Fig. 4: Generation of axonal and dendritic probability density functions.
From: Full-scale scaffold model of the human hippocampus CA1 area
a, 3D meshes of CA1 (pink), CA2 (light green) and subiculum (dark green) generated by stacking the segmentation boundaries of hippocampal subregions. b, Left: orientation planes were generated for each PC (black spots) according to the relative distances of PCs from CA2 and subiculum (Methods). Axons (black dotted line) are created in the orientation plane and project towards subiculum adapting to CA1 surface gyrification (Methods). The inset shows the reconstruction from experimental data of the entire morphology of a murine CA1 PC (Janelia Research Campus http://mouselight.janelia.org/). Note the directionality of PC axons from CA3 side to subiculum. c, Schematic representation of the axon modelling procedure. The points of the CA1 surface laying on the orientation plane are connected through a spline line defining a tubular volume (150 μm radius). d. Left: example of modelled PC axons (orange and blue thick lines) running in the SO from PC somas placement towards subiculum. Right: 100 randomly selected PC axons running in the external part of the SP from PC placement towards subiculum. e. Left: realistic morphology of PCs (basal dendrites in brown and apical in blue, adapted from ref. 53), oriented within a transversal CA1 hippocampal slice. Right: the probability density functions are represented as two cones with colour code respecting the realistic morphology.
