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3D Objects Counter

    TODO component: {"content"=>"sc.fiji:3D\\_Objects\\_Counter"}

    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.


    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/.