Measuring/counting grey pixels within an area

[joaopgcs]

Hello.
I have a question, which is probably a basic one, but I need to get it clear so I can move on with this part of my work.
I have pictures (grey or red fluorescence photographs) in which I want to count the number of positive pixels (grey or red) to obtain a percentage of positive fluorescent area within a given area (which I select). There is always a bit of background, so I want to set image j to recognize only those with an intensity over X.

Can someone help me on this?

Thanks