Application of stVAE on E12.5 mouse embryo obtained from Stereo-seq. Top three rows, the proportions of the five osteoblast subtypes inferred by stVAE, DestVI, and Stereoscope are displayed on each spot. The fourth row, expression levels of the five corresponding top-ranked marker genes are displayed; Bottom row, the Spearman’s rank correlations between the inferred cell type proportions and expression levels of the top two marker genes for each of the five osteoblast subtypes.