afspm: A framework for manufacturer-agnostic automation in scanning probe microscopy

Scanning probe microscopy (SPM) is a valuable technique by which one can investigate the physical characteristics of the surfaces of materials. However, its throughput is hampered by the time-consuming nature of running an experiment and the significant domain knowledge required. Recent studies have shown the value of multiple forms of automation in improving this, but their use is limited due to the difficulty of integrating them with SPMs other than the one it was developed for. We have built a framework that allows for tasks written with it to be run on multiple SPM systems. Our framework defines generic commands and data structures that are passed among separate software processes, with the final SPM commands sent to the microscope after passing through an SPM-specific translator. The use of configuration files allows automation logic to be further decoupled from experiment specifics. A mediation layer permits background tasks to intermittently control the microscope, fixing detected experiment problems. Our framework has been tested on various SPM controllers, validating that it can integrate with all existing scripting interfaces types. An automated experiment was run to ensure overall running beyond integration testing.