ImageJ

3D ImageJ Suite (3DSuite)
Author	Thomas Boudier, Jean Ollion
Update site	3D ImageJ Suite
Maintainer	Thomas Boudier
Source	on GitHub
Initial release	25/09/2012, V2.0
Latest version	30/10/2019, V3.96
Development status	stable, active
Category	3D, Analysis, Filtering, Segmentation, Mathematical morphology

3D ImageJ Suite

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

Migrating 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 : Media:NEUBIAS_3DSuite.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.

Author

Thomas Boudier

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, Academia Sinica, Taipei, Taiwan.

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

Features

This suite is composed of :

• 3D Filters (mean, median, max, min, tophat, max local, ...) and Edge and symmetry filter
• 3D Segmentation (iterative thresholding, spots segmentation, watershed, ...)
• 3D Mathematical Morphology tools (fill holes, binary closing, distance map, ...)
• 3D RoiManager (3D display and analysis of 3D objects)
• 3D Analysis (Geometrical measurements, Mesh measurements, Convex hull, ...)
• 3D MereoTopology (Relationship between objects)
• 3D Tools (Drawing ellipsoids and lines, cropping, ...)

A 2D/3D spatial statistics plugin is also available.

Installation

From version 2.7, 3D ImageJ Suite is available in Fiji as an Fiji update site. The Java8 and ImageScience update sites must be activated in Fiji, see instructions here].

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.

You have also to manually download and copy into your plugins directory the imagescience.jar library from here.

Download

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

NEW 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 Media:3d_viewer-mcib.zip, just unzip the file in the plugins directory).

Java 1.8 or later is required. The imagescience library is required  : download here.

Bundle : Media:Mcib3d-suite3.96.3.zip

Sources are available on GitHub for core and plugins.

Citation

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

License

GPL distribution (see license). Sources available on Github (see Download)

Acknowledgements

The 3D suite would like to thanks the developers of the following plugins :

• Imagescience
• LocalThickness
• ConvexHull3D
• 3D Object Counter
• Droplet Counter
• and P. Andrey, J.-F. Gilles.

Links

• BoneJ2
• 3D Shapes
• 3D Annotation Tool
• 3D Viewer
• MorphoLibJ

Change Log

• 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.