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3D Objects Counter

1,543 bytes added, 19:52, 13 November 2009
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| website = [http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:3d_object_counter:start]
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The 3D Object Counter.java linked in the info box here is by Fabrice Cordelieres.
V2.0 plugin is now contained in Fiji; just use [[Update_Fiji|Help>Update Fiji]] to get it.
== What does it do ? ==
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's manual ==
The plugin's manual might be downloaded from [http://imagejdocu.tudor.lu/lib/exe/fetch.php?media=plugin:analysis:3d_object_counter:3d-oc.pdf ImageJ's wiki (follow this link)]
 
== Install/Update ==
v2.0 plugin is now contained in Fiji; just use [[Update_Fiji|Help>Update Fiji]] to get it.
 
== Reference ==
The original plugin was published here:
[http://www3.interscience.wiley.com/cgi-bin/fulltext/118727584/PDFSTART S. Bolte & F. P. Cordelières, A guided tour into subcellular colocalization analysis in light microscopy, Journal of Microscopy, Vol. Volume 224, Pt Issue 3 December 2006: 213-232] == 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, ppor (at your option) any later version. 213–232 Received 13 April 2006This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; accepted 28 June 2006 Blackwell Publishing Ltd TUTORIAL REVIEW without even the implied warranty of MERCHANTABILITY or FITNESS FOR A guided tour into subcellular colocalization analysis in lightmicroscopy SPARTICULAR 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. BOLTE & Forg/licenses/ http://www. Pgnu. CORDELIÈRESorg/licenses/]. 
[[Category:Plugins]]
[[Category:Particle analysis]]
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