This site contains the source code as well as binaries of the ImageJ plugin Ratio Calculator.
For now, you can download the plugin and try it for yourself, proper documentation will be added.
The easiest way to get the plugin running:
Copy the files Ratio_Calculator.jar, ratio_calculator.txt, and commons-math3-3.0.jar from the Downloads section to your ImageJ/Fiji plugins folder.
It also helps to place the file Ratio Spectrum.lut into your ImageJ/Fiji luts folder.
Optionally, you can also copy the macro toolsets Ratios Macro.txt and Intensities Macro.txt to your ImageJ/Fiji macros/toolsets folder.
If you want to change the default options, edit the file ratio_calculator.txt.
In the most recent version, the final analysis of data generated by the ImageJ plugin is conducted in R, see the scripts in the respective folder.
A detailed description of the Ratio Calculator plugin and downstream analyses can be found in the manual.