Colocalization JACoP Batch process macro

[mykstax]

Hello,
I am new to the group, and somewhat new to creating macros, and batch processing.
I am trying to use the JACoP plug-in on many images from different culture conditions.
I would like to automate this, but am not sure how. I have the "red images" in one folder, and the "green images" in another, and they have the same file name. If anyone could help me figure out how to set up a batch process for JACoP to pull files from their respective folders for analysis, and move through all the images, I would really appreciate it!
Thanks,
Mike