Trying to attack the problem from a different direction:
in reply to Controlling a non-perl GUI
What kind of interface does the microscope use to connect to the PC?
If it is serial (standard RS-232 or some bastardization of it), chances are that it uses simple ASCII commands to drive the microscope. You could capture and reverse-engineer those commands more easily than a proprietary binary file format.
Even if it is USB, those are sometimes realized with a serial-to-USB converter inside or outside the unit, and even if it is a proprietary USB-based protocol, you might have some chance of deciphering it.
Remote controlling a GUI that was not designed to be remote controlled seems like a really desperate last ditch effort to me (i.e. resort to this only if all else fails).