatory T_level_2_directional_ratio | For a given cell type, the level 2 directional ratio captures the dominant orientation at the second decomposition level by dividing the maximum directional energy (horizontal, vertical, or diagonal) by the level's total energy. This dimensionless metric is well-suited for cross-case comparisons. |
| vnu2mx3x2rzq | Th,Treg,B,A,MFp,G | Regulatory T_level_3_directional_ratio | For a given cell type, the level 3 directional ratio reflects the balance among the directional components at the third decomposition level by computing the maximal directional energy divided by the sum of all directional energies at that level. Its normalized nature makes it robust for comparison across different tumor patches. |
| vnu2mx3x2rzq | Th,Treg,B,A,MFp,G | Regulatory T_normalized_wavelet_energy | For a given cell type, the normalized wavelet energy provides a normalized measure of the overall spatial complexity by dividing the total wavelet energy (accumulated over all levels) by the number of non-zero pixels in the density map. This adjustment ensures the metric is comparable between patient cases with differing ROI sizes. |
| vnu2mx3x2rzq | Th,Treg,B,A,MFp,G | B Cells_level_1_directional_ratio | For a given cell type, the level 1 directional ratio is a normalized value derived from the ratio of the maximum value among horizontal, vertical, and diagonal detail energies to the total energy at that level. It succinctly captures the predominant directional feature in the tissue-based spatial analysis. |
| vnu2mx3x2rzq | Th,Treg,B,A,MFp,G | B Cells_level_2_directional_ratio | For a given cell type, the level 2 directional ratio offers a normalized metric indicating the dominant directional energy at the second wavelet level by evaluating the ratio between the highest directional component and the combined energy. This facilitates inter-patient comparisons regarding spatial infiltration patterns. |
| vnu2mx3x2rzq | Th,Treg,B,A,MFp,G | B Cells_level_3_directional_ratio | For a given cell type, the level 3 directional ratio is a normalized measure assessing the directional preference at the third wavelet level, calculated by taking the maximum directional energy over the total energy. Its dimensionless form makes it suitable for comparative analysis across different cases. |
| vnu2mx3x2rzq | Th,Treg,B,A,MFp,G | B Cells_normalized_wavelet_energy | For a given cell type, the normalized wavelet energy sums the energy contributions across all wavelet levels and then normalizes this sum by the count of non-zero cells within the spatial density map. This normalization enables robust comparisons among patients by mitigating variations in ROI sizes. |
| vnu2mx3x2rzq | Th,Treg,B,A,MFp,G | APC_level_1_directional_ratio | For a given cell type, the level 1 directional ratio is computed by dividing the largest energy value among the wavelet detail coefficients (horizontal, vertical, or diagonal) at level one by the total energy at that level, rendering a dimensionless metric that facilitates cross-case comparison. |
| vnu2mx3x2rzq | Th,Treg,B,A,MFp,G | APC_level_2_directional_ratio | For a given cell type, the level 2 directional ratio is a normalized indicator of directional dominance at the second decomposition level, computed as the maximum directional energy divided by the aggregate energy. This ratio is effective for standardizing spatial complexity assessments between cases. |
| vnu2mx3x2rzq | Th,Treg,B,A,MFp,G | APC_level_3_directional_ratio | For a given cell type, the level 3 directional ratio is a scale-free metric computed from the highest directional energy relative to the total energy from the third wavelet decomposition level, thus allowing for consistent comparative analysis of tissue infiltration patterns. |
| vnu2mx3x2rzq | Th,Treg,B,A,MFp,G | APC_normalized_wavelet_energy | For a given cell type, the normalized wavelet energy is a comprehensive, normalized measure of the spatial complexity. It is derived by aggregating wavelet energy values across all decomposition levels and then dividing by the number of contributing pixels in the density map, ensuring uniform comparison across different patient samples. |
| vnu2mx3x2rzq | Th,Treg,B,A,MFp,G | PDPN+ Myofibroblasts_level_1_directional_ratio | For a given cell type, the level 1 directional ratio is a ratio metric that indicates which directional component (horizontal, vertical, or diagonal) contributes most significantly to the overall energy at the first wavelet level. Its normalized character makes it ideal for comparing spatial patterns between patients. |
| vnu2mx3x2rzq | Th,Treg,B,A,MFp,G | PDPN+ Myofibroblasts_level_2_directional_ratio | For a given cell type, the level 2 directional ratio reflects the relative predominance of one directional detail over others at the second wavelet decomposition level, with its normalized nature ensuring comparability of spatial complexity assessments across cases. |
| vnu2mx3x2rzq | Th,Treg,B,A,MFp,G | PDPN+ Myofibroblasts_level_3_directional_ratio | For a given cell type, the level 3 directional ratio captures the relative importance of the dominant directional energy against the total energy from the third level of wavelet decomposition. Being a ratio, it is inherently normalized and suitable for comparative analysis. |
| vnu2mx3x2rzq | Th,Treg,B,A,MFp,G | PDPN+ Myofibroblasts_normalized_wavelet_energy | For a given cell type, the normalized wavelet energy quantifies the overall complexity of the spatial distribution by summing energies from all wavelet levels and adjusting for the size of the region of interest. This normalization allows for fair comparisons between different tumor patches. |
| vnu2mx3x2rzq | Th,Treg,B,A,MFp,G | Granulocytes_level_1_directional_ratio | For a given cell type, the level 1 directional ratio represents a normalized metric that captures the directional bias in the spatial infiltration pattern at the first wavelet decomposition level, computed as the maximum of the directional energies divided by the total energy. |
| vnu2mx3x2rzq | Th,Treg,B,A,MFp,G | Granulocytes_level_2_directional_ratio | For a given cell type, the level 2 directional ratio is determined by the ratio of the highest directional energy component (horizontal, vertical, or diagonal) to the total energy at the second level. This normalized ratio effectively highlights the dominant spatial orientation. |
| vnu2mx3x2rzq | Th,Treg,B,A,MFp,G | Granulocytes_level_3_directional_ratio | For a given cell type, the level 3 directional ratio is a dimensionless metric computed by dividing the maximum directional energy by the cumulative energy at the third wavelet level, thereby quantifying directional dominance in a normalized fashion. |
| vnu2mx3x2rzq | Th,Treg,B,A,MFp,G | Granulocytes_normalized_wavelet_energy | For a given cell type, the normalized wavelet energy metric is achieved by summing the energy contributions across all decomposition levels and then normalizing by the number of non-zero density map pixels. This normalization makes the measure robust and comparable across varied cases. |
| vodgl29jsmql | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | FRACTAL_DIMENSION | FRACTAL_DIMENSION represents the weighted fractal dimension calculated from the spatial distribution of 14 different cell types within a tumor patch. It is obtained using a box-counting method applied to cell centroids, where cell contributions are weighted according to predefined values. This parameter is normalized and facilitates comparison across patient cases by capturing the complexity of cell infiltration patterns—higher values indicate more complex spatial arrangements. |
| vodgl29jsmql | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | FD_R_SQUARED | FD_R_SQUARED is a numeric metric representing the R² value from the linear regression on the log-log plot of weighted box counts versus the inverse of box sizes used in the fractal dimension calculation. This parameter serves as an indicator of the quality of the fractal dimension fit, ensuring that the estimated fractal dimension is robust and can be reliably compared across different tumor regions. |
| volt7qo50nvq | Th,Treg | TH_TREG_RATIO | TH_TREG_RATIO represents the normalized ratio of helper T lymphocytes to regulatory T lymphocytes found in the stromal compartment of tumor patches. Unlike raw cell counts, this ratio is normalized and enables comparison across different patients and tumor regions. It captures the balance between the cells (where a higher ratio may indicate a more effective anti-tumor immune response) and is derived from the cell counts obtained from filtered cells within the stroma. |
| vq9t1t6g7ct6 | Th,MFp | TH_DENSITY_PER_MM2 | TH_DENSITY_PER_MM2: This parameter represents the density of T helper cells (CD4+ T cells) present in the perivascular regions, normalized to one square millimeter. It is calculated by dividing the count of T helper cells within the perivascular area by the area (expressed in mm²), allowing for direct comparison between different patient cases. |
| vq9t1t6g7ct6 | Th,MFp | MFP_DENSITY_PER_MM2 | MFP_DENSITY_PER_MM2: This parameter measures the density of PDPN+ myofibroblasts within the perivascular areas, expressed as the number of cells per square millimeter. By normalizing the cell counts to the area, it provides a standardized metric that can be compared across various patient samples. |
| vq9t1t6g7ct6 | Th,MFp | TH_MFP_DENSITY_RATIO | TH_MFP_DENSITY_RATIO: This parameter is the ratio of the density of T helper cells to the density of PDPN+ myofibroblasts in the perivascular regions. It effectively compares the relative abundance of these cell types by using their normalized densities, offering a robust metric for inter-patient and inter-region comparisons. |
| vsl9skkib73i | B,MFp,Ff,G | max_circularity_b_cell | max_circularity_b_cell measures the highest nucleus circularity value among B cells located in the stromal regions of breast cancer tissues. The circularity is computed using the formula (4π × area) / (perimeter²), resulting in a value between 0 and 1, where a value equal to 1 indicates a perfectly circular nucleus. |
| vsl9skkib73i | B,MFp,Ff,G | max_circularity_myofibroblast_pdpn | max_circularity_myofibroblast_pdpn captures the maximum nucleus circularity for PDPN+ myofibroblasts in the stroma. This parameter assesses how circular the nucleus of these cells is, with values derived from direct measurements of cell polygon properties and normalized to a scale from 0 to 1. |
| vsl9skkib73i | B,MFp,Ff,G | max_circularity_fibroblast_fsp1 | max_circularity_fibroblast_fsp1 represents the maximum nuclear circularity found among FSP1+ fibroblasts in the stromal compartment. It uses the same circularity computation to gauge the shape of the nuclei and provides a normalized numeric value between 0 and 1 for inter-patient comparisons. |
| vsl9skkib73i | B,MFp,Ff,G | max_circularity_granulocyte | max_circularity_granulocyte reflects the maximum nuclear circularity observed among granulocytes in the stromal region. The parameter is calculated through a standardized formula ensuring that the results, ranging from 0 to 1, are directly comparable across different patient cases. |
| vvqphwrabuop | MFp,A,F,G | avg_area_MFp | avg_area_MFp: The average nuclear area of PDPN-positive myofibroblasts in the stromal compartment. It is calculated by summing the nuclear areas of all PDPN-positive myofibroblasts and dividing by their count, resulting in a normalized metric suitable for comparing different patient cases. |
| vvqphwrabuop | MFp,A,F,G | avg_area_A | avg_area_A: The average nuclear area of antigen-presenting cells within the stromal compartment. This parameter is obtained by averaging the nuclear areas of these cells, ensuring normalization by accounting for the cell count, thus being comparable across patient cases. |
| vvqphwrabuop | MFp,A,F,G | avg_area_F | avg_area_F: The average nuclear area of FSP1-negative fibroblasts in the stromal compartment. This measure is computed by dividing the total nuclear area of these cells by the number of cells, providing a normalized and comparable parameter. |
| vvqphwrabuop | MFp,A,F,G | avg_area_G | avg_area_G: The average nuclear area of granulocytes in the stromal compartment. Derived by averaging the nuclear areas of granulocytes, this parameter is normalized to facilitate comparisons between different groups or patient cases. |
| vvqphwrabuop | MFp,A,F,G | ratio_MFp_to_A | ratio_MFp_to_A: The ratio of the average nuclear area of PDPN-positive myofibroblasts to that of antigen-presenting cells. This normalized parameter provides an insight into comparative cell size differences between these two populations. |
| vvqphwrabuop | MFp,A,F,G | ratio_MFp_to_F | ratio_MFp_to_F: The ratio of the average nuclear area of PDPN-positive myofibroblasts to the average nuclear area of FSP1-negative fibroblasts. It is a normalized metric that allows for direct comparisons of cell size relationships across patches and patient cases. |
| vvqphwrabuop | MFp,A,F,G | ratio_MFp_to_G | ratio_MFp_to_G: The ratio of the average nuclear area of PDPN-positive myofibroblasts to that of granulocytes. This parameter offers a normalized comparison of nuclear size between these cell types in the stromal compartment. |
| vxvl7dfbxs58 | Tc,Treg,Ff,MFp | Tc_adjacency_ratio | Tc_adjacency_ratio represents the proportion of cytotoxic T cells that are found to be directionally adjacent to vessels. It is calculated by dividing the number of cytotoxic T cells meeting the directional adjacency criteria by the total count of cytotoxic T cells. This normalized ratio enables meaningful comparisons across different samples and patient cases. |
| vxvl7dfbxs58 | Tc,Treg,Ff,MFp | Treg_adjacency_ratio | Treg_adjacency_ratio defines the normalized proportion of regulatory T cells that are directionally adjacent to vessels. It is derived by dividing the count of regulatory T cells fulfilling the spatial and directional criteria by the overall number of regulatory T cells present in the patch, making it suitable for cross-sample analyses. |
| vxvl7dfbxs58 | Tc,Treg,Ff,MFp | Ff_adjacency_ratio | Ff_adjacency_ratio indicates the proportion of fibroblasts that are FSP1+ and exhibit directional adjacency to vessel structures. It is a normalized metric calculated as the ratio of the number of FSP1+ fibroblasts adjacent to vessels to the total number of FSP1+ fibroblasts, ensuring comparability between different cases. |
| vxvl7dfbxs58 | Tc,Treg,Ff,MFp | MFp_adjacency_ratio | MFp_adjacency_ratio measures the directional vessel adjacency of PDPN+ myofibroblasts. This parameter is computed by dividing the number of PDPN+ myofibroblasts that are appropriately oriented and within the defined proximity to vessel boundaries by the total count of PDPN+ myofibroblasts, yielding a normalized ratio. |
| vxvl7dfbxs58 | Tc,Treg,Ff,MFp | overall_adjacency_ratio | overall_adjacency_ratio is an aggregate metric representing the combined proportion of all four cell types that are directionally adjacent to vessels. It is calculated by summing the counts of directionally adjacent cells across the cell types and dividing by the total cell count for these cell types, providing a unified, normalized measure for differential patient comparisons. |
| w14uo7vvix39 | Treg,MFp | treg_nuclear_perimeter_mean | treg_nuclear_perimeter_mean: This parameter represents the average nuclear perimeter (measured in micrometers) of regulatory T cells within the tumor stroma. It is derived by selecting only stroma-resident cells identified as regulatory T cells, computing the perimeter of each cell's nucleus based on its polygon shape, and then averaging these values. Since it is an average metric, it is normalized across different patient cases. |
| w14uo7vvix39 | Treg,MFp | myofib_pdpn_nuclear_perimeter_mean | myofib_pdpn_nuclear_perimeter_mean: This parameter indicates the average nuclear perimeter (in micrometers) of PDPN+ myofibroblasts in the stroma. It is obtained by filtering for cells classified as PDPN+ myofibroblasts from the stroma cells, calculating the nuclear perimeter for each using polygon geometry, and finding their mean value. This average measurement allows for comparisons across different patches and patient cases. |
