Calibrating coordinate system alignment in a scanning transmission electron microscope using a digital twin

In four-dimensional scanning transmission electron microscopy (4D STEM) a focused beam is scanned over a specimen and a diffraction pattern is recorded at each position using a pixelated detector. During the experiment, it must be ensured that the scan coordinate system of the beam is correctly calibrated relative to the detector coordinate system. Various simplified and approximate models are used implicitly and explicitly for understanding and analyzing the recorded data, requiring translation between the physical reality of the instrument and the abstractions used in data interpretation. Here, we introduce a calibration method where interactive live data processing in combination with a digital twin is used to match a set of models and their parameters with the action of a real-world instrument.