3D object counter

This plugin allows counting objects in 3D, and getting some measurements about each object found.


Fabrice P. Cordelières, Institut Curie, Orsay (France). Fabrice.Cordelieres at curie.u-psud.fr


This plugin:

  1. counts the number of 3D objects in a stack.
  2. 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.
  3. 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. To find out more, download the plugin's manual from here.


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.

More information in the plugin's manual downloadable from here.


When using the “3D Object Counter” plugin for publication, please refer to 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 FAQ section, on ImageJ’s website. A copy of your paper being sent to my e-mail address would also be greatly appreciated !


Simply download 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.



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/.

Copyright (C) 2005 Fabrice P. Cordelières


plugin/analysis/3d_object_counter/start.txt · Last modified: 2013/05/17 16:39 by mutterer
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