===== 3D Roi Manager  =====
This plugin adds a 3D Roi Manager to ImageJ and should be used as a complement to [[plugin:analysis:3d_object_counter:start|3D Objects Counter]].

===== Author =====
Thomas Boudier
===== Features =====
A tutorial can be found [[tutorial:working:tutorial_for_3d_roi_manager|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

{{:plugin:stacks:3d_roi_manager:3d_manager_general2.png|}}

===== 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 [[plugin:analysis:3d_object_counter:start|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 {{:plugin:stacks:3d_ij_suite:macrosfunctionsroimanager3d.pdf|here}}. Here are examples of macros : 

  * {{:plugin:stacks:3d_roi_manager:macromanager3d2_measure.ijm|Basic use of measurements, save and close window}}
  * {{:plugin:stacks:3d_roi_manager:macromanager3d_quantifmultichannel.ijm|Example for signal quantification}}
  * {{:plugin:stacks:3d_roi_manager:macromanager3d_quantifmultichannel2.ijm|Example 2 for signal quantification}}
  * {{:plugin:stacks:3d_ij_suite:macromanager3d2_selected.ijm|Example to get the list of selected objects}}
  * {{:plugin:stacks:3d_roi_manager:macromanager3d2_centres.ijm|Draw a sphere at position of objects centre}}
  * {{:plugin:stacks:3d_ij_suite:macromanager3d2_minmax.ijm|Find the smallest and biggest object}}
  * {{:plugin:stacks:3d_ij_suite:macromanager3d2_colorsize.ijm|Colorize the objects based on their volume}}
  * {{:plugin:stacks:3d_ij_suite:macromanager3d2_colorsviewer3d.ijm|Displays the objects in 3D viewer with random colors}}
  * {{:plugin:stacks:3d_roi_manager:macromanager3d2_lutviewer3d.ijm|Displays the objects in 3D viewer with LUT colors}}
  * {{:plugin:stacks:3d_ij_suite:macromanager3d2_cluster.ijm|Finds clusters based on closest object}} 


===== Download =====
For details go to the [[plugin:stacks:3d_ij_suite:start|3D ImageJ Suite]].

ImageJ 1.47 or later is required. Java3D is also required.

Java 1.6 or later is required.
===== Citation =====
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. [[http://dx.doi.org/10.1093/bioinformatics/btt276|doi]]
===== License =====
GPL distribution (see [[http://www.cecill.info/index.en.html|license]]).




===== Change log =====

  * 29/10/2012  V2.3 : new macro functions for 3D Manager
  * 21/03/2013  V2.5 : new design for 3D Manager
  * 24/10/2013  V2.7 : 32-bits segmentation for large number of objects (>65535)
  * 03/06/2014  V2.8 : load/save objects with calibration
  * 03/10/2014  V2.9 : new Results Tables for 3DManager
  * 21/11/2014  V3.0 : closest object in selection for 3D Manager + Macros functions to save results for 3D Manager
  * 27/04/2015  V3.1 : bug in colocalisation (rare objects configuration) + improved split
  * 05/06/2015  V3.3 : new function closeResults saveResults 3DManager + exclude on edges
  * 20/08/2015  V3.4 : quantification in 32-bits images with NaN values
  * 07/12/2015  V3.6 : option to sync between 3D Viewer selected object and 3DManager
  * 10/04/2017  V3.9 : new LookNFeel for interface, handling hyperstacks
  * 14/03/2018  V3.92: Bug fixes and improvements + new Roi3D overlay in 3DManager
  * 19/10/2018  V3.93: Bug fixes and improvements + numbers objects within objects (Quantif) + manual classification (press 0,1,2, ..)
  * 15/01/2019  V3.94: Improved interface, actioning buttons will not freeze interface.