Difference between revisions of "3D Objects Counter"

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| website                = [http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:3d_object_counter:start]
 
| website                = [http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:3d_object_counter:start]
 
}}
 
}}
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:
 
The original  plugin was published here:
[http://www3.interscience.wiley.com/cgi-bin/fulltext/118727584/PDFSTART Journal of Microscopy, Vol. 224, Pt 3 December 2006, pp. 213–232 Received 13 April 2006; accepted 28 June 2006 Blackwell Publishing Ltd TUTORIAL REVIEW A guided tour into subcellular colocalization analysis in lightmicroscopy S. BOLTE & F. P. CORDELIÈRES]
+
[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, Volume 224, Issue 3: 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, 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/].
 +
 
  
  
 
[[Category:Plugins]]
 
[[Category:Plugins]]
 
[[Category:Particle analysis]]
 
[[Category:Particle analysis]]

Revision as of 13:52, 13 November 2009

3D Object Counter (ImageJ)
Author Fabrice Cordelieres
Maintainer Daniel White
File ???
Source ???
Initial release  ????
Latest version  ????
Development status maintained actively as of 11/2009
Category Particle analysis
Website [1]



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 ImageJ's wiki (follow this link)

Install/Update

v2.0 plugin is now contained in Fiji; just use Help>Update Fiji to get it.

Reference

The original plugin was published here: S. Bolte & F. P. Cordelières, A guided tour into subcellular colocalization analysis in light microscopy, Journal of Microscopy, Volume 224, Issue 3: 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, 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/.