JACoP
This page describes Just Another Colocalization Plugin, not the Java Constraint Programming solver.
This plug-in is a compilation of co-localization tools.
Authors
Fabrice P. Cordelières, Bordeaux Imaging Center (France). Fabrice.Cordelieres at gmail dot com Susanne Bolte, IFR 83, Paris (France). Susanne.Bolte at upmc.fr
Features
JACoP allows:
Calculating a set of commonly used co-localization indicators:
- Pearson’s coefficient
- Overlap coefficient
- k1 & k2 coefficients
- Manders’ coefficient
Generating commonly used visualizations:
- Cytofluorogram
Having access to more recently published methods:
- Costes’ automatic threshold
- Li’s ICA
- Costes’ randomization
- Objects based methods (2 methods: distances between centres and centre-particle coincidence)
All methods are implemented to work on 3D datasets.
Description
JACoP has been totaly re-written, based on user feedback. The interface has been re-designed to offer full access to all the options, based on a unique Swing frame.
It includes a “Zoom/Reset button” which allows the user to set the two selected images side-by-side, automatically adapting the zoom. For each method selected, the user’s attention is drawn on options to set, by highlighting the appropriate tab by turning its caption to red.
References/Citation
When using the current plugin for publication, please refer to our review (see below), to this webpage and of course to ImageJ. A copy of your paper being sent to both of our e-mail adresses would also be greatly appreciated!
doi:10.1111/j.1365-2818.2006.01706.x
JACoP v2.0 was released for the second ImageJ User and Developer Conference in November 2009. The conference proceedings related the plugin is available 1.
Installation
Simply download JACoP_.jar to the Plugins folder of ImageJ, restart ImageJ and use the “JACoP” command in the Plugins menu.
Download
Plugin available here: JACoP_.jar
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 https://www.gnu.org/licenses/.
Copyright (C) 2006 Susanne Bolte & Fabrice P. Cordelières
Changelog
2.0 (07/11/2008):
- New interface: one window presenting all options
- JACoP is now fully macro recordable
- Added the objects based method
- Added the “Zoom/Reset button” allowing to set the two selected images side-by-side, automatically adapting the zoom.
2.1 (01/04/2010):
- Fixed a bug leading to an error in the Manders’ coefficients calculation when applying a threshold to images.
2.1.1 (20/08/2010):
- Fixed a bug about distance based co-localization when calling the function from a macro.
