{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T15:20:39Z","timestamp":1775575239808,"version":"3.50.1"},"reference-count":40,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2022,11,9]],"date-time":"2022-11-09T00:00:00Z","timestamp":1667952000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01 GM127527"],"award-info":[{"award-number":["R01 GM127527"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000952","name":"Paul G. Allen Family Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000952","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    Organoids have immense potential as\n                    <jats:italic>ex vivo<\/jats:italic>\n                    disease models for drug discovery and personalized drug screening. Dynamic changes in individual organoid morphology, number, and size can indicate important drug responses. However, these metrics are difficult and labor-intensive to obtain for high-throughput image datasets. Here, we present OrganoID, a robust image analysis platform that automatically recognizes, labels, and tracks single organoids, pixel-by-pixel, in brightfield and phase-contrast microscopy experiments. The platform was trained on images of pancreatic cancer organoids and validated on separate images of pancreatic, lung, colon, and adenoid cystic carcinoma organoids, which showed excellent agreement with manual measurements of organoid count (95%) and size (97%) without any parameter adjustments. Single-organoid tracking accuracy remained above 89% over a four-day time-lapse microscopy study. Automated single-organoid morphology analysis of a chemotherapy dose-response experiment identified strong dose effect sizes on organoid circularity, solidity, and eccentricity. OrganoID enables straightforward, detailed, and accurate image analysis to accelerate the use of organoids in high-throughput, data-intensive biomedical applications.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1010584","type":"journal-article","created":{"date-parts":[[2022,11,9]],"date-time":"2022-11-09T14:07:14Z","timestamp":1668002834000},"page":"e1010584","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":102,"title":["OrganoID: A versatile deep learning platform for tracking and analysis of single-organoid dynamics"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8530-4956","authenticated-orcid":true,"given":"Jonathan M.","family":"Matthews","sequence":"first","affiliation":[]},{"given":"Brooke","family":"Schuster","sequence":"additional","affiliation":[]},{"given":"Sara Saheb","family":"Kashaf","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0866-8801","authenticated-orcid":true,"given":"Ping","family":"Liu","sequence":"additional","affiliation":[]},{"given":"Rakefet","family":"Ben-Yishay","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0425-1408","authenticated-orcid":true,"given":"Dana","family":"Ishay-Ronen","sequence":"additional","affiliation":[]},{"given":"Evgeny","family":"Izumchenko","sequence":"additional","affiliation":[]},{"given":"Le","family":"Shen","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2117-3184","authenticated-orcid":true,"given":"Christopher R.","family":"Weber","sequence":"additional","affiliation":[]},{"given":"Margaret","family":"Bielski","sequence":"additional","affiliation":[]},{"given":"Sonia S.","family":"Kupfer","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5123-9992","authenticated-orcid":true,"given":"Mustafa","family":"Bilgic","sequence":"additional","affiliation":[]},{"given":"Andrey","family":"Rzhetsky","sequence":"additional","affiliation":[]},{"given":"Sava\u015f","family":"Tay","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2022,11,9]]},"reference":[{"issue":"6","key":"pcbi.1010584.ref001","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1016\/j.devcel.2016.08.014","article-title":"Organoids: Modeling Development and the Stem Cell Niche in a Dish.","volume":"38","author":"K Kretzschmar","year":"2016","journal-title":"Developmental Cell"},{"issue":"7","key":"pcbi.1010584.ref002","first-page":"852","volume":"9","author":"E Driehuis","year":"2019","journal-title":"Oral Mucosal Organoids as a Potential Platform for Personalized Cancer Therapy. Cancer Discovery"},{"issue":"5","key":"pcbi.1010584.ref003","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1016\/j.molmed.2017.02.007","article-title":"Disease Modeling in Stem Cell-Derived 3D Organoid Systems","volume":"23","author":"D Dutta","year":"2017","journal-title":"Trends in Molecular Medicine"},{"issue":"1\u20132","key":"pcbi.1010584.ref004","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1016\/j.cell.2017.11.010","article-title":"A Living Biobank of Breast Cancer Organoids Captures Disease Heterogeneity","volume":"172","author":"N Sachs","year":"2018","journal-title":"Cell"},{"issue":"1","key":"pcbi.1010584.ref005","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1146\/annurev-cancerbio-030518-055702","volume":"3","author":"H Clevers","year":"2019","journal-title":"Organoid Models for Cancer Research. 