The 24 swc files in this directory were generated numerically based on the 24 prototypes - CA3 pyramidal cells from the Amaral archive (one virtual neuron for each prototype). Labels (a-x) in the figure correspond to the digital file names that contain remodeled virtual cells. As in the original Amaral files, apical dendrites in the remodeled files have kind=3, and basal dendrites have kind=4 (second field in the swc format). The name of the original data file for each remodeled cell can be found in the following table:
In each figure (a-x), the 2 panels show the X-Y view of the original (bottom) and the remodeled (top) cells. X and Y are not the original axes, but the first two principal components (singular values) of the distribution of nodes. Therefoe, each shown planar projection is a projection that has a maximal spread. Cells are aligned with their basal dendrites pointed right. The scale (different on each plot) can be determined based on the distance (600 microns) between the two somata of each pair. The remodeling algorithm and further details are given in [1] (Figure 5). In brief, the algorithm [1] consists of 2 steps: (1) extracting the dendrogram from the original cell, and (2) embedding the dendrogram into 3D, starting from the soma. During step (2), a random orientation for each dendritic segment is generated based on a linear combination of the parent link direction and the direction toward the soma.
References:
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