{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T12:42:12Z","timestamp":1786711332377,"version":"build-2736575974"},"posted":{"date-parts":[[2026,8,11]]},"group-title":"Bioinformatics","reference-count":24,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,8,11]],"date-time":"2026-08-11T00:00:00Z","timestamp":1786406400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["1R01DE032178"],"award-info":[{"award-number":["1R01DE032178"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100032878","name":"Georgia Cancer Center","doi-asserted-by":"crossref","award":["MCGFD01068"],"award-info":[{"award-number":["MCGFD01068"]}],"id":[{"id":"10.13039\/100032878","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,8,11]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>Single-cell spatial transcriptomics can connect molecular cell states with tissue morphology, but this promise depends on accurate registration to histopathology. In serial sections, however, tissue borders often differ because of sectioning artifacts, staining variability, and field-of-view acquisition, limiting conventional area-based registration. We developed AnchorR, an expert-guided workflow for coarse-grained alignment of hematoxylin and eosin (H&amp;E) images with CosMx Spatial Molecular Imaging data. Bioinformaticians first define and color-code cell types in Seurat, and pathologists then identify corresponding internal landmarks using QuPath overlays. AnchorR combines these paired landmarks to estimate affine transformations, quantify residual error, and support visual quality control and anchor refinement.<\/jats:p>\n                <jats:p>Using six oral pre-cancerous tissue sections, we identified 60 cross-modal landmarks. Fitting each section independently reduced mean landmark error from 121.5 \u00b5m with a single whole-slide transformation to 14.6 \u00b5m. Cross-validation further showed that increasing the number of anchors improved robustness, with nine-anchor fits achieving approximately 20 \u00b5m error, or about one cell diameter.<\/jats:p>\n                <jats:p>AnchorR is designed to complement automated computer-vision methods by providing reliable tissue-level alignment when border mismatch makes global registration difficult. By creating a shared workspace for pathologists and bioinformaticians, it operationalizes an expert-in-the-loop approach and makes feature-based multimodal registration accessible without specialized computer-vision expertise or high-performance computing.<\/jats:p>","DOI":"10.64898\/2026.08.05.742985","type":"posted-content","created":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T03:35:20Z","timestamp":1786505720000},"source":"Crossref","is-referenced-by-count":0,"title":["AnchorR: A QuPath and R interface for collaborative exploration of spatial transcriptomics and histology"],"prefix":"10.64898","author":[{"given":"Caitlin A","family":"Morris","sequence":"first","affiliation":[{"name":"Institute of Bioinformatics, University of Georgia, Athens, GA, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William C","family":"Bastian","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics, University of Georgia, Athens, GA, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Cui","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Cancer Immunology, Inflammation & Tolerance Program, Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zoya","family":"Kurago","sequence":"additional","affiliation":[{"name":"Department of Oral Biology and Diagnostic Sciences, Dental College of Georgia, Medical College of Georgia, Georgia Cancer Center, Augusta University, Augusta, GA, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3418-9203","authenticated-orcid":false,"given":"Eugene F","family":"Douglass","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics, University of Georgia, Athens, GA, United States"},{"name":"Department of Pharmaceutical and Biomedical Sciences, Innovations in Drug Discovery (IDD), University of Georgia, Athens, GA, United States"},{"name":"Precision One Health Initiative, University of Georgia College of Veterinary Medicine, Athens, GA, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026081405201006000_2026.08.05.742985v1.1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-022-01483-z"},{"key":"2026081405201006000_2026.08.05.742985v1.2","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-020-01033-y"},{"key":"2026081405201006000_2026.08.05.742985v1.3","doi-asserted-by":"publisher","DOI":"10.1007\/s12105-025-01876-x"},{"key":"2026081405201006000_2026.08.05.742985v1.4","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giaf035"},{"key":"2026081405201006000_2026.08.05.742985v1.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.media.2018.02.004"},{"key":"2026081405201006000_2026.08.05.742985v1.6","doi-asserted-by":"publisher","DOI":"10.7860\/JCDR\/2013\/6170.3541"},{"key":"2026081405201006000_2026.08.05.742985v1.7","doi-asserted-by":"crossref","unstructured":"Borovec, J. 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