Abstract Spatial transcriptomics allows for the measurement of gene expression within native tissue context, thereby improving our understanding of how cell states are modulated by their microenvironment. Despite technological advancements, computational methods to link cell states with their microenvironment and perform comparative analysis across different samples and conditions are still underdeveloped. To address this, we introduce TissueMosaic ( Tissue MOtif-based SpAtial Inference across Conditions ), a self…