Extended Data Fig. 10: Classical morphometric do not recapitulate MorphOMICs observations.

a: Box plots for the selected features process length, number of branches, terminal- and branching points of control (n_♀= 926, n_♂= 894), and CK-p25_1w (n_♀= 219, n_♂= 194), CK-p25_2w (n_♀= 264, n_♂= 492), CK-p25_6w (n_♀= 858, n_♂= 462) mice (1-, 2- and 6-weeks after doxycycline withdrawal, respectively) in the frontal cortex (FC). 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 showing 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). b, c: Bootstrapped and UMAP representations of an extended set of morphological classifiers (see Supplementary Table 3) applied to females (left) and males (right) in 5xFAD (b) and developmental time points (c) with highlighted frontal cortex (calculation without cochlear nucleus and cerebellum for simplicity). Each dot represents an averaged extended set of morphometric classifiers across 30 microglia that form the bootstrap population. d: Morphometric UMAP of the bootstrapped comprehensive 27 morphometrics set showing regional heterogeneity of microglia in adult healthy mice. Brain regions are color-coded. e: Reference atlas for each brain region represented as Palantir reconstruction containing both sexes.n_samples = 300(B-D) and n_samples = 200 (E) per condition (see also Methods: Average and bootstrapped persistence images).