Extended Data Fig. 9: Spotiphy’s imputation to out-spot increases information density of ST data.
From: Spotiphy enables single-cell spatial whole transcriptomics across an entire section
a, Quantification of all detectable nuclei/cells including both in-spot and non-capture areas from WT and AD samples. b, The workflow of pseudo single-cell resolution image generation. c, Schematic overview of Gaussian processes for cell-type proportion imputation. d, e, Cell type annotation of individual cells in selected FOVs of cerebral cortex. Dots in d represent all detectable nuceli, color-coded for cell type. Grey circles represent the transcriptomic spots in the Visium data. Dashed white lines have been added to allow for easier comparison. e, Depicts whole cells, color-coded for cell type. The cell boundaries depicted for the Xenium (upper panel) and Spotiphy (lower panel) data were inferred through those methods’ respective pipelines. Color legend in Fig. 6. Scale bars in d, e: 100 μm.
