One of the drawbacks of super macro photography is that every little issue, whether that be damage to a crystal, or crud, dust or lint, is magnified (duh!) and can become a problem that has to be dealt with.
Yes you can clean your specimen before you take the photos, using a blast of air, an ultrasonic cleaner, or other methods, but even then, there can still be dirt attached, whether that is due to static, just being stubborn, or something else.
And there may be reasons why you can’t clean a specimen. It might be too fragile, water soluble, or permanently mounted (and you don’t want to have to remount it), or it might be just sheer laziness on your part (often guilty, your honour!). 😆
Below is a specimen of brown rhombohedral siderite (after calcite?), chabazite-Na (herschelite), and a needle of apatite with orange chlorite grown on it (in front of siderite).
The first photo is after I cleaned up (digitally removed) the bits of rock dust sprinkled over the crystals. In this case, I used the Spot Healing Brush in my photo editing tool of choice, PhotoScape X. This available as a free or paid version for Windows here (I use the free version).
The second photo is before I cleaned it up.
And as has been a recent focus in Mineral Matters, the third photo is an old one of mine from 2007.
Below: Siderite, Chabazite-Na, Chlorite, Apatite, Bicker's Quarry, Dargaville, North Island, New Zealand Width of view 3mm. Click on the image below for a higher resolution version.
Wow! What a difference! That's amazing! Like magic!
(You can see how little microphotography I do! (as well as how hard up for "words" I am, sometimes)