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plugin:analysis:3d_object_counter:start [2019/04/12 13:13] (current)
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 +====== 3D object counter ======
 +**This plugin allows counting objects in 3D, and getting some measurements about each object found.
 +===== Author =====
 +Fabrice P. Cordelières,​ Bordeaux Imaging Center (France). Fabrice.Cordelieres at gmail dot com 
 +===== Features =====
 +This plugin:
 +  - counts the number of 3D objects in a stack.
 +  - quantifies for each found object the following parameters:
 +    * Integrated density;
 +    * Mean of the gray values;
 +    * Standard deviation of the gray values;
 +    * Minimum gray value;
 +    * Maximum gray value;
 +    * Median of the gray values;
 +    * Mean distance from the geometrical centre of the object to surface;
 +    * Standard deviation of the distance to surface;
 +    * Median distance to surface;
 +    * Centroid;
 +    * Centre of mass;
 +    * Bounding box.
 +  - generates results representations such as:
 +    * Objects'​ map;
 +    * Surface voxels'​ map;
 +    * Centroids'​ map;
 +    * Centres of masses'​ map.
 +As ImageJ'​s "​Analyze Particles"​ function, 3D-OC also has a "​redirect to" option, allowing one image to be taken as a mask to quantify intensity related parameters on a second image. //​**{{:​plugin:​analysis:​3d_object_counter:​3d-oc.pdf|To find out more, download the plugin'​s manual from here.}}**//
 +===== Description =====
 +This plugin is composed of two parts:
 +  * The "3D-OC Set Measurements"​ part allows to define the parameters to calculate and fix some options.
 +  * The "3D-OC Object Counter"​ part to run the analysis.
 +//​**{{:​plugin:​analysis:​3d_object_counter:​3d-oc.pdf|More information in the plugin'​s manual downloadable from here.}}**//
 +===== References/​Citation =====
 +When using the “3D Object Counter” plugin for publication,​ please refer to [[http://​​pubmed/​17210054|S. Bolte & F. P. Cordelières,​ A guided tour into subcellular colocalization analysis in light microscopy, Journal of Microscopy, Volume 224, Issue 3: 213-232]], to this webpage and of course to ImageJ, as explained in the [[http://​​ij/​docs/​faqs.html|FAQ section, on ImageJ’s website]]. A copy of your paper being sent to my e-mail address would also be greatly appreciated !
 +===== Installation =====
 +Simply download {{:​plugin:​analysis:​3d_object_counter:​3d-oc_.jar|}} to the Plugins folder of ImageJ, use the "​Help/​Update Menus" function to refresh the plugins'​ menu and use the “3D Object Counter/Set Measurements” and "“3D Object Counter/3D object counter"​ commands in the Plugins menu.
 +===== Downloads =====
 +{{:​plugin:​analysis:​3d_object_counter:​3d-oc_.jar|The plugin is available from here}}
 +{{:​plugin:​analysis:​3d_object_counter:​3d-oc.pdf|The plugin'​s manual is available from here.}}
 +===== License =====
 +This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see [[http://​​licenses/​|http://​​licenses/​]].
 +Copyright (C) 2005 Fabrice P. Cordelières
 +===== Changelog =====
plugin/analysis/3d_object_counter/start.txt · Last modified: 2019/04/12 13:13 (external edit)