{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T07:10:24Z","timestamp":1788851424791,"version":"build-2803163510"},"posted":{"date-parts":[[2025,12,13]]},"group-title":"Developmental Biology","reference-count":64,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,12,13]],"date-time":"2025-12-13T00:00:00Z","timestamp":1765584000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nd\/4.0\/"}],"funder":[{"name":"NIH-NICHD","award":["P01HD084387"],"award-info":[{"award-number":["P01HD084387"]}]},{"name":"NIH-NIAMS","award":["R01AR072009"],"award-info":[{"award-number":["R01AR072009"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,4]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>\n                  Motile cilia generate fluid flows that are essential for normal development and physiology. Cilia display diverse beating waveforms, and while pronounced defects are strongly associated with motile ciliopathies, subtler alterations also influence disease manifestations. Finer quantification of ciliary dynamics is therefore critical for understanding ciliopathies, but the heterogeneity of cilia beating makes accurate and robust characterization challenging. Here, we present CiliaIO, a machine learning-based tool for quantification of motile cilia morphodynamics. Using this platform, we discovered subtle but highly significant regional differences in ciliary waveforms in the zebrafish spinal cord. To demonstrate the tool\u2019s efficacy, we used CiliaIO to capture and quantify subtle ciliary defects in a novel\n                  <jats:italic>bbs2<\/jats:italic>\n                  allele that causes a late-onset scoliosis phenotype. These results provide a workflow for additional fine-scale analyses of ciliary morphodynamics that will be important for understanding motile ciliopathy.\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>SUMMARY STATEMENT<\/jats:title>\n                  <jats:p>Accurate and automatized cilia quantification is a challenging task. CiliaIO overcomes these challenges using a machine learning-based framework that automatically detects and quantifies cilia morphodynamics.<\/jats:p>\n                <\/jats:sec>","DOI":"10.64898\/2025.12.10.693099","type":"posted-content","created":{"date-parts":[[2025,12,13]],"date-time":"2025-12-13T19:05:13Z","timestamp":1765652713000},"source":"Crossref","is-referenced-by-count":0,"title":["CiliaIO: Machine learning reveals spatial patterns of cilia beating dynamics in the zebrafish spinal cord"],"prefix":"10.64898","author":[{"given":"Ece","family":"Atayeter","sequence":"first","affiliation":[{"name":"Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA"},{"name":"Department of Nutrition and Pediatrics, Dell Pediatric Research Institute, The University of Texas at Austin, Austin, TX 78723, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason","family":"Ho","sequence":"additional","affiliation":[{"name":"Chandra Family Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, Texas 78712, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Talon G.","family":"Blottin","sequence":"additional","affiliation":[{"name":"Department of Nutrition and Pediatrics, Dell Pediatric Research Institute, The University of Texas at Austin, Austin, TX 78723, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ilyena B.","family":"Joe","sequence":"additional","affiliation":[{"name":"Department of Nutrition and Pediatrics, Dell Pediatric Research Institute, The University of Texas at Austin, Austin, TX 78723, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ron","family":"Sistrunk","sequence":"additional","affiliation":[{"name":"Department of Nutrition and Pediatrics, Dell Pediatric Research Institute, The University of Texas at Austin, Austin, TX 78723, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2962-5314","authenticated-orcid":false,"given":"Bo","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Developmental Biology, Washington University School of Medicine, S Euclid Avenue, St. Louis, MO 63110, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lilianna Solnica","family":"Krezel","sequence":"additional","affiliation":[{"name":"Department of Developmental Biology, Washington University School of Medicine, S Euclid Avenue, St. Louis, MO 63110, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas","family":"Gerstlauer","sequence":"additional","affiliation":[{"name":"Chandra Family Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, Texas 78712, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John B.","family":"Wallingford","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9668-6497","authenticated-orcid":false,"given":"Ryan S.","family":"Gray","sequence":"additional","affiliation":[{"name":"Department of Nutrition and Pediatrics, Dell Pediatric Research Institute, The University of Texas at Austin, Austin, TX 78723, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026090723551334000_2025.12.10.693099v2.1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1084576"},{"key":"2026090723551334000_2025.12.10.693099v2.2","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-025-02981-z"},{"key":"2026090723551334000_2025.12.10.693099v2.3","doi-asserted-by":"publisher","DOI":"10.1242\/dev.175794"},{"key":"2026090723551334000_2025.12.10.693099v2.4","doi-asserted-by":"publisher","DOI":"10.1136\/jmedgenet-2019-106424"},{"key":"2026090723551334000_2025.12.10.693099v2.5","doi-asserted-by":"publisher","DOI":"10.1186\/s13244-023-01487-6"},{"key":"2026090723551334000_2025.12.10.693099v2.6","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-026-75076-8"},{"key":"2026090723551334000_2025.12.10.693099v2.7","doi-asserted-by":"publisher","DOI":"10.1038\/ncb2042"},{"key":"2026090723551334000_2025.12.10.693099v2.8","unstructured":"Bradski, G ., 2000. 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