The main problem that I am having is that the oscilloscope X and Y amplifiers do not provide enough range or offset to easily control where the scan pattern hits the sample. I knew this would be a problem, so I included small mechanical X and Y stages for the specimen in the microscope. I even designed a vacuum-safe rotary passthrough into the vaccum chamber. The biggest problem is just connecting the rotary passthrough to the stage itself with a right-angle and/or flexible shaft arrangement. Space is very tight and the shaft must move with the stage, making for a difficult mechanical design.
