Fig. 4

Crescendo batch correction increases ability to visualize and detect spatial gene–gene correlations. A Example schematics of gene–gene pairs that have a high spatial cross-correlation index (SCI) and a low SCI. B Comparison of SCIs for all fibroblast and myeloid cell gene–gene pairs before batch correction vs. after batch correction. C In these and following plots, scRNA-seq is plotted in UMAP space, while spatial slices are plotted in physical space. Spatial locations of fibroblasts and endothelial cells (top). Gene expression visualization of JAG2 in endothelial cells and NOTCH3 in fibroblasts (bottom). SCIs are listed for each spatial sample before and after batch correction. D Spatial locations of myeloid cells and fibroblasts (top). Gene expression visualization of CCR3 in myeloid cells and CCL11 in fibroblasts (bottom). SCIs are listed for each spatial sample before and after batch correction