Fig. 3: UniCell allows for deconvolution of tumor microenvironments across varying cancer subtypes with unique histologic features.

a (left) Hematoxylin & Eosin (H&E) stained section of a breast invasive adenocarcinoma (BRCA) sample with human-derived pathological annotations (provided with source data) overlaid. (right) UniCell Deconvolve Base (UCDBase) predicted distribution of key cell types in the tumor microenvironment for a sequential section derived from the same sample (n = 1). b Box plots of feature attribution weights (x-axis) for genes (y-axis) indicative of select cell types predicted to be present in the BRCA spatial sample. Sample sizes represent the top 2% (n = 51) of individual total spatial capture spots by predicted fraction for that given cell type (Source Data File—Fig. 3b). c (left) Hematoxylin & Eosin (H&E) stained section of a prostate adenocarcinoma (PRAD) sample with human-derived pathological annotations (provided with source data) overlaid. (right) UCDBase predicted distribution of key cell types in the tumor microenvironment for a sequential section derived from the same sample (n = 1). d Box plots of feature attribution weights (x-axis) for genes (y-axis) indicative of select cell types predicted to be present in the PRAD spatial sample. Sample sizes represent the top 2% (n = 88) of individual total spatial capture spots by predicted fraction for that given cell type (Source Data File—Fig. 3d). e (left) Hematoxylin & Eosin (H&E) stained section of a colorectal adenocarcinoma (COAD) sample. (right) UCDBase predicted distribution of key cell types in the tumor microenvironment for a sequential section derived from the same sample (n = 1). f Box plots of feature attribution weights (x-axis) for genes (y-axis) indicative of select cell types predicted to be present in the COAD spatial sample. Sample sizes represent the top 2% (n = 63) of individual total spatial capture spots by predicted fraction for that given cell type (Source Data File—Fig. 3f). For scale bars on the right-side of a, c, and e, these represent the fraction (range 0–1) a given spatial coordinate is predicted to be composed of a given cell type. For boxplots in b, d, and f, the center line, box limits and box whiskers correspond to the median, first and third quartiles, and the 1.5x interquartile range, respectively. Individual data points are superimposed over each boxplot.