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Nevertheless, the absence of deconvolution methods that simultaneously model multi\u2010modal features has impeded progress in understanding cellular heterogeneity in spatial contexts. To address this issue, SpaDA is developed, a novel spatially aware domain adaptation method that integrates multi\u2010modal data (i.e., transcriptomics, histological images, and spatial locations) from SRT to accurately estimate the spatial distribution of cell types. SpaDA utilizes a self\u2010expressive variational autoencoder, coupled with deep spatial distribution alignment, to learn and align spatial and graph representations from spatial multi\u2010modal SRT data and single\u2010cell RNA sequencing (scRNA\u2010seq) data. This strategy facilitates the transfer of cell type annotation information across these two similarity graphs, thereby enhancing the prediction accuracy of cell type composition. The results demonstrate that SpaDA surpasses existing methods in cell type deconvolution and the identification of cell types and spatial domains across diverse platforms. Moreover, SpaDA excels in identifying spatially colocalized cell types and key marker genes in regions of low\u2010quality measurements, exemplified by high\u2010resolution mouse cerebellum SRT data. In conclusion, SpaDA offers a powerful and flexible framework for the analysis of multi\u2010modal SRT datasets, advancing the understanding of complex biological systems.<\/jats:p>","DOI":"10.1002\/smtd.202401163","type":"journal-article","created":{"date-parts":[[2024,12,3]],"date-time":"2024-12-03T02:13:57Z","timestamp":1733192037000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Spatially Aware Domain Adaptation Enables Cell Type Deconvolution from Multi\u2010Modal Spatially Resolved Transcriptomics"],"prefix":"10.1002","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3285-2235","authenticated-orcid":false,"given":"Lequn","family":"Wang","sequence":"first","affiliation":[{"name":"Key Laboratory of Systems Biology Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences  Shanghai 200031 China"},{"name":"Key Laboratory of 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