Computer-implemented methods for controlling a charged particle microscopy system include estimating a drift of a stage of the charged particle microscopy system based on an image sequence, and automatically adjusting a stage settling wait duration based on the drift estimate. Charged particle microscopy systems include an imaging system, a movement stage, and a processor and memory configured with computer-executable instructions that, when executed, cause the processor to estimate a stage settling duration of the movement stage based on an image sequence obtained with the imaging system, and automatically adjust a stage settling wait duration for the movement stage based on the stage settling duration.