Application of QuadST to a MERFISH data set from mouse cortex. (A) Spatial map by annotated cell types in the MERFISH data. (B) UMAP by cell type and cortical layer. (C) Partial R-squared by cell type and cortical layer. (D) Number of significant ICGs by anchor–neighbor cell-type pairs. (E) Directional association scores of ICGs and all other genes among all anchor–neighbor cell pairs.