Measuring fluorescent intensity in different compartement

hi everyone,
i am going to measure fluorescent intensity in cytoplasm and nucleus which were stained with different antibody, could anyone please tell me how can i measure them, i can not measure it by Co-localization plugins because they are not actually in the same region so there is not any co localization between them.

Hello there,
Try to do a simple thresholding first to see if you can differentiate both the regions, followed by using the ‘Analyze Particle’ tool. Alternatively you could also try the Trainable Weka Segmentation plugin to do the segmentation for you.
-Praveen