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Colocalization Finder


  • Christophe Laummonerie
  • Jerome Mutterer, CNRS.
  • Philippe Carl (maintainer), UMR7213, Strasbourg, France


  • 2004/02/02: First version
  • 2005/01/28: Version 1.1: statistical methods added.
  • 2006/08/29: Version 1.2
    • ratio bars non destructively displayed
    • works with any closed ROI
    • Fire LUT better diplayed
    • You now have to click in the ROI to update overaly image(s) and statistics
  • 2016/03/21: Version 1.3
    • replacement of the deprecated functions (getBoundingRect, IJ.write) by the new ones
    • extension of the plugin for whatever picture dynamics
    • addition of a plot (with legends, ticks (minor and major), labels) within the scatter plot
    • the selected points within the overlay picture are updated as soon as the ROI in the scatter plot is modified or dragged over
    • possibility to move the ROI position (within the scatter plot) from the mouse position within the overlay picture
    • possibility to set ROIs with given colors with a mouse double click
    • possibility to generate the x or y histogram with a Gaussian fit in order to extract the histogram maximum position by using the numeric pad 4/6 or 2/8 keys
  • 2019/10/14: Version 1.4:
    • addition of scripting possibilities illustrated within the macro example that can be downloaded here: macro1 and macro2 .
    • colocalization calculations are performed using double parameters instead of float
  • 2021/01/28: Version 1.6:
    • possibility to choose the size of the scatter plot upon start of the plugin
    • addition of a label panel at the bottom of the scatterPlot picture displaying the limits of the scatterPlot Roi selection
    • addition of a “Set” button at the bottom left of the scatterPlot picture allowing so set the limits of the scatterPlot graph and/or of the scatterPlot Roi (the 'g' key gives the same features)
    • the possibility to set ROIs with given colors with a mouse double click has been erased (due to the ImageJ 1.53c 26 June 2020 update) and replaced by a Ctrl + mouse click user action


  • Source: Contained in the JAR file.
  • Installation: Download Colocalization_Finder.jar to the plugins folder, or subfolder, restart ImageJ, and there will the “Colocalization Finder…” new command in the Plugins menu.


This plugin displays a correlation diagram for two images (8bits, same size). Drawing a rectangular selection on this diagram allows you to highlight corresponding pixels on a RGB overlap of the original images, and if selected, on a 3rd image. Analysis can be restricted to pixels having values with a minimum ratio. Selection settings are logged to a results window.

Parts of this code were taken from plugins by W. Rasband, P. Bourdoncle, and G. Chinga. Example results:

The results table with computer Pearson's correlation, Overlap coefficient, contribution of both channels to OC, Slope and intercept of the linear regression,% pixels selected, min and max in both channels.

plugin/analysis/colocalizationfinder/start.txt · Last modified: 2022/03/07 10:21 by mutterer