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

Thomas Boudier (thomas dot boudier at snv dot jussieu dot fr)

A tutorial (for the previous version) 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 colocalisation 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 :

• Find the smallest and biggest object
• Colorize the objects based on their volume
• Displays the objects in 3D viewer with random colors
• Finds clusters based on closest object

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 :

E. Iannuccelli, F. Mompart, J. Gellin, Y. Lahbib, M. Yerle et T. Boudier.(2010) NEMO: a tool for analyzing gene and chromosome territory distributions from 3D-FISH experiments. Bioinformatics Jan. 14. E. Iannuccelli et al. 2010.

GPL distribution (see licence ). Sources for plugins are available freely. Sources for core are available on request.

Interaction with 3D viewer (21/09/2011)

New version using Swing interface (25/09/2012)

* 29/10/2012 V2.3 : new macro functions for 3D Manager

* 21/03/2013 V2.5 : new design for 3D Manager