Colocalization analysis w/ ICA and JACoP

Posted by sibert on Jun 01, 2010; 4:28pm
URL: http://imagej.273.s1.nabble.com/Colocalization-analysis-w-ICA-and-JACoP-tp3687953.html

Hello,

I would like to analyze the colocalization of two proteins in some fluorescent images.  Based on what I've read, I'd like to use the ICA method by Li et al. (J. Neurosci. 24:4070, 2004)

So far, I've tried the Intensity Correlation Analysis plugin and JACoP.

These plugins always provide different values for the Intensity Correlation Quotient (ICQ) as well as the Pearson's coefficient and Mander's coefficients for the same images.  I've tried both plugins with identical thresholds and without thresholds.  Adjusting the threshold does not appear to have any effect on the ICQ from JACoP.

The ICQ from JACoP seems to be excessively high, even when minimal colocalization is visible the value given is generally > 0.3.  Whereas the ICA plugin returns values of ~.28 when the proteins appear highly colocalized (such an image returns ~.44 in JACoP).

The Pearson's and Mander's coefficients are also generally higher in JACoP than ICA.

Unfortunately, I don't know Java well enough to determine how these calculations are being done in the source code.  It isn't clear to me from any documentation why the values are not identical between the two plugins.

Can anyone provide some insight as to why these plugins are providing different values for the same analysis and how I may discern which of the plugins is providing accurate calculations?