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CIN may result from chromosome mis-segregation errors and excessive chromatin is frequently packaged in micronuclei (MN), which can be enumerated to quantify CIN. The assessment of CIN remains a predominantly manual and time-consuming task. Here, we present micronuclAI, a pipeline for automated and reliable quantification of MN of varying size and morphology in cells stained only for DNA. micronuclAI can achieve close to human-level performance on various human and murine cancer cell line datasets. The pipeline achieved a Pearson\u2019s correlation of 0.9278 on images obtained at 10X magnification. We tested the approach in otherwise isogenic cell lines in which we genetically dialed up or down CIN rates, and on several publicly available image datasets where we achieved a Pearson\u2019s correlation of 0.9620. Given the increasing interest in developing therapies for CIN-driven cancers, this method provides an important, scalable, and rapid approach to quantifying CIN on images that are routinely obtained for research purposes. We release a GUI-implementation for easy access and utilization of the pipeline.<\/jats:p>","DOI":"10.1038\/s42003-025-07796-4","type":"journal-article","created":{"date-parts":[[2025,3,4]],"date-time":"2025-03-04T10:48:42Z","timestamp":1741085322000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["micronuclAI enables automated quantification of micronuclei for assessment of chromosomal instability"],"prefix":"10.1038","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8411-4854","authenticated-orcid":false,"given":"Miguel A.","family":"Ibarra-Arellano","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1370-8684","authenticated-orcid":false,"given":"Lindsay A.","family":"Caprio","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aroj","family":"Hada","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Niklas","family":"Stotzem","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luke L.","family":"Cai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9439-6509","authenticated-orcid":false,"given":"Shivem B.","family":"Shah","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zachary H.","family":"Walsh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5410-6586","authenticated-orcid":false,"given":"Johannes C.","family":"Melms","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Florian","family":"W\u00fcnneman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kresimir","family":"Bestak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ibrahim","family":"Mansaray","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2379-6702","authenticated-orcid":false,"given":"Benjamin","family":"Izar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9391-5722","authenticated-orcid":false,"given":"Denis","family":"Schapiro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,3,4]]},"reference":[{"key":"7796_CR1","doi-asserted-by":"publisher","first-page":"16226","DOI":"10.1073\/pnas.202617399","volume":"99","author":"MA Nowak","year":"2002","unstructured":"Nowak, M. 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(Zenodo, 2025). https:\/\/doi.org\/10.5281\/ZENODO.14848935.","DOI":"10.5281\/ZENODO.14848935"}],"container-title":["Communications Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-07796-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-07796-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-07796-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,3,4]],"date-time":"2025-03-04T10:58:13Z","timestamp":1741085893000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-07796-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3,4]]},"references-count":60,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["7796"],"URL":"https:\/\/doi.org\/10.1038\/s42003-025-07796-4","relation":{},"ISSN":["2399-3642"],"issn-type":[{"value":"2399-3642","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,3,4]]},"assertion":[{"value":"24 May 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 February 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"4 March 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"D.S. reports funding from Cellzome, a GSK company and received honorariums from Immunai, Noetik, Alpenglow and Lunaphore. B.I. is a consultant for or received honoraria from Volastra Therapeutics, Johnson & Johnson\/Janssen, Novartis, Eisai, AstraZeneca and Merck, and has received research funding to Columbia University from Agenus, Alkermes, Arcus Biosciences, Checkmate Pharmaceuticals, Compugen, Immunocore, Regeneron, and Synthekine. All other authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"361"}}