Fig. 2

High-resolution functional structures of mouse PDOX brain sections can be identified using unsupervised clustering and automated cell type identification based on spatial gene expression. a Unsupervised clustering of mouse spots from cerebellum regions in PDOX sections based on gene expression. By this data-driven approach, each cluster precisely corresponded to known anatomical layers of mouse cerebellum. b Heat map of cluster marker genes depicts the top five differentially expressed genes in each cluster. c Spot gene enrichment scores of top ten most differentially expressed genes in each cluster, consistent with clustering results shown in a, but with additional information on gene expression heterogeneity within each cluster. d High-resolution cell types identified by reference-based annotation (see ‘Methods’) were concordant with and expanded upon pathological annotation of the H&E sections. Independent annotations by a brain pathologist for the H&E tissue image are shown as close contours overlaid with the mouse/mix spot cell types. Sample control C is shown as a representative. d1–d4 Enlarged regions of interest from d (red boxes) showing mouse cell types consistent with distinct histological features, but with higher resolution reflecting important heterogeneity. d1 Dominant cell types indicated at each layer are as expected, with oligodendrocyte precursor cells in the white matter (inner-layer), granule and unipolar brush cells in the granule layer (dark, middle layer), and Purkinje cells in the molecular layer (outer layer). d2 ‘Macrophage with Hemosiderin’ pathological feature contained exclusively meninges and microglia. d3 ‘Mouse macrophage/lymphocytes’ area was predominantly astrocytes, microglia and meninges. d4 ‘Mouse meningeal arteries’ corresponded to vasculature cell types; meninges, endothelial cells, pericytes and microglia. IGL internal granule layer, ML molecular layer, OPC oligodendrocyte precursor cells, PJ Purkinje, WM white matter