Fig. 1

Crescendo directly corrects gene expression. A Harmony batch corrects lower-dimensional embeddings like principal components that are visualized with a 2-dimensional UMAP. B Crescendo extends Harmony to batch correct genes expression, which can similarly be visualized in a UMAP. C Spatial transcriptomics allows for visualization of gene expression in the context of cellular locations. Due to batch effects, gene expression can be poorly expressed and spatial patterns can be obscured. Crescendo infers the gene expression of a cell, which facilitates the visualization and spatial pattern recognition of gene expression. Representative distributions of simulated gene expression before (D) and after (E) Crescendo batch correction. Batch-associated and cell-type-associated variance metrics before (F) batch correction and after (G) batch correction. H Calculated batch-variance ratio and cell-type-variance ratio metrics based on F–G