Nichesphere is an sc-verse compatible Python library which allows the user to find differential co-localization domains / niches based on cell type pair co-localization probabilities in different conditions. Cell type pair co-localization probabilities can be obtained in different ways, for example, through deconvolution of spatial transcriptomics / PIC-seq data (getting the probabilities of finding each cell type in each spot / multiplet) ; or counting cell boundaries overlaps for each cell type pair in single cell spatial data (MERFISH , CODEX …).
It also offers the possibility to look at biological process based differential communication among differential co-localization domains based on Ligand-Receptor pairs expression data, such as results from CrossTalkeR [ref.].
You can find our documentation and an application example on the Myocardial Infarction atlas data from Kuppe et. al. 2022 here: https://nichesphere.readthedocs.io/en/latest/