Fig. 2: Clustering, spatial annotation and computational validation using established scRNA-seq data.

a Visualization of cell type co-localization by Pearson correlations (left). Positive correlation values indicate spatial co-localization of cell types while negative values represent spatial segregation. Non-significant correlations are highlighted with magenta borders. UMAP embedding of single cell data of the Mouse Cell Atlas (MCA)⁴¹ grouped by annotated cell types (bottom right). Numeration behind the cell types represent annotation of MCA data (B cell-1: Fcmr high, -2: Jchain high, Dendritic cell-1: Cst3 high, -2: Siglec high, Epithelial cell-1: Spp1 high, -2: /, Erythroblast-1: Hbb-bs high, -2: Hbb-bt high, Hepatocyte-1: Fabp1 high, -2: mt-Nd4 high, T cell-1: Gzma high, -2: Trbcs2 high). Encircled clusters in the plot refer to pericentral or periportal hepatocytes of MCA data. Quantile scales of cell-proportions annotated as pericentral and periportal hepatocytes (Methods) are mapped on Spatial Transcriptomics spot data (top right). b Visualization of spots representing gene expression profiles of cluster 1 (portal vein, blue) and cluster 2 (central vein, red) on H&E stained tissue (right), compared with visual histology annotations of central- (red circles) and portal- (blue circles) veins (left) (scale bar indicates 500 µm). c Pearson correlations of genes expressed in cluster 1 and 2 ordered by their first principal component (Methods). Genes with high expression in the pericentral cluster (cluster 2) show negative correlation with genes highly expressed in the periportal cluster (cluster 1) and vice versa. Genes present within cluster 1 or cluster 2 exhibit positive correlation with genes in the same cluster. d Projection of selected marker genes for central venous expression (Glul, top) and periportal expression (Sds, bottom) in UMAP space and spots under the tissue (scale bar indicates 500 µm).