| w14uo7vvix39 | Treg,MFp | nuclear_perimeter_difference | nuclear_perimeter_difference: This parameter measures the difference between the mean nuclear perimeters of regulatory T cells and PDPN+ myofibroblasts. It is computed by subtracting the average nuclear perimeter of the PDPN+ myofibroblasts from that of the regulatory T cells. This comparative parameter is normalized, facilitating direct comparisons between patient samples. |
| w403eke5odfx | TU,G | MEAN_DISTANCE_TUMOR_TO_GRANULOCYTE_PERIVASCULAR | The parameter calculates the average Euclidean distance (in micrometers) between tumor cells and granulocytes within the perivascular region, defined as the area within 50 micrometers around blood vessels. In practice, for each tumor patch, vessel areas are expanded by a buffer to create a perivascular region, and only cells within these regions are considered. Tumor cells and granulocytes are identified, and the Euclidean distances between all possible tumor-granulocyte pairs are computed. The resulting mean value reflects the spatial relationship between tumor cells and inflammatory granulocytes, thereby offering insight into local inflammation which may impact tumor progression. This metric is normalized as it represents an averaged distance per patch, making it comparable across different patient cases. |
| w7q9jwhivst1 | M,Ff,E | COLOC_INDEX_OVERALL | COLOC_INDEX_OVERALL represents the overall co-localization index calculated as the arithmetic mean of the individual co-localization ratios between the three cell types (macrophages, FSP1+ fibroblasts, and endothelial cells) within the tumor stroma. This metric provides a normalized value that allows for comparison across different patient cases or patches. |
| w7q9jwhivst1 | M,Ff,E | COLOC_RATIO_MACRO_FSP1 | COLOC_RATIO_MACRO_FSP1 quantifies the co-localization of macrophages and FSP1+ fibroblasts by computing the ratio of cell pairs that are within a defined spatial threshold to the total possible pairs. This normalized metric enables comparisons across different tumor regions. |
| w7q9jwhivst1 | M,Ff,E | COLOC_RATIO_MACRO_ENDO | COLOC_RATIO_MACRO_ENDO represents the co-localization ratio between macrophages and endothelial cells. It is calculated as the normalized proportion of cell pairs that are within the spatial threshold, making it suitable for comparisons between patient cases. |
| w7q9jwhivst1 | M,Ff,E | COLOC_RATIO_FSP1_ENDO | COLOC_RATIO_FSP1_ENDO calculates the co-localization ratio between FSP1+ fibroblasts and endothelial cells, using a similar method to the other ratios, providing a normalized metric that can be compared across different samples. |
| wbbesoq9enca | Tc,Th,Treg | combined_infiltration_ratio | combined_infiltration_ratio represents a normalized metric of immune cell infiltration in the stromal compartment of breast cancer tissue. It is calculated as the sum of cytotoxic (CD8+) and helper (CD4+) T cell counts divided by the regulatory T cell count, with a small epsilon added to avoid division by zero. This ratio provides a comparative measure across different patient cases by balancing anti-tumor cells against regulatory cells. |
| wcosb53vrhz3 | TU,Tc | CYTOTOXIC_TO_TUMOR_RATIO | The cytotoxic-to-tumor ratio measures the normalized relationship between cytotoxic T cells and tumor cells in the epithelial compartment. It is computed by dividing the number of cytotoxic T cells by the number of tumor cells, with a defined output of 0 when there are no tumor cells. This parameter provides a standardized assessment of the immune response relative to tumor burden, making it useful for comparing different patient cases. |
| wdpqwzg10pnj | TU,Tc,Th,Treg,B,P,M,MFp,MF,F | median_dist_to_vessel_TU | This parameter measures the median distance from tumor (epithelial) cells to the nearest vessel. It is computed by calculating the distance from the centroid of each tumor cell to all vessel polygons and then taking the median, providing a numeric metric that allows comparison across different patient cases. |
| wdpqwzg10pnj | TU,Tc,Th,Treg,B,P,M,MFp,MF,F | median_dist_to_vessel_Tc | This parameter measures the median distance from CD8+ T cells to the nearest vessel. The approach involves finding the minimum distance from each CD8+ T cell’s centroid to any vessel polygon and aggregating these distances using the median, thus normalizing the spatial measure for cross-patient analysis. |
| wdpqwzg10pnj | TU,Tc,Th,Treg,B,P,M,MFp,MF,F | median_dist_to_vessel_Th | This parameter measures the median distance from CD4+ T helper cells to the closest vessel. Each cell's centroid is evaluated against vessel locations; the nearest distance is recorded, and the median of these distances offers a normalized numeric value useful for comparing different tumor patches. |
| wdpqwzg10pnj | TU,Tc,Th,Treg,B,P,M,MFp,MF,F | median_dist_to_vessel_Treg | This parameter measures the median distance from regulatory T cells (Treg) to the nearest vessel. It operates by computing distances from the cell centroids to available vessel boundaries and then determining the median, resulting in a numeric and normalized metric. |
| wdpqwzg10pnj | TU,Tc,Th,Treg,B,P,M,MFp,MF,F | median_dist_to_vessel_B | This parameter measures the median distance from B cells to the nearest vessel by computing the minimum distance from each B cell's centroid to any vessel polygon and aggregating the values using the median. The resulting numeric value is normalized for comparison purposes. |
| wdpqwzg10pnj | TU,Tc,Th,Treg,B,P,M,MFp,MF,F | median_dist_to_vessel_P | This parameter measures the median distance from plasma cells to the nearest vessel. The process involves determining the smallest distance from each plasma cell’s centroid to vessel boundaries and then using the median value to provide a normalized numeric metric. |
| wdpqwzg10pnj | TU,Tc,Th,Treg,B,P,M,MFp,MF,F | median_dist_to_vessel_M | This parameter measures the median distance from macrophages to the nearest vessel. By evaluating each macrophage's centroid against vessel polygons and taking the median of the minimum distances, it generates a numeric, normalized measurement applicable across patient cases. |
| wdpqwzg10pnj | TU,Tc,Th,Treg,B,P,M,MFp,MF,F | median_dist_to_vessel_MFp | This parameter measures the median distance from PDPN-positive myofibroblasts to the nearest vessel. It involves calculating the minimum distance for each of these cells from its centroid to vessel outlines and then computing the median, resulting in a numeric and comparable metric. |
| wdpqwzg10pnj | TU,Tc,Th,Treg,B,P,M,MFp,MF,F | median_dist_to_vessel_MF | This parameter measures the median distance from myofibroblasts (without PDPN) to the nearest vessel. The distances are calculated from cell centroids to the closest vessel polygon and aggregated using the median to form a normalized numeric value. |
| wdpqwzg10pnj | TU,Tc,Th,Treg,B,P,M,MFp,MF,F | median_dist_to_vessel_F | This parameter measures the median distance from fibroblasts to the nearest vessel. The measurement is derived by computing the shortest distance from each fibroblast's centroid to the set of vessel polygons and then taking the median, yielding a normalized numeric value useful for cross-case comparisons. |
| wfuyjg7g39ax | TU,Treg,A,B,P,F,E | mean_cluster_area | mean_cluster_area represents the average area (in square micrometers) of cell clusters formed by the spatial union of Voronoi polygons. This parameter reflects the typical size of the clusters and is comparable across patient patches because each patch is processed similarly. |
| wfuyjg7g39ax | TU,Treg,A,B,P,F,E | mean_cluster_perimeter | mean_cluster_perimeter is the average perimeter (in micrometers) of the detected cell clusters. It quantifies the boundary length of clusters and serves as a standardized measure of cluster shape irregularity. |
| wfuyjg7g39ax | TU,Treg,A,B,P,F,E | mean_cluster_compactness | mean_cluster_compactness is the average compactness metric of the clusters, calculated using the formula (4π * Area) / (Perimeter^2). This dimensionless ratio indicates how circular the clusters are, with a value of 1 representing a perfectly round shape. |
| wfuyjg7g39ax | TU,Treg,A,B,P,F,E | max_cluster_compactness | max_cluster_compactness identifies the highest compactness value among all clusters. It highlights the most circular cluster within a given patch and is normalized for comparative analysis. |
| wfuyjg7g39ax | TU,Treg,A,B,P,F,E | min_cluster_compactness | min_cluster_compactness denotes the lowest compactness value among the clusters, reflecting the most irregularly shaped cluster in the patch, thus providing insight into spatial heterogeneity. |
| wfuyjg7g39ax | TU,Treg,A,B,P,F,E | TU_proportion_in_clusters | TU_proportion_in_clusters refers to the proportion of tumor cells (designated as TU) among all cells present in the clusters. As a ratio, it is normalized and enables comparison between different patient cases. |
| wfuyjg7g39ax | TU,Treg,A,B,P,F,E | Treg_proportion_in_clusters | Treg_proportion_in_clusters represents the proportion of regulatory T cells within the clusters. This metric is also normalized, serving to assess the spatial distribution of immune cells. |
| wfuyjg7g39ax | TU,Treg,A,B,P,F,E | A_proportion_in_clusters | A_proportion_in_clusters measures the proportion of antigen presenting cells (A) in the clusters, offering a normalized indicator of their abundance relative to the total clustered cells. |
| wfuyjg7g39ax | TU,Treg,A,B,P,F,E | B_proportion_in_clusters | B_proportion_in_clusters indicates the normalized proportion of B cells in the clusters, facilitating cross-sample comparisons of immune cell spatial distribution. |
| wfuyjg7g39ax | TU,Treg,A,B,P,F,E | P_proportion_in_clusters | P_proportion_in_clusters represents the proportion of plasma cells (P) relative to total clustered cells, presented as a normalized value for inter-case comparisons. |
| wfuyjg7g39ax | TU,Treg,A,B,P,F,E | F_proportion_in_clusters | F_proportion_in_clusters is the normalized measure of fibroblasts (F) present within the clusters, providing insight into stromal component representation in the tissue. |
| wfuyjg7g39ax | TU,Treg,A,B,P,F,E | E_proportion_in_clusters | E_proportion_in_clusters denotes the proportion of endothelial cells (E) in the clusters, offering a normalized metric to evaluate vascular cell distribution in the examined regions. |
| wg1gv4tckqtc | TU,Treg,MF,Ff,B | TU_GRADIENT_SLOPE | TU_GRADIENT_SLOPE measures the rate of change in nuclear area for tumor cells along a spatial gradient. It is computed using a linear regression of nuclear area against the normalized x-coordinate, ensuring that the measurement is comparable across different patient cases. |
| wg1gv4tckqtc | TU,Treg,MF,Ff,B | TU_BIN_DIFFERENCE | TU_BIN_DIFFERENCE represents the difference in mean nuclear area between the higher and lower gradient intervals for tumor cells. This normalized dissociation score captures variations in tumor cell morphology independent of raw cell counts. |
| wg1gv4tckqtc | TU,Treg,MF,Ff,B | Treg_GRADIENT_SLOPE | Treg_GRADIENT_SLOPE captures the spatial change in nuclear morphology for regulatory T cells by quantifying the regression slope of nuclear area versus the normalized x-coordinate, thus providing a normalized metric for patient comparisons. |
| wg1gv4tckqtc | TU,Treg,MF,Ff,B | MF_GRADIENT_SLOPE | MF_GRADIENT_SLOPE quantifies the rate at which the nuclear area of myofibroblasts changes along the normalized spatial gradient. This slope serves as a normalized measure of morphological dissociation. |
| wg1gv4tckqtc | TU,Treg,MF,Ff,B | MF_BIN_DIFFERENCE | MF_BIN_DIFFERENCE is the difference between the average nuclear areas in the high and low gradient bins for myofibroblasts, offering a normalized insight into spatial morphological variations. |
| wg1gv4tckqtc | TU,Treg,MF,Ff,B | Ff_GRADIENT_SLOPE | Ff_GRADIENT_SLOPE evaluates the gradient-based change in nuclear area for fibroblasts FSP1+ by calculating the linear regression slope with respect to the normalized x-coordinate. This parameter is scaled to allow direct comparisons between patches. |
| wg1gv4tckqtc | TU,Treg,MF,Ff,B | Ff_BIN_DIFFERENCE | Ff_BIN_DIFFERENCE calculates the difference in mean nuclear area between the high and low gradient bins for fibroblasts FSP1+, providing a normalized dissociation score that highlights spatial changes in cell morphology. |
| wg1gv4tckqtc | TU,Treg,MF,Ff,B | B_GRADIENT_SLOPE | B_GRADIENT_SLOPE measures the slope of the nuclear area for B lymphocytes against the normalized x-coordinate. Because the x-coordinate is normalized, this parameter reflects the morphological gradient in a manner that is comparable across patient cases. |
| wg1gv4tckqtc | TU,Treg,MF,Ff,B | B_BIN_DIFFERENCE | B_BIN_DIFFERENCE represents the difference in average nuclear area between high and low gradient bins for B lymphocytes. It serves as a normalized measure of the morphological shift across the spatial gradient. |
| wgm6ynukrjfl | TU,Tc,Th,Treg,B,P,M,MFp,Ff,E | MST_length_ratio | MST_length_ratio measures the average edge length in the minimum spanning tree that connects key cellular players (epithelial cells, CD8 T cells, CD4 T cells, regulatory T cells, B cells, plasma cells, macrophages, myofibroblasts, fibroblasts, and endothelial cells) within a tumor region. This parameter is computed by first filtering cells to include only the specified types, then calculating the pairwise distances between cell centroids, and finally generating a minimum spanning tree to obtain the total edge length. The total length is normalized by dividing by the number of edges (number of cells minus one), yielding a ratio that allows cross-patient and cross-region comparisons. Lower values indicate tighter spatial clustering, which may correlate with more aggressive tumor characteristics. |
| whc5ayfrn6bp | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_vessel_contact_diversity_score | weighted_vessel_contact_diversity_score is a normalized metric representing the overall diversity of cell types in contact with vessel structures. It is computed as the weighted average of the Shannon diversity indices of individual vessels, with each vessel's contribution weighted by its area. This allows for comparisons across different patient cases, as the measure accounts for both diversity and the relative size of each vessel. |
| whc5ayfrn6bp | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | mean_vessel_shannon_index | mean_vessel_shannon_index is the arithmetic mean of the individual Shannon diversity indices of all vessels within an image patch. Being a normalized measure derived from the cell type diversity, it facilitates comparison between different cases by summarizing the overall diversity in vessel contacts. |
| whc5ayfrn6bp | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | max_vessel_shannon_index | max_vessel_shannon_index denotes the highest Shannon diversity index observed among all vessels in a given image patch. This parameter highlights the vessel with the greatest cell type diversity and is normalized, making it a suitable metric for comparing different patient regions. |
| wleeojltvzby | TU | CV_TU_VESSEL_DIST | CV_TU_VESSEL_DIST: This parameter represents the coefficient of variation of the distances from tumor cells to their nearest vessels in the epithelial compartment. It is a normalized, dimensionless measure calculated by dividing the standard deviation by the mean distance (with a small epsilon added to prevent division by zero). This ratio provides insight into the relative variability of tumor cell proximity to vascular structures, allowing meaningful comparisons between different patient cases. |
| wleeojltvzby | TU | MEAN_TU_VESSEL_DIST | MEAN_TU_VESSEL_DIST: This is the average distance, in micrometers, from all tumor cells in the epithelial compartment to the nearest vessel. By computing the arithmetic mean of the recorded distances, it offers a central measure of tumor cell positioning relative to vessels that is comparable across different patient samples. |
| wleeojltvzby | TU | STD_TU_VESSEL_DIST | STD_TU_VESSEL_DIST: This parameter quantifies the standard deviation of the distances from tumor cells to the nearest vessel, measured in micrometers. It reflects the spread or dispersion of these distance values from the mean, providing an understanding of the variability in tumor cell-vessel interactions. |
