====== 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:3doc-sm.jpg|}}{{:plugin:analysis:3d_object_counter:3doc-redir.jpg|}}

//**{{: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://www.ncbi.nlm.nih.gov/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://rsbweb.nih.gov/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://www.gnu.org/licenses/|http://www.gnu.org/licenses/]].

Copyright (C) 2005 Fabrice P. Cordelières
===== Changelog =====