A focused ion beam (FIB) is used to mill beam spots into a substrate at a variety of ion beam column settings to form a set of training images that are used to train a convolutional neural network. After the neural network is trained, an ion beam can be adjusted by obtaining spot image which is processed with the neural network. The neural network can provide a magnitude and direction of defocus,aperture position, lens adjustments, or other ion beam or ion beam column settings. In some cases, adjustments are not made by the neural network, but serve to indicate that the ion beam and associated ion column continue to operate stably, and additional adjustment is not required.
Optical alignment correction using convolutional neural network evaluation of beam image