{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:25:39Z","timestamp":1792787139430,"version":"4.5.0"},"reference-count":0,"publisher":"SPIE-Intl Soc Optical Eng","issue":"05","license":[{"start":{"date-parts":[[2025,9,4]],"date-time":"2025-09-04T00:00:00Z","timestamp":1756944000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Department of Defense","award":["HT9425-23-1-0003"],"award-info":[{"award-number":["HT9425-23-1-0003"]}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01DK135597"],"award-info":[{"award-number":["R01DK135597"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2040462"],"award-info":[{"award-number":["2040462"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"name":"NSF NAIRR Pilot Award","award":["NAIRR240055"],"award-info":[{"award-number":["NAIRR240055"]}]},{"name":"The Leona M. and Harry B. Helmsley Charitable Trust","award":["G-1903-03793"],"award-info":[{"award-number":["G-1903-03793"]}],"id":[{"id":"https:\/\/ror.org\/011x6n313","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Med. Imag."],"published-print":{"date-parts":[[2025,9,4]]},"abstract":"<jats:p>PurposeRecent developments in computational pathology have been driven by advances in vision foundation models (VFMs), particularly the Segment Anything Model (SAM). This model facilitates nuclei segmentation through two primary methods: prompt-based zero-shot segmentation and the use of cell-specific SAM models for direct segmentation. These approaches enable effective segmentation across a range of nuclei and cells. However, general VFMs often face challenges with fine-grained semantic segmentation, such as identifying specific nuclei subtypes or particular cells.ApproachIn this paper, we propose the molecular empowered all-in-SAM model to advance computational pathology by leveraging the capabilities of VFMs. This model incorporates a full-stack approach, focusing on (1)\u00a0annotation\u2014engaging lay annotators through molecular empowered learning to reduce the need for detailed pixel-level annotations, (2)\u00a0learning\u2014adapting the SAM model to emphasize specific semantics, which utilizes its strong generalizability with SAM adapter, and (3)\u00a0refinement\u2014enhancing segmentation accuracy by integrating molecular oriented corrective learning.ResultsExperimental results from both in-house and public datasets show that the all-in-SAM model significantly improves cell classification performance, even when faced with varying annotation quality.ConclusionsOur approach not only reduces the workload for annotators but also extends the accessibility of precise biomedical image analysis to resource-limited settings, thereby advancing medical diagnostics and automating pathology image analysis.<\/jats:p>","DOI":"10.1117\/1.jmi.12.5.057501","type":"journal-article","created":{"date-parts":[[2025,9,4]],"date-time":"2025-09-04T17:39:13Z","timestamp":1757007553000},"page":"1-12","source":"Crossref","is-referenced-by-count":0,"title":["Fine-grained multiclass nuclei segmentation with molecular empowered all-in-SAM model"],"prefix":"10.1117","volume":"12","author":[{"given":"Xueyuan","family":"Li","sequence":"first","affiliation":[{"name":"Vanderbilt University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Can","family":"Cui","sequence":"additional","affiliation":[{"name":"Vanderbilt University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruining","family":"Deng","sequence":"additional","affiliation":[{"name":"Vanderbilt University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yucheng","family":"Tang","sequence":"additional","affiliation":[{"name":"NVIDIA Corporation"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quan","family":"Liu","sequence":"additional","affiliation":[{"name":"Vanderbilt University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1848-079X","authenticated-orcid":false,"given":"Tianyuan","family":"Yao","sequence":"additional","affiliation":[{"name":"Vanderbilt University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6376-4292","authenticated-orcid":false,"given":"Shunxing","family":"Bao","sequence":"additional","affiliation":[{"name":"Vanderbilt University Medical Center"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naweed","family":"Chowdhury","sequence":"additional","affiliation":[{"name":"Vanderbilt University Medical Center"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4265-7492","authenticated-orcid":false,"given":"Haichun","family":"Yang","sequence":"additional","affiliation":[{"name":"Vanderbilt University Medical Center"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2096-8065","authenticated-orcid":false,"given":"Yuankai","family":"Huo","sequence":"additional","affiliation":[{"name":"Vanderbilt University"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"189","container-title":["Journal of Medical Imaging"],"original-title":[],"link":[{"URL":"https:\/\/www.spiedigitallibrary.org\/journals\/journal-of-medical-imaging\/volume-12\/issue-05\/057501\/Fine-grained-multiclass-nuclei-segmentation-with-molecular-empowered-all-in\/10.1117\/1.JMI.12.5.057501.full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T20:40:57Z","timestamp":1790196057000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.spiedigitallibrary.org\/journals\/journal-of-medical-imaging\/volume-12\/issue-05\/057501\/Fine-grained-multiclass-nuclei-segmentation-with-molecular-empowered-all-in\/10.1117\/1.JMI.12.5.057501.full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9,4]]},"references-count":0,"journal-issue":{"issue":"05","published-online":{"date-parts":[[2025,9,1]]}},"URL":"https:\/\/doi.org\/10.1117\/1.jmi.12.5.057501","relation":{},"ISSN":["2329-4302","2329-4310"],"issn-type":[{"value":"2329-4302","type":"print"},{"value":"2329-4310","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,9,4]]}}}