High-throughput, organ-scale 3D tubule tracking using TubuleMAP

High-throughput, organ-scale 3D tubule tracking using TubuleMAP | 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 Article High-throughput, organ-scale 3D tubule tracking using TubuleMAP Chetan Poudel, David Brenes, Wenhui Xie, Yvonne Guan, Pedro Vasquez, and 14 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9510358/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 Advances in tissue clearing and lightsheet microscopy enable mesoscale imaging of intact and convoluted tubular networks, yet analytical tools to map tubule continuity and assess injury patterns within and across tubules are limited. Here, we introduce TubuleMAP, a semi-automated pipeline for 3D tubule tracking and reconstruction that adapts to various morphological and staining patterns, leverages parallel processing of terabyte-scale data for large-scale analysis of tubular networks, and uses a napari interface for human oversight. Using TubuleMAP, we reconstruct 1,000 intact mouse nephrons in ~1-millimeter-thick kidney slab with ~400-fold higher throughput and ≤1% human effort compared to prior approaches. These reconstructions enable analysis of mesoscale nephron organization, quantitative profiling of pathologic morphologies, whole-nephron cytometry, and identification of rare morphologies at unprecedented scales. We demonstrate generalizability by reconstructing all seminiferous tubules in a mouse testis within a day. TubuleMAP is released as an open-source Python package. Biological sciences/Biological techniques/Software Biological sciences/Biological techniques/Microscopy/Light-sheet microscopy Biological sciences/Computational biology and bioinformatics/Image processing Full Text Additional Declarations Yes there is potential Competing Interest. J.T.C.L. is a cofounder, equity holder, and board member of Alpenglow Biosciences, Inc., which has licensed the 3D pathology technologies developed in his lab, including patents related to open-top light-sheet (OTLS) microscopy. S.J.S. is a consultant for Lumen Biosciences. The other authors report no competing interests. Supplementary Files SupplementaryVideo3.mp4 Supplementary Video 3 SupplementaryVideo6.mp4 Supplementary Video 6 SupplementaryVideo2.mp4 Supplementary Video 2 SupplementaryVideo7.mp4 Supplementary Video 7 SupplementaryVideo9.mp4 Supplementary Video 9 SupplementaryVideo5.mp4 Supplementary Video 5 SupplementaryVideo8.mp4 Supplementary Video 8 SupplementaryVideo4.mp4 Supplementary Video 4 SupplementaryVideo1.mp4 Supplementary Video 1 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-9510358","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":629057702,"identity":"60a9a219-a394-4004-b546-e86776a939c3","order_by":0,"name":"Chetan 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