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Your sharpie photo indicates that your bevels arms not meeting. If the bevels had been fully set, then the sharpie mark would have been eliminated.

What is the brand and model of the microscope?

I analyze chromosomes at 1000x and the working distance is so close I cannot imagine how you would have been able to illuminate the bevel from...

OK, so as stated above, the rolling X stroke is going to be what you'll need. If you are not familiar with it, there are plenty of descriptions and videos of it around here. Continued use of the...

I assume that the photos indicate a marker test, showing where contact was, and was not, made on the hone. Is that correct, and was that just from one stroke? The marker wear also shows contact on...