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JaCoP

JACoP



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.

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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 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.