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Updated: May 8, 2026
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High-resolution Time-lapse Imaging and Automated Analysis of Microtubule Dynamics in Living Human Umbilical Vein Endothelial Cells
Published on: August 13, 2016
High-throughput, organ-scale 3D tubule tracking using TubuleMAP
Chetan Poudel1,2,3, David Brenes4,5, Wenhui Xie1,6
1University of Washington, Department of Chemistry, Seattle, WA, USA.
Research Square
|May 7, 2026
Summary
TubuleMAP is a new open-source tool for reconstructing complex tubular networks like kidney nephrons. This 3D tubule mapping software significantly speeds up analysis and reduces manual effort for mesoscale imaging studies.
Area of Science:
- Biomedical Imaging
- Computational Biology
- Renal Physiology
Background:
- Mesoscale imaging of intact tubular networks is advancing with tissue clearing and lightsheet microscopy.
- Analytical tools for mapping tubule continuity and injury patterns in 3D are currently limited.
Purpose of the Study:
- To develop and validate TubuleMAP, a semi-automated pipeline for 3D tubule tracking and reconstruction.
- To enable large-scale analysis of tubular networks from terabyte-scale imaging data.
Main Methods:
- TubuleMAP employs a semi-automated pipeline for 3D tubule tracking and reconstruction.
- The pipeline adapts to diverse morphological and staining patterns and uses parallel processing.
- A napari interface allows for human oversight and interaction.
Main Results:
- TubuleMAP reconstructed 1,000 intact mouse nephrons from ~1-millimeter-thick kidney tissue.
- Analysis achieved ~400-fold higher throughput with ≤1% human effort compared to previous methods.
- Generalizability demonstrated by reconstructing all seminiferous tubules in a mouse testis within one day.
Conclusions:
- TubuleMAP enables unprecedented scale analysis of tubular organization and pathology.
- The tool facilitates whole-nephron cytometry and identification of rare morphologies.
- TubuleMAP is released as an open-source Python package for broad accessibility.
