Difference between revisions of "3D Objects Counter"

Line 4: Line 4:
| maintainer        =  [mailto:white_at_mpi-cbg_dot_de Daniel White]
| maintainer        =  [mailto:white_at_mpi-cbg_dot_de Daniel White]
| author                = Fabrice Cordelieres
| author                = Fabrice Cordelieres
| filename              = [http://rsb.info.nih.gov/ij/plugins/track/_3D_objects_counter.class ???]  
| filename              = [http://imagejdocu.tudor.lu/lib/exe/fetch.php?media=plugin:analysis:3d_object_counter:3d-oc_.jar 3d-oc_.jar]  
| source                = [http://rsb.info.nih.gov/ij/plugins/track/_3D_objects_counter.class ???]
| source                = [http://imagejdocu.tudor.lu/lib/exe/fetch.php?media=plugin:analysis:3d_object_counter:3d-oc_.jar Contained within the jar file]
| released              = ????
| released              = 15/06/2005
| latest version        = ????
| latest version        = 12/08/2009
| status                = maintained actively as of 11/2009
| status                = maintained actively as of 11/2009
| category              = [[:Category:Particle analysis|Particle analysis]]
| category              = [[:Category:Particle analysis|Particle analysis]]

Revision as of 14:57, 13 November 2009

3D Object Counter (ImageJ)
Author Fabrice Cordelieres
Maintainer Daniel White
File 3d-oc_.jar
Source Contained within the jar file
Initial release 15/06/2005
Latest version 12/08/2009
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)


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


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


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/.