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

bioRxiv (Cold Spring Harbor Laboratory) 2026 Preprint Open access

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Authors: Chetan Poudel, David Brenes, Wenhui Xie, Yvonne Guan, Pedro Vasquez, Naren Mahadevan, Eesha Konatham, Nina Fan, Ziyu Guo, Nicolas J Porter, Madeline K. Wong, Michelle M. Martinez
+7 more Ruben M. Sandoval, Kenneth William Dunn, Pierre C. Dagher, Diana G. Eng, Stuart J. Shankland, Jonathan Liu, Joshua C. Vaughan
DOI: 10.64898/2026.04.23.720231
Cited by: 1

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

Fields of Study & Subjects

Renal and related cancers Digital Holography and Microscopy Microtubule and mitosis dynamics

Publication details

Journal / source
bioRxiv (Cold Spring Harbor Laboratory)
Publisher
openRxiv
Publication date
27 April 2026
Language
EN
Document type
Preprint