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0The paper introduces scNiche, an innovative computational framework designed to identify and characterize cell niches using single-cell resolution spatial omics data. By integrating multi-view features—including the molecular profiles of individual cells and their surrounding microenvironments—the tool successfully deciphers complex tissue structures and cellular interactions. The researchers validated scNiche across diverse biological contexts, such as mapping the tumor-immune interface in human breast cancer and tracking tissue remodeling during liver failure. Benchmarking results demonstrate that this method outperforms existing technologies in accuracy and scalability, effectively handling datasets containing millions of cells. Ultimately, the source highlights how scNiche enables a deeper understanding of how local environments shape cellular phenotypes in both healthy and diseased states.
References:
Qian J, Shao X, Bao H, Fang Y, Guo W, Li C, Li A, Hua H, Fan X. Identification and characterization of cell niches in tissue from spatial omics data at single-cell resolution. Nat Commun. 2025 Feb 16;16(1):1693. doi: 10.1038/s41467-025-57029-9. PMID: 39956823; PMCID: PMC11830827.
