Disclosed herein are scientific instrument support systems, as well as related methods, apparatus, computing devices, and computer-readable media. For example, some embodiments provide a scientific instrument comprising an ion-beam instrument configured to generate an ion beam including first and second sub-beams; an electron-beam instrument including a charged-particle-beam (CPB) lens having an adjustable setting controlling a magnetic force applied to the first and second sub-beams; and a computing device. The computing device is configured to: acquire an image by causing the ion-beam instrument to scan the ion beam across a sample using a selected setting of the CPB lens of the electron-beam instrument, apply automated image processing to the image to quantify an amount of spatial misalignment of the first and second sub-beams at the sample, and control the CPB lens of the electron-beam instrument to a setting based on the amount of spatial misalignment within the image.