We have successfully used ImageJ software to measure fluorescent microscopic images. You may check the method and results of the attached article in addition to the ImageJ user guide to set up your system.
Please tell us more. Do you want to know the shape of labeled elements, the amount of space they occupy, the correlation to other labels or features in the image? Give us an idea and we can help you.
Muthana's link should be quite helpful, but it might be a bit overwhelming if you have no experience. Filling in your desired outcome will help us guide you to a solution.