Extended Data Fig. 6: Deep count autoencoder denoising of Visium and spatial ATAC.
From: Solid-phase capture and profiling of open chromatin by spatial ATAC
a. Visium clusters based on original (same as in Fig. 2a) or denoised gene counts. b. Heatmap displaying the percentage of spots being assigned to the clusters obtained from original or denoised Visium data. c. UMAP on denoised expression colored by cluster. d. Visualization of gene expression normalized counts before and after denoising on E15.5 sections. e. Clusters based on original or denoised spatial ATAC peak counts (same as in Fig. 1c, shown for comparison). f. Heatmap displaying the percentage of spots being assigned to the clusters obtained from original or denoised spatial ATAC data g. UMAP on denoised peaks colored by cluster. h. Visualization of normalized peak accessibility before and after denoising on E12.5 sections. Scale bars are 500 µm.
