3D Tools

This plugin adds 3D tools to ImageJ.


Thomas Boudier


The plugin comprises tools for 3D drawing :

  • Drawing 3D line
  • Drawing 3D ellipsoids in any direction
  • Drawing in stacks as volumes
  • Drawing in 3D viewer as surfaces

A 3D crop is available (cubic or spherical cropping), it works also with a list of points in the RoiManager to automatically crop all positions and save them.

A 3D radial distribution is available, it computes the mean value of pixel in surrounding spherical layers.

A plugin to draw contours of 3D objects, using a 3D labeled image as input.

3D random ellipsoids

3D random ellipsoids : Macro


For details go to the 3D ImageJ Suite.


GPL distribution (see licence ). Sources for plugins are available freely. Sources for core are available on request.


  • 24/10/2013 core V2.7 : plugin to draw slices of 3D objects
  • 27/04/2015 core V3.1 : bug in colocalisation (rare objects configuration) + improved split + poles in ellipsoid fitting
plugin/stacks/3d_tools/start.txt · Last modified: 2015/08/20 10:50 by tboudier
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