Fig. 2

Crescendo facilitates visualization of genes across spatial transcriptomics datasets of serial sections from whole mouse brain tissue. A The Vizgen MERSCOPE platform was used to assay three coronal mouse brain tissue slices [37]. B Cell state classifications of cells based on marker genes. C Spatial locations of broad cell types. Gene expression distributions across slices for Gpr34 (D) and Rxfp1 (G). Spatial locations of cell types with the highest expression Gpr34 (E) and Rxfp1 (H). Gene expression visualizations in physical space before and after Crescendo batch correction for Gpr34 (F) and Rxfp1 (I). J Scatter plots of batch-variance ratio (BVR) and cell-type-variance ratio (CVR) metrics calculated for all 483 genes across 5 different batch correction algorithms. Purple dashed vertical line is at CVR = 0.5 and the purple dashed horizontal line is at BVR = 1. Red at BVR < 1 and CVR ≥ 0.5 is the target zone for genes that were batch corrected well