Fig. 5: Integrating H&E image, pathology label, deconvolution, and clustering identifies TLS and tumor subtypes in Visium.

a For lung sample L1, TLS markers show boundary of TLS after BayesSpace resolution enhancement, which validates the TLS ___location by pathology label in Visium. In the consecutive section of L1 in GeoMx, at the same tissue ___location where the TLS was identified in Visium, we zoomed in to check the TLS markers expression level in the TME ROI compared to its neighboring Islet ROI. Black arrows point to the Other AOI, where the B-cell signal is expected to appear. Sample L1 - Visium: 944 spots; GeoMx: 25 AOIs. b For breast sample B3, two regions were similar in H&E, labeled as tumor by pathologist, and deconvolution majority voted as single tumor type from Chromium; two spatially distinct tumor subtypes appeared with spatially-aware clustering in Visium. c In the consecutive section of B3 in GeoMx, the ROI-s were mapped to the two regions identified by Visium. The Malignant AOI-s show distinct clusters in the reduced dimension. Deconvolution results for each AOI are displayed as pie charts. Sample B3 - Visium: 2156 spots; GeoMx: 23 AOIs. d Volcano plot of Differential Expression (DE) analysis between selected clusters from (b) (moderated t-test, two-sided). Genes for which there are existing drugs are highlighted (see further information in Supplementary Data 8). e Volcano plot of DE analysis between two Malignant AOI clusters in (c) (Wilcoxon’s Rank Sum test, two-sided). Genes that are mutually DE in both Visium and GeoMx are highlighted with black outline. f Upset plot showing number of distinct DE genes identified by Visium, GeoMx, and Chromium, and their combinations. Images above are representative of 2 samples. Source data are provided as a Source Data file.