Transferring ROI within channels of a composite image

Hi all,

I am doing an image analysis research project that focuses on the actin cytoskeleton. I have several three-channelled composite images: C1-Nucleus, C-2-Actin, C-3-Antibody.

I aim to quantify the actin cytoskeleton using the ImageJ plugin, ‘AnalyzeSkeleton 2D/3D’. However, this plugin analyses all cell’s cytoskeleton as a whole. The project would be more objective if I could add individual cells to the ROI manager and use this plugin to analyse each cell’s cytoskeleton independently.

My problem:

The images are very compact and thus, difficult to properly segment, and I have tried the following workflow - split-channel > merge C-1 & C-3 > filter (Gaussian blur, R=10) > thresholding > dilate > dilate > watershed > analysis particles > add to ROI manager.
This workflow gives me a clear, distinct outline of each cell, but I can not transfer the ROI to the C-2 image.

I wonder if this is possible or if anyone has any suggestion I could try?