| wleeojltvzby | TU | MIN_TU_VESSEL_DIST | MIN_TU_VESSEL_DIST: The minimum distance recorded, in micrometers, from any tumor cell in the epithelial compartment to its nearest vessel. This parameter highlights the cell that is in closest proximity to a vascular structure within the analyzed patch. |
| wleeojltvzby | TU | MAX_TU_VESSEL_DIST | MAX_TU_VESSEL_DIST: The maximum distance, in micrometers, from any tumor cell to the nearest vessel in the tumor region. It identifies the cell that is farthest from any vessel, offering insight into the range of cellular locations relative to the vasculature. |
| wleeojltvzby | TU | MEDIAN_TU_VESSEL_DIST | MEDIAN_TU_VESSEL_DIST: This parameter indicates the median distance, in micrometers, from tumor cells to their nearest vessels. Representing the middle value in the ordered list of distances, it provides a robust measure of central tendency that is less influenced by extreme values. |
| wleeojltvzby | TU | Q1_TU_VESSEL_DIST | Q1_TU_VESSEL_DIST: The 25th percentile of the distances, in micrometers, from tumor cells to the nearest vessels. It signifies that 25% of the measured distances are below this value, helping to characterize the lower end of the distribution of distances. |
| wleeojltvzby | TU | Q3_TU_VESSEL_DIST | Q3_TU_VESSEL_DIST: The 75th percentile distance, in micrometers, from tumor cells to the nearest vessels. This parameter shows that 75% of distance values fall below this threshold, thus describing the upper segment of the distribution. |
| wleeojltvzby | TU | IQR_TU_VESSEL_DIST | IQR_TU_VESSEL_DIST: The interquartile range, in micrometers, is calculated as the difference between the 75th and 25th percentiles of the measured distances. This value captures the spread of the middle 50% of the data, reflecting the variability in tumor cell distances from the vessels. |
| wp8jk75518qv | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | WEIGHTED_PATH_COMPLEXITY_MEAN | WEIGHTED_PATH_COMPLEXITY_MEAN represents the average complexity score of vessel-to-epithelial paths within a tissue patch. Each complexity score is obtained by multiplying the weighted cell count (where each cell is assigned a weight based on its type) by the tortuosity (the ratio of the actual path length to the straight-line distance). This mean value is normalized and allows comparison across different patient cases. |
| wp8jk75518qv | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | WEIGHTED_PATH_COMPLEXITY_MAX | WEIGHTED_PATH_COMPLEXITY_MAX denotes the maximum complexity score among all the detected vessel-to-epithelial paths in a patch. It reflects the highest level of interaction complexity, combining both the weighted cell count and the geometrical tortuosity. This metric is normalized by design for cross-case comparisons. |
| wp8jk75518qv | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | WEIGHTED_PATH_COMPLEXITY_MIN | WEIGHTED_PATH_COMPLEXITY_MIN indicates the minimum complexity score among the identified paths. It captures the least complex transition pathway, derived from the weighted sum of cell counts and the tortuosity measure. Being an average derived metric, it is normalized for comparative analysis. |
| wp8jk75518qv | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | WEIGHTED_PATH_COMPLEXITY_STD | WEIGHTED_PATH_COMPLEXITY_STD is the standard deviation of the complexity scores across vessel-to-epithelial paths. This parameter measures the variability in path complexity within the tissue region, and it is a normalized statistic that facilitates the comparison of heterogeneity across different patient cases. |
| wp8jk75518qv | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | TORTUOSITY_MEAN | TORTUOSITY_MEAN is the average tortuosity of the paths, where tortuosity is calculated as the ratio between the actual path length (the sum of distances between consecutive cell centroids along the transition) and the direct straight-line distance between a vessel and the nearest epithelial cell. This ratio is inherently normalized, enabling accurate inter-case comparisons. |
| wp8jk75518qv | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | WEIGHTED_CELL_COUNT_MEAN | WEIGHTED_CELL_COUNT_MEAN represents the average weighted cell count along the paths. The weighted cell count is computed by multiplying the count of each cell type by a predetermined weight that reflects its importance. Averaging these counts across all detected paths yields a normalized metric for comparative analysis across different tumor regions. |
| wrksmliat8ji | Treg,Th,B,P,M,G | Treg_proportion | Treg_proportion measures the normalized fraction of regulatory T cells that are in direct contact with vessel structures. It is computed by dividing the count of Treg cells intersecting or being within a defined small buffer around the vessels by the total number of Treg cells, ensuring comparability across different patient cases. |
| wrksmliat8ji | Treg,Th,B,P,M,G | Helper T cells_proportion | Helper T cells_proportion measures the normalized ratio of helper T cells that interact with vessel structures. It is calculated by assessing the number of helper T cells whose nuclei polygons come into contact with a buffered vessel boundary compared to the overall tally of helper T cells. |
| wrksmliat8ji | Treg,Th,B,P,M,G | B cells_proportion | B cells_proportion quantifies the proportion of B cells in direct contact with vessels. This normalized parameter is derived by dividing the number of B cells that intersect or lie within a small buffered region around the vessels by the total B cell count, making it suitable for comparative studies. |
| wrksmliat8ji | Treg,Th,B,P,M,G | Plasma cells_proportion | Plasma cells_proportion represents the normalized proportion of plasma cells that are located in close contact with vessel structures. It is determined by comparing the count of plasma cells in proximity to vessels against the total count of plasma cells. |
| wrksmliat8ji | Treg,Th,B,P,M,G | Macrophages_proportion | Macrophages_proportion is a parameter that captures the normalized fraction of macrophages that are in direct contact with vessels. This ratio, calculated as the number of macrophages meeting the contact criteria divided by the total macrophage count, facilitates comparison across different tumor regions. |
| wrksmliat8ji | Treg,Th,B,P,M,G | Granulocytes_proportion | Granulocytes_proportion quantifies the fraction of granulocytes in contact with vessel structures in a normalized manner. It is computed by taking the number of granulocytes that intersect or are within a small buffer around the vessels and dividing it by the total number of granulocytes. |
| wrksmliat8ji | Treg,Th,B,P,M,G | overall_proportion | overall_proportion provides an aggregate, normalized measure of the fraction of all selected immune cells (including Treg, helper T cells, B cells, plasma cells, macrophages, and granulocytes) that are in direct contact with vessel structures. It is calculated by dividing the total count of immune cells interacting with vessels by the overall count of immune cells, enabling cross-case comparison. |
| wrrsj5nt795d | TU,Tc,Th,Ff | TU_Tc_scale0_coherence | TU_Tc_scale0_coherence: A normalized measure of local wavelet coherence at the finest scale between tumor cells (TU) and cytotoxic T cells (Tc). It quantifies the similarity of fine-scale spatial variations in cell density along the stromal boundary. |
| wrrsj5nt795d | TU,Tc,Th,Ff | TU_Tc_scale1_coherence | TU_Tc_scale1_coherence: A normalized measure of local wavelet coherence at the second finest scale between tumor cells (TU) and cytotoxic T cells (Tc), representing mid-frequency spatial correlation along the interface. |
| wrrsj5nt795d | TU,Tc,Th,Ff | TU_Tc_scale2_coherence | TU_Tc_scale2_coherence: A normalized measure of local wavelet coherence at a coarser scale between tumor cells (TU) and cytotoxic T cells (Tc), capturing lower frequency spatial interactions along the boundary. |
| wrrsj5nt795d | TU,Tc,Th,Ff | TU_Tc_scale3_coherence | TU_Tc_scale3_coherence: A normalized measure of local wavelet coherence at the coarsest scale between tumor cells (TU) and cytotoxic T cells (Tc), reflecting broad-scale spatial pattern similarities along the tumor-stroma interface. |
| wrrsj5nt795d | TU,Tc,Th,Ff | TU_Tc_mean_coherence | TU_Tc_mean_coherence: The average local wavelet coherence across all scales between tumor cells (TU) and cytotoxic T cells (Tc), providing an overall indicator of multi-scale spatial association along the boundary. |
| wrrsj5nt795d | TU,Tc,Th,Ff | TU_Tc_max_coherence | TU_Tc_max_coherence: The maximum localized wavelet coherence value observed across all scales between tumor cells (TU) and cytotoxic T cells (Tc), highlighting the strongest level of spatial correlation along the interface. |
| wrrsj5nt795d | TU,Tc,Th,Ff | TU_Th_scale0_coherence | TU_Th_scale0_coherence: A normalized measure of local wavelet coherence at the finest scale between tumor cells (TU) and helper T cells (Th), quantifying high-frequency spatial interaction at the stromal boundary. |
| wrrsj5nt795d | TU,Tc,Th,Ff | TU_Th_scale1_coherence | TU_Th_scale1_coherence: A normalized measure of local wavelet coherence at a slightly coarser scale between tumor cells (TU) and helper T cells (Th), representing intermediate spatial pattern correspondence along the boundary. |
| wrrsj5nt795d | TU,Tc,Th,Ff | TU_Th_scale2_coherence | TU_Th_scale2_coherence: A normalized measure of local wavelet coherence at a coarser scale between tumor cells (TU) and helper T cells (Th), capturing lower frequency spatial relationships along the interface. |
| wrrsj5nt795d | TU,Tc,Th,Ff | TU_Th_scale3_coherence | TU_Th_scale3_coherence: A normalized measure of local wavelet coherence at the coarsest scale between tumor cells (TU) and helper T cells (Th), reflecting broad-scale spatial pattern alignment along the tumor-stroma interface. |
| wrrsj5nt795d | TU,Tc,Th,Ff | TU_Th_mean_coherence | TU_Th_mean_coherence: The mean wavelet coherence across all wavelet scales between tumor cells (TU) and helper T cells (Th), offering a consolidated measure of spatial correlation along the boundary. |
| wrrsj5nt795d | TU,Tc,Th,Ff | TU_Th_max_coherence | TU_Th_max_coherence: The maximum wavelet coherence value across all scales between tumor cells (TU) and helper T cells (Th), indicating the highest degree of spatial coupling detected along the interface. |
| wrrsj5nt795d | TU,Tc,Th,Ff | TU_Ff_scale0_coherence | TU_Ff_scale0_coherence: A normalized measure of local wavelet coherence at the finest scale between tumor cells (TU) and FSP1+ fibroblasts (Ff), quantifying high-frequency co-variation in spatial cell distribution along the stromal boundary. |
| wrrsj5nt795d | TU,Tc,Th,Ff | TU_Ff_scale1_coherence | TU_Ff_scale1_coherence: A normalized measure of local wavelet coherence at an intermediate scale between tumor cells (TU) and FSP1+ fibroblasts (Ff), reflecting moderate level spatial association along the interface. |
| wrrsj5nt795d | TU,Tc,Th,Ff | TU_Ff_scale2_coherence | TU_Ff_scale2_coherence: A normalized measure of local wavelet coherence at a coarser scale between tumor cells (TU) and FSP1+ fibroblasts (Ff), capturing lower frequency spatial relationships along the boundary. |
| wrrsj5nt795d | TU,Tc,Th,Ff | TU_Ff_scale3_coherence | TU_Ff_scale3_coherence: A normalized measure of local wavelet coherence at the coarsest scale between tumor cells (TU) and FSP1+ fibroblasts (Ff), highlighting broad-scale spatial correlation along the tumor-stroma interface. |
| wrrsj5nt795d | TU,Tc,Th,Ff | TU_Ff_mean_coherence | TU_Ff_mean_coherence: The average coherence across all wavelet scales between tumor cells (TU) and FSP1+ fibroblasts (Ff), summarizing the multi-scale spatial correlation along the boundary. |
| wrrsj5nt795d | TU,Tc,Th,Ff | TU_Ff_max_coherence | TU_Ff_max_coherence: The maximum coherence observed over all scales between tumor cells (TU) and FSP1+ fibroblasts (Ff), indicating the strongest spatial alignment between their distributions. |
| wrrsj5nt795d | TU,Tc,Th,Ff | Tc_Th_scale0_coherence | Tc_Th_scale0_coherence: A normalized measure of local wavelet coherence at the finest scale between cytotoxic T cells (Tc) and helper T cells (Th), indicating high-frequency co-occurrence patterns along the stromal interface. |
| wrrsj5nt795d | TU,Tc,Th,Ff | Tc_Th_scale1_coherence | Tc_Th_scale1_coherence: A normalized measure of local wavelet coherence at an intermediate scale between cytotoxic T cells (Tc) and helper T cells (Th), representing mid-level spatial correlation along the boundary. |
| wrrsj5nt795d | TU,Tc,Th,Ff | Tc_Th_scale2_coherence | Tc_Th_scale2_coherence: A normalized measure of local wavelet coherence at a coarser scale between cytotoxic T cells (Tc) and helper T cells (Th), detailing lower frequency spatial interactions across the interface. |
| wrrsj5nt795d | TU,Tc,Th,Ff | Tc_Th_scale3_coherence | Tc_Th_scale3_coherence: A normalized measure of local wavelet coherence at the coarsest scale between cytotoxic T cells (Tc) and helper T cells (Th), capturing broad-scale spatial dynamics along the tumor-stroma interface. |
| wrrsj5nt795d | TU,Tc,Th,Ff | Tc_Th_mean_coherence | Tc_Th_mean_coherence: The mean wavelet coherence value across all scales between cytotoxic T cells (Tc) and helper T cells (Th), providing an overall assessment of their spatial interaction along the boundary. |
| wrrsj5nt795d | TU,Tc,Th,Ff | Tc_Th_max_coherence | Tc_Th_max_coherence: The maximum coherence value across all scales between cytotoxic T cells (Tc) and helper T cells (Th), highlighting the peak of spatial correlation detected along the interface. |
| wrrsj5nt795d | TU,Tc,Th,Ff | Tc_Ff_scale0_coherence | Tc_Ff_scale0_coherence: A normalized measure of local wavelet coherence at the finest scale between cytotoxic T cells (Tc) and FSP1+ fibroblasts (Ff), describing high-frequency spatial synchronization along the stromal boundary. |
| wrrsj5nt795d | TU,Tc,Th,Ff | Tc_Ff_scale1_coherence | Tc_Ff_scale1_coherence: A normalized measure of local wavelet coherence at an intermediate wavelet scale between cytotoxic T cells (Tc) and FSP1+ fibroblasts (Ff), indicating moderate spatial correlation along the interface. |
| wrrsj5nt795d | TU,Tc,Th,Ff | Tc_Ff_scale2_coherence | Tc_Ff_scale2_coherence: A normalized measure of local wavelet coherence at a coarser scale between cytotoxic T cells (Tc) and FSP1+ fibroblasts (Ff), reflecting lower frequency spatial alignment along the boundary. |
| wrrsj5nt795d | TU,Tc,Th,Ff | Tc_Ff_scale3_coherence | Tc_Ff_scale3_coherence: A normalized measure of local wavelet coherence at the coarsest scale between cytotoxic T cells (Tc) and FSP1+ fibroblasts (Ff), capturing broad-scale spatial correlations along the tumor-stroma interface. |
| wrrsj5nt795d | TU,Tc,Th,Ff | Tc_Ff_mean_coherence | Tc_Ff_mean_coherence: The average wavelet coherence value across all scales between cytotoxic T cells (Tc) and FSP1+ fibroblasts (Ff), summarizing their overall spatial interdependence along the boundary. |
| wrrsj5nt795d | TU,Tc,Th,Ff | Tc_Ff_max_coherence | Tc_Ff_max_coherence: The maximum wavelet coherence observed across scales between cytotoxic T cells (Tc) and FSP1+ fibroblasts (Ff), indicating the highest degree of spatial correlation along the interface. |
| wrrsj5nt795d | TU,Tc,Th,Ff | Th_Ff_scale0_coherence | Th_Ff_scale0_coherence: A normalized measure of local wavelet coherence at the finest wavelet scale between helper T cells (Th) and FSP1+ fibroblasts (Ff), capturing high-frequency spatial co-variation along the stromal boundary. |
| wrrsj5nt795d | TU,Tc,Th,Ff | Th_Ff_scale1_coherence | Th_Ff_scale1_coherence: A normalized measure of local wavelet coherence at an intermediate scale between helper T cells (Th) and FSP1+ fibroblasts (Ff), indicating a moderate level of spatial pattern correspondence along the boundary. |
| wrrsj5nt795d | TU,Tc,Th,Ff | Th_Ff_scale2_coherence | Th_Ff_scale2_coherence: A normalized measure of local wavelet coherence at a coarser scale between helper T cells (Th) and FSP1+ fibroblasts (Ff), reflecting lower frequency spatial interactions along the tumor-stroma interface. |
