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Related Concept Videos

Microtubules01:35

Microtubules

There are three types of cytoskeletal structures in eukaryotic cells—microfilaments, intermediate filaments, and microtubules. With a diameter of about 25 nm, microtubules are the thickest of these fibers. Microtubules carry out a variety of functions that include cell structure and support, transport of organelles, cell motility (movement), and the separation of chromosomes during cell division.

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Related Experiment Video

Updated: May 8, 2026

High-resolution Time-lapse Imaging and Automated Analysis of Microtubule Dynamics in Living Human Umbilical Vein Endothelial Cells
10:25

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
PubMed
Summary
This summary is machine-generated.

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.

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Related Experiment Videos

Last Updated: May 8, 2026

High-resolution Time-lapse Imaging and Automated Analysis of Microtubule Dynamics in Living Human Umbilical Vein Endothelial Cells
10:25

High-resolution Time-lapse Imaging and Automated Analysis of Microtubule Dynamics in Living Human Umbilical Vein Endothelial Cells

Published on: August 13, 2016

High-resolution Imaging and Analysis of Individual Astral Microtubule Dynamics in Budding Yeast
10:23

High-resolution Imaging and Analysis of Individual Astral Microtubule Dynamics in Budding Yeast

Published on: April 20, 2017

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.