Fig. 2: Visualization of soma depths and cortical layer assignments of excitatory neuronal morphologies showing mostly a continuum with distinct clusters only in deeper layers.

A Top view of the EM volume with approximate visual areas indicated. All neurons with their soma origin within the red boundary were used for analysis. B Distribution of complete neurons (N) and fragments (F) along cortical depth as determined by our classifier based on the morphological embeddings. C Distribution of excitatory neurons (E) and interneurons (I) along cortical depth. D Classifier prediction for cortical layer origin based on the learned morphological embeddings. E t-SNE embedding (perplexity = 300) of the vector embeddings of excitatory neuronal morphologies colored by the respective soma depth (in μm) of the neurons relative to the pia (n = 32,571). F t-SNE embedding colored by cortical layer assignments as predicted by a cross-validated classifier trained on the morphological embeddings as features and a subset of manually labeled excitatory neurons (n = 922). G Cross-section of the brain volume depicting soma positions of neurons colored by their assigned cortical layer. Cortical layer thicknesses for primary visual cortex (V1) (left) and higher visual areas (HVA) (right) given as mean  ± standard deviation. H t-SNE embedding of excitatory neuronal morphologies colored by expert-defined cell types. I Example morphologies of the expert-defined cell types. Source data are provided as a Source Data file.