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A Petri net was used to model, analyze, and ultimately control a novel laboratory robotic system designed to automatically image protein crystallization experiments per user-specified schedules. Flexibility in system operation was necessary in order to accommodate unpredictable experimental tray entry and removal by crystallographers, as well as on-the-fly modification of imaging schedules to account for unplanned events or delays. A Petri net model of the system was created and analyzed. The Petri net was implemented in software, interfaced with the system hardware, and used to operate the integrated system. The Petri net controlled automated crystallization imaging system has been in daily use for well over one full year.