Abstract: There is provided systems and methods for electron microscopy imaging, including a method for imaging a sample using a charged particle microscope, the method comprising: acquiring an initial image of a surface of the sample using the charged particle microscope; receiving an indication of one or more initial areas of interest for one or more auto-functions for the charged particle microscope; acquiring a series of subsequent images of subsequent surfaces of the sample using the charged particle microscope. Wherein, for each subsequent image, acquiring said subsequent image comprises exposing the respective subsequent surface of the sample; identifying, one or more areas of interest corresponding to the one or more initial areas of interest; and imaging the respective subsequent surface wherein imaging the respective subsequent surface comprises applying the one or more auto-functions based on at least one of the identified areas of interest corresponding to the one or more initial areas of interest.