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However, existing computational approaches lack the intrinsic flexibility to universally process both spatial multi\u2010modal and multi\u2010omics data. Here, we introduce STransformer, a unified deep learning framework designed to seamlessly accommodate a comprehensive landscape of spatial data. By simultaneously capturing short\u2010range cellular interactions and tissue\u2010wide semantic patterns, it extracts robust representations to accurately dissect complex tissue heterogeneity. Systematic evaluations across diverse species, tissue types, and data modalities highlight its profound versatility. For spatial multi\u2010modal data, STransformer delineates intricate anatomical structures in the human cortex, uncovers pathological mechanisms in Alzheimer's disease, and characterizes dynamic spatiotemporal developmental trajectories during chicken cardiogenesis. Scaling to spatial multi\u2010omics data, STransformer synergizes spatial transcriptomic and proteomic profiles to decipher intricate immune microenvironments within the human tonsil, and jointly analyzes spatial epigenomic and transcriptomic data to infer regulatory mechanisms in the mouse embryonic brain. Consequently, STransformer serves as a highly versatile and robust analytical framework for advancing our understanding of tissue heterogeneity and disease\u00a0pathogenesis.<\/jats:p>","DOI":"10.1002\/advs.75969","type":"journal-article","created":{"date-parts":[[2026,6,9]],"date-time":"2026-06-09T20:00:11Z","timestamp":1781035211000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Accurately Deciphering Tissue Heterogeneity From Spatial Multi\u2010Modal and Multi\u2010Omics With STransformer"],"prefix":"10.1002","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6004-4174","authenticated-orcid":false,"given":"Xingyi","family":"Li","sequence":"first","affiliation":[{"name":"School of Computer Science Northwestern Polytechnical University Xi'an Shaanxi China"},{"name":"Shenzhen Research Institute of Northwestern Polytechnical University Shenzhen Guangdong China"},{"name":"Faculty of Data Science City 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