AI-driven deciphering of cell niches with single-cell and spatial omics: a new perspective for traditional Chinese medicine research

The therapeutic effects of traditional Chinese medicine (TCM) are characterized by holistic and systematic regulation of the organism, typically achieved through coordinating tissue microenvironments and multicellular interactions. However, conventional molecular biology approaches struggle to precisely characterize cellular composition, spatial architecture, and associated microenvironment (cell niche) at the tissue level, constraining a comprehensive understanding of the mechanism of action of TCM. In recent years, the rapid advancement of single-cell and spatial omics technologies, together with artificial intelligence (AI)-driven computational methods, has enabled systematic deciphering of cell niches within complex tissues, offering new opportunities for TCM research. Centered on the cell niche, this review outlines its conceptual development and research progress, with a particular focus on recent advances in AI-assisted cell niche analysis based on single-cell and spatial omics data. We further summarize representative scenarios of cell niche analysis in TCM research, while discussing current challenges and future directions, highlighting its potential to provide a new perspective and analytical paradigm in TCM.