{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T13:09:47Z","timestamp":1789650587654,"version":"4.0.0"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T00:00:00Z","timestamp":1789603200000},"content-version":"vor","delay-in-days":16,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U54AG075936"],"award-info":[{"award-number":["U54AG075936"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R35GM154865"],"award-info":[{"award-number":["R35GM154865"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Spatial transcriptomics (ST) enables measurement of gene expression while preserving spatial organization within tissues. Accurate reconstruction of single-cell transcriptomes requires precise whole-cell segmentation, yet many ST experiments provide only nuclear staining images, making reliable inference of cell boundaries difficult. Here we introduce Halo, a pretrained segmentation model that reconstructs whole-cell boundaries by integrating nuclear morphology with the spatial distribution of RNA transcripts. Halo converts transcript coordinates into molecular density maps that are processed jointly with DAPI images using a Cellpose-SAM segmentation architecture. Halo is pretrained on multimodal Xenium data from 12 tissue types and can be directly applied to new datasets without additional training, providing a ready-to-use alternative to supervised approaches that require dataset-specific fitting. Across diverse tissues, Halo achieves substantially higher agreement with the 10$\\times$ multimodal reference segmentation than existing methods, in terms of both cell boundaries and RNA-to-cell assignments, while requiring only DAPI staining and transcript spatial information. Improved segmentation leads to more reliable cell-type identification and more accurate estimation of cell morphological features. By providing a pretrained, generalizable model for whole-cell reconstruction, Halo enables scalable and reproducible cell segmentation for image-based ST.<\/jats:p>","DOI":"10.1093\/bib\/bbag515","type":"journal-article","created":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T11:37:36Z","timestamp":1788521856000},"source":"Crossref","is-referenced-by-count":0,"title":["Halo: a pretrained model for whole-cell segmentation from nuclei images in spatial transcriptomics"],"prefix":"10.1093","volume":"27","author":[{"given":"Xingyuan","family":"Zhang","sequence":"first","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, Duke University School of Medicine , 2424 Erwin Road, Durham, NC, 27705 ,","place":["United States"]},{"name":"Program of Computational Biology and Bioinformatics, Duke University School of Medicine , 2424 Erwin Road, Durham, NC, 27705 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haotian","family":"Zhuang","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, Duke University School of Medicine , 2424 Erwin Road, Durham, NC, 27705 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhicheng","family":"Ji","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, Duke University School of Medicine , 2424 Erwin Road, Durham, NC, 27705 ,","place":["United States"]},{"name":"Program of Computational Biology and Bioinformatics, Duke University School of Medicine , 2424 Erwin Road, Durham, NC, 27705 ,","place":["United 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