Is there a recommendation for a software/FiJi-ImageJ plugin/workflow for quantifying ratio of expression of a protein between nucleus and cytoplasm (or the nuclei and the rest of the photo) in absence of cell membrane marker. Only the Nuclei are marked by DAPI.
CellProfiler may be able to do this very easily depending on the appearance of your cytoplasmic protein. Is it generally cytosolic? Meaning, can you see the whole shape of the cell to the point where you can differentiate adjacent cells?
The Intensity Ratio Nuclei Cytoplasm Tool, for Image J, has work well for me (immunofluoerescence in cell culture). It quantifies how much of your signal colocalizes with your nuclear staining. It doesn't make a difference between cytosolic and extracellular signal, so you just have to be sure of not having any background signal outside the cells.
Here is the tool:
http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Intensity_Ratio_Nuclei_Cytoplasm_Tool
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