This plugin adds a 3D Roi Manager to ImageJ and should be used as a complement to 3D Objects Counter.
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 licence ). Sources for plugins are available freely. Sources for core are available on request.