# Colocalization Finder

## Authors

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

### History

-   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](http://punias.free.fr/ImageJ/download/Colocalization_Finder_Macro1.ijm)
        and
        [macro2](http://punias.free.fr/ImageJ/download/Colocalization_Finder_Macro2.ijm)
        .
    -   colocalization calculations are performed using double
        parameters instead of float

```{=html}
<!-- -->
```
     * 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 &quot;Set&quot; 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 

#### Installation

-   Source: Contained in the JAR file.
-   Installation: Download
    [Colocalization_Finder.jar](http://punias.free.fr/ImageJ/download/Colocalization_Finder.jar)
    to the plugins folder, or subfolder, restart ImageJ, and there will
    the \"Colocalization Finder\...\" new command in the Plugins menu.

#### Description

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:
![](/plugin/analysis/colocalizationfinder/cf_images.png)

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/cf_table.png)