(A) Experiment schematic whereby spatial transcriptomics was performed on VML-injured tibialis anterior muscles at 7 days after injury. (B) Representative image showing tissue annotation into 3 zones — a defect zone, a zone of intact muscle, and a transition zone between them. (C) Representative distribution of unique molecular identifiers shows higher read counts at the location of the defect. (D) GO Term analysis showing upregulated terms within each zone compared with the other 2 zones. Differentially expressed genes were calculated using Wilcoxon Rank Sum Test with post hoc analysis. Log₂ fold change > 0.25 and adjusted P < 0.05 was considered significant. (E) Integration of spatial transcriptomics data sets with matched, cell type–annotated scRNA-Seq data sets using Seurat label transfer. (Left) Representative spatial overlays. (Right) Quantification. **P < 0.01, *P < 0.05, by 1-way ANOVA with Tukey’s post hoc analysis. n = 4 muscles from 2 male and 2 female mice. Color bars indicate prediction scores. (F) Immunohistological stains confirm the spGEX-predictions of cell localization within the different zones. (Left) Representative images. Scale bars: 500 μm. (Right) Quantifications. **P < 0.01, *P < 0.05, by 1-way ANOVA with Tukey’s post hoc analysis. n = 3–4 muscles from 2 male and 2 female mice. ***P < 0.001, ****P < 0.0001. Magnification, 20×.