Atom interferometers require precise control of digital, analog, and radio frequency signals for effective operation. In this paper, we propose and implement a control system for mobile atom interferometers. The system consists of a microcontroller and peripherals to synthesize radio frequency signals and to read or write analog signals. We use the system to operate a mobile atomic gravimeter by controlling 7 analog outputs, 16 digital outputs, 2 radio frequency channels, and 1 analog input. Our control system eliminates dead time between repetitions of the measurement and, consequently, improves the sampling rate of our atomic gravimeter, while maintaining the sensitivity per repetition compared to the system based on a desktop computer.
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