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. 2022 Jul 5;39(2):213–244. doi: 10.1007/s12264-022-00897-8

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© The Author(s) 2022

Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 6 — Phenotypic and functional heterogeneity of microglia in the glial scar. A Spatial maps showing the distribution of 6 microglia clusters in the glial scar at different time points after injury. B Bar plot showing the fraction of all spots comprising each subpopulation at different time points after injury. C Jitterplot showing the top 5 differentially-expressed genes (DEGs) in each subpopulation. D Definition of the boundary areas to study the interaction between two neighboring microglia clusters in the scar. Regions 2 spots wide along the boundary lines in each cluster are selected. E Dot plot showing the mean interaction scores between neighboring clusters at the boundaries for ligand-receptor pairs. The ligand-receptor pairs are listed on the left. The size of a circle denotes the p-value, and the color denotes the mean interaction score. F, G Trajectory of microglia in the glial scar. H Heat map showing the changes in genes expression along a spatial trajectory. I Correlation of the expression of CD74, Gpr17, and laminin with pseudotime. J Spatial maps showing the GSVA score of the cardiac muscle contraction pathway enrichment in cluster 1 cells at different time points after injury. K Violin plots and spatial maps showing the expression of Plxnb2 at different time points after injury. L Violin plots and spatial maps showing the expression of Gpr37l1 at different time points after injury. M Spatial maps showing the expression of selected DEGs in spots that cross the fibroblast scar and form bridges at 14 dpi. N IF-stained 14-dpi scars for Nxpe3 (red) and DAPI (blue) (scale bars, 200 µm). O Violin plots showing the expression of selected genes contributing to microglia-organized scar-free spinal cord repair in neonatal mice.