HiPR-FISH Spatial Mapping of Cheese Rind Microbial Communities

This dataset is associated with this HiPR-FISH Spatial Mapping of Cheese Rind Microbial Communities pub from Arcadia Science.

HiPR-FISH spatial imaging was used to look at the distribution of microbes within five distinct microbial communities growing on the surface of aged cheeses. Probe design and imaging was performed by Kanvas Biosciences. 

This dataset includes the following:

• For each field of view (roughly 135µm x 135µm; 7 FOVs per each cheese specimen):
  • A fluorescence intensity image (*_spectral_max_projection.png/.tif).
  • A pseudo-colored microbe-labeled image (*_identification.png/.tif).
  • A data frame contains each identified microbe's identity, position, and size (*_cell_information.csv).
  • A segmented mask for microbiota (*_segmentation.png/.tif)
  • A spatial proximity graph for each species close to each other, showing the spatial enrichment over random distribution (*_spatialheatmap.png).
  • A corresponding data frame used to generate the spatial proximity graph (*_absolute_spatial_association.csv) and dataframe for the average of 500 random shuffles of the taxa (*_randomized_spatial_association_matrix.csv). 
• For each cheese specimen:
  • A widefield image with FOVs located on the image (*_WF_overlay.png).
• In general:
  • A png showing the color legend for each species. (ARC1_taxa_color_legend.png)
  • A data frame showing the environmental location of each FOV in the cheese (RIND/CURD) and the location of each FOV relative to FOV 1. (ARC1_Cheese_Map.csv).
  • A vignette showing an example of each cell and its false coloring according to its taxonomic identification (ARC1_detected_species_representative_cell_vignette.png).
  • Sequences used as input in probe design (16S_18S_forKanvas.fasta).
  • A CSV file containing the sequences that belong to each ASV (ARC1_sequences_to_ASVs.csv).
  • Plots of log-transformed counts for each microbe detected across all FOVs, and broken down for each cheese (*detected_species_absolute_abundance.png).
  • CSVs containing pairwise correlation of FOVs based on spatial association (ARC1_spatial_association_FOV_correlation.csv) and microbial abundance (ARC1_abundance_FOV_correlation.csv).
  • Plots of spatial association matrices, aggregated for different cheeses and different locations (RIND vs CURD) (*samples_*loc_relative_spatial_association.png).
  • CSV containing the principle component coordinates for each FOV (ARC1_abundance_FOV_PCA.csv, ARC1_spatial_association_FOV_PCA.csv).
  • CSV containing the mean fold-change in number of edges between each ASV and the corresponding p-value when compared to the null state (random spatial association matrices) (ARC1_spatial_enrichment_significance.csv).