Fig. 2: Formulation of neuronal connectivity and difference between morphological features and connectivity features of single neurons.

a, A schematic overview of the definition of arbor domains and potential connectivity. Left: neurons are categorized into soma-location types (s-types) based on their cell body location in the CCFv3 anatomical region. Within each s-type, morphological coordinates are clustered using a GMM, forming arbor domains. A dendritic arbor domain contains a major number of somas. Right: overlapping voxels between axonal and dendritic domains define the potential connectivity. b, A schematic illustration of dendritic arbor domains for SSp neurons in middle sections of the CCFv3 atlas outline (left, coronal half-view; right, sagittal half-view). c, A heat map of potential connectivity for VPM neurons, which project to SSp heavily. The horizontal axis indicates the dendritic domains (as indicated by the prefix ‘d’) with renumbered identifiers denoting the domain center coordinates in b (see Supplementary Table 4 for a complete list of domains); only the top-25 domains with the greatest variances are shown for clarity, while the entire feature vector was used in clustering. The vertical axis indicates the clustered VPM neurons. The dendrogram on the left shows hierarchical clustering of the potential connectivity feature vectors of neurons. The orange lines indicate cluster boundaries in the heatmap. The color bar shows the number of overlapping voxels between a neuron of interest and dendritic domains. d, Horizontal view of VPM neurons overlaid on the CCFv3 contour colored by the clusters obtained from potential connectivity. e, A comparison of clustering results based on morphology features only (top) and based on joint feature vectors by concatenating morphology and connectivity features (bottom). Top left: a scatter plot of MOp, SUB and VPL s-types. The horizontal axis indicates the total length of the neurons in μm. The vertical axis indicates the maximum branch order. Bottom left: 3D scatter plot of the total length, maximum branch order and first component of a PCA of the potential connectivity matrix. The c-types obtained are colored with different shades of each s-type color. Right: heat maps showing the overlap between paired s-type point clouds in scatter plots, with color indicating the misclassification percentage using SVM classification.