How can I organize multi-measure output table?

I have a stack of images of cells with both phase and fluorescence images. With the phase images, I am able to use Find Maxima and Analyze Particles to extract an outline of each cell in each frame into the ROI Manager. I would then like to get the fluorescence intensities in each frame from these ROIs. If I use Measure in the ROI Manager, I get a big list of intensities with no information on which frame it came from. If I run Multi-Measure, it measures each ROI in every single frame, not only in its native frame.

Is there a straightforward way to get an organized table of fluorescence intensities using ROIs, which includes information on which frame each measurement came from? I do not need to track the cells, only extract their fluorescence from each frame.

Thanks for any help!

You can enable the frame information in the “Set Measurements” dialog to get the stack position:

Exactly for this kind of analysis I created an action to transfer multiple ROI selections from a stack or single image (all pixels within the ROI in a selected datatype) to R to create statistical analysis from ROI-Manager measurements.

Here is an older flash video demonstration: