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3D object counter

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


Fabrice P. Cordelières, Bordeaux Imaging Center (France). Fabrice.Cordelieres at gmail dot com


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

Copyright (C) 2005 Fabrice P. Cordelières


plugin/analysis/3d_object_counter/start.txt · Last modified: 2019/04/12 13:13 by

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