An electron microscope and method of operating an electron microscope (1) has an electron beam source (11) for producing an electron beam, a noise canceling aperture (12) for detecting a part of the beam, an amplifier (42), an effective value calculating circuit (44) for extracting DC components of the output signal from the amplifier (42), a detector (15) for detecting a signal obtained in response to impingement of the beam on a sample (A), a preamplifier circuit (20), an amplifier circuit (30), a dividing circuit (54) for performing a division based on the output signal from the amplifier circuit (30) and on the output signal from the amplifier (42), and a multiplier circuit (58) for performing multiplication of the output signal from the dividing circuit (54) and the output from the effective value calculating circuit (44).