The newest generation of computer-controlled electron microscopes incorporates the ability to perform adjustments to microscopy conditions by comparing pairs of images and altering the conditions accordingly. Automation of electron microscope adjustments offers the advantages of accuracy, precision, efficiency, the ability to incorporate the adjustments into other automated procedures, and, for radiation-sensitive specimens, minimal exposure to the beam.

At present, automated functions include determination of eucentric height, focus, astigmatism, orientation and location of the stage tilt axis, centering of an image feature, and rotation center alignment. It is possible to automate other functions, so this list may be incomplete. In general, these functions are accomplished by induced image shifts, and, in many cases, the automated functions are completely analogous to the corresponding manual ones.