A method of calibrating a Scanning Transmission Charged-Particle Microscope, operable in a non-scanning mode, whereby said beam is relatively broad, and a scanning mode, whereby said beam is relatively narrow and an image is formed as a function of scan position of said beam, the method comprising: providing a calibration specimen on said specimen holder; in non-scanning mode, using said detector to form a calibration image of the calibration specimen, using a given configuration of said imaging system; utilizing a known dimension of said calibration specimen and comparing it to a corresponding dimension in said calibration image to calibrate a characteristic dimension of a field of view of said detector; and, in scanning mode, recording a beam pattern of said beam in the calibrated field of view of said detector, and examining the recorded beam pattern to derive a geometric aspect thereof.