Colocalization_Finder

Authors: Christophe Laummonerie,
Jerome Mutterer, Institut de Biologie Moleculaire des Plantes, Strasbourg, France.
Philippe Carl (maintainer), UMR7021, Strasbourg, France.
History: 2004/02/02: First version: Parts of the initial code were taken from plugins by W. Rasband, P. Bourdoncle, and G. Chinga.
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 examples that can be downloaded here and here.
- the colocalization calculations are performed using double parameters instead of float
2019/12/15: Version 1.5:
- possibility to add a selection within the Composite picture to restric the analysis to a given selection
- addition of synchronized background thread for smoothly updating the calculations on the fly
Source: Contained in the JAR file. To open a JAR file, change the extension from ".jar" to ".zip" and double click on it.
or
Download Colocalization_Finder.java.
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.
or
Download Colocalization_Finder.java to the plugins folder or subfolder. Compile and run it using Plugins/Compile and Run. Restart ImageJ and there will be a new "Colocalization Finder..." command in the Plugins menu or its submenu.
Description and features: This plugin displays a correlation diagram (called scatterPlot picture) from two initial pictures having the same size together with a RGB overlap of the original images (called Composite picture).
The user interface of the plugin provides the following features:
- Drawing or modifying a selection within the scatterPlot allows to highlight the corresponding pixels on the composite picture.
If the selection within the scatterPlot is deleted, it is automatically regenerated to its initial settings (i.e. covering all the scatterPlot).
- Drawing or modifying a selection within the Composite picture allows to restric the analysis to the given selection and will regenerate the corresponding scatterPlot picture accordingly.
- The analysis results of a given cross (i.e. scatterPlot and Composite pictures) selection can be generated with a single click inside either one of the selections.
- As a double click inside either one of the selections (of the scatterPlot or Composite picture) will as well generate the given cross selection analysis results, but additionally add the scatterPlot selection within the roiManager attributing a given color to the corresponding ROI and colorizing the selected pixels within the Composite picture with the same attributed color.
- By pressing the Ctrl key and moving the mouse over the Composite picture, the selection within the scatterPlot will be moving over placing it's center to the scatterPlot settings of the corresponding Composite picture pixel.
- By pressing the numeric pad 4/6 or 2/8 keys, the x or y intensity histograms will be generated together with a Gaussian fit in order to extract the histogram maximum position.

Example results:
[CF_images]

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.
[CF_table]

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