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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/.
