====== 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)
\\
NB: 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.\\
{{:plugin:analysis:jacop_2.0:just_another_colocalization_plugin:jacop_interface.jpg|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 {{:plugin:analysis:jacop_2.0:just_another_colocalization_plugin:jacop_ijconf2008.pdf|here}}. 

===== Installation =====
Simply download {{:plugin:analysis:jacop_2.0:just_another_colocalization_plugin:jacop_.jar|JACoP_.jar}} to the Plugins folder of ImageJ, restart ImageJ and use the "JACoP" command in the Plugins menu.
===== Download =====
Plugin available here: {{:plugin:analysis:jacop_2.0:just_another_colocalization_plugin:jacop_.jar|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 [[http://www.gnu.org/licenses/|http://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.