case_images: PMC4701943_01
case_images: (A) Intracellularly injected layer III pyramidal neuron of the human cingulate cortex visualized in 3D from high-resolution confocal stacks of images. (B) Three-dimensional reconstruction of the complete morphology of the cell shown in (A). (C,D) Higher magnification images of (A,B), respectively, showing basal dendritic segments to illustrate the reconstruction of the dendritic shafts and spines. Scale bar (in D): 100 mum in (A,B) and 20 mum in (C,D).
case_images: fnana-09-00159-g001.jpg
case_images: PMC4701943_01_fnana-09-00159-g001.jpg
case_images: F1
case_images: The injected cell was fully imaged at high magnification using tile scan mode in a Leica TCS 4D confocal scanning laser attached to a Leitz DMIRB fluorescence microscope (Figure 1). Dendritic shafts and spines were individually reconstructed in 3D from the high-resolution confocal stacks of images (Figures 1C,D) using Imaris 7.6.5, Filament Tracer module (Bitplane AG, Zurich, Switzerland).
case_images: Content-Based Information Retrieval (CBIR) system operation scheme.
case_images: fnana-09-00159-g002.jpg
case_images: PMC4701943_01_fnana-09-00159-g002.jpg
case_images: F2
case_images: Figure 2 depicts the main operations involved in a CBIR system.
case_images: Graphical user interface (GUI) of PyramidalExplorer showing the cell comparison query result concerning Spine Area, from the human pyramidal neuron in a global view (A) and in a zoom in view (B). Values are represented by color code. Red colors represent highest values whereas blue colors represent the lowest values. White frame in the main window highlights the spine visualized in the Detail viewer widget.
case_images: fnana-09-00159-g003.jpg
case_images: PMC4701943_01_fnana-09-00159-g003.jpg
case_images: F3
case_images: The graphical user interface (GUI) comprises a main window and four additional auxiliary widgets (Figure 3A). The user can interact with the whole scenario using the mouse for pan, rotate and zoom operations (Figure 3B). Color codes are also mapped in the Score column as a visual reference to highlight the level of similarity achieved with a particular score (see Figures 3 and 4). Figure 3A shows the result of applying a Cell Distribution query, concerning the Spine Area. Figures 3A and 4A show the whole dendritic tree, but shafts can be hidden if users want to focus only on the spines (i.e., assigning a transparent color to the dendritic shaft).
case_images: Graphical user interface (GUI) of PyramidalExplorer showing the spine comparison query results concerning Spine Area, from the human pyramidal neuron in a global view (A) and in a zoom in view (B). Values are represented by color code. Red represents the most similar spines with respect to the query set (shown at the bottom, right-hand corner), while blue shows the most different spines. This query set specifically displays the comparison of one selected spine (which is also shown in the Detail viewer widget) with the most similar spines of the dataset. White frame in the main window highlights the spine visualized in the Detail viewer widget.
case_images: fnana-09-00159-g004.jpg
case_images: PMC4701943_01_fnana-09-00159-g004.jpg
case_images: F4
case_images: Color codes are also mapped in the Score column as a visual reference to highlight the level of similarity achieved with a particular score (see Figures 3 and 4). By contrast, Figure 4A shows the result of applying a Spine Comparison query to the spine area. Figures 3A and 4A show the whole dendritic tree, but shafts can be hidden if users want to focus only on the spines (i.e., assigning a transparent color to the dendritic shaft). When Spine Comparison is selected, the image of the query set defined by the user is displayed (Figures 4A,B; bottom, right-hand corner).
case_images: Cell comparison query result from the human pyramidal neuron concerning Spine Volume (A); Spine Volume and Length (B,C); Maximum Diameter and Mean Neck Diameter (D,E); and Membrane Potential Peak (F). Values are represented by color code. Red colors represent the highest values whereas blue colors represent the lowest values. Higher magnification images of the apical dendrites are shown on the right (inset). Arrows indicate representative spines of the highest values, which are also shown on the Detail viewer widget at the bottom right. See results for further details.
case_images: fnana-09-00159-g005.jpg
case_images: PMC4701943_01_fnana-09-00159-g005.jpg
case_images: F5
case_images: For example, we can interactively discover that the spines with the largest volumes are found in the main apical dendrite, while some :but not all: collateral and basal dendrites have a particularly high percentage of large spines (Figure 5A). If we additionally select the Length feature, we can visualize the position of the largest and longest spines (Figure 5B), which is different from the position of the largest and shortest spines (Figure 5C). As another example, if we select Maximum Spine Diameter and Spine Neck Mean Diameter, we can visualize the position of the spines with the largest heads and the thinnest necks (Figure 5D), which have a different distribution in the arbor from those which do not have the largest heads and have the thickest necks (Figure 5E). As shown in Figure 5F, particular dendrites display different membrane potential peak values, as do particular dendritic segments within the same dendrite.