Table of Contents

3D ImageJ Suite

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

Author

Thomas Boudier email, Academia Sinica, Taipei, Taiwan.

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

Features

This “suite” is composed of :

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 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 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. The imagescience library is required : download. Bundle : mcib3d-suite3.96.zip

Core library : mcib3d-core-3.96.jar

Plugins : mcib3d_plugins-3.96.jar

The ConvexHull3D plugin is required only for mesh measurements : quickhull jar

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 and : P. Andrey, J.-F. Gilles.

Change Log