Figure 6. Single-cell and spatial analysis of the multiplexed error-robust fluorescence in situ hybridization (MERFISH) liver sample.

(A) UMAP plots of MERFISH data colored by manually annotated clusters or by normalized, log-transformed, and scaled expression of example marker genes. (B) Spatial plot of MERFISH dataset alone, colored by manually annotated cell types in (A). Inset highlights spatial co-localization of periportal endothelial cells and hepatocytes (gray and brown, respectively) and pericentral endothelial cells and hepatocytes (olive and pink, respectively). (C) DAPI stain of the liver sample. White box indicates the same inset region as in panel (C). (D) Spatial plot of MERFISH dataset using scANVI predicted cell type labels. Legend is the same as in panel (B). (E) Cell type composition for scRNA-seq and MERFISH datasets. Each point in (A, B, D) represents a single cell. (F) Confusion matrix of MERFISH cell type annotations between the manual method and scANVI predictions. The rows for other endothelial cells and hepatocytes (“o-EC” and “o-hep”) are blank because none of the manual annotations were in these groups. In addition, the row for bile duct epithelial cells is noisy because none of the scRNA-seq reference cells possessed this annotation. Cell type abbreviations are as follows: “IC,” “immune cell”; “o-EC,” “other endothelial cell”; “KC,” “Kupffer cell”; “HSC,” “hepatic stellate cell”; “o-hep,” “other hepatocyte”; “PP-hep,” “periportal hepatocyte”; “PC-hep,” “pericentral hepatocyte”; “PP-EC,” “periportal endothelial cell”; “PC-EC,” “pericentral endothelial cell”; “BD-EC,” “bile duct epithelial cell.”