Fig. 6: Spotiphy outputs pseudo-single-cell-resolved whole-transcriptome images.
From: Spotiphy enables single-cell spatial whole transcriptomics across an entire section
a,b, Cell-type annotation of individual nuclei and cells in selected FOVs in the HPF. Dots in a represent all detectable nuclei color coded for cell type. Gray circles represent the transcriptomic spots in the Visium data. Dashed white lines have been added to allow for easier comparison. Cells in b are color coded by cell type. The cell boundaries depicted for the Xenium (top) and Spotiphy (bottom) data were inferred through those methods’ respective pipelines; scale bars, 100 μm; Astro, astrocytes; Oligo, oligodendrocytes. c,d, The mean absolute error (MAE) and mean squared error (MSE) of the cell-type imputation generated by Spotiphy, Tangram and CytoSPACE for each cell. Xenium data were used as the ground truth; STY in-spot, image with only cells inside the spots; STY out-spot, image with only cells outside the spots; STY merge, image with all cells included.
