You would take scraping from gills, scales etc and view with the microscope-the water itself already contains most of the bacteria that causes illness in the fish like flex-the fish immunity it what keeps it at bay or from infecting them along with good husbandry
A microscope is great to have in the fish room-I wish I had a newer model that you could hook up to the computer to view the slide and then you could post them on the computer too...that would be so neat....to share scraping/findings...etc.....I bet there are even site you could send them to for diagnosis or evaluation at least...