Can anyone help me figure out how to fix this and what it is. I have taken the objective off and it seems to still show once I put my finger underneath the light, not sure what it is or where it has come from as the last time I used the microscope it was perfectly fine.
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The dirt symptoms are not clear to me from your photo. The image on screen looks like a sample that is not quite in focus.
Looks strange to me too. I’m no stranger to dust in the system, but it normally shows as dark spots, smudges, or strands. The most annoying is dust on your Pi Camera sensor, which is a pain to clean (and trying to clean it can leave behind streaks which are even worse!)
If you remove your camera from the rest of the microscope optics while still plugged in and wave it around under a light (though moving it while live is generally not recommended and can lead to disaster, so I only do it to diagnose this!) you should be able to at least determine if the aberration is on the camera itself or if there’s weird dust etc. coming from the optics module or tube lens.
My guess would be it’s camera-related, but even that looks out-of-focus and I haven’t seen it before. I’m guessing you’ve completely reset any image calibrations too?