Automated 3D Morphometric Analysis Reveals Nuclear Hypertrophy and Reduced Cell Density in cdh2-Deficient Zebrafish Embryos

Automated 3D Morphometric Analysis Reveals Nuclear Hypertrophy and Reduced Cell Density in cdh2-Deficient Zebrafish Embryos | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Automated 3D Morphometric Analysis Reveals Nuclear Hypertrophy and Reduced Cell Density in cdh2 -Deficient Zebrafish Embryos Yashwant Nama This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8986693/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract The mechanical regulation of nuclear volume is a fundamental yet under-explored aspect of embryogenesis. We developed an automated computational framework in Python to quantify 3D nuclear morphometry in zebrafish (Danio rerio) embryos. Applying this pipeline to cdh2-CRISPR mutant image stacks from the BioImage Archive (Accession: S-BIAD1405), we observed pronounced nuclear hypertrophy associated with reduced cadherin-mediated adhesion. Using voxel scaling factors verified in ImageJ (pixel width/height = 0.991492 µm; z spacing = 1.0 µm; consistent across WT and mutant stacks), we observed a ≈12.0% increase in median nuclear volume (1,606 vs. 1,434 voxels; Mann–Whitney U, p = 0.0407), while nearest-neighbor distances remained broadly similar, suggesting that local packing is comparatively preserved. These results support a model in which cadherin-dependent mechanical coupling contributes to nuclear size homeostasis. We provide biological insight into the mechanobiological role of cdh2 and an open-source workflow for reproducible volumetric analysis in complex 3D biological systems. Computational Biology Bioinformatics Systems Biology Stem Cell & Developmental Cell Biology 3D Morphometrics N-cadherin Zebrafish Embryology Mechanobiology Python Nuclear Volume Regulation. Full Text Additional Declarations The authors declare no competing interests. Supplementary Files Supplementary.pdf Supplementary Material: Code and Data Availability Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-8986693","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":598069561,"identity":"10487799-d971-481c-810b-598cdb88371f","order_by":0,"name":"Yashwant Nama","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA80lEQVRIiWNgGAWjYDADAzBZAcTMzA0kaDlwBqSFkRQtB9tAJAEt5uynEz8wttnZm0skP3v8cV5tNH87UMuPim04tVj25G6WYGxLTtw5I83c4OC247kzDjM2MPacuY3bPQdyNwC1MCcY3E4wkzi47VhuA1ALM2MbHi3n327+wdhWb29wO/2bxME5x3LnE9RyI3cb0JbDjBtu5wBtaajJ3UBYy9ttFgnnjiduuP+mTOLMsQO5G4FaDuL1y/nczTc+lFXbG5w5vk2ioqYud975wwcf/KjArQUMEtngzMNg8gB+9SDwB86qI6x4FIyCUTAKRhwAAHzEYxurZSi+AAAAAElFTkSuQmCC","orcid":"https://orcid.org/0009-0003-3443-4413","institution":"Independent Researcher, Jaipur, Rajasthan, India","correspondingAuthor":true,"prefix":"","firstName":"Yashwant","middleName":"","lastName":"Nama","suffix":""}],"badges":[],"createdAt":"2026-02-27 10:21:08","currentVersionCode":1,"declarations":{"humanSubjects":false,"vertebrateSubjects":true,"conflictsOfInterestStatement":false,"humanSubjectEthicalGuidelines":false,"humanSubjectConsent":false,"humanSubjectClinicalTrial":false,"humanSubjectCaseReport":false,"vertebrateSubjectEthicalGuidelines":true},"doi":"10.21203/rs.3.rs-8986693/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-8986693/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":104399906,"identity":"5b121425-8537-4361-b694-396be4006d17","added_by":"auto","created_at":"2026-03-11 12:08:08","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1604741,"visible":true,"origin":"","legend":"","description":"","filename":"NamaYZebrafishMorphometrics2026.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8986693/v1_covered_9d80cd76-102d-42d1-84a8-c294e88df924.pdf"},{"id":103726049,"identity":"b4eb82af-8778-4c21-ac00-ad19fe0a36f1","added_by":"auto","created_at":"2026-03-02 08:22:49","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":93616,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eSupplementary Material: Code and Data Availability\u003c/strong\u003e\u003c/p\u003e","description":"","filename":"Supplementary.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8986693/v1/fd0e5b4389f9d87c39d8e272.pdf"}],"financialInterests":"The authors declare no competing interests.","formattedTitle":"\u003cp\u003eAutomated 3D Morphometric Analysis Reveals Nuclear Hypertrophy and Reduced Cell Density in\u003cem\u003e cdh2\u003c/em\u003e-Deficient Zebrafish Embryos\u003c/p\u003e","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"Independent Researcher","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"3D Morphometrics, N-cadherin, Zebrafish Embryology, Mechanobiology, Python, Nuclear Volume Regulation.","lastPublishedDoi":"10.21203/rs.3.rs-8986693/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8986693/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eThe mechanical regulation of nuclear volume is a fundamental yet under-explored aspect of embryogenesis. 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