Extended Data Fig. 3: Inferred spatial cell type distributions using AMBA volumetric ISH.

a, Inferred spatial distribution of three neuronal cell types, by correlating transcriptomic profiles with Allen Mouse Brain Atlas (AMBA-ISH), on eight a-p (left-to-right) sections, with amygdala nuclei labeled. For every cluster and every voxel, a correlation coefficient heatmap is shown (dark, high; white, low). b, Spatial correlation of all amygdala neuron clusters with the dissected amygdala nuclei, related or neighboring regions, and other higher-order gray matter structures. Regions are sorted by correlation similarity, cell types by dendrogram order. Region names are colored according to the AMBA convention; regions that were not (fully) dissected are in italic; higher-order amygdala regions are in bold. c, Up: Neuronal cell type taxonomy in dendrogram order of scRNA-seq clusters (note; VGLUT2 switched with VGLUT1 compared to Fig. 1), and below; neuronal cell type taxonomy by regional correlation; that is, cell types are arranged according to similarity in correlation with regions analyzed in b. The dendrogram is colored by cell class, ‘spatial clusters’ (that is cell types most strongly correlated in their spatial enrichment) with highest correlating regions indicated on dendrogram branches. Cell types are linked between the two classifications to reveal the relation of their scRNA-seq and spatial clustering.