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3D Objects Counter

3D Objects Counter
Project Fiji
URL https://imagej.net/3D_Objects_Counter
Source on GitHub
License GPLv3
Release 2.0.1
Date Sat Apr 29 22:18:19 CDT 2017
Development status Stable
Support status Partial
Team
Founders Fabrice Cordelieres
Leads Daniel James White
Developers -
Debuggers -
Reviewers Daniel James White
Support Daniel James White
Maintainers Daniel James White, Curtis Rueden
Contributors Fabrice Cordelieres, Johannes Schindelin, Niko Ehrenfeuchter, Mark Hiner

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.

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/.