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.