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===== 3D ImageJ Suite =====
This "suite" provides plugins to enhance 3D capabilities of ImageJ.  

===== Author =====
Thomas Boudier  {{:plugin:stacks:3d_ij_suite:email.png|email}}, [[http://www.imb.sinica.edu.tw/en/|Academia Sinica]], Taipei, Taiwan.

With many contributions from J. Ollion, Laboratoire Jean Perrin, Paris, France.
===== Features =====

This "suite" is composed of : 

  * [[plugin:filter:3d_filters:start|3D Filters]] (mean, median, max, min, tophat, max local, ...) and [[plugin:filter:3d_edge_and_symmetry_filter:start|edge and symmetry filter]]
  * [[plugin:segmentation:3d_spots_segmentation:start|3D Segmentation]] (iterative thresholding, spots segmentation, watershed, ...)
  * [[plugin:morphology:3d_mathematical_morphology_:start|3D Mathematical Morphology]] tools (fill holes, binary closing, distance map, ...)
  * [[plugin:stacks:3d_roi_manager:start|3D RoiManager]] (3D display and analysis of 3D objects)
  * [[plugin:analysis:3d_analysis:start|3D Analysis]] (Geometrical measurements, Mesh measurements, Convex hull, ...)
  * [[plugin:analysis:3d_mereotopology:start|3D MereoTopology]] (Relationship between objects)
  * [[plugin:stacks:3d_tools:start|3D Tools]] (Drawing ellipsoids and lines, cropping, ...)

A 2D/3D [[plugin:analysis:spatial_statistics_2d_3d:start|spatial statistics]] plugin is also available.

===== Installation =====
From version 2.7, 3D ImageJ Suite is available in Fiji as an [[http://fiji.sc/List_of_update_sites|Fiji update site]]. The **Java8** and **ImageScience** update sites must be activated in Fiji, see instructions [[https://imagej.net/Following_an_update_site|here]]. 

You can also install 3D ImageJ Suite [[plugin:stacks:3d_ij_suite:start#download|manually]] and unzip it in your plugins folder. The various plugins will appear in the menu //3D// of the plugins list.
You have also to manually download and copy into your plugins directory the **imagescience.jar** library from [[http://www.imagescience.org/meijering/software/featurej/|here]].


===== Download =====
ImageJ 1.47 or later is required. Java3D is also required, check that [[http://rsbweb.nih.gov/ij/plugins/3d-viewer/|3D Viewer]] is working. 

**NEW** From version 3.83 and later the new version 4.0.1 of 3D_Viewer is required (please remove the 3D_Viewer plugin provided by ImageJ and replace it by {{:plugin:stacks:3d_ij_suite:3d_viewer-mcib.zip|this version}}, just unzip the file in the plugins directory). 

Java 1.8 or later is required. **The [[http://www.imagescience.org/meijering/software/featurej/|imagescience]] library is required ** : [[http://www.imagescience.org/meijering/software/download/imagescience.jar|download]]. 
**Bundle** : {{:plugin:stacks:3d_ij_suite:mcib3d-suite3.96.zip|}}

Core library : {{:plugin:stacks:3d_ij_suite:mcib3d-core-3.96.jar|}}

Plugins : {{:plugin:stacks:3d_ij_suite:mcib3d_plugins-3.96.jar|}}

The [[http://rsbweb.nih.gov/ij/plugins/3d-convex-hull/index.html| ConvexHull3D]] plugin is required only for mesh measurements : {{:plugin:stacks:3d_ij_suite:quickhull3d-1.0.0.jar|quickhull jar}}

Sources are available on [[https://github.com/|GitHub]] for [[https://github.com/mcib3d/mcib3d-core|core]] and [[https://github.com/mcib3d/mcib3d-plugins|plugins]]. 

===== Citation =====
If you use the 3D suite for your publication please cite : 

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]]). Sources available on Github (see Download) 

===== Acknowledgements =====
The 3D suite would like to thanks the developers of the following plugins :  [[http://www.imagescience.org/meijering/software/featurej/|Imagescience]],  [[https://www.optinav.info/Local_Thickness.htm|LocalThickness]],  [[http://rsbweb.nih.gov/ij/plugins/3d-convex-hull/index.html| ConvexHull3D]],  [[plugin:analysis:3d_object_counter:start|3D Object Counter]], [[plugin:analysis:droplet_counter:start|droplet]] and : P. Andrey, J.-F. Gilles. 

===== Links =====

  * [[http://bonej.org/|BoneJ]] 
  * [[plugin:analysis:droplet_counter:start|DropletCounter]]
  * [[https://sites.google.com/site/learnimagej/plugins/3d-shape|3D Shapes]]
  * [[plugin:utilities:annotation_roi_3d:start|3D Annotation Tool]]
  * [[plugin:analysis:3d_object_counter:start|]]
  * [[http://3dviewer.neurofly.de/|3D Viewer]]
  * [[http://www.optinav.com/Local_Thickness.htm|Local Thickness]]

===== Change Log =====
  * 25/09/2012 V2.0 : first version 
  * 28/09/2012 V2.1 : corrected bug in display (Ellipsoid3D and RoiManager3D)
  * 12/10/2012 V2.2 : calibration bug fixed in spatial statistics
  * 22/10/2012 V2.3 : bug fixed for filters3D with 32-bits images
  * 29/10/2012 V2.3 : new macro functions for 3D Manager 
  * 08/02/2013 V2.4 : new plugin MereoTopology 3D
  * 21/03/2013 V2.5 : new design for 3D Manager
  * 28/05/2013 V2.6 : bug fixes and improvements, new filters openGray and closeGray
  * 24/10/2013 V2.7 : new segmentation Iterative thresholding; check for required libraries at startup; 32-bits segmentation and labelling
  * 21/03/2014 V2.71: bug fix in Segment3D
  * 03/06/2014 V2.8 : new plugin shape analysis. 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 + poles in ellipsoid fitting
  * 25/05/2015 V3.2 : improved watershed (especially for flat regions)
  * 05/06/2015 V3.3 : new function closeResults saveResults 3DManager + exclude on edges
  * 20/08/2015 V3.4 : redesigned Watershed, Record Iterative Thresholding, Quantification in 32-bits images with NaN values
  * 01/09/2015 V3.5 : compatibility with ImageScience 3.0
  * 07/12/2015 V3.6 : bug fixes, new edge and symmetry filters, sync between 3D Viewer select object and 3DManager
  * 02/03/2016 V3.7 : bug fixes, new plugin exclude objects on borders
  * 18/03/2016 V3.71: new plugin 3D Maxima Finder
  * 30/03/2016 V3.74: bug fixed in EDT
  * 04/07/2016 V3.82: compatibility with new version of 3D viewer, improvements and bug fixes
  * 22/08/2016 V3.83: New plugin Radial Distance Area Ratio (RDAR), Watershed improved
  * 10/04/2017 V3.9 : Display computing time and ETC for filters, new LooknFeel for Manager  
  * 05/01/2018 V3.91: Bug fixes and improvements
  * 14/03/2018 V3.92: Bug fixes and improvements. New Roi3D overlay in 3DManager
  * 19/10/2018 V3.93: Bug fixes and improvements. New plugins MultiColoc, EVF radial analysis and density 
  * 15/01/2019 V3.94: Bug fixes and improvements. 3D Manager interface improved.
  * 30/10/2019 V3.96: Bug fixes and improvements. New plugins distances and interactions.