| wrrsj5nt795d | TU,Tc,Th,Ff | Th_Ff_scale3_coherence | Th_Ff_scale3_coherence: A normalized measure of local wavelet coherence at the coarsest scale between helper T cells (Th) and FSP1+ fibroblasts (Ff), highlighting broad-scale spatial synchronization along the boundary. |
| wrrsj5nt795d | TU,Tc,Th,Ff | Th_Ff_mean_coherence | Th_Ff_mean_coherence: The averaged coherence value over all wavelet scales between helper T cells (Th) and FSP1+ fibroblasts (Ff), providing a comprehensive measure of multi-scale spatial correlation along the stromal boundary. |
| wrrsj5nt795d | TU,Tc,Th,Ff | Th_Ff_max_coherence | Th_Ff_max_coherence: The highest wavelet coherence value found across all scales between helper T cells (Th) and FSP1+ fibroblasts (Ff), indicating the peak spatial alignment between the two cell types along the interface. |
| wssd0oy0qw29 | Tc,B | tc_nucleus_mean_diameter | Mean nuclear diameter of cytotoxic T cells: This parameter measures the average diameter of the nuclei of cytotoxic T cells located in epithelial regions near vessels. The measurement is obtained by calculating the area of the nucleus using polygon data, converting the area into an equivalent diameter, and presenting the value in micrometers, which allows for normalized, comparative analysis across different patient cases. |
| wssd0oy0qw29 | Tc,B | b_nucleus_mean_diameter | Mean nuclear diameter of B lymphocytes: This parameter represents the average nuclear diameter of B lymphocytes in epithelial regions adjacent to vessels. The diameter is derived from the computed area of the nucleus using an equivalent circle formula, resulting in a normalized measure (in micrometers) suitable for cross-case comparisons. |
| wssd0oy0qw29 | Tc,B | tc_b_diameter_ratio | Cytotoxic T cell to B lymphocyte nuclear diameter ratio: This parameter is defined as the ratio of the mean nuclear diameter of cytotoxic T cells to that of B lymphocytes. Being a dimensionless ratio, it provides a normalized metric to compare the relative nuclear sizes between the two cell types across different patient samples. |
| wssi1pi8gq2u | M | macrophage_nucleus_area_variance | macrophage_nucleus_area_variance: This parameter quantifies the variance of the nuclear areas of macrophages located in the stromal regions of a tumor patch. It captures the degree of heterogeneity in nuclear size, reflecting potential differences in the functional state of macrophages and providing a metric useful for comparing variations across patient cases. |
| wssi1pi8gq2u | M | macrophage_nucleus_area_mean | macrophage_nucleus_area_mean: This parameter represents the average nucleus area of macrophages in the stromal compartments of a tumor patch. It summarizes the central tendency of nuclear sizes and allows for comparisons between different patients by providing a standardized measure. |
| wssi1pi8gq2u | M | macrophage_nucleus_area_std | macrophage_nucleus_area_std: This parameter measures the standard deviation of the nuclear areas of macrophages within the stromal regions of a tumor patch. It indicates the spread or dispersion of the nuclear size measurements around the mean, offering insight into the variability of cell morphology across patient samples. |
| wz73bkbox1et | TU | SKEWNESS | SKEWNESS: This parameter measures the asymmetry of the distribution of tumor cell nucleus areas in the epithelial compartment. It is a dimensionless statistic where positive values indicate that the distribution's tail extends to the right and negative values indicate a left-skew. Being derived from the distribution of nucleus areas, it can be compared across different patient cases. |
| wz73bkbox1et | TU | MEAN_AREA | MEAN_AREA: This parameter represents the average area of tumor cell nuclei within the epithelial compartment. Calculated as the arithmetic mean of the measured areas, it is a normalized metric, assuming standardized measurement procedures, and is useful for comparing tumor regions across patient cases. |
| wz73bkbox1et | TU | MEDIAN_AREA | MEDIAN_AREA: This parameter is the median value of the tumor cell nucleus area distribution, providing a robust central tendency measure that is less sensitive to outliers than the mean. It is suitable for cross-case comparisons given that the image and analysis protocols are consistent. |
| wz73bkbox1et | TU | STD_AREA | STD_AREA: The standard deviation of tumor cell nucleus areas quantifies the spread or dispersion of the area measurements in the epithelial compartment. As a normalized measure of variability, it allows for meaningful comparisons between different patient samples. |
| wz73bkbox1et | TU | MIN_AREA | MIN_AREA: This parameter indicates the smallest measured tumor cell nucleus area in the epithelial compartment for a given patch. While reflecting an extreme value, it is calculated under consistent conditions, making it comparable across cases. |
| wz73bkbox1et | TU | MAX_AREA | MAX_AREA: This metric captures the largest observed tumor cell nucleus area within the epithelial compartment. Like the minimum area, it is derived using standardized measurement methods, allowing for valid comparisons among different patient cases. |
| wzg8q0yr7rt6 | TU,M,Th,Treg,B,MFp,MF,Ff | Persistence_Score | The Persistence_Score quantifies the relative proportion of fibroblast-immune interactions that occur across different tissue compartments. It is calculated as the ratio of the weighted score of cross-compartment interactions (where the weight is the inverse of the Euclidean distance between interacting cells) to the total weighted score of all fibroblast-immune interactions. This ratio is normalized, allowing for comparison across different patient cases, and provides an indication of how persistent or sustained these cross-boundary interactions are, relative to the overall interaction landscape. |
| wzi8uk0f32u5 | Treg,M | avg_treg_convexity | avg_treg_convexity represents the average convexity of regulatory T cell nuclei within a tumor patch. Convexity is computed as the ratio of the polygon area of the nucleus to the area of its convex hull, providing a normalized measure of the nucleus shape that can be compared across different patient cases. |
| wzi8uk0f32u5 | Treg,M | avg_macrophage_convexity | avg_macrophage_convexity corresponds to the average convexity of macrophage nuclei in a tumor patch. Similar to the Treg measure, it is calculated as the ratio of the nucleus area to its convex hull area, serving as a normalized metric to assess cell shape irregularities across various samples. |
| wzi8uk0f32u5 | Treg,M | convexity_difference | convexity_difference is the numerical difference between the average convexity of regulatory T cell nuclei and that of macrophage nuclei. This parameter highlights the disparity in nucleus shape between these two cell types, offering a normalized comparison that aids in understanding potential biological differences in the tumor microenvironment. |
| wzteyvwizcdu | Tc,MF | tc_minor_axis_mean | tc_minor_axis_mean: This parameter represents the mean minor axis length of the nucleus of cytotoxic T cells (identified as 't_cell_cd8') measured in micrometers for each patch. It is derived by averaging the minor axis lengths computed from the minimum rotated rectangle of each cytotoxic T cell nucleus. |
| wzteyvwizcdu | Tc,MF | tc_minor_axis_median | tc_minor_axis_median: This parameter shows the median minor axis length of cytotoxic T cell nuclei measured in micrometers. It provides a central value of the distribution of the minor axis lengths across the analyzed cytotoxic T cells in a patch. |
| wzteyvwizcdu | Tc,MF | tc_minor_axis_std | tc_minor_axis_std: This parameter calculates the standard deviation of the minor axis lengths of cytotoxic T cell nuclei, offering insight into the variability in nuclear shape among these cells within the patch. |
| wzteyvwizcdu | Tc,MF | tc_minor_axis_min | tc_minor_axis_min: This parameter records the minimum minor axis length observed among all cytotoxic T cell nuclei in a patch, measured in micrometers. |
| wzteyvwizcdu | Tc,MF | tc_minor_axis_max | tc_minor_axis_max: This parameter records the maximum minor axis length observed among all cytotoxic T cell nuclei in a patch, measured in micrometers. |
| wzteyvwizcdu | Tc,MF | mf_minor_axis_mean | mf_minor_axis_mean: This parameter represents the mean minor axis length of the nucleus of PDPN- myofibroblasts (identified as 'myofibroblast') measured in micrometers for each patch. It is derived by averaging the computed minor axis lengths from the corresponding myofibroblast nuclei. |
| wzteyvwizcdu | Tc,MF | mf_minor_axis_median | mf_minor_axis_median: This parameter shows the median minor axis length of PDPN- myofibroblast nuclei measured in micrometers, indicating the central tendency of the distribution for these cells in a patch. |
| wzteyvwizcdu | Tc,MF | mf_minor_axis_std | mf_minor_axis_std: This parameter calculates the standard deviation of the minor axis lengths of PDPN- myofibroblast nuclei, highlighting the variability in nuclear morphological features across these cells. |
| wzteyvwizcdu | Tc,MF | mf_minor_axis_min | mf_minor_axis_min: This parameter records the minimum minor axis length observed among PDPN- myofibroblast nuclei in a patch, measured in micrometers. |
| wzteyvwizcdu | Tc,MF | mf_minor_axis_max | mf_minor_axis_max: This parameter records the maximum minor axis length observed among PDPN- myofibroblast nuclei in a patch, measured in micrometers. |
| wzteyvwizcdu | Tc,MF | diff_minor_axis_mean | diff_minor_axis_mean: This parameter represents the difference between the mean minor axis lengths of cytotoxic T cell nuclei and PDPN- myofibroblast nuclei (measured in micrometers). It allows for direct comparison of the two cell types in terms of nuclear morphology. |
| wzteyvwizcdu | Tc,MF | ratio_minor_axis_mean | ratio_minor_axis_mean: This parameter indicates the ratio of the mean minor axis length of cytotoxic T cell nuclei to that of PDPN- myofibroblast nuclei. The value is calculated with a small constant added to the denominator to avoid division by zero, facilitating comparisons across patches. |
| x4g92dxxt12p | TU,Tc,Th,B,P,G,MFp,MF | GRANULOCYTE_AVG_ELONGATION_INDEX | GRANULOCYTE_AVG_ELONGATION_INDEX: This parameter represents the average ratio between the major and minor axes of the minimum rotated rectangles that bound each granulocyte cluster. It captures the typical elongation of clusters and is a normalized, dimensionless measure suitable for comparing spatial patterns across different patient patches. |
| x4g92dxxt12p | TU,Tc,Th,B,P,G,MFp,MF | GRANULOCYTE_WEIGHTED_AVG_ELONGATION_INDEX | GRANULOCYTE_WEIGHTED_AVG_ELONGATION_INDEX: This metric is calculated by taking a weighted average of the elongation indices from all granulocyte clusters, where each cluster’s contribution is weighted by its cell count. By emphasizing larger clusters, it provides a normalized measure of overall cluster shape that can be reliably compared between cases. |
| x4g92dxxt12p | TU,Tc,Th,B,P,G,MFp,MF | GRANULOCYTE_MAX_ELONGATION_INDEX | GRANULOCYTE_MAX_ELONGATION_INDEX: This is the highest elongation index observed among all granulocyte clusters within a patch. It identifies the most elongated cluster and, being a ratio, offers a normalized measure that facilitates direct comparison across patient samples. |
| x4g92dxxt12p | TU,Tc,Th,B,P,G,MFp,MF | GRANULOCYTE_MIN_ELONGATION_INDEX | GRANULOCYTE_MIN_ELONGATION_INDEX: This parameter denotes the smallest elongation index among granulocyte clusters, reflecting the cluster with the most circular or least elongated shape. It is expressed as a normalized, dimensionless ratio that can be used for inter-case comparisons. |
| x4g92dxxt12p | TU,Tc,Th,B,P,G,MFp,MF | GRANULOCYTE_MEDIAN_ELONGATION_INDEX | GRANULOCYTE_MEDIAN_ELONGATION_INDEX: The median elongation index across all granulocyte clusters, this metric provides a robust central tendency measure of cluster shape. Since it is based on ratios, it is normalized and can be used to compare different patient regions. |
| x4g92dxxt12p | TU,Tc,Th,B,P,G,MFp,MF | GRANULOCYTE_PERCENT_IN_STROMA | GRANULOCYTE_PERCENT_IN_STROMA: This parameter quantifies the percentage of granulocyte cells present in the stroma regions relative to the total granulocyte count in the sample. As a percentage, it is normalized and facilitates comparison of spatial distribution across different patient cases. |
| x52tjpinkrbu | Treg,MFp | TREG_PDPN_MYOFIB_PROPORTION_WITHIN_20UM | TREG_PDPN_MYOFIB_PROPORTION_WITHIN_20UM measures the fraction of regulatory T cells in the stromal compartment that are located within a 20 µm radius from a PDPN-positive myofibroblast. This parameter is computed by dividing the number of T cells meeting the proximity criterion by the total number of regulatory T cells in the stroma, resulting in a normalized metric that facilitates comparison across different tumor regions and patient cases. |
| x52tjpinkrbu | Treg,MFp | TREG_PDPN_MYOFIB_MEAN_MIN_DISTANCE | TREG_PDPN_MYOFIB_MEAN_MIN_DISTANCE quantifies the average minimum distance from each regulatory T cell to the nearest PDPN-positive myofibroblast in the stroma. This metric reflects the overall spatial proximity between the two cell types in a normalized manner, allowing for meaningful cross-sample comparisons. |
| x52tjpinkrbu | Treg,MFp | TREG_PDPN_MYOFIB_MEDIAN_MIN_DISTANCE | TREG_PDPN_MYOFIB_MEDIAN_MIN_DISTANCE represents the median of the minimum distances from each regulatory T cell to its closest PDPN-positive myofibroblast. This robust statistical measure provides insight into the typical spatial separation between these cells and is normalized for comparative analysis. |
| x52tjpinkrbu | Treg,MFp | TREG_PDPN_MYOFIB_STD_MIN_DISTANCE | TREG_PDPN_MYOFIB_STD_MIN_DISTANCE indicates the variability in the minimum distances from regulatory T cells to the nearest PDPN-positive myofibroblast by calculating the standard deviation. It offers an understanding of the dispersion in spatial relationships in a normalized way, enabling reliable comparisons across different patient samples. |
| xayfqponm3qc | TU | MEDIAN_FD | MEDIAN_FD represents the median fractal dimension of tumor cell nuclei in epithelial regions. This parameter is computed by applying a box-counting algorithm to each valid tumor cell nucleus polygon and then taking the median value of the resulting fractal dimensions, serving as a normalized metric for comparing nuclear complexity across different patient cases. |
| xayfqponm3qc | TU | MEAN_FD | MEAN_FD is the average fractal dimension of tumor cell nuclei within the epithelial compartment. It is calculated by averaging the fractal dimensions determined through a box-counting method for each valid tumor cell, providing a normalized overall measure of nuclear boundary complexity. |
| xayfqponm3qc | TU | STD_FD | STD_FD is the standard deviation of the fractal dimensions of tumor cell nuclei, quantifying the variability in nuclear shape complexity among the analyzed cells. This normalized statistic helps assess the distribution spread of fractal dimension values, making comparisons valid across different cases. |
| xayfqponm3qc | TU | MIN_FD | MIN_FD denotes the minimum fractal dimension value observed among the tumor cell nuclei. As a normalized metric derived from the box-counting fractal analysis, it indicates the lower bound of nuclear complexity measured in the epithelial tumor spots. |
| xayfqponm3qc | TU | MAX_FD | MAX_FD refers to the maximum fractal dimension recorded among tumor cell nuclei. This parameter, derived in a normalized manner, reflects the upper bound of nuclear complexity observed in the specimen. |
| xayfqponm3qc | TU | Q1_FD | Q1_FD is the first quartile (25th percentile) of the fractal dimensions of tumor cell nuclei. It is a normalized statistical measure that delineates the point below which 25% of the computed fractal dimensions fall, thereby characterizing the lower spread of the complexity distribution. |
| xayfqponm3qc | TU | Q3_FD | Q3_FD is the third quartile (75th percentile) of the fractal dimensions. This normalized parameter indicates that 75% of the fractal dimension values are below this threshold, thus describing the upper segment of the complexity distribution. |
