Fig. 1

Celloscope overview. A The total number of cells for each spot is estimated based on a H&E image. Optionally, regions of interest are annotated. H&E image source: 10x Genomics. B Prior knowledge on marker genes is given as the model’s input, in a form of a binary matrix, together with ST data on marker gene expression in spots (C). D The graphical representation of Celloscope. Gray nodes correspond to the observed variables, double circled to deterministic ones, while the remaining nodes correspond to hidden variables. Arrows represent probabilistic dependencies. Model’s variables are described in Table 1 and hyperparameters in Table 2. E Cell type decomposition in each spot using Celloscope is performed via MCMC inference