Fig. 1: Spot swapping in human brain sample LIBD_151507.

a H&E-stained image. Scale bar is 1 mm. b Unique molecular identifier (UMI) total counts in the background decrease with increasing distance from the tissue. Tissue and background spot annotations are taken from Maynard et al. ⁹. The perimeter delineating tissue and background is shown in white; also shown in white are tissue spots originally called background in Maynard et al. ⁹ that appear to contain tissue in the H&E image. The spots shown in white have been removed from the summaries shown in c–f to ensure that the effects shown are not due to spots on the tissue-background boundary, or to tissue in the background. c UMI count densities for tissue and background spots show relatively high counts in the background. d Counts of the top 50 genes from a select tissue region (upper), from a nearby background region (middle), and from a distant background region (bottom) show the similarity between expression in tissue spots and nearby background spots due to spot swapping from tissue to background, an effect that decreases as distance from the tissue increases. The positions of the three regions are shown in Supplementary Fig. 2. e Graph-based clustering of all spots identifies 9 clusters, visualized in uniform manifold approximation and projection (UMAP) plot. f Spots on the slide are colored by their cluster membership shown in e. Black arrows highlight areas of spot swapping of signal from tissue to background.