I’m measuring the ratio of NF-kB intensity in the nucleus to the cytoplasm, but would like to use the ‘ring region’ (around the nucleus) for the cytoplasm measure.
Currently, my pipeline is as follows:
- IdentifyPrimaryObjects - segment nuclei using Hoechst stain
- ExpandOrShrinkObjects - expand nuclei by 4px
- IdentifyTertiaryObjects - subtract the nucleus region from the expanded region to obtain the ring region
I would like to constrain the ring region within the boundaries of the cytoplasm. I am able to segment the cytoplasm but unsure how to crop the ring region/expand the nucleus region within the cytoplasm boundaries.
Note I am already able to calculate a nucleus to whole cytoplasm ratio but have found better readings in other image analysis software in using the ring region, due to large differences in cytoplasm shape between and within lines.
I very much appreciate any suggestions as I am new to Cell Profiler and keen to use it a lot more from now on! Thank you