Fig. 3: Cell type classification of large and small cell fragments via aggregated embeddings.

a, 3D renderings of representative proofread neuron and glia cells, for a selected subset of the types used in the mouse and human datasets. The pyramidal cell axon is cut off to fit. Cells are oriented from white matter (WM) to pia. b, Rendering of representative cutouts from a pyramidal dendrite (top inset) and axon (bottom inset). Different size cutouts are defined by the skeleton node aggregation radius R. c, Cell type classifiers are trained on top of SegCLR embeddings after aggregation into a mean embedding over the cutout. d, Cell typing performance of shallow ResNet classifiers over different aggregation radii for the six labeled cell types in the human dataset. Zero radius corresponds to a single unaggregated embedding node. Error bars are s.d. (n = 20 subsamples). See Supplementary Table 2 for the number of training samples per class. e, Confusion matrix for the 6-class human cell type task at a 10 μm aggregation radius. GT, ground truth. f, Illustration of SegCLR cell type predictions over the extent of a single basket cell from the mouse test set. The orange areas are predicted correctly, while the sparse black areas show mispredictions. g, Cell typing performance for the mouse dataset. The 13-class task (black) uses all of the ground truth-labeled classes, while the 10-class task (green) combines all pyramidal cell labels into a single class. The 6-class task (blue) further reduces the neuronal labels into excitatory and inhibitory groups, comparable to the labels available on the human dataset (d). Error bars are s.d. (n = 20 subsamples). See Supplementary Table 2 for the number of training samples per class. h, Confusion matrix for the mouse 13-class cell type task at a 25 μm aggregation radius. Colored boxes indicate the group of four pyramidal cell types that were collapsed into the 10-class task, and the five excitatory and four inhibitory types collapsed into the 6-class task in g. Abbreviations: AC, astrocyte; BC, basket cell; BPC, bipolar cell; E, excitatory neuron; I, inhibitory interneuron; MC, Martinotti cell; MGC, microglia cell; NGC, neurogliaform cell; OGC, oligodendrocyte cell; OPC, oligodendrocyte precursor cell; P2–6, cortical layer 2–6 pyramidal cell; THLC, thalamocortical axon. Scale bars: a, neuronal 100 μm, glia 25 μm; b,f, 100 μm;.