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plugin:stacks:3d_roi_manager:start [2019/01/23 04:52]
plugin:stacks:3d_roi_manager:start [2019/04/12 11:13] (current)
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 +
 +===== 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.
 +