Weka segmentation in cell profiler

We have generated a data set in wide filed time lapse format. We have phase contrast images and two fluorescent images for every time point. These cells are stained with a lipid stain that changes from red to green with treatment. I can segment the phase contrast images with weka segmentation in Fiji. But we have a lot of images and therefore I would like to use cell profiler. After segmentation I wanted to measure the green and red intensities in the areas that are determined to contain cells. I tried to use Image J in cell profiler today but I cannot figure out how to do weka segmentation within cell profiler. Is it possible to run this plug in within cell profiler?
I was thinking of just measure the intensity in the entire images and divide the intensities . This would be easier however the green channel is very noisy and I think I first need to determine which areas of the image contains cells before I look at intensities.
Best regards

Integration with ImageJ really only works in CP 2.1.1 at the moment- it’s broken in 2.2 and will be going away entirely by 2.4 but according to this forum post from last year it’s difficult to integrate the two even in that version.

If you want to use CP, my recommendation would be to either directly segment in CP (it’s trickier with brightfield than fluorescence, but it often can be done) or to use Weka or the newer versions of Ilastik to segment and then export your segmentation maps for measurement in CP.