Extended Data Fig. 10: Spotiphy’s imputation to loss nuclei increases information density of Slide-tags data.
From: Spotiphy enables single-cell spatial whole transcriptomics across an entire section
a, Alignment of AD sample Visium H&E image and hippocampus plot from Slide-tags data of. b, c, Closer look at same hippocampus region of AD sample with 3,193 nuclei detected by Spotiphy segmentation. b, nuclei are color-coded with blue to indicate their location on the H&E image. c, nuclei are color-coded for cell type annotated by Spotiphy. Grey circles represent transcriptomic spots from Visium data. Scale bars in a–c: 500 μm. d, e, UMAP projection of 4,032 cells including Slide-tags data and iscRNA data. Clusters are labeled according to their cell type (d) or data-of-origin (e). f, Heatmaps displaying the expression patterns of the marker gene sets from the original article in Slide-tags data and iscRNA data. g, Cell-type proportions of the Slide-tags data and iscRNA data.
