{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T02:03:16Z","timestamp":1775268196364,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,1,20]],"date-time":"2024-01-20T00:00:00Z","timestamp":1705708800000},"content-version":"vor","delay-in-days":19,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004837","name":"Ministerio de Ciencia e Innovaci\u00f3n","doi-asserted-by":"publisher","award":["PID2020-118768RJ-I00"],"award-info":[{"award-number":["PID2020-118768RJ-I00"]}],"id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007320","name":"AECC","doi-asserted-by":"publisher","award":["LABAE222994MAUV"],"award-info":[{"award-number":["LABAE222994MAUV"]}],"id":[{"id":"10.13039\/100007320","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The toroidal nucleus is a novel chromosomal instability (CIN) biomarker which complements the micronucleus. Understanding the specific biological stresses leading to the formation of each CIN-associated phenotype requires the evaluation of large panels of biological images collected from different genetic backgrounds and environmental conditions. However, the quantification of toroidal nuclei is currently a manual process which is unviable on a large scale.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present QATS (QuAntification of Toroidal nuclei in biological imageS), a tool that automates the identification of toroidal nuclei, minimizing false positives while highly agreeing with the manual quantifications. Additionally, QATS identifies micronuclei for a convenient comparison of both CIN biomarkers. QATS is an open-source ImageJ plugin with a user-friendly interface that enables a wide scientific community to easily assess the frequency of CIN biomarkers for the determination of CIN levels in cellular models.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>QATS is an ImageJ plugin freely available at http:\/\/www.toroidalnucleus.org\/qats. The user manual and the images used for the evaluation of QATS are included in the website. Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae026","type":"journal-article","created":{"date-parts":[[2024,1,21]],"date-time":"2024-01-21T01:14:33Z","timestamp":1705799673000},"source":"Crossref","is-referenced-by-count":5,"title":["QATS: an ImageJ plugin for the quantification of toroidal nuclei in biological images"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9131-9089","authenticated-orcid":false,"given":"Carles","family":"Pons","sequence":"first","affiliation":[{"name":"Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology (BIST) , 08028 Barcelona, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4220-7272","authenticated-orcid":false,"given":"Caroline","family":"Mauvezin","sequence":"additional","affiliation":[{"name":"Department of Biomedicine, Faculty of Medicine, University of Barcelona , 08036 Barcelona, Spain"},{"name":"August Pi i Sunyer Biomedical Research Institute (IDIBAPS) , 08036 Barcelona, Spain"}]}],"member":"286","published-online":{"date-parts":[[2024,1,19]]},"reference":[{"key":"2024012817140516400_btae026-B1","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1080\/15548627.2020.1764727","article-title":"Lysosomal degradation ensures accurate chromosomal segregation to prevent chromosomal instability","volume":"17","author":"Almacellas","year":"2021","journal-title":"Autophagy"},{"key":"2024012817140516400_btae026-B2","doi-asserted-by":"crossref","DOI":"10.26508\/lsa.202101160","article-title":"Nuclear ingression of cytoplasmic bodies accompanies a boost in autophagy","volume":"5","author":"Garcia","year":"2022","journal-title":"Life Sci Alliance"},{"key":"2024012817140516400_btae026-B3","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1016\/S0002-9440(10)63958-2","article-title":"Abnormal nuclear shape in solid tumors reflects mitotic instability","volume":"158","author":"Gisselsson","year":"2001","journal-title":"Am J Pathol"},{"key":"2024012817140516400_btae026-B4","doi-asserted-by":"crossref","first-page":"1501","DOI":"10.1038\/s41467-020-15279-9","article-title":"Degree and site of chromosomal instability define its oncogenic potential","volume":"11","author":"Hoevenaar","year":"2020","journal-title":"Nat Commun"},{"key":"2024012817140516400_btae026-B5","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.ceb.2021.01.004","article-title":"Causes and consequences of micronuclei","volume":"70","author":"Krupina","year":"2021","journal-title":"Curr Opin Cell Biol"},{"key":"2024012817140516400_btae026-B6","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1038\/nmeth.2083","article-title":"Annotated high-throughput microscopy image sets for validation","volume":"9","author":"Ljosa","year":"2012","journal-title":"Nat Methods"},{"key":"2024012817140516400_btae026-B7","doi-asserted-by":"crossref","first-page":"e9243","DOI":"10.15252\/msb.20199243","article-title":"Systematic genetics and single-cell imaging reveal widespread morphological pleiotropy and cell-to-cell variability","volume":"16","author":"Mattiazzi Usaj","year":"2020","journal-title":"Mol. 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