Cell by cell nuclear cytoplasm intensity ratio measurment


I am trying to figure out how to measure gene expression intensities cell by cell (the confocal images have at least 100 cells in it that was taken at 20X). I’ve tried using the Intensity Ration Nuclei Cytoplasm Tool in ImageJ but it measures the ratio of the cells and takes an average of all the cells in the image. Is there a way to measure the ratio cell by cell?

This is the link for tool I have tried, as mentioned. https://www.researchgate.net/deref/http%3A%2F%2Fdev.mri.cnrs.fr%2Fprojects%2Fimagej-macros%2Fwiki%2FIntensity_Ratio_Nuclei_Cytoplasm_Tool


Hi @Joanna_Maddela,

you can not do this with the Intensity_Ratio_Nuclei_Cytoplasm_Tool .

The problem will often be to separate the cells (the cytoplasm) from each other. If it is possible to do this for your images, the rest should be straight forward.

Best regards,