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JaCoP

    JACoP

    This page describes “"”J”"”ust “"”A”"”nother “"”Co”"”localization “"”P”"”lugin, 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.

    JACoP v2.0: The new interface

    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 [https://doi.org/10.1111/j.1365-2818.2006.01706.x|(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. A copy of your paper being sent to both of our e-mail adresses would also be greatly appreciated !

    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.