Fig. 3: Cell morphology spaces summarize cell shapes across heterogeneous cell types.

a UMAP representation of the cell morphology space of 70,510 cells from a cubic millimeter volume of the mouse visual cortex profiled by the MICrONS program using two-photon microscopy, microtomography, and serial electron microscopy⁴³. The representation is colored by the cell populations identified by clustering of the cell morphology space. The morphology of randomly sampled cells from several populations is shown for reference. The magnification is indicated in cases where the morphology of the cells has been zoomed in to facilitate visualization. b The position of 185 cells that were manually annotated by the MICrONS program is indicated in the UMAP representation, showing consistency with the structure of the cell morphology space. c The UMAP representation of the cell morphology space is colored by the cortical layer of each cell. The morphology space recapitulates morphological differences between neurons and astrocytes from different cortical layers. d The part of the UMAP representation corresponding to astrocytes is colored by the volume of the minimum-size box containing the astrocyte. Astrocytes in the lower part of the UMAP have smaller dimensions than at the top. For reference, the morphology of 4 astrocytes is also shown. e Boxplot summarizing the distribution of the angle of the major axis of astrocytes from different layers with respect to the pial surface (n = 4763 cells). Astrocytes from layer 2/3 are elongated perpendicularly with respect to the pial surface. For reference, the part of the UMAP representation corresponding to astrocytes colored by the cortical layer each also shown. Boxplots denote the median (line), interquartile range (box), min(max(x), Q3 + 1.5 IQR) (upper whisker), and max(min(x), Q1 − 1.5 IQR) (lower whisker). f The ability of CAJAL to identify morphological differences between neurons of different molecular type and T cells from different anatomical locations is evaluated in comparison to four general algorithms for cell morphometry and according to three different metrics of performance. The dashed line indicates the accuracy of a random classifier. CTS score: cell-type separation score. Source data are provided as a Source data file.