{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T17:55:03Z","timestamp":1785779703180,"version":"3.56.0"},"reference-count":13,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T00:00:00Z","timestamp":1785715200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000069","name":"National Institute of Arthritis and Musculoskeletal and Skin Diseases","doi-asserted-by":"publisher","award":["AR074417"],"award-info":[{"award-number":["AR074417"]}],"id":[{"id":"10.13039\/100000069","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>\n                    Zebrafish (\n                    <jats:italic>Danio rerio<\/jats:italic>\n                    ) are an important model for the study of musculoskeletal genetics, development, disease, regeneration, and evolution. While micro-computed tomography (microCT) allows for the assessment of quantitative 3D morphometric measures related to body size and shape and lean mass in adult zebrafish, computing these measures is typically a labor-intensive process. The purpose of this study was to develop fully automatic methods for the calculation of lean volume, fineness ratio, anterior and posterior swim bladder length, and standard length from microCT scans of adult zebrafish. Here, we show that built-in functions in the open-source software FIJI\/ImageJ can be combined into fully automated methods to compute these measures. We show that measures computed by automated methods compare favorably to those computed using manual and semi-automated methods while significantly improving the throughput of data collection and eliminating inter-observer variability. We have implemented these methods as ImageJ macros, providing an accessible tool to facilitate the use of microCT for body morphometric analyses in adult zebrafish.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0354249","type":"journal-article","created":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T17:23:52Z","timestamp":1785777832000},"page":"e0354249","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Automatic body morphometric analysis of adult zebrafish using microCT"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-2900-5610","authenticated-orcid":true,"given":"Mohammed Mushtak","family":"Kanani","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9760-3761","authenticated-orcid":true,"given":"Ronald Young","family":"Kwon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,8,3]]},"reference":[{"key":"pone.0354249.ref001","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1016\/j.bone.2017.05.001","article-title":"Utility of quantitative micro-computed tomographic analysis in zebrafish to define gene function during skeletogenesis","volume":"101","author":"JF Charles","year":"2017","journal-title":"Bone"},{"key":"pone.0354249.ref002","article-title":"MicroCT-based phenomics in the zebrafish skeleton reveals virtues of deep phenotyping in a distributed organ system","volume":"6","author":"M Hur","year":"2017","journal-title":"Elife"},{"issue":"8","key":"pone.0354249.ref003","doi-asserted-by":"crossref","first-page":"9116","DOI":"10.1096\/fj.201802654RR","article-title":"Scleraxis genes are required for normal musculoskeletal development and for rib growth and mineralization in zebrafish","volume":"33","author":"E Kague","year":"2019","journal-title":"FASEB J"},{"key":"pone.0354249.ref004","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1007\/978-1-0716-4306-8_28","article-title":"MicroCT Scanning and Analysis of the Zebrafish Skeleton","volume":"2885","author":"AE G\u00f3mez","year":"2025","journal-title":"Methods Mol Biol"},{"issue":"12","key":"pone.0354249.ref005","doi-asserted-by":"crossref","first-page":"1695","DOI":"10.1093\/jbmr\/zjae171","article-title":"Standardization of bone morphometry and mineral density assessments in zebrafish and other small laboratory fishes using X-ray radiography and micro-computed tomography","volume":"39","author":"E Kague","year":"2024","journal-title":"J Bone Miner Res"},{"issue":"3","key":"pone.0354249.ref006","article-title":"Phenomics-Based Quantification of CRISPR-Induced Mosaicism in Zebrafish","volume":"10","author":"CJ Watson","year":"2020","journal-title":"Cell Syst"},{"issue":"2","key":"pone.0354249.ref007","doi-asserted-by":"crossref","DOI":"10.1242\/bio.058948","article-title":"Computational anatomy and geometric shape analysis enables analysis of complex craniofacial phenotypes in zebrafish","volume":"11","author":"KM Diamond","year":"2022","journal-title":"Biol Open"},{"issue":"11","key":"pone.0354249.ref008","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1010496","article-title":"wnt16 regulates spine and muscle morphogenesis through parallel signals from notochord and dermomyotome","volume":"18","author":"CJ Watson","year":"2022","journal-title":"PLoS Genet"},{"issue":"2","key":"pone.0354249.ref009","doi-asserted-by":"crossref","DOI":"10.1093\/jbmrpl\/ziae159","article-title":"Loss of cped1 does not affect bone and lean tissue in zebrafish","volume":"9","author":"K Alvarado","year":"2024","journal-title":"JBMR Plus"},{"issue":"12","key":"pone.0354249.ref010","doi-asserted-by":"crossref","first-page":"2975","DOI":"10.1002\/dvdy.22113","article-title":"Normal table of postembryonic zebrafish development: staging by externally visible anatomy of the living fish","volume":"238","author":"DM Parichy","year":"2009","journal-title":"Dev Dyn"},{"issue":"10","key":"pone.0354249.ref011","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0075422","article-title":"Body fineness ratio as a predictor of maximum prolonged-swimming speed in coral reef fishes","volume":"8","author":"JA Walker","year":"2013","journal-title":"PLoS One"},{"issue":"2","key":"pone.0354249.ref012","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1016\/j.ydbio.2009.04.035","article-title":"Development of zebrafish swimbladder: The requirement of Hedgehog signaling in specification and organization of the three tissue layers","volume":"331","author":"CL Winata","year":"2009","journal-title":"Dev Biol"},{"issue":"7","key":"pone.0354249.ref013","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/nmeth.2019","article-title":"Fiji: an open-source platform for biological-image analysis","volume":"9","author":"J Schindelin","year":"2012","journal-title":"Nat Methods"}],"container-title":["PLOS One"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0354249","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T17:23:55Z","timestamp":1785777835000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0354249"}},"subtitle":[],"editor":[{"given":"Joel Harrison","family":"Gayford","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,8,3]]},"references-count":13,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2026,8,3]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0354249","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,3]]}}}