19-08-2012

1/4

3D Roi Manager and 3D Analysis

3D Roi Manager and 3D Analysis

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

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

Features
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 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

ImageJ Documentation Wiki - http://imagejdocu.tudor.lu/

3D Roi Manager and 3D Analysis

2/4

19-08-2012

Description
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. In order to use the installed commands you need to activate them with Ext.install(RoiManager3D_);

http://imagejdocu.tudor.lu/

Printed on 2012/08/19 04:46

19-08-2012

3/4

3D Roi Manager and 3D Analysis

3D cluster analysis : Macro (done by Jean-Franois Gilles)

Installation
Download and copy the two jars in your plugins folder.

Download
Core library : mcib3d-core.jar Plugins : mcib3d_plugins.jar 3d-manager-measure.png 3d_clusters.png 165149 2011/09/21 12:14 42097 2011/03/17 13:38 2011/03/17 14:05 2011/09/21 12:59

macromanager3ddistanceanalysiscluster.ijm 5994 macromanager3ddistanceanalysiscluster2.ijm 9274

ImageJ Documentation Wiki - http://imagejdocu.tudor.lu/

3D Roi Manager and 3D Analysis

4/4

19-08-2012

macros_roimanager3d_en.pdf

43826 2011/03/17 12:25

Citation
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..

License
Sources are available here.

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

Known Bugs
The about button does not seem to work with Fiji and some ImageJ versions.

From: http://imagejdocu.tudor.lu/ - ImageJ Documentation Wiki Permanent link: http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_roi_manager:start Last update: 2012/03/19 11:45

http://imagejdocu.tudor.lu/

Printed on 2012/08/19 04:46