Fig. 4: Comparison of cell segmentation.

a Comparison of platform-derived automatic cell segmentation and manual nuclear segmentation across Stereo-seq v1.3, CosMx 6K, and Xenium 5K HCC sections. For each platform, a 250 × 250 μm region is shown. H&E staining for Stereo-seq v1.3 and multi-channel immunofluorescent staining for CosMx 6K and Xenium 5K are shown. Left column, automatically segmented cell boundaries. Middle column, manually segmented nuclear boundaries. Right column, overlay of automatic and manual segmentations, where white polygons denote automatic segmentations, and blue-filled masks in Stereo-seq v1.3 and yellow polygons in CosMx 6K and Xenium 5K indicate manual segmentations. Scale bars, 50 μm. b Number of automatically segmented cells and manually segmented nuclei per 100 × 100 μm bin across platforms (n = 125 bins per platform per cancer type). Each data point represents one bin. Center lines indicate the median value, and lower and upper hinges represent the 25th and 75th percentiles, respectively. The whiskers denote 1.5× the interquartile range. c Log₂-transformed transcript and gene counts per cell across platforms. For ST platforms, the platform-derived automatic segmentations were used. Left: all detected genes included. Right: only retained genes shared across scRNA-seq, CosMx 6K, and Xenium 5K. Each data point represents one cell. Center lines indicate the median value, and lower and upper hinges represent the 25th and 75th percentiles, respectively. The whiskers denote 1.5× the interquartile range. d Joint density plots showing the expression of exclusive marker pairs within cells in COAD. Only cells with ≥1 transcript of either marker gene were included. Color intensity indicates the density of cells. e Expression correlation of 36 gene pairs expected to be exclusively expressed in distinct major lineages. Pearson correlation was computed across either cells or 8 × 8 μm bins. Each data point represents one marker pair (n = 36). Lower values indicate better separation of marker pairs. Center lines indicate the median value, and lower and upper hinges represent the 25th and 75th percentiles, respectively. The whiskers denote 1.5× the interquartile range. Source data are provided as a Source Data file.