Hi, Bernadette
I never used Nuclear fast red, but I found that hematoxylin is probably the best: a drop on the specimen will color it, it resists through processing and since you are going to stain with H&E anyway, it blends in with your staining and doesn't leave a different color on your slides.
I also worked in a hospital where they used mercurochrome to mark there tissue, that will also resist through processing.
 
Dolores

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