Automation in quantum logic experiments with cold molecular ions

Modern experiments with cold molecular ions have reached a high degree of complexity requiring frequent sample preparation, state initialization and protocol execution while demanding precise control over multiple devices and laser sources. To maintain a high experimental duty cycle and robust measurement conditions, automation becomes essential. We present a fully automated control system for the preparation of trapped state-selected molecular ions and subsequent quantum logic-based experiments. Adaptive feedback routines based on real-time image analysis introduce and identify single molecular ions in atomic-ion Coulomb crystals. By appropriate manipulation of the trapping potentials, excess atomic ions are released from the trap to produce dual-species two-ion strings, here Ca$^+-$N$_2^+$. After mass and state identification of the molecular ion, nanosecond-level synchronization of laser pulses employing the Sinara/ARTIQ framework and real-time data analysis enable quantum-logic-spectroscopic measurements. The present automated control system enables robust, unsupervised operation over extended periods resulting in an increase of the number of experimentation cycles by about a factor of ten compared to manual operation and a factor of about eight in loaded molecules in typical practical situations. The modular, distributed design of the system provides a scalable blueprint for similar molecular-ion experiments.