3D ImageJ Suite

This suite provides plugins to enhance 3D capabilities of ImageJ.

Updated contents from 3D Suite on ImageJ Documentation Website.

The pdf of the NEUBIAS academy presentation "Introduction to 3D Analysis with 3D ImageJ suite" is available : (pdf).

The associated video is available on YouTube. The QAs are available on the image.sc forum.

The associated project for automation is available in TAPAS.


Thomas Boudier, Centrale Méditerranée, Nice Campus, France.

You can contact me on image.sc @ThomasBoudier.

With many contributions from J. Ollion, Laboratoire Jean Perrin, Paris, France.


This suite is composed of plugins to perform different tasks on image stacks :

  • Filters for pre- and post-filtering. Filters can be used to reduce noise (see median filter in 3D Fast Filters). Some filters (edge and symmetry or maxima finder) can help detect seeds for further segmentation (such as spot segmentation or watershed)

  • Binary filters will improve thresholding or segmentation results such as fill holes or exclude objects on edges. For labelled image close labels can help make objects shape more compact. Maps can also be created such as distance map to compute distance from all pixels to the border of the labelled objects.

  • Segmentation for objects detection. Thresholding will create a binary image and can be performed using Adjust/Threshold. Labelling will detect the different objects in a binary image (see simple, hysteresis or iterative segmentation plugins). For seeds-based detection watershed segmentation can be used. Custom segmentation plugins are also available for spots or nuclei (in culture cells images).

  • Analysis to perform various 3D measurements of the objects, such as geometry, shape, or -intensity-. Relationships between objects can also be studied with plugins such as distances or co-localisation. Finally 3D spatial organisation can be assessed with plugins such as EVF Analysis or Spatial Statistics.

  • The 3D Manager interface acts a a manager for 3D objects, to perform measurements.

  • Various tools are also available, especially to create 3D Shapes or Draw 3D contours as Rois.


From version 2.7, 3D ImageJ Suite is available in Fiji as an update site. The Java8 update site must be activated in Fiji. For versions 2 and 3, the ImageScience update site must also be activated in Fiji.

You can also install 3D ImageJ Suite manually (see download section) and unzip it in your plugins folder. The various plugins will appear in the menu 3D of the plugins list.

For versions 2 and 3, you have also to manually download and copy into your plugins directory the imagescience.jar library from here.


ImageJ 1.47 or later is required. Java3D is also required, check that 3D Viewer is working.

From version 3.83 and later, for ImageJ users the new version 4.0.1 of 3D Viewer is required (please remove the 3D Viewer plugin provided by ImageJ and replace it by this version, just unzip the file in the plugins directory).

Java 1.8 or later is required. For versions 2 and 3, the imagescience library is required : download here.

Sources are available on Framagit for core and plugins.


If you use the 3D suite for your publication, please cite :

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 GPLv3. Sources available on Framagit (see Download).


The 3D suite would like to thank P. Andrey, J.-F. Gilles and the developers of the following plugins :

Change Log

  • 19/04/2023 V4.1.5: Bug fixes, seeds option for segmentation.
  • 20/03/2023 V4.1.2: Bug fixes. Intensity Mode Non Zero. Plugin Voxelizer.
  • 26/01/2023 V4.1.0: New design for 3DManager. New Macro Extensions. New plugin Merge Labels.
  • 23/09/2022 V4.0.93: New Center-Border distances. Improved 3D Maxima Finder. Testing new 3D Manager.
  • 30/06/2022 V4.0.88: Minor changes.
  • 08/04/2022 V4.0.87: Improved Measurements. New method FillHoles in BinaryCloseLabels.
  • 09/02/2022 V4.01: Changed Value to Label for segmented objects. Corrected bugs in Analysis.
  • 05/01/2022 V4.01: Redesigned code for 3D Objects and measurements; new plugins and organisation.
  • 30/10/2019 V3.96: Bug fixes and improvements. New plugins distances and interactions.
  • 15/01/2019 V3.94: Bug fixes and improvements. 3D Manager interface improved.
  • 19/10/2018 V3.93: Bug fixes and improvements. New plugins MultiColoc, EVF radial analysis and density.
  • 14/03/2018 V3.92: Bug fixes and improvements. New Roi3D overlay in 3DManager.
  • 05/01/2018 V3.91: Bug fixes and improvements.
  • 10/04/2017 V3.9 : Display computing time and ETC for filters, new LooknFeel for Manager.
  • 22/08/2016 V3.83: New plugin Radial Distance Area Ratio (RDAR), Watershed improved.
  • 04/07/2016 V3.82: compatibility with new version of 3D viewer, improvements and bug fixes.
  • 30/03/2016 V3.74: bug fixed in EDT.
  • 18/03/2016 V3.71: new plugin 3D Maxima Finder.
  • 02/03/2016 V3.7 : bug fixes, new plugin exclude objects on borders.
  • 07/12/2015 V3.6 : bug fixes, new edge and symmetry filters, sync between 3D Viewer select object and 3DManager.
  • 01/09/2015 V3.5 : compatibility with ImageScience 3.0.
  • 20/08/2015 V3.4 : redesigned Watershed, Record Iterative Thresholding, Quantification in 32-bits images with NaN values.
  • 05/06/2015 V3.3 : new function closeResults saveResults 3DManager + exclude on edges.
  • 25/05/2015 V3.2 : improved watershed (especially for flat regions).
  • 27/04/2015 V3.1 : bug in colocalisation (rare objects configuration) + improved split + poles in ellipsoid fitting.
  • 21/11/2014 V3.0 : closest object in selection for 3D Manager. Macros functions to save results for 3D Manager.
  • 03/10/2014 V2.9 : new Results Tables for 3DManager.
  • 03/06/2014 V2.8 : new plugin shape analysis. Load/save objects with calibration.
  • 21/03/2014 V2.71: bug fix in Segment3D.
  • 24/10/2013 V2.7 : new segmentation Iterative thresholding; check for required libraries at startup; 32-bits segmentation and labelling.
  • 28/05/2013 V2.6 : bug fixes and improvements, new filters openGray and closeGray.
  • 21/03/2013 V2.5 : new design for 3D Manager.
  • 08/02/2013 V2.4 : new plugin MereoTopology 3D.
  • 29/10/2012 V2.3 : new macro functions for 3D Manager.
  • 22/10/2012 V2.3 : bug fixed for filters3D with 32-bits images.
  • 12/10/2012 V2.2 : calibration bug fixed in spatial statistics.
  • 28/09/2012 V2.1 : corrected bug in display (Ellipsoid3D and RoiManager3D).
  • 25/09/2012 V2.0 : first version.