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plugin:stacks:3d_ij_suite:start [2019/01/31 03:57]
plugin:stacks:3d_ij_suite:start [2019/05/06 00:08] (current)
tboudier [Installation]
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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}},​ [[https://​www.wehi.edu.au/​|Walter & Eliza Hall Institute]],​ Melbourne, Australia.
 +
 +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-suite3.94.zip|}}
 +
 +Core library : {{:​plugin:​stacks:​3d_ij_suite:​mcib3d-core3.94.jar|}}
 +
 +Plugins : {{:​plugin:​stacks:​3d_ij_suite:​mcib3d_plugins3.94.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]], ​ [[http://​www.optinav.com/​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.