| xayfqponm3qc | TU | IQR_FD | IQR_FD is the interquartile range of fractal dimensions, calculated as the difference between Q3_FD and Q1_FD. It is a normalized measure that captures the spread of the central 50% of fractal dimension values, thereby highlighting the dispersion in nuclear complexity. |
| xbi078ftsuls | TU,Tc,Th,Treg,B,P | STROMA_IG_ACTIVATION_INDEX | STROMA_IG_ACTIVATION_INDEX represents a normalized metric measuring the balance between humoral and T cell-driven immune responses in the stroma region. It is calculated by dividing the sum of B cell and plasma cell counts by the total count of T cells (including CD8, CD4, and regulatory T cells) and then normalizing that ratio by the epithelial (tumor) cell count. This normalization enables consistent comparison across different patient cases and tissue patches. |
| xbyua52k32a4 | TU,B,P,Treg | TU_mean_distance_variance | TU_mean_distance_variance: This parameter represents the mean variance of distances measured from tumor cells to all neighboring cells of different types (B cells, plasma cells, and regulatory T cells). It quantifies the spatial heterogeneity in the tumor microenvironment and is normalized to allow comparisons across different patient cases. |
| xbyua52k32a4 | TU,B,P,Treg | TU_median_distance_variance | TU_median_distance_variance: This parameter captures the median variance of distances from tumor cells to their neighboring immune cells. It provides a robust central measure of spatial heterogeneity in the tumor microenvironment across various patches. |
| xbyua52k32a4 | TU,B,P,Treg | B_mean_distance_variance | B_mean_distance_variance: This parameter reflects the mean variance of distances calculated from B lymphocytes to all neighboring cells of other types (tumor, plasma, regulatory T cells). It is a normalized measure indicating the average spread or dispersion of B cell interactions within the tissue. |
| xbyua52k32a4 | TU,B,P,Treg | B_median_distance_variance | B_median_distance_variance: This is the median value of the variance of distances from B cells to neighboring cells, offering a robust metric for evaluating the spatial dispersion patterns of B cells in tumor regions. |
| xbyua52k32a4 | TU,B,P,Treg | P_mean_distance_variance | P_mean_distance_variance: This parameter measures the mean variance of distances from plasma cells to their neighboring cells (tumor cells, B cells, regulatory T cells). It provides insight into the average spatial heterogeneity of plasma cells and is normalized for cross-case comparisons. |
| xbyua52k32a4 | TU,B,P,Treg | P_median_distance_variance | P_median_distance_variance: The median variance of distances from plasma cells to other cell types captures a robust metric of spatial variability, representing the central tendency of plasma cell dispersion. |
| xbyua52k32a4 | TU,B,P,Treg | Treg_mean_distance_variance | Treg_mean_distance_variance: This parameter represents the mean variance of distances from regulatory T cells to neighboring cells (tumor, B, and plasma cells), reflecting the average spatial distribution and local arrangement heterogeneity of these cells in the tumor patch. |
| xbyua52k32a4 | TU,B,P,Treg | Treg_median_distance_variance | Treg_median_distance_variance: The median variance of distances from regulatory T cells to cells of other types provides a robust measure of spatial organization, minimizing the effect of outliers and supporting normalized comparisons. |
| xbyua52k32a4 | TU,B,P,Treg | overall_mean_distance_variance | overall_mean_distance_variance: This parameter aggregates the mean variance of distances across all analyzed cells (of all types), delivering a comprehensive metric of spatial heterogeneity for the entire tumor patch that is normalized across cases. |
| xbyua52k32a4 | TU,B,P,Treg | overall_median_distance_variance | overall_median_distance_variance: This parameter captures the overall median variance of distances from all cells, offering a robust summary statistic of the general spatial arrangement variability present within each tumor patch. |
| xdkg05lggrvt | B,Treg | B_CELL_PERCENTAGE_STROMA | B_CELL_PERCENTAGE_STROMA quantifies the normalized percentage of B cells among all cells present in the stromal compartment of a tumor patch. It is computed by dividing the number of B cells by the total number of stromal cells and multiplying by 100, thereby providing a direct measure that can be compared across different patient cases. |
| xdkg05lggrvt | B,Treg | TREG_CELL_PERCENTAGE_STROMA | TREG_CELL_PERCENTAGE_STROMA quantifies the normalized percentage of regulatory T cells present in the stromal compartment of a tumor patch. This parameter is derived by dividing the number of regulatory T cells by the total number of stromal cells and multiplying by 100, ensuring that the measure is expressed as a normalized percentage suitable for comparative analysis. |
| xdkg05lggrvt | B,Treg | B_TREG_RATIO_STROMA | B_TREG_RATIO_STROMA measures the normalized ratio of the percentage of B cells to the percentage of regulatory T cells in the stromal compartment of a tumor patch. It is obtained by dividing the B cell percentage by the Treg cell percentage, using a small epsilon value for cases where the Treg percentage is very low to prevent division by zero. This ratio facilitates direct comparison of the relative presence of B cells versus regulatory T cells across different cases. |
| xfbt4xtsmgo1 | TU,Tc,B,P,M,MF,E | epithelial_cell_stromal_proportion | epithelial_cell_stromal_proportion: This parameter measures the proportion of tumor (epithelial) cells that are located in the stromal compartment relative to the total number of tumor cells. It provides a normalized metric to compare tumor compartmentalization across different patient cases. |
| xfbt4xtsmgo1 | TU,Tc,B,P,M,MF,E | t_cell_cd8_stromal_proportion | t_cell_cd8_stromal_proportion: This parameter quantifies the proportion of cytotoxic T cells (CD8+ T cells) that are found in the stromal compartment rather than in the epithelial compartment, offering a normalized view of the immune cell distribution. |
| xfbt4xtsmgo1 | TU,Tc,B,P,M,MF,E | b_cell_stromal_proportion | b_cell_stromal_proportion: This parameter represents the ratio of B cells located in the stromal compartment compared to the overall B cell count, serving as a normalized indicator of B cell distribution within the tissue microenvironment. |
| xfbt4xtsmgo1 | TU,Tc,B,P,M,MF,E | plasma_cell_stromal_proportion | plasma_cell_stromal_proportion: This parameter denotes the normalized proportion of plasma cells residing in the stromal compartment relative to the total plasma cells, which aids in understanding their compartmental distribution. |
| xfbt4xtsmgo1 | TU,Tc,B,P,M,MF,E | macrophage_stromal_proportion | macrophage_stromal_proportion: This parameter reflects the normalized proportion of macrophages in the stroma compared to the total macrophage number, facilitating comparisons between different tumor patches. |
| xfbt4xtsmgo1 | TU,Tc,B,P,M,MF,E | myofibroblast_stromal_proportion | myofibroblast_stromal_proportion: This parameter calculates the proportion of non-PDPN myofibroblasts in the stromal compartment relative to their total, serving as a normalized index to assess their spatial distribution in the tissue. |
| xfbt4xtsmgo1 | TU,Tc,B,P,M,MF,E | endothelial_cell_stromal_proportion | endothelial_cell_stromal_proportion: This parameter measures the normalized proportion of endothelial cells found in the stromal compartment, aiding in evaluating vascular or structural patterns in the tissue. |
| xfbt4xtsmgo1 | TU,Tc,B,P,M,MF,E | compartmental_distribution_index | compartmental_distribution_index: This composite parameter is the arithmetic mean of the stromal proportions of the seven cell types under consideration. It provides a normalized overall index reflecting the distribution of diverse cell types between the stromal and epithelial compartments, making it suitable for comparing different patient cases. |
| xhfougiytmwk | MFp,MF,M,E,Tc,B | MFp_eccentricity_variance | MFp_eccentricity_variance measures the variance of nuclear eccentricity values for PDPN+ Myofibroblasts located in the stromal compartment. The metric is derived by computing the eccentricity of each nucleus polygon using eigenvalue analysis of the polygon's covariance matrix, reflecting the heterogeneity of cell shape across analyzed patches. |
| xhfougiytmwk | MFp,MF,M,E,Tc,B | MF_eccentricity_variance | MF_eccentricity_variance measures the variance of nuclear eccentricity values for PDPN- Myofibroblasts in the stromal area. It is calculated by first validating the cell's nucleus polygon and then computing its eccentricity. The variance across cells indicates the degree of morphological diversity among these cells. |
| xhfougiytmwk | MFp,MF,M,E,Tc,B | M_eccentricity_variance | M_eccentricity_variance measures the variance of nuclear eccentricity values for Macrophages found in the stroma. This parameter is generated by extracting the nucleus polygon for each cell, calculating its eccentricity from the eigenvalues of the covariance matrix, and then computing the variance. This reflects the heterogeneity in nuclear morphology within the macrophage population. |
| xhfougiytmwk | MFp,MF,M,E,Tc,B | E_eccentricity_variance | E_eccentricity_variance measures the variance in nuclear eccentricity values of Endothelial cells in the stroma. The parameter is obtained by assessing the cell's nuclear shape and computing its eccentricity via eigenvalue decomposition. The variance provides insight into the variability of cell shape, which is relevant for comparing different tumor regions. |
| xhfougiytmwk | MFp,MF,M,E,Tc,B | Tc_eccentricity_variance | Tc_eccentricity_variance measures the variance of nuclear eccentricity values for Cytotoxic T Cells in the stromal compartment. It involves processing the nucleus polygon of each cell, calculating its eccentricity, and then determining the variance. This metric is used to understand the diversity of nuclear morphology among cytotoxic T cells. |
| xhfougiytmwk | MFp,MF,M,E,Tc,B | B_eccentricity_variance | B_eccentricity_variance measures the variance of nuclear eccentricity values for B Cells present in the stroma. The procedure includes validating the nucleus polygon of each cell, computing its eccentricity through covariance matrix eigenvalue analysis, and calculating the variance across these values. The resulting parameter facilitates comparison of morphological heterogeneity between different patient cases. |
| xm6ooy3md5vl | Tc,B,M,MFp,TU | mean_nuclear_solidity_Tc | mean_nuclear_solidity_Tc: Measures the average nuclear solidity for cytotoxic T cells (CD8+). Nuclear solidity is calculated as the ratio of the nucleus area to the convex hull area, representing the morphological compactness and helping to compare characteristics across different patient cases. |
| xm6ooy3md5vl | Tc,B,M,MFp,TU | mean_nuclear_solidity_B | mean_nuclear_solidity_B: Measures the average nuclear solidity for B cells, using the ratio of nucleus area to its convex hull area. This normalized metric facilitates the comparison of B cell nuclear morphology across various tumor patches. |
| xm6ooy3md5vl | Tc,B,M,MFp,TU | mean_nuclear_solidity_M | mean_nuclear_solidity_M: Represents the average nuclear solidity for macrophages. By computing the ratio of the nuclear area to the convex area, it standardizes cellular shape measurements, making it a reliable normalized parameter for inter-case comparisons. |
| xm6ooy3md5vl | Tc,B,M,MFp,TU | mean_nuclear_solidity_MFp | mean_nuclear_solidity_MFp: Quantifies the average nuclear solidity for PDPN+ myofibroblasts. This parameter is derived from the ratio of nucleus area to convex hull area, normalized to allow meaningful comparisons of nuclear morphology across different patches and patient samples. |
| xm6ooy3md5vl | Tc,B,M,MFp,TU | mean_nuclear_solidity_TU | mean_nuclear_solidity_TU: Assesses the average nuclear solidity for tumor cells (epithelial cells) by calculating the ratio of the nuclear area to the convex hull area. This normalized measurement aids in evaluating tumor cell morphological variations across different patient cases. |
| xm6ooy3md5vl | Tc,B,M,MFp,TU | combined_mean_nuclear_solidity | combined_mean_nuclear_solidity: Provides a combined, overall measure of nuclear solidity by computing the simple arithmetic mean of the five individual cell type mean nuclear solidity values. This comprehensive parameter offers a standardized approach for comparing nuclear characteristics across patient cases. |
| y1414n5nxbjj | Treg,Th,Ff,B,TU | Th_mean_density_gradient | Th_mean_density_gradient: This parameter measures the average magnitude of the density gradient vectors for helper T cells. It is computed by identifying neighboring cells within a fixed radius, calculating the displacement vectors from each helper T cell to its neighbors, summing these vectors to determine a density gradient, and then taking the mean magnitude over all cells. This provides an indication of the strength of local directional clustering in each patch and is normalized since it represents an average value. |
| y1414n5nxbjj | Treg,Th,Ff,B,TU | Th_std_density_gradient | Th_std_density_gradient: This parameter captures the variability (standard deviation) in the density gradient magnitudes for helper T cells across a patch. It reflects the spread or consistency of directional clustering and is computed over all helper T cells in the region. |
| y1414n5nxbjj | Treg,Th,Ff,B,TU | Th_mean_anisotropy | Th_mean_anisotropy: Representing the average anisotropy measure for helper T cells, this parameter quantifies the directional alignment of cell infiltrates. The anisotropy is derived by calculating the angular dispersion (using cosine and sine components of displacement vectors) and normalizing the resultant vector length to a scale of 0 to 1. The mean value over all cells makes it comparable across different patches. |
| y1414n5nxbjj | Treg,Th,Ff,B,TU | Th_std_anisotropy | Th_std_anisotropy: This parameter denotes the standard deviation of the anisotropy values for helper T cells. It expresses the variation in directional alignment among cells within a patch, ensuring that differences in infiltration patterns are quantitatively captured. |
| y1414n5nxbjj | Treg,Th,Ff,B,TU | Ff_mean_density_gradient | Ff_mean_density_gradient: This metric is the average magnitude of density gradient vectors computed for FSP1+ fibroblasts. It assesses how strongly the fibroblasts are directionally clustered by averaging the computed displacements of neighboring fibroblasts across a patch. |
| y1414n5nxbjj | Treg,Th,Ff,B,TU | Ff_std_density_gradient | Ff_std_density_gradient: This metric measures the variability in the density gradient magnitudes for FSP1+ fibroblasts. It reflects the heterogeneity of directional clustering within the region by calculating the standard deviation of the gradient magnitudes. |
| y1414n5nxbjj | Treg,Th,Ff,B,TU | B_mean_density_gradient | B_mean_density_gradient: For B cells, this parameter captures the mean magnitude of density gradient vectors. It is calculated by summing the displacement vectors from B cells to nearby B cells (within a fixed radius) and averaging the resulting magnitudes, thus providing a normalized indicator of spatial clustering. |
| y1414n5nxbjj | Treg,Th,Ff,B,TU | B_std_density_gradient | B_std_density_gradient: This parameter represents the standard deviation of the density gradient magnitudes for B cells. It quantifies the variability in the directional clustering strength and serves as a normalized measure across different patches. |
| y1414n5nxbjj | Treg,Th,Ff,B,TU | B_mean_anisotropy | B_mean_anisotropy: This parameter reflects the average anisotropy (directional alignment) of B cells by computing the normalized resultant length from the displacement vectors within the neighborhood. A higher value (on a scale of 0 to 1) indicates more organized, directional infiltration. |
| y1414n5nxbjj | Treg,Th,Ff,B,TU | B_std_anisotropy | B_std_anisotropy: This parameter gives the standard deviation of the anisotropy measures for B cells across a patch. It captures the variation in the consistency of directional alignment among B cells. |
