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3D Roi Manager

This plugin adds a 3D Roi Manager to ImageJ and should be used as a complement to 3D Objects Counter.


Thomas Boudier


A tutorial can be found here.

* 3D thresholding and segmentation

* 3D quantitative measurements (volume, surface, feret, ellipsoid fitting, …)

* 3D intensity measurements (min, max, mean, integrated density, …)

* 3D distance measurements (centre to centre, centre to border, border to border, radial distance, eccentricity)

* 3D co-localisation and contact surface

* 3D split (tries to split the object in two)

* 3D angle (between 3 objects)

* 3D list of voxels

* Can interact with 3D Viewer

* Macro recordable


This plugin acts as a RoiManager for 3D objects, the image can be segmented directly within the plugin via the 3D segment button.

Typically the objects would have been segmented with the 3D Objects Counter plugin. Then use the Add Image button to import the objects into the 3D RoiManager.

The measurements and options can be set in 3D Manager Options.

The functions works on selected objects, you can choose to select only one object with MonoSelect or multiple selection with MultiSelect. If no objects are selected, the functions will work on all objects.

The list of available macros functions are available here. Here are examples of macros :


For details go to the 3D ImageJ Suite.

ImageJ 1.47 or later is required. Java3D is also required.

Java 1.6 or later is required.


When using the 3D Roi Manager plugin for publication, please refer to :

J. Ollion, J. Cochennec, F. Loll, C. Escudé, T. Boudier. (2013) TANGO: A Generic Tool for High-throughput 3D Image Analysis for Studying Nuclear Organization. Bioinformatics 2013 Jul 15;29(14):1840-1. doi


GPL distribution (see license).

Change log

  • 29/10/2012 V2.3 : new macro functions for 3D Manager
  • 21/03/2013 V2.5 : new design for 3D Manager
  • 24/10/2013 V2.7 : 32-bits segmentation for large number of objects (>65535)
  • 03/06/2014 V2.8 : load/save objects with calibration
  • 03/10/2014 V2.9 : new Results Tables for 3DManager
  • 21/11/2014 V3.0 : closest object in selection for 3D Manager + Macros functions to save results for 3D Manager
  • 27/04/2015 V3.1 : bug in colocalisation (rare objects configuration) + improved split
  • 05/06/2015 V3.3 : new function closeResults saveResults 3DManager + exclude on edges
  • 20/08/2015 V3.4 : quantification in 32-bits images with NaN values
  • 07/12/2015 V3.6 : option to sync between 3D Viewer selected object and 3DManager
  • 10/04/2017 V3.9 : new LookNFeel for interface, handling hyperstacks
  • 14/03/2018 V3.92: Bug fixes and improvements + new Roi3D overlay in 3DManager
  • 19/10/2018 V3.93: Bug fixes and improvements + numbers objects within objects (Quantif) + manual classification (press 0,1,2, ..)
  • 15/01/2019 V3.94: Improved interface, actioning buttons will not freeze interface.
plugin/stacks/3d_roi_manager/start.txt · Last modified: 2019/04/12 13:13 by

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