Fig. 4: Multi-modality of Visium and GeoMx data visualized with H&E and fluorescence image, pathology label, and deconvolution.
a Pathology label visualized on H&E image of Visium sample B1_4. b Deconvolution cell type fractions plotted as scattered pie charts for each spot visualized on H&E image of Visium sample B1_4. c Pathological regions of interest (ROI-s) visualized on fluorescence images of GeoMx sample B1_3. d Up to four AOI segments have their outlines complement each other in an ROI. Deconvolution cell type fractions plotted as pie charts for each area of illumination (AOI) segment within each ROI. Sample B1 - Visium: 1988 spots; GeoMx: 24 AOIs. Pathology label and deconvolution agreement for breast, lung and DLBCL in Visium (e) and GeoMx (f) samples. Heatmap is labelled by the average cell type deconvolution fraction per pathology label or AOI label, colored by square root of the number. g Lymphocyte resolution zoomed in on H&E image, pathology annotation, deconvolution shown as scatterpie of cell type fractions, and individual deconvolution fraction for cell type of interest in Visium sample B1_4. At the same spatial ___location, ROI and AOI outlines (if any) were shown on the consecutive section of GeoMx sample B1_3. The individual deconvolution fraction of B-cells is shown spatially in the TME ROI. The T-cell region identified in Visium did not have an ROI sampled exactly head-to-head in GeoMx. h Malignant cell subtypes visualized across various modalities for consecutive sections of Visium and GeoMx sample D3. Deconvolution is able to depict the spatial transitioning in Visium of tumor cell types annotated in Chromium. The absence of Tu_D3_FAM3C and the existence of Tu_D3_dividing can be validated in GeoMx at the same spatial ___location. Sample D3 - Visium: 4951 spots; GeoMx: 23 AOIs. i Tumor and epithelium cell subtypes visualized across various modalities for consecutive sections of Visium and GeoMx sample D6. Sample D6 - Visium: 1649 spots; GeoMx: 19 AOIs. Images above are representative of 3 samples. Source data are provided as a Source Data file.