| y1414n5nxbjj | Treg,Th,Ff,B,TU | TU_mean_density_gradient | TU_mean_density_gradient: For tumor cells, this measure captures the mean magnitude of density gradient vectors. It is determined by summing displacement vectors from each tumor cell to its neighboring tumor cells and averaging these magnitudes, serving as a normalized measure of the directional clustering behavior within the patch. |
| y1414n5nxbjj | Treg,Th,Ff,B,TU | TU_std_density_gradient | TU_std_density_gradient: This parameter reflects the standard deviation of the density gradient magnitudes for tumor cells. It quantifies the variability in the clustering strength among tumor cells, ensuring normalized comparisons between different patches. |
| y1414n5nxbjj | Treg,Th,Ff,B,TU | TU_mean_anisotropy | TU_mean_anisotropy: This parameter measures the average anisotropy for tumor cells, quantifying the degree of directional alignment of the tumor cells' spatial positions. It is calculated as a normalized measure (ranging from 0 to 1) based on the distribution of displacement vector directions, allowing for meaningful comparison between patient cases. |
| y1414n5nxbjj | Treg,Th,Ff,B,TU | TU_std_anisotropy | TU_std_anisotropy: This parameter denotes the standard deviation of the anisotropy values for tumor cells. It captures the variability in the directional infiltration patterns of tumor cells within a patch and is computed in a normalized manner. |
| y2gcevewl4qb | TU,M,G,MFp,MF,Ff,F | Inflammatory_Fibroblast_to_Tumor_Ratio | The Inflammatory_Fibroblast_to_Tumor_Ratio parameter quantifies the relative abundance of inflammatory and fibroblast cells compared to tumor cells within a tissue patch. It is computed by summing the counts of several cell types (macrophages, granulocytes, myofibroblasts with PDPN, myofibroblasts, FSP1-positive fibroblasts, and normal fibroblasts) and then normalizing this total by the number of epithelial tumor cells. This normalized ratio allows for meaningful comparisons across different patient cases and image patches, ensuring a valid numeric metric for analyzing the tumor microenvironment. |
| yf4daew6y9b2 | P,G,MFp,E | Plasma Cells_median_form_factor | Plasma Cells_median_form_factor: This parameter represents the median nuclear form factor for plasma cells located in the stromal regions of breast cancer tissue. It is derived by measuring the area and perimeter of each plasma cell's nuclear polygon and applying the formula (4π × area / perimeter²). The resulting value reflects how close the nuclear shape is to a perfect circle (a value of 1 indicates a perfect circle), allowing for normalized comparisons across different patient cases. |
| yf4daew6y9b2 | P,G,MFp,E | Granulocytes_median_form_factor | Granulocytes_median_form_factor: This parameter captures the median nuclear form factor for granulocytes in the stromal areas. It is based on the computed nuclear shape descriptor (using area and perimeter measurements) that quantifies the regularity of the nuclei. The normalization achieved by taking the median enables direct comparisons across multiple patient samples. |
| yf4daew6y9b2 | P,G,MFp,E | PDPN+ Myofibroblasts_median_form_factor | PDPN+ Myofibroblasts_median_form_factor: This parameter denotes the median nuclear form factor for PDPN+ myofibroblasts within the stromal compartment. The nuclear form factor is calculated using the standardized formula, representing the degree of nuclear shape regularity. By computing the median value, the parameter becomes normalized and suitable for comparing tumor patches across various patient cases. |
| yf4daew6y9b2 | P,G,MFp,E | Endothelial Cells_median_form_factor | Endothelial Cells_median_form_factor: This parameter indicates the median nuclear form factor for endothelial cells in the stroma. It is calculated by applying the nuclear shape formula to the area and perimeter measurements of the cells, resulting in a value that reflects the circularity of the nucleus. The use of the median ensures that the parameter is normalized and comparable between different patient cases. |
| yjfu3to5orr6 | Th,M | TH_FRACTAL_DIM_MEAN | TH_FRACTAL_DIM_MEAN represents the average fractal dimension of the nuclear boundaries of T helper cells in the stromal compartment. It is computed using a box-counting method on nuclear polygons and provides a normalized measure of the complexity of the nucleus shape. |
| yjfu3to5orr6 | Th,M | TH_FRACTAL_DIM_STD | TH_FRACTAL_DIM_STD represents the standard deviation of the fractal dimensions calculated for the nuclear boundaries of T helper cells in stroma. It indicates the variability in nuclear complexity across these cells and is normalized for comparison across patient cases. |
| yjfu3to5orr6 | Th,M | TH_FRACTAL_DIM_MIN | TH_FRACTAL_DIM_MIN represents the minimum fractal dimension value obtained from the T helper cell nuclei in the stromal region. It reflects the lowest observed measurement of nuclear boundary complexity among these cells. |
| yjfu3to5orr6 | Th,M | TH_FRACTAL_DIM_MAX | TH_FRACTAL_DIM_MAX represents the maximum fractal dimension value obtained from the T helper cell nuclei in the stromal region. It reflects the highest observed measurement of nuclear complexity among these cells. |
| yjfu3to5orr6 | Th,M | MACRO_FRACTAL_DIM_MEAN | MACRO_FRACTAL_DIM_MEAN represents the average fractal dimension of the nuclear boundaries of macrophage cells in the stroma. This normalized metric is computed similarly as for T helper cells, providing a comparative measurement of nuclear complexity. |
| yjfu3to5orr6 | Th,M | MACRO_FRACTAL_DIM_STD | MACRO_FRACTAL_DIM_STD represents the standard deviation of the fractal dimensions calculated for macrophage cell nuclei in the stromal area. It indicates the degree of variation in nuclear complexity among these macrophage cells. |
| yjfu3to5orr6 | Th,M | MACRO_FRACTAL_DIM_MIN | MACRO_FRACTAL_DIM_MIN represents the minimum fractal dimension value from the macrophage nuclei in stroma, highlighting the lowest observed nuclear complexity among these cells. |
| yjfu3to5orr6 | Th,M | MACRO_FRACTAL_DIM_MAX | MACRO_FRACTAL_DIM_MAX represents the maximum fractal dimension value from the macrophage nuclei in stroma, highlighting the highest observed nuclear complexity among these cells. |
| yjfu3to5orr6 | Th,M | FRACTAL_DIM_DIFFERENCE | FRACTAL_DIM_DIFFERENCE represents the difference between the mean fractal dimensions of T helper cells and macrophages in the stroma. It is calculated by subtracting the macrophage mean fractal dimension from the T helper cell mean, yielding a normalized measure useful for comparing activation states between the two cell types. |
| yl93nke75yie | MFp,Ff,M,E,G,TU | avg_eccentricity_MFp | avg_eccentricity_MFp: This parameter measures the average nucleus eccentricity for PDPN+ Myofibroblasts. It is calculated by extracting the nucleus shape as a polygon, computing the covariance of its coordinates, and using the eigenvalues to determine the lengths of the major and minor axes. The eccentricity, a normalized value between 0 (perfect circle) and 1 (highly elongated), quantifies how deformed the nuclei are, providing an indicator of cell morphology influenced by a high-stress tumor microenvironment. |
| yl93nke75yie | MFp,Ff,M,E,G,TU | avg_eccentricity_Ff | avg_eccentricity_Ff: This parameter represents the average nucleus eccentricity for FSP1+ Fibroblasts. It relies on the same approach of extracting nucleus polygon data, performing covariance and eigenvalue analysis, and computing the ratio of the minor to major axis lengths to derive a normalized eccentricity measure. This value effectively captures the elliptical deformation of fibroblast nuclei relevant to tumor behavior. |
| yl93nke75yie | MFp,Ff,M,E,G,TU | avg_eccentricity_M | avg_eccentricity_M: This parameter reflects the average nucleus eccentricity for Macrophages. The measurement involves assessing the nucleus shape polygon, center-aligning its coordinates, determining the principal axes from the eigenvalues of the covariance matrix, and calculating a normalized eccentricity. The resulting value indicates morphological alterations in macrophage nuclei associated with the tumor microenvironment. |
| yl93nke75yie | MFp,Ff,M,E,G,TU | avg_eccentricity_E | avg_eccentricity_E: This parameter denotes the average nucleus eccentricity for Endothelial Cells. It is derived by analyzing the polygon representation of the nucleus, computing the covariance matrix of the coordinates, and evaluating the eigenvalues to obtain the major and minor axis lengths. The calculated eccentricity, ranging from 0 to 1, offers a normalized measure of the cell’s nuclear shape distortion. |
| yl93nke75yie | MFp,Ff,M,E,G,TU | avg_eccentricity_G | avg_eccentricity_G: This parameter is the average nucleus eccentricity for Granulocytes. The underlying process involves extracting the nucleus polygon coordinates, applying statistical techniques to compute the principal axes, and subsequently determining the eccentricity. The normalized value serves to compare the level of elongation in granulocyte nuclei across different tumor regions. |
| yl93nke75yie | MFp,Ff,M,E,G,TU | avg_eccentricity_TU | avg_eccentricity_TU: This parameter quantifies the average nucleus eccentricity for Tumor Cells. It is computed by processing the nucleus shape obtained from polygon data, evaluating the shape's variance through eigenvalue analysis, and determining the elongation with respect to a circle. The normalized eccentricity value facilitates comparisons of nuclear morphology among tumor cells. |
| yl93nke75yie | MFp,Ff,M,E,G,TU | avg_eccentricity_all | avg_eccentricity_all: This parameter provides the overall average nucleus eccentricity across all analyzed cell types. It is computed by aggregating the individual eccentricities of PDPN+ Myofibroblasts, FSP1+ Fibroblasts, Macrophages, Endothelial Cells, Granulocytes, and Tumor Cells. The final value is normalized and represents a comprehensive indicator of nuclear shape deformation within the tumor microenvironment. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | all_cell_type_weighted_buffer_thickness | all_cell_type_weighted_buffer_thickness represents the overall weighted sum of immune cell buffer thickness around tumor cells. It is calculated by summing the product of the average minimal distance from tumor cells to each immune cell subtype and the relative abundance of that subtype, offering a normalized measure for comparing different patient cases. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_min_dist_Tc | avg_min_dist_Tc measures the average minimal distance from tumor cells to CD8+ T cells (cell type code 'Tc'). It reflects the typical spatial separation between tumor cells and these cytotoxic immune cells. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_min_dist_Th | avg_min_dist_Th denotes the average minimal distance from tumor cells to CD4+ T cells (cell type code 'Th'). This parameter indicates the typical gap between tumor cells and helper T cells. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_min_dist_Treg | avg_min_dist_Treg indicates the average minimal distance from tumor cells to regulatory T cells (cell type code 'Treg'). It captures how close tumor cells are to immune cells that may modulate immune response. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_min_dist_B | avg_min_dist_B reports the average minimal distance from tumor cells to B cells (cell type code 'B'). It quantifies the spatial proximity of tumor cells to B lymphocytes. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_min_dist_P | avg_min_dist_P provides the average minimal distance from tumor cells to plasma cells (cell type code 'P'). It shows how spatially near tumor cells are to antibody-producing cells. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_min_dist_M | avg_min_dist_M measures the average minimal distance from tumor cells to macrophages (cell type code 'M'). This parameter reflects the closeness of tumor cells to phagocytic immune cells. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_min_dist_G | avg_min_dist_G captures the average minimal distance from tumor cells to granulocytes (cell type code 'G'). It indicates the spatial relationship between tumor cells and granulocytic immune cells. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_min_dist_MFp | avg_min_dist_MFp represents the average minimal distance from tumor cells to myofibroblast cells expressing podoplanin (cell type code 'MFp'). It measures the proximity of tumor cells to these specialized stromal cells. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_min_dist_MF | avg_min_dist_MF reflects the average minimal distance from tumor cells to myofibroblasts (cell type code 'MF'), revealing their spatial association with tumor cells. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_min_dist_Ff | avg_min_dist_Ff indicates the average minimal distance from tumor cells to fibroblast cells expressing FSP1 (cell type code 'Ff'), which shows the closeness to a specific fibroblast subtype. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_min_dist_F | avg_min_dist_F provides the average minimal distance from tumor cells to general fibroblasts (cell type code 'F'). It quantifies the spatial interactions between tumor cells and fibroblastic stromal components. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_min_dist_E | avg_min_dist_E denotes the average minimal distance from tumor cells to endothelial cells (cell type code 'E'), reflecting the proximity of tumor cells to blood vessel lining cells. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | avg_min_dist_A | avg_min_dist_A measures the average minimal distance from tumor cells to ap cells (cell type code 'A'), indicating the spatial separation between tumor cells and this immune cell subset. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | rel_abundance_Tc | rel_abundance_Tc represents the relative abundance of CD8+ T cells among all immune cells. It is a normalized proportion that allows comparison across patient cases. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | rel_abundance_Th | rel_abundance_Th denotes the relative abundance of CD4+ T cells in the immune cell population, providing a normalized fraction of these helper cells. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | rel_abundance_Treg | rel_abundance_Treg indicates the relative abundance of regulatory T cells among all immune cells, ensuring the measurement is normalized for comparability. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | rel_abundance_B | rel_abundance_B reflects the relative proportion of B cells within the entire immune cell population, offering a normalized metric. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | rel_abundance_P | rel_abundance_P provides the normalized relative abundance of plasma cells, calculated as the count of plasma cells divided by the total immune cell count. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | rel_abundance_M | rel_abundance_M denotes the normalized relative abundance of macrophages, assessing their proportion in the immune cell compartment. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | rel_abundance_G | rel_abundance_G measures the relative abundance of granulocytes as a fraction of total immune cells, ensuring a normalized comparison. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | rel_abundance_MFp | rel_abundance_MFp represents the normalized relative abundance of myofibroblast cells with podoplanin expression among immune and stromal cells. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | rel_abundance_MF | rel_abundance_MF indicates the normalized relative abundance of myofibroblasts, calculated as their count divided by total immune cells. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | rel_abundance_Ff | rel_abundance_Ff reflects the normalized relative abundance of fibroblast cells expressing FSP1 among all immune cells. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | rel_abundance_F | rel_abundance_F provides the normalized fraction of fibroblasts within the immune cell population. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | rel_abundance_E | rel_abundance_E denotes the normalized relative abundance of endothelial cells, showing their proportion relative to the total number of immune cells. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | rel_abundance_A | rel_abundance_A represents the normalized relative abundance of ap cells among the immune cell population. