JACoP Default Threshold

[iwilliams91]

Hi all,
I'm using JACoP to evaluate the colocalization between two fluorescent probes. Specifically, I want to calculate the Manders Correlation Coefficients (MCCs), M1 and M2. From what I understand, these coefficients are very sensitive to background and therefore a rigorous and unbiased thresholding method is necessary.

When I use JACoP, I only check "M1&M2 coefficients." The "Threshold" tab at the bottom of the interface lights up and when I click on it, it has already thresholded the two images, presumably by some default method. My questions: 1) What is this default threshold method? 2) Is this default thresholding in JACoP sufficiently rigorous and unbiased for MCC calculation?

Any help would be greatly appreciated.

Ian