{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T10:21:47Z","timestamp":1783506107377,"version":"3.55.0"},"posted":{"date-parts":[[2026,7,6]]},"reference-count":49,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T00:00:00Z","timestamp":1783296000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"crossref","award":["R01DK083345"],"award-info":[{"award-number":["R01DK083345"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"crossref","award":["R21DK136083"],"award-info":[{"award-number":["R21DK136083"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,7,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>Nephrons are the functional units of the kidney; within each nephron, the glomerulus is the initial site of selective filtration that allows removal of waste products while preserving proteins in the bloodstream. Each glomerulus consists of a network of capillaries surrounded by specialized epithelial cells, podocytes, which mediate selective filtration. Abnormalities in glomerular structure impair renal function, resulting in proteinuria and kidney disease. Although several microscopy-based approaches exist to characterize glomerular architecture and structural abnormalities, quantitative analysis is often limited by labor-intensive image segmentation. In this study we present a semi-automated approach for segmentation and analysis of glomerular architecture from three-dimensional confocal microscopy data. Using mTmG transgenic mice that express membrane-associated EGFP in podocytes and membrane-associated tdTomato across all other cell types, we reconstruct podocyte processes and glomerular capillaries from volumetric renal images. This semi-automated approach reduces manual segmentation effort and supports more efficient, standardized analysis of glomerular architecture in three-dimensional confocal microscopy datasets.<\/jats:p>","DOI":"10.64898\/2026.07.03.736410","type":"posted-content","created":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T10:15:13Z","timestamp":1783332913000},"source":"Crossref","is-referenced-by-count":0,"title":["Semi-automated reconstruction of glomerular architecture from 3D confocal microscopy data"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-4430-9920","authenticated-orcid":false,"given":"Yoseph M","family":"Loyd","sequence":"first","affiliation":[{"name":"Dept. of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse NY 13210"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sharon E.","family":"Chase","sequence":"additional","affiliation":[{"name":"Dept. of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse NY 13210"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7008-9069","authenticated-orcid":false,"given":"Mira","family":"Krendel","sequence":"additional","affiliation":[{"name":"Dept. of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse NY 13210"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026070803100873000_2026.07.03.736410v1.1","doi-asserted-by":"publisher","DOI":"10.34067\/KID.0006492020"},{"key":"2026070803100873000_2026.07.03.736410v1.2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx180"},{"key":"2026070803100873000_2026.07.03.736410v1.3","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1016\/j.kint.2018.06.034","article-title":"Kidney-on-a-chip: untapped opportunities","volume":"94","year":"2018","journal-title":"Kidney Int"},{"key":"2026070803100873000_2026.07.03.736410v1.4","first-page":"745319","article-title":"Podocyte Foot Process Effacement Precedes Albuminuria and Glomerular Hypertrophy in CD2-Associated Protein Deficient Mice","volume":"8","year":"2021","journal-title":"Front Med (Lausanne)"},{"key":"2026070803100873000_2026.07.03.736410v1.5","doi-asserted-by":"publisher","DOI":"10.1145\/361002.361007"},{"key":"2026070803100873000_2026.07.03.736410v1.6","doi-asserted-by":"publisher","DOI":"10.1016\/j.kint.2025.08.028"},{"key":"2026070803100873000_2026.07.03.736410v1.7","doi-asserted-by":"publisher","DOI":"10.1369\/0022155419849388"},{"key":"2026070803100873000_2026.07.03.736410v1.8","doi-asserted-by":"publisher","DOI":"10.1152\/ajprenal.00251.2012"},{"key":"2026070803100873000_2026.07.03.736410v1.9","doi-asserted-by":"publisher","DOI":"10.1038\/ki.2008.413"},{"key":"2026070803100873000_2026.07.03.736410v1.10","first-page":"68","article-title":"Implementation of Bernsen\u2019s locally adaptive binarization method for gray scale images","volume":"7","year":"2017","journal-title":"The Online Journal of Science and Technology"},{"key":"2026070803100873000_2026.07.03.736410v1.11","doi-asserted-by":"publisher","DOI":"10.1002\/pro.3235"},{"key":"2026070803100873000_2026.07.03.736410v1.12","doi-asserted-by":"publisher","DOI":"10.1093\/ndt\/gfm344"},{"key":"2026070803100873000_2026.07.03.736410v1.13","doi-asserted-by":"publisher","DOI":"10.1177\/002215540305101203"},{"key":"2026070803100873000_2026.07.03.736410v1.14","doi-asserted-by":"publisher","DOI":"10.1038\/srep08993"},{"key":"2026070803100873000_2026.07.03.736410v1.15","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0106621"},{"key":"2026070803100873000_2026.07.03.736410v1.16","doi-asserted-by":"publisher","DOI":"10.1007\/s10157-020-01854-3"},{"key":"2026070803100873000_2026.07.03.736410v1.17","doi-asserted-by":"publisher","DOI":"10.1039\/C8LC00495A"},{"key":"2026070803100873000_2026.07.03.736410v1.18","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1681\/ASN.2007111172","article-title":"Disruption of Myosin 1e promotes podocyte injury","volume":"20","year":"2009","journal-title":"Journal of the American Society of Nephrology : JASN"},{"key":"2026070803100873000_2026.07.03.736410v1.19","doi-asserted-by":"crossref","first-page":"295","DOI":"10.23876\/j.krcp.20.017","article-title":"Severity of foot process effacement is associated with proteinuria in patients with IgA nephropathy","volume":"39","year":"2020","journal-title":"Kidney Res Clin Pract"},{"key":"2026070803100873000_2026.07.03.736410v1.20","doi-asserted-by":"crossref","first-page":"976043","DOI":"10.3389\/fcell.2022.976043","article-title":"A zebrafish model of congenital nephrotic syndrome of the Finnish type","volume":"10","year":"2022","journal-title":"Front Cell Dev Biol"},{"key":"2026070803100873000_2026.07.03.736410v1.21","doi-asserted-by":"crossref","unstructured":"Li, L. , Y. 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