{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T17:36:06Z","timestamp":1790616966933,"version":"4.1.0"},"reference-count":31,"publisher":"The Company of Biologists","issue":"2","license":[{"start":{"date-parts":[[2022,2,17]],"date-time":"2022-02-17T00:00:00Z","timestamp":1645056000000},"content-version":"vor","delay-in-days":2,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100009992","name":"Seattle Children's Research Institute","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100009992","id-type":"DOI","asserted-by":"crossref"}]},{"name":"National Science Foundation","award":["DBI\/1759883"],"award-info":[{"award-number":["DBI\/1759883"]}]},{"name":"National Science Foundation","award":["OAC\/1939505"],"award-info":[{"award-number":["OAC\/1939505"]}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["AR074417"],"award-info":[{"award-number":["AR074417"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,2,15]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>Due to the complexity of fish skulls, previous attempts to classify craniofacial phenotypes have relied on qualitative features or sparce 2D landmarks. In this work we aim to identify previously unknown 3D craniofacial phenotypes with a semiautomated pipeline in adult zebrafish mutants. We first estimate a synthetic \u2018normative\u2019 zebrafish template using MicroCT scans from a sample pool of wild-type animals using the Advanced Normalization Tools (ANTs). We apply a computational anatomy (CA) approach to quantify the phenotype of zebrafish with disruptions in bmp1a, a gene implicated in later skeletal development and whose human ortholog when disrupted is associated with Osteogenesis Imperfecta. Compared to controls, the bmp1a fish have larger otoliths, larger normalized centroid sizes, and exhibit shape differences concentrated around the operculum, anterior frontal, and posterior parietal bones. Moreover, bmp1a fish differ in the degree of asymmetry. Our CA approach offers a potential pipeline for high-throughput screening of complex fish craniofacial shape to discover novel phenotypes for which traditional landmarks are too sparce to detect. The current pipeline successfully identifies areas of variation in zebrafish mutants, which are an important model system for testing genome to phenome relationships in the study of development, evolution, and human diseases.<\/jats:p>\n                  <jats:p>This article has an associated First Person interview with the first author of the paper.<\/jats:p>","DOI":"10.1242\/bio.058948","type":"journal-article","created":{"date-parts":[[2022,1,24]],"date-time":"2022-01-24T05:05:23Z","timestamp":1643000723000},"source":"Crossref","is-referenced-by-count":21,"title":["Computational anatomy and geometric shape analysis enables analysis of complex craniofacial phenotypes in zebrafish"],"prefix":"10.1242","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8639-6795","authenticated-orcid":false,"given":"Kelly M.","family":"Diamond","sequence":"first","affiliation":[{"name":"Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9514-7774","authenticated-orcid":false,"given":"Sara M.","family":"Rolfe","sequence":"additional","affiliation":[{"name":"Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA"},{"name":"Friday Harbor Marine Laboratories, University of Washington, San Juan, WA 98250, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ronald Y.","family":"Kwon","sequence":"additional","affiliation":[{"name":"Department of Orthopedics and Sports Medicine, University of Washington, Seattle, WA 98195, USA"},{"name":"Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7921-9018","authenticated-orcid":false,"given":"A. Murat","family":"Maga","sequence":"additional","affiliation":[{"name":"Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA"},{"name":"Division of Craniofacial Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98105, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"237","published-online":{"date-parts":[[2022,2,17]]},"reference":[{"key":"2022021709072673900_BIO058948C1","doi-asserted-by":"publisher","first-page":"393","DOI":"10.1111\/2041-210X.12035","article-title":"Geomorph: An r package for the collection and analysis of geometric morphometric shape data","volume":"4","author":"Adams","year":"2013","journal-title":"Methods Ecol. 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