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PCA and standard Louvain clustering using the top 50 PCs were used to detect 15 broad clusters across the TBI sample (Figs. S2 and 2c). Clusters were split further if they were spatially separated within the tissue using the stLearn sub-clustering option. Each cluster was annotated using the well-defined anatomical regions given by the Allen Mouse Brain Atlas28. Data were visualised in both UMAP and ForceAtlas2 space59 (Fig. S2).
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