A charged particle beam microscope system is operated in a transmission imaging mode. During the operation, the charged particle beam microsystem directs a charged particle beam to the sample to produce images. A time series of beam tilts is applied in a pattern to the charged particle beam directed to the sample to produce a sequence of images. At least some of the images in the sequence of images are captured while the charged particle beam is transitioning between one beam tilt in the time series of beam tilts and a sequentially adjacent beam tilt in the time series of beam tilts. The pattern is configured to induce image changes between the images in the sequence of images that are indicative of optical aberrations in the charged particle beam microscope system.