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. 2022 Sep 30;25(10):1379–1393. doi: 10.1038/s41593-022-01167-6

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 3 — a: Heat-map of classification accuracy between pairs of brain regions using stable ranks for different bootstrap sizes. Numbers indicates the percentage of microglia correctly assigned in the classification task, averaged over 10 repeated cross-validations. 1, perfect assignment; 0.5 random assignment. b: Sholl curves for each brain region. Data are presented as mean number of processes (points) ± SD that intersect with a series of concentric Sholl spheres centered on the soma and spaced at 5 µm. For number of animals per condition and region see Supplementary Table 4, 5. c: Bootstrapped and UMAP visualized Sholl-analyzed microglia, color-coded for each brain region. Each dot represents a bootstrapped Sholl analysis. Each plot has a set radius step size (1, 3, 5, 7, 10 µm). Olfactory bulb (OB), frontal cortex (FC), dentate gyrus (DG), somatosensory cortex (S1), substantia nigra (SN), cochlear nucleus (CN), and cerebellum (CB). n_samples = 300 per condition (see also Methods: Average and bootstrapped persistence images). SD: standard deviation.