Difference between revisions of "JaCoP"

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= JACoP =
 
= JACoP =
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{{Notice | This page describes '''J'''ust '''A'''nother '''Co'''localization '''P'''lugin, not the [http://jacop.org Java Constraint Programming solver].}}
  
 
'''This plug-in is a compilation of co-localization tools.'''
 
'''This plug-in is a compilation of co-localization tools.'''
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== References/Citation ==
 
== 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 !
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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}}.  
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JACoP v2.0 was released for the second ImageJ User and Developer Conference in November 2009. The conference proceedings related the plugin is available [https://conference.imagej.net/2008/jacop_ijconf2008.pdf|here].
  
 
== Installation ==
 
== 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.
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Simply download  
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[https://imagejdocu.list.lu/_media/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 ==
 
== Download ==
  
Plugin available here: {{:plugin:analysis:jacop_2.0:just_another_colocalization_plugin:jacop_.jar|JACoP_.jar}}
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Plugin available here: [https://imagejdocu.list.lu/_media/plugin/analysis/jacop_2.0/just_another_colocalization_plugin/jacop_.jar JACoP_.jar]
  
 
== License ==
 
== 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/].
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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/ https://www.gnu.org/licenses/].
  
 
Copyright (C) 2006 Susanne Bolte & Fabrice P. Cordelières  
 
Copyright (C) 2006 Susanne Bolte & Fabrice P. Cordelières  

Latest revision as of 11:01, 11 February 2020

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.

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.