If there is a clear difference between neurofilament contents within cytoplasm, you can take pictures of GFAP immunofluorescense and compare IMF strength from them. T.K.
Depends on the strength of your signal, but you might find the method described in our paper useful. We wanted to compare the relative amount of extreme fluorescence between different samples, and found a way to do that in ImageJ using black and white images and defining a standardized threshold. The method is described in the paper and example given in Figure 2. Another group has since successfully used the same method.
I hope you find a suitable method!
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