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Vessel3DTracer is an ImageJ plugin for segmentation and quantification of hollow and filled 3D vasculature.

Download the plugin

  1. Download Vessel3DTracer.jar
  2. Place it into the plugins folder of ImageJ or Fiji


The image should represent bright vasculature on dark background, in 8-bit z-stack.


The software provided here is a plugin for ImageJ/Fiji, which has a public domain license and runs on several platforms: Linux, Windows, and Mac OS X.

Conditions of use

This software is free to use for research purposes, but it should not redistributed without our consent.

In addition, adequate citations and acknowledgments are expected to be included whenever results based on Vessel3DTracer are presented or published.

Vessel 3DTracer is written by



Hollow vasculature segmentation

Hollow vasculature segmentation.

Download example images for hollow vasculature segmentation.

Filled vasculature segmentation

Filled vasculature segmentation.

Download example images for filled vasculature segmentation.

Binary mask re-segmentation

Download example images for binary mask re-segmentation.


Segmentation of vasculature

Manual edition

  • Deletion of branch
  • Partial deletion of branch
  • Manual connection of two branches
  • Manual drawing of a new branch


  • Skeleton
  • Mask
  • Measurements of the vascular network



In case you have further questions about the software, please contact Marta Trusohamn.