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While effective for capturing end\u2010stage outcomes, these methods offer limited insight into the cellular mechanisms driving tissue remodeling, hindering efforts to rationally design better biomaterials. Transcriptomics has revolutionized our understanding of gene activity driving cellular function, yet remains underutilized in biomaterial evaluation. Recent advances in high\u2010resolution spatial transcriptomics now enable precise mapping of gene expression within tissue, offering detailed insight into cellular states and spatial organization. To align biomaterial research with advances in spatial biology, we develop a bioinformatics workflow for the Xenium platform to analyze in vivo responses to implanted materials. Applying this workflow to evaluate electrospun polycaprolactone (PCL) scaffolds implanted subcutaneously in mice, we identify spatially distinct macrophage and fibroblast subpopulations with unique gene expression profiles. Spatial analyses show shared phenotypic features between co\u2010localized macrophages and fibroblasts, oriented from the scaffold body to its surface. Gene ontology linked these spatial transitions to functional roles, with immune cell recruitment occurring within the scaffold and fibrosis at the surface. These transitions were not detectable by histology, highlighting spatial transcriptomics as a powerful approach for uncovering cellular dynamics and enabling better biologically\u2010informed design of biomaterials.<\/jats:p>","DOI":"10.1002\/advs.202513242","type":"journal-article","created":{"date-parts":[[2026,2,15]],"date-time":"2026-02-15T13:19:27Z","timestamp":1771161567000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Developing a Single\u2010Cell Spatial Transcriptomics Workflow for In Vivo Evaluation of Implanted Biomaterials"],"prefix":"10.1002","volume":"13","author":[{"given":"Alex H.P.","family":"Chan","sequence":"first","affiliation":[{"name":"School of Medical Sciences Faculty of Health and Medicine Charles Perkins Centre University of Sydney  Sydney New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunfei","family":"Hu","sequence":"additional","affiliation":[{"name":"School of Medical Sciences Faculty of Health and Medicine Charles Perkins Centre University of Sydney  Sydney New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Billie","family":"Pardavi","sequence":"additional","affiliation":[{"name":"School of Medical Sciences Faculty of Health and Medicine Charles Perkins Centre University of Sydney  Sydney New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xueying","family":"Xu","sequence":"additional","affiliation":[{"name":"School of Medical Sciences Faculty of Health and Medicine Charles Perkins Centre University of Sydney  Sydney New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Angus J.","family":"Grant","sequence":"additional","affiliation":[{"name":"School of Medical Sciences Faculty of Health and Medicine Charles Perkins Centre University of Sydney  Sydney New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven G.","family":"Wise","sequence":"additional","affiliation":[{"name":"School of Medical Sciences Faculty of Health and Medicine Charles Perkins Centre University of Sydney  Sydney New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lipin","family":"Loo","sequence":"additional","affiliation":[{"name":"School of Medical Sciences Faculty of Health and Medicine Charles Perkins Centre University of Sydney  Sydney New South Wales Australia"},{"name":"School of Life and Environmental Sciences Faculty of Science Charles Perkins Centre University of Sydney  Sydney New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2670-2882","authenticated-orcid":false,"given":"Richard P.","family":"Tan","sequence":"additional","affiliation":[{"name":"School of Medical Sciences Faculty of Health and Medicine Charles Perkins Centre University of Sydney  Sydney New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,2,15]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1039\/D4TB00705K"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jacbts.2018.10.004"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1002\/adhm.202301571"},{"key":"e_1_2_10_5_1","unstructured":"I. 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