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_dist_Tc | weighted_dist_Tc is the weighted distance contribution of CD8+ T cells. It is computed by multiplying the average minimal distance from tumor cells to CD8+ T cells by their relative abundance, thereby normalizing the spatial metric by their prevalence. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_dist_Th | weighted_dist_Th measures the weighted distance for CD4+ T cells by combining their average minimal distance to tumor cells with their relative abundance. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_dist_Treg | weighted_dist_Treg reflects the weighted distance for regulatory T cells, deriving from the product of their average minimal distance from tumor cells and their relative abundance in the immune cell mix. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_dist_B | weighted_dist_B quantifies the weighted contribution of B cells by calculating the product of their average minimal distance to tumor cells and their relative fraction among immune cells. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_dist_P | weighted_dist_P computes the weighted distance for plasma cells by multiplying their average minimal distance by their normalized relative abundance. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_dist_M | weighted_dist_M is the weighted distance for macrophages, obtained by combining the average minimal distance from tumor cells to macrophages with their relative abundance. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_dist_G | weighted_dist_G measures the contribution of granulocytes to the overall spatial metric by weighting their average minimal distance to tumor cells with their normalized abundance. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_dist_MFp | weighted_dist_MFp calculates the weighted distance for myofibroblast cells expressing podoplanin by integrating their average minimal distance and relative proportion. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_dist_MF | weighted_dist_MF quantifies the weighted contribution of myofibroblasts by multiplying their average minimal distance by their relative abundance. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_dist_Ff | weighted_dist_Ff provides the weighted distance for fibroblast cells expressing FSP1 by combining the average minimal distance from tumor cells to these cells with their normalized relative abundance. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_dist_F | weighted_dist_F computes the weighted distance for fibroblasts with a similar approach, using the average minimal distance and relative abundance of fibroblasts. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_dist_E | weighted_dist_E is the weighted distance for endothelial cells, obtained by multiplying their average minimal distance from tumor cells by their normalized relative abundance. |
| yldxliwbr70c | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_dist_A | weighted_dist_A represents the weighted distance for ap cells, calculated by the product of the average minimal distance from tumor cells and their relative abundance. |
| yogau6ioii2u | M,A,MF,B | clustering_coefficient | The parameter 'clustering_coefficient' quantifies the degree of interconnectedness among specific cell types (macrophages, antigen presenting cells, myofibroblasts, and B cells) located in the stromal compartment of breast cancer tissues. It is computed as the average of local clustering coefficients obtained from a graph constructed using cell-to-cell distances within a predefined threshold. The value ranges between 0 and 1, where 0 indicates no clustering and 1 indicates full clustering. This metric is normalized and numeric, making it suitable for comparing different patient cases across tumor patches. |
| yp01k80kt2kw | P,Tc,F,MFp | mean_fractal_dim_all_cells | mean_fractal_dim_all_cells: This parameter represents the average fractal dimension of the cell boundaries for all cells analyzed near the tumor boundary. It quantifies the overall complexity and irregularity of the cell membranes, offering a normalized metric that facilitates comparison across different patient cases. |
| yp01k80kt2kw | P,Tc,F,MFp | std_fractal_dim_all_cells | std_fractal_dim_all_cells: This parameter reflects the standard deviation of the fractal dimensions measured for all cells near the tumor boundary. It provides insight into the variability in boundary complexity among the cells, enabling an assessment of heterogeneity in the tumor microenvironment. |
| yp01k80kt2kw | P,Tc,F,MFp | max_fractal_dim_all_cells | max_fractal_dim_all_cells: This parameter captures the highest observed fractal dimension among all analyzed cells near the tumor boundary. It indicates the extreme level of boundary irregularity in the cell population, valuable for understanding potential outliers in morphological patterns. |
| yp01k80kt2kw | P,Tc,F,MFp | min_fractal_dim_all_cells | min_fractal_dim_all_cells: This parameter denotes the lowest fractal dimension recorded among cells near the tumor boundary, representing the least complex or most regular cell boundaries. It acts as a baseline metric for comparison with higher values. |
| yp01k80kt2kw | P,Tc,F,MFp | mean_fractal_dim_per_cluster | mean_fractal_dim_per_cluster: This parameter is the average of the mean fractal dimensions calculated for each identified cell cluster. By normalizing the complexity measurement at the cluster level, it allows for comparative analysis of clusters across different patients or tissue patches. |
| yp01k80kt2kw | P,Tc,F,MFp | std_fractal_dim_per_cluster | std_fractal_dim_per_cluster: This parameter represents the standard deviation of the average fractal dimensions across cell clusters. It provides a measure of how much the complexity of cell boundaries varies between different clusters. |
| yp01k80kt2kw | P,Tc,F,MFp | mean_fractal_dim_plasma_cell | mean_fractal_dim_plasma_cell: This parameter indicates the average fractal dimension specifically for plasma cells located near the tumor boundary. It serves as a normalized measure to compare the morphological complexity of plasma cell boundaries against other cell types in the microenvironment. |
| yp01k80kt2kw | P,Tc,F,MFp | std_fractal_dim_plasma_cell | std_fractal_dim_plasma_cell: This parameter denotes the standard deviation of the fractal dimensions for plasma cells near the tumor boundary, assessing the variation in boundary complexity among plasma cells. |
| yp01k80kt2kw | P,Tc,F,MFp | mean_fractal_dim_t_cell_cd8 | mean_fractal_dim_t_cell_cd8: This parameter represents the mean fractal dimension calculated for cytotoxic T cells (CD8 positive) near the tumor boundary. It quantifies the average boundary complexity of these immune cells and assists in comparing their morphological features in different cases. |
| yp01k80kt2kw | P,Tc,F,MFp | std_fractal_dim_t_cell_cd8 | std_fractal_dim_t_cell_cd8: This parameter captures the standard deviation of fractal dimensions for cytotoxic T cells near the tumor boundary, highlighting the heterogeneity in their boundary irregularity. |
| yp01k80kt2kw | P,Tc,F,MFp | mean_fractal_dim_fibroblast | mean_fractal_dim_fibroblast: This parameter measures the average fractal dimension for fibroblasts near the tumor boundary. It provides a normalized metric that represents the typical irregularity of fibroblast cell boundaries, facilitating comparisons across patients. |
| yp01k80kt2kw | P,Tc,F,MFp | std_fractal_dim_fibroblast | std_fractal_dim_fibroblast: This parameter reflects the variability in the fractal dimensions observed in fibroblasts near the tumor boundary, indicating how consistently the fibroblast morphology manifests within the analyzed patches. |
| yp01k80kt2kw | P,Tc,F,MFp | mean_fractal_dim_myofibroblast_pdpn | mean_fractal_dim_myofibroblast_pdpn: This parameter represents the mean fractal dimension calculated for PDPN+ myofibroblasts near the tumor boundary. It offers a normalized measure of the complexity of these cells’ boundaries and assists in comparative analysis with other cell types. |
| yp01k80kt2kw | P,Tc,F,MFp | std_fractal_dim_myofibroblast_pdpn | std_fractal_dim_myofibroblast_pdpn: This parameter denotes the standard deviation of the fractal dimensions for PDPN+ myofibroblasts, reflecting how variable the boundary complexity is among these cells in the tumor microenvironment. |
| ys577yk6m402 | B,F,MFp,TU | B_cell_0_30 | B_cell parameters: Each parameter labeled 'B_cell_X_Y' measures the normalized percentage of B cells whose angular orientation, relative to the centroid of their nearest vessel, falls within a specific 30-degree segment (e.g., from 0 to 30 degrees, 30 to 60 degrees, etc.). The value is normalized by the total count of B cells, enabling comparison across different tumor patches. |
| ys577yk6m402 | B,F,MFp,TU | B_cell_30_60 | Fibroblast parameters: Each parameter labeled 'Fibroblast_X_Y' quantifies the normalized percentage of fibroblasts (specifically fibroblasts FSP1-) that lie within a defined 30-degree angular sector around the nearest vessel's centroid. This normalization by the total fibroblast count facilitates inter-case comparisons of their spatial distribution. |
| ys577yk6m402 | B,F,MFp,TU | B_cell_60_90 | Myofibroblast_PDPN parameters: Each 'Myofibroblast_PDPN_X_Y' parameter indicates the normalized percentage of PDPN-positive myofibroblasts positioned in a particular 30-degree bin relative to the centroid of their closest vessel. The normalization process ensures that the measurement reflects relative distribution independent of absolute cell numbers. |
| ys577yk6m402 | B,F,MFp,TU | B_cell_90_120 | Tumor_cell parameters: Each parameter under the 'Tumor_cell_X_Y' series captures the normalized percentage of tumor cells located within a specific 30-degree angular segment around the center of the nearest vessel. The percentage is derived by dividing the cell count in a given bin by the total tumor cell count, thereby allowing standardized comparisons across different regions. |
| ysubxwa9u50o | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | STROMA_EPITHELIUM_RATIO | STROMA_EPITHELIUM_RATIO is a normalized numeric parameter that represents the ratio of stromal cells to epithelial tumor cells. It is computed by dividing the total count of stromal cells by the epithelial cell count (with a small epsilon added to avoid division by zero), resulting in a dimensionless value that enables comparison across different patient cases and tissue patches. |
| ywogbwbo8i62 | Th | SPATIAL_ENTROPY_HELPER_T | SPATIAL_ENTROPY_HELPER_T is a normalized metric that measures the spatial entropy of the distribution of helper T cells (CD4+ T cells) within a tissue region. It is computed by dividing the tissue area into spatial bins, counting the helper T cells in each bin, calculating the Shannon entropy from the probability distribution of cell counts, and then normalizing this value by the maximum possible entropy (which is the logarithm of the number of bins that contain cells). This normalization, resulting in values between 0 and 1, allows for direct comparisons across different patient cases and tissue patches. |
| yxdk4zryfxt9 | Treg | AVG_MIN_DIST_TREG_TO_VESSEL_STROMA | This parameter represents the average minimal Euclidean distance between regulatory T lymphocytes (Tregs) and the nearest blood vessels within the stromal compartment of tumor tissue. It is calculated by measuring the distance from each Treg cell's nucleus to every vessel polygon, selecting the smallest distance for each Treg cell, and then averaging these minimal distances across all Treg cells present in each analyzed patch. The computed value, expressed in micrometers, is normalized across different patches or patient cases, ensuring comparability between them. |
| z156wpl7twp7 | F,Ff,MFp,M | fibroblast_wave_ratio | fibroblast_wave_ratio measures the relative distribution of normal fibroblast cells around epithelial clusters by computing the ratio of cells located in the outer ring (20-40 μm from the epithelial boundary) to those in the inner ring (0-20 μm). This ratio is a normalized numeric metric that reflects the extent of peripheral infiltration of fibroblasts, making it comparable across different patient cases. |
| z156wpl7twp7 | F,Ff,MFp,M | fibroblast_fsp1_wave_ratio | fibroblast_fsp1_wave_ratio quantifies the infiltration pattern of FSP1 positive fibroblasts by calculating the ratio of cells in the outer infiltration ring (20-40 μm from the epithelial boundary) relative to those in the inner ring (0-20 μm). This normalized numeric parameter is designed to assess the spatial distribution of an activated fibroblast subset and enable cross-patient comparisons. |
| z156wpl7twp7 | F,Ff,MFp,M | myofibroblast_pdpn_wave_ratio | myofibroblast_pdpn_wave_ratio assesses the spatial distribution of PDPN positive myofibroblasts by computing the ratio between the number of cells found in the outer ring (20-40 μm) and those in the inner ring (0-20 μm) around epithelial clusters. Being a normalized numeric value, it indicates the degree of myofibroblast infiltration, allowing for standardized comparison across tissue samples. |
| z156wpl7twp7 | F,Ff,MFp,M | macrophage_wave_ratio | macrophage_wave_ratio evaluates the infiltration behavior of macrophages by calculating the ratio of cells in the outer ring (20-40 μm) to those in the inner ring (0-20 μm) relative to the epithelial boundary. This parameter is numeric and normalized, thus ensuring that it is suitable for comparing macrophage peripheral infiltration patterns across different cases. |
| z1trsknj4kjz | MF | CV_PDPN_NEG_MF_NUCLEUS_CONVEXITY | CV_PDPN_NEG_MF_NUCLEUS_CONVEXITY represents the coefficient of variation of the nuclear convexity values of PDPN- myofibroblast cells in stromal compartments. It is calculated by dividing the standard deviation of the convexity values by their mean, thereby quantifying the relative variability and morphological diversity in the nuclear shape. |
| z1trsknj4kjz | MF | MEAN_PDPN_NEG_MF_NUCLEUS_CONVEXITY | MEAN_PDPN_NEG_MF_NUCLEUS_CONVEXITY is the average of the nuclear convexity values of PDPN- myofibroblasts in the stromal regions. It provides a central measure for the typical nuclear convexity across the cells. |
| z1trsknj4kjz | MF | STD_PDPN_NEG_MF_NUCLEUS_CONVEXITY | STD_PDPN_NEG_MF_NUCLEUS_CONVEXITY is the standard deviation of the nuclear convexity values among PDPN- myofibroblasts in stromal compartments. This parameter measures how spread out the convexity measurements are, reflecting variation in cell shape. |
| z1trsknj4kjz | MF | MIN_PDPN_NEG_MF_NUCLEUS_CONVEXITY | MIN_PDPN_NEG_MF_NUCLEUS_CONVEXITY indicates the smallest value observed for nuclear convexity among the PDPN- myofibroblasts in the stromal compartments, highlighting the lower bound of the shape descriptor. |
| z1trsknj4kjz | MF | MAX_PDPN_NEG_MF_NUCLEUS_CONVEXITY | MAX_PDPN_NEG_MF_NUCLEUS_CONVEXITY represents the largest nuclear convexity value in PDPN- myofibroblasts from the stromal compartments, documenting the upper bound for the measured cell shapes. |
| z1trsknj4kjz | MF | MEDIAN_PDPN_NEG_MF_NUCLEUS_CONVEXITY | MEDIAN_PDPN_NEG_MF_NUCLEUS_CONVEXITY is the median of the nuclear convexity values for PDPN- myofibroblasts in stromal regions. This robust statistic provides a central tendency measure that is less affected by outliers compared to the mean. |
| z466w60je98k | A,B,E,Ff,G,Th,Treg,TU | Average_Distance | Average_Distance represents the mean Euclidean distance between the centroids of spatial clusters of the three key cell types (granulocytes, FSP1+ fibroblasts, and antigen presenting cells). This metric is computed as an average over all pairwise distances between clusters, making it normalized for comparing different patient cases. Lower values indicate that the clusters are in closer proximity, which may be indicative of an altered tumor microenvironment. |
| z466w60je98k | A,B,E,Ff,G,Th,Treg,TU | Distance_Variation | Distance_Variation quantifies the standard deviation of the pairwise Euclidean distances calculated between the centroids of the spatial clusters. It provides a measure of the uniformity in the spatial organization of the key cell types. Since it is a normalized statistically derived value (variation across clusters), it allows for reliable comparisons across different patient cases, with lower values signifying a more uniform cluster distribution. |
