Extended Data Fig. 1: Classic morphometry analysis and intrinsic variability of microglial morphology.

a: Box plots for the following morphometric features: process length, number of branches, and terminal and branching points for traced adult C57BL/6J microglia across different brain regions color-coded: CB (cerebellum, n = 299), CN (cochlear nucleus, n = 498), FC (frontal cortex, n = 926), DG (dentate gyrus, n = 902), OB (olfactory bulb, n = 796), S1 (somatosensory cortex, n = 719), SN (substantia nigra, n = 1050) from at least six animals. For number of animals per condition and region see also Supplementary Table 5. Box denotes first and last quartile with central line indicating the median. Whiskers: range of quantities. Open circle: outliers. Next, matrices with color-coded p-values for the pairwise comparison of each morphometric. Kruskal-Wallis test, Bonferroni correction using Dunn’s test, * p < 0.05, ** p < 0.01 (see Supplementary Table 1, 3). b: Example of a 3D-traced microglia and its conversion to a persistence image. Top: left, Imaris-traced skeleton of a microglia. Scale bar: 10 µm. Right, formatted rooted microglia tree, which is used for the persistence plots. Bottom: persistence barcode (left), persistence diagram (middle), and persistence image (right) exactly matching the rooted tree. c: Hierarchically-ordered heat map for pairwise TMD intrinsic distances between average persistence images from microglia across brain regions from Fig. 1a. d-e: UMAP plots of the entire microglial population size (grey) with color-highlighted brain regions (d) or animals (e). Each dot represents a single persistence image. (e) Triangle and circle for females and males, respectively. Each animal is color-coded.