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Nat Biomed Eng","volume":"4","author":"DJ Richards","year":"2020","journal-title":"Internet]"},{"issue":"2","key":"pcbi.1010584.ref008","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1038\/s41563-020-00804-4","article-title":"Rethinking organoid technology through bioengineering","volume":"20","author":"E Garreta","year":"2020","journal-title":"Nature Materials"},{"key":"pcbi.1010584.ref009","article-title":"Spectroscopic label-free microscopy of changes in live cell chromatin and biochemical composition in transplantable organoids","author":"G Pettinato","year":"2021","journal-title":"Sci Adv"},{"key":"pcbi.1010584.ref010","article-title":"Screening for modulators of the cellular composition of gut epithelia via organoid models of intestinal stem cell differentiation","author":"BE Mead","year":"2022","journal-title":"Nature Biomedical 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Wiedenmann","year":"2021","journal-title":"Nat Biomed Eng"},{"issue":"9","key":"pcbi.1010584.ref014","doi-asserted-by":"crossref","first-page":"875","DOI":"10.1038\/s41551-020-0576-z","article-title":"Three-dimensional single-cell imaging for the analysis of RNA and protein expression in intact tumour biopsies","volume":"4","author":"N Tanaka","year":"2020","journal-title":"Nat Biomed Eng"},{"issue":"7","key":"pcbi.1010584.ref015","doi-asserted-by":"crossref","first-page":"744","DOI":"10.1177\/2472555220915827","article-title":"Comparison of Cell and Organoid-Level Analysis of Patient-Derived 3D Organoids to Evaluate Tumor Cell Growth Dynamics and Drug Response.","volume":"25","author":"S Kim","year":"2020","journal-title":"SLAS Discov"},{"issue":"6","key":"pcbi.1010584.ref016","doi-asserted-by":"crossref","first-page":"1756","DOI":"10.1038\/s41596-019-0160-8","article-title":"High-resolution 3D imaging of fixed and cleared organoids","volume":"14","author":"JF Dekkers","year":"2019","journal-title":"Nature Protocols"},{"issue":"1","key":"pcbi.1010584.ref017","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1186\/s12915-021-00958-w","article-title":"Long-term live imaging and multiscale analysis identify heterogeneity and core principles of epithelial organoid morphogenesis.","volume":"19","author":"L Hof","year":"2021","journal-title":"BMC Biol"},{"issue":"12","key":"pcbi.1010584.ref018","doi-asserted-by":"crossref","first-page":"1425","DOI":"10.1038\/s41587-019-0137-8","article-title":"Gene editing for immune cell therapies","volume":"37","author":"SR Bailey","year":"2019","journal-title":"Nature Biotechnology"},{"issue":"8","key":"pcbi.1010584.ref019","doi-asserted-by":"crossref","first-page":"2190","DOI":"10.1016\/j.celrep.2018.01.087","article-title":"A Roadmap for Human Liver Differentiation from Pluripotent Stem Cells.","volume":"22","author":"LT Ang","year":"2018","journal-title":"Cell 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Long","year":"2020","journal-title":"BMC Bioinformatics"},{"key":"pcbi.1010584.ref040","doi-asserted-by":"crossref","first-page":"v7","DOI":"10.1093\/annonc\/mdj941","article-title":"Cellular pharmacology of gemcitabine","volume":"17","author":"E Mini","year":"2006","journal-title":"Annals of Oncology"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1010584","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,11,9]],"date-time":"2022-11-09T14:07:57Z","timestamp":1668002877000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1010584"}},"subtitle":[],"editor":[{"given":"Dina","family":"Schneidman-Duhovny","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,11,9]]},"references-count":40,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2022,11,9]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1010584","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2022.01.13.476248","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,11,9]]}}}