| z6nutrbp82yc | Th,B | avg_min_distance_th_b | The parameter 'avg_min_distance_th_b' quantifies the spatial proximity between helper T lymphocytes and B lymphocytes by computing the average of the minimum Euclidean distances measured between these two cell types within tumor patches. The measure is derived by first calculating the minimum distance from each helper T cell to any B cell and vice versa, then combining these values into a single average. This numeric metric is normalized in the sense that it offers a consistent basis for comparison across different patient cases and tumor regions, thereby supporting analyses of coordinated adaptive immune responses. |
| z6w4h6xg73kg | TU,Th,Treg,B,P,M,E,A | median_distance | median_distance is a measure of the central tendency of the spatial distances calculated as the median of the minimum Euclidean distances from each tumor cell to the nearest endothelial or antigen-presenting cell. This parameter captures a normalized metric in the sense that it reflects a consistent and comparable spatial relationship between tumor and vascular or antigen-presenting cells across different patient cases. |
| z6w4h6xg73kg | TU,Th,Treg,B,P,M,E,A | composite_metric | composite_metric is a normalized composite parameter that adjusts the median spatial distance by incorporating the level of B cell and plasma cell infiltration. It is calculated by dividing the median distance by (1 + B_plasma_count), thereby providing a dimensionless measure that accounts for the influence of immune cell density on the spatial proximity between tumor cells and vascular/AP cells. |
| z77a1t1h3mgb | B,E,Ff,G,M,MFp,Th,Treg,TU | CO_ALIGNMENT_SCORE | CO_ALIGNMENT_SCORE is a normalized metric ranging from 0 to 1 that quantifies the alignment between fibroblast-endothelial cell pairs and nearby immune clusters. It is calculated by taking the mean angle between the cells' connecting vector and the vector pointing from their midpoint to the nearest immune cluster, dividing by 90, and subtracting from 1. A score of 1 indicates perfect alignment, while a score of 0 indicates random or poor alignment. |
| z77a1t1h3mgb | B,E,Ff,G,M,MFp,Th,Treg,TU | MEAN_ANGLE | MEAN_ANGLE represents the average of all angles (in degrees) computed between the vector connecting each fibroblast to its matched endothelial cell and the vector from their midpoint to the nearest immune cluster. This metric provides an overall measure of directional alignment across a tumor patch. |
| z77a1t1h3mgb | B,E,Ff,G,M,MFp,Th,Treg,TU | STD_ANGLE | STD_ANGLE is the standard deviation of the computed angles, offering insight into the variability and consistency of the angular alignment. A lower value indicates that the alignment across cell pairs is more consistent. |
| z77a1t1h3mgb | B,E,Ff,G,M,MFp,Th,Treg,TU | MIN_ANGLE | MIN_ANGLE records the smallest angle observed among all valid fibroblast-endothelial pairs, reflecting the instance of best alignment within the analyzed tumor region. |
| z77a1t1h3mgb | B,E,Ff,G,M,MFp,Th,Treg,TU | MAX_ANGLE | MAX_ANGLE records the largest angle observed among all valid fibroblast-endothelial pairs, indicating the worst-case deviation in alignment within the tumor patch. |
| z77a1t1h3mgb | B,E,Ff,G,M,MFp,Th,Treg,TU | MEDIAN_ANGLE | MEDIAN_ANGLE is the median value of the computed angles, providing a robust central measure that is less sensitive to extreme values, and helps in understanding the typical alignment behavior. |
| z9a5v2seq50o | Tc,Th,Treg,B,M,P,G,A | Tc_avg_dist | Tc_avg_dist measures the average spatial distance of CD8+ cytotoxic T cells from the epithelial-stromal boundary. This normalized metric is computed by summing the distances from individual T cells to the boundary and dividing by the number of such cells in each tumor patch, allowing for comparison between different patient cases. |
| z9a5v2seq50o | Tc,Th,Treg,B,M,P,G,A | Th_avg_dist | Th_avg_dist quantifies the average distance of CD4+ T helper cells to the boundary between tumor and stroma. It reflects the spatial positioning of these cells relative to the interface by averaging distance measurements for all detected T helper cells within each region. |
| z9a5v2seq50o | Tc,Th,Treg,B,M,P,G,A | Treg_avg_dist | Treg_avg_dist represents the mean distance of T regulatory cells from the epithelial-stromal boundary. It is computed by measuring the shortest distance from each regulatory T cell to the boundary and then averaging these distances, offering a normalized spatial distribution metric in a tumor patch. |
| z9a5v2seq50o | Tc,Th,Treg,B,M,P,G,A | B_avg_dist | B_avg_dist calculates the average distance of B cells from the tumor-stroma interface. This parameter is derived by computing the distances of individual B cells to the defined boundary and averaging them, providing insights into their clustering behavior relative to the tumor periphery. |
| z9a5v2seq50o | Tc,Th,Treg,B,M,P,G,A | M_avg_dist | M_avg_dist is the normalized metric that reflects the mean distance of macrophages from the epithelial-stromal boundary. It is obtained by averaging the minimal distances calculated for each macrophage, thereby indicating their spatial relationship to the tumor boundary. |
| z9a5v2seq50o | Tc,Th,Treg,B,M,P,G,A | P_avg_dist | P_avg_dist measures the average distance of plasma cells to the epithelial-stromal interface. The parameter is computed by aggregating the distances of individual plasma cells to the boundary and normalizing by their count within each tumor patch. |
| z9a5v2seq50o | Tc,Th,Treg,B,M,P,G,A | G_avg_dist | G_avg_dist denotes the average spatial distance of granulocytes from the tumor-stroma boundary. It is calculated by taking the mean of all individual distance measurements from granulocytes to the boundary, providing a normalized metric to compare across different patient patches. |
| z9a5v2seq50o | Tc,Th,Treg,B,M,P,G,A | A_avg_dist | A_avg_dist quantifies the average distance of antigen presenting cells from the epithelial-stromal boundary. This parameter is determined by averaging the distances of each antigen presenting cell from the defined boundary, serving as a normalized spatial indicator for immune cell distribution. |
| z9ohhkmh3n6a | Tc,Th,Treg,M,MFp,MF | MEDIAN_NUCLEUS_AREA_DIFF_IMMUNE_MYOFIBRO | MEDIAN_NUCLEUS_AREA_DIFF_IMMUNE_MYOFIBRO represents the difference between the median nucleus area of immune cells and the median nucleus area of myofibroblast cells in regions of high tumor density. This parameter captures the relative divergence in nuclear size between these two cell groups under tumor-induced stress. |
| z9ohhkmh3n6a | Tc,Th,Treg,M,MFp,MF | MEDIAN_NUCLEUS_AREA_IMMUNE | MEDIAN_NUCLEUS_AREA_IMMUNE denotes the median area of the nuclei of immune cells (including various T-cell subtypes and macrophages) in patches where tumor cell density is high. It provides a robust measure of typical nuclear size within the immune compartment. |
| z9ohhkmh3n6a | Tc,Th,Treg,M,MFp,MF | MEDIAN_NUCLEUS_AREA_MYOFIBRO | MEDIAN_NUCLEUS_AREA_MYOFIBRO indicates the median nucleus area for myofibroblast cells in high tumor density regions. It serves as a central measure to understand the typical nuclear morphology of these cells under the influence of the tumor microenvironment. |
| z9ohhkmh3n6a | Tc,Th,Treg,M,MFp,MF | MEAN_NUCLEUS_AREA_IMMUNE | MEAN_NUCLEUS_AREA_IMMUNE refers to the average nucleus area of immune cells located in high tumor density regions. This parameter is useful to observe variations in the overall cell size profile compared across patient cases. |
| z9ohhkmh3n6a | Tc,Th,Treg,M,MFp,MF | MEAN_NUCLEUS_AREA_MYOFIBRO | MEAN_NUCLEUS_AREA_MYOFIBRO represents the average nucleus area of myofibroblast cells in areas of high tumor density. It provides insights into the central tendency of nuclear sizes for these cells under tumor stress conditions. |
| z9ohhkmh3n6a | Tc,Th,Treg,M,MFp,MF | STD_NUCLEUS_AREA_IMMUNE | STD_NUCLEUS_AREA_IMMUNE is the standard deviation of nucleus areas for immune cells in high tumor density regions. This parameter quantifies the variability of nuclear sizes, thereby highlighting the heterogeneity within the immune cell population. |
| z9ohhkmh3n6a | Tc,Th,Treg,M,MFp,MF | STD_NUCLEUS_AREA_MYOFIBRO | STD_NUCLEUS_AREA_MYOFIBRO is the standard deviation of the nucleus areas of myofibroblast cells in regions with a high density of tumor cells. It measures the dispersion in nuclear size, indicating heterogeneity in the myofibroblast population. |
| zbdn6b6c69pr | MF,MFp,M,A,G,TU | NUCLEAR_AREA_DIFF_PDPN_POS_NEG | NUCLEAR_AREA_DIFF_PDPN_POS_NEG represents the normalized difference in the average nuclear area between PDPN positive myofibroblasts and PDPN negative fibroblasts in the stroma of breast cancer tissue. It is calculated by subtracting the average nuclear area of PDPN negative fibroblasts from that of PDPN positive myofibroblasts, providing a comparison metric across different tumor regions. |
| zbdn6b6c69pr | MF,MFp,M,A,G,TU | AVG_NUCLEAR_AREA_PDPN_NEG | AVG_NUCLEAR_AREA_PDPN_NEG is the normalized average nuclear area (measured in square micrometers) of PDPN negative fibroblasts located in the stroma. It is computed by averaging the nuclear areas from individual cell polygons, allowing for direct comparisons between different patient cases. |
| zbdn6b6c69pr | MF,MFp,M,A,G,TU | AVG_NUCLEAR_AREA_PDPN_POS | AVG_NUCLEAR_AREA_PDPN_POS is the normalized average nuclear area (measured in square micrometers) of PDPN positive myofibroblasts within the stromal compartment. This parameter is derived by averaging the nuclear areas of the cells and is useful for comparing morphological differences across tumor patches from various patients. |
| zj2oc4udnby2 | TU,Tc,Th,Treg,B,M | IMMUNE_SYNERGY_SCORE | IMMUNE_SYNERGY_SCORE represents a normalized measure of the immune environment by calculating the difference between the number of activating immune cells (CD8 T-cells, CD4 T-cells, and B cells) and the number of suppressive immune cells (T-reg cells and macrophages) around tumor cells, divided by the total number of tumor cells. This score provides a comparative value across patient cases and tissue patches. |
| zj2oc4udnby2 | TU,Tc,Th,Treg,B,M | ACTIVATING_IMMUNE_RATIO | ACTIVATING_IMMUNE_RATIO is the normalized proportion of activating immune cells relative to the total immune cells present near tumor cells. It reflects the balance of beneficial immune responses within the tumor microenvironment and facilitates comparisons between different cases. |
| zj2oc4udnby2 | TU,Tc,Th,Treg,B,M | SUPPRESSIVE_IMMUNE_RATIO | SUPPRESSIVE_IMMUNE_RATIO indicates the proportion of suppressive immune cells among all immune cells in proximity to tumor cells. As a normalized ratio, it enables effective comparison of the suppressive aspects of the immune response between different patient samples. |
| zj2oc4udnby2 | TU,Tc,Th,Treg,B,M | AVG_ACTIVATING_PER_TUMOR | AVG_ACTIVATING_PER_TUMOR is the average count of activating immune cells detected per tumor cell. This metric is normalized by the number of tumor cells, providing a per-cell measure that can be used to compare the intensity of tumor-associated immune activation across different samples. |
| zj2oc4udnby2 | TU,Tc,Th,Treg,B,M | AVG_SUPPRESSIVE_PER_TUMOR | AVG_SUPPRESSIVE_PER_TUMOR is the average number of suppressive immune cells found around each tumor cell. This normalized metric allows for direct comparison of the degree of immune suppression among various tumor regions. |
| zj2oc4udnby2 | TU,Tc,Th,Treg,B,M | AVG_TOTAL_IMMUNE_PER_TUMOR | AVG_TOTAL_IMMUNE_PER_TUMOR reflects the average total immune cell count (including both activating and suppressive cells) per tumor cell. This parameter is normalized to the tumor cell count, offering a comprehensive view of the overall immune cell presence around tumor cells and enabling cross-sample comparisons. |
| zppsx211lhe4 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | fragmentation_index | fragmentation_index: This parameter measures the ratio of the number of contiguous clusters of epithelial tumor cells to the total number of epithelial tumor cells. It is a normalized metric that enables comparison across different tumor patches, with higher values indicating increased fragmentation and potentially more invasive behavior. |
| zppsx211lhe4 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | non_epithelial_to_epithelial_ratio | non_epithelial_to_epithelial_ratio: This parameter represents the ratio of the total count of non-epithelial cells (cells that are not classified as epithelial tumor cells) to the total count of epithelial tumor cells. It is normalized, capturing the relative contribution of the tumor microenvironment to the overall cellular composition of the tumor region. |
| zppsx211lhe4 | TU,Tc,Th,Treg,B,P,M,G,MFp,MF,Ff,F,E,A | weighted_fragmentation_index | weighted_fragmentation_index: This parameter is derived by multiplying the fragmentation index by the expression (1 + non_epithelial_to_epithelial_ratio). It integrates both the fragmentation of the epithelial cells and the influence of surrounding non-epithelial cells, providing a normalized metric that can be used to predict invasive behavior across different patient cases. |
| zrjyna9uwsi3 | Tc,Th,Treg,E | overall_clustering_coefficient | overall_clustering_coefficient: This parameter measures the average clustering coefficient across all analyzed cells in the network, quantifying the degree to which cells tend to group or cluster together. It is a normalized ratio that enables comparison across different patient cases by reflecting the overall spatial interconnectedness of the cell network. |
| zrjyna9uwsi3 | Tc,Th,Treg,E | cd8_clustering_coefficient | cd8_clustering_coefficient: This parameter represents the average clustering coefficient calculated specifically for CD8+ cytotoxic T cells. It provides a normalized measure of the extent to which these cells form local clusters, allowing for comparison of their spatial organization across different samples. |
| zrjyna9uwsi3 | Tc,Th,Treg,E | cd4_clustering_coefficient | cd4_clustering_coefficient: This parameter gives the average clustering coefficient for CD4+ helper T cells. It is a normalized ratio that indicates the tendency of these cells to cluster together within the tissue, supporting comparisons across various patient patches. |
| zrjyna9uwsi3 | Tc,Th,Treg,E | endothelial_clustering_coefficient | endothelial_clustering_coefficient: This parameter denotes the average clustering coefficient for endothelial cells. By measuring the degree to which these cells are interconnected in the spatial network, it serves as a normalized metric that can be compared across different tumor regions. |
| zrjyna9uwsi3 | Tc,Th,Treg,E | mixed_cluster_percent | mixed_cluster_percent: This parameter expresses the percentage of clusters that contain at least two different cell types. It is a normalized percentage that provides insight into the heterogeneity of cell clusters, thereby reflecting the level of diverse cellular interactions in the microenvironment. |
| zrjyna9uwsi3 | Tc,Th,Treg,E | cd8_near_vessels_percent | cd8_near_vessels_percent: This parameter calculates the percentage of CD8+ T cells that are in close proximity to endothelial cells. Being a normalized percentage, it enables the assessment of how frequently these T cells interact with blood vessels across different patient cases. |
| zrjyna9uwsi3 | Tc,Th,Treg,E | cd4_near_vessels_percent | cd4_near_vessels_percent: This parameter measures the percentage of CD4+ helper T cells that are located near endothelial cells. It provides a normalized value that can be compared between different tumor regions to evaluate the spatial relationship between these cells and the vasculature. |
| zrjyna9uwsi3 | Tc,Th,Treg,E | treg_near_vessels_percent | treg_near_vessels_percent: This parameter denotes the percentage of regulatory T cells that have spatial connections with endothelial cells. As a normalized metric, it offers a means to compare the potential interaction or proximity of these cells to blood vessels across various samples. |