Fig. 2: Evaluation of false positives.
a Spatial distribution of gene calls (left) and negative control calls (right) in COAD samples profiled by CosMx 6K and Xenium 5K. Color intensity indicates mean call count per probe in each 8 × 8 μm bin. b Total call counts and Moran’s I for common genes (2552), platform-specific genes (3623 for CosMx 6K and 2449 for Xenium 5K), negative probes (NegProbe, 20 for CosMx 6K and 40 for Xenium 5K), and negative codes (NegCode, 324 for CosMx 6K and 609 for Xenium 5K) detected by CosMx 6K and Xenium 5K across the shared regions shown in (a). Each data point represents one target. 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 Histogram showing the log10-transformed signal proportions of individual negative probes and codes, pooled across COAD, HCC, and OV tissues. d H&E staining and transcript distribution inside and outside COAD tissue regions. Red dashed line outlines the Stereo-seq v1.3 region used for diffusion analysis; solid lines mark extra-tissue regions with high transcript levels. Color intensity indicates mean-normalized transcript count of each 8 × 8 μm bin. Scale bars, 1 mm. e Evaluation of transcript diffusion in COAD. The x-axis and y-axis represent the mean-normalized transcript counts and the distance to tissue edge for bins outside the tissue, respectively. Color intensity indicates the number of bins. f Ratio of the mean transcript count in extra-tissue bins to that in intra-tissue bins. Hollow circles indicate the ratio calculated for each of the three cancer types (n = 3). Data are presented as mean values +/− SEM. Source data are provided as a Source Data file.
