Bleigh
The best bad influence
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Don’t scrape it hard. You just need to run the side of the fish. Shouldn’t cause it any discomfort. If it does, you’re doing it wrong.
To expand, if you were to put gloves on, catch the fish in your hand, and rub a finger on the area that’s infected, then wipe this on a slide, I’d imagine this would give you a good idea of what may be going on, microscopically. If you wanted to make more certain you got something, use the flat side of a toothpick to gently, yet firmly (oxymoron I know) scrape the side that’s infected and place this on your microscope slide.
One project I worked on involved analysis of devil ray mucous. Initially the collections weren’t invasive at all. Unfortunately we realized the enzyme we were looking for was only produced when the ray was injured. We had to puncture (small puncture and it was healed in less than 2 days) the fins to start the production in order to study it in the mucous.
The collection should be more non-invasive for your clownfish, but obviously you don’t need to puncture your fish to look for microorganisms around the infected area.
I do agree that it probably doesn’t matter what it is, she needs to be treated. My only concern is whether it will be a recurring issue due to an underlying issue and how to best avoid future infections.