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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.

Biorxiv : the Preprint Server for Biology
|May 7, 2026
PubMed
Summary
This summary is machine-generated.

TubuleMAP is a new open-source pipeline for 3D tubule reconstruction. It enables high-throughput analysis of complex tubular networks like nephrons and seminiferous tubules, significantly reducing human effort.

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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
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Published on: August 13, 2016

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Published on: April 20, 2017

Area of Science:

  • Biomedical Imaging
  • Computational Biology
  • Histology

Background:

  • Mesoscale imaging of intact tubular networks is advancing with tissue clearing and lightsheet microscopy.
  • Analytical tools for 3D tubule mapping, continuity assessment, and injury pattern analysis are currently limited.

Purpose of the Study:

  • To develop a semi-automated pipeline, TubuleMAP, for 3D tubule tracking and reconstruction.
  • To enable large-scale analysis of complex tubular networks with high throughput and reduced human effort.

Main Methods:

  • TubuleMAP is a semi-automated pipeline utilizing parallel processing for terabyte-scale data.
  • It adapts to diverse morphological and staining patterns and includes a napari interface for human oversight.
  • The pipeline performs 3D tubule tracking and reconstruction.

Main Results:

  • Reconstructed 1,000 intact mouse nephrons from ~1-millimeter-thick kidney tissue with ~400-fold higher throughput and <1% human effort.
  • Demonstrated generalizability by reconstructing all seminiferous tubules in a mouse testis within a day.
  • Enabled mesoscale nephron organization analysis, quantitative profiling of pathologies, and whole-nephron cytometry.

Conclusions:

  • TubuleMAP provides a powerful tool for analyzing complex tubular structures at unprecedented scales.
  • The open-source pipeline facilitates detailed investigation of tissue architecture and pathology.
  • This technology advances the study of tubular networks in various biological contexts.