Fig. 3: Integration of ST data with H&E images.

Left panel: Following generation of spatial transcriptomic (ST) data using the Xenium platform, H&E staining can be performed on the same section. The ST data can be integrated with the H&E image and be visualised overlying the H&E morphology. This step allows for confirmation of architectural preservation and cellular morphology, as well as visual confirmation of appropriate cellular segmentation. The panel shows H&E image of a BMT, with three distinct cell groups highlighted (purple, blue and yellow indicating lymphocytes, stromal and erythroid groups respectively, clockwise from top right). Right panel: H&E-based annotation. (Top and middle BMTs) Regions in which cell annotation is compromised (e.g. due to haemorrhage or crush) should be negatively annotated for removal from downstream analysis. Areas of architectural preservation are positively annotated for subsequent spatial analysis. (Bottom BMT) Each discrete positively annotated region (here representing an intertrabecular space) is indicated by a different colour.