Identification of multicellular niches and niche-regulated cell states using NicheScope v1

NicheScope is a computational framework for identifying multicellular niches (MCNs) and their associated niche-regulated cell states (NRCSs) from spatial transcriptomics data. This protocol describes the workflow for preparing spatial transcriptomics data, quantifying local neighborhood cell-type composition, selecting candidate niche genes, detecting MCNs through nonnegative sparse canonical correlation analysis, and interpreting the resulting niche scores, niche genes, and niche cell types. A reproducible demonstration using Xenium lymph node data is provided in the NicheScope GitHub repository.