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This textbook provides practicing scientists and engineers a primer on the Atmel AVR microcontroller. Our approach is to provide the fundamental skills to quickly get up and operating with this internationally popular microcontroller. The Atmel ATmega16 is used as a representative sample of the AVR line. The knowledge you gain on the ATmega16 can be easily translated to every other microcontroller in the AVR line. We cover the main subsystems aboard the ATmega16, providing a short theory section followed by a description of the related microcontroller subsystem with accompanying hardware and software to exercise the subsytem. In all examples, we use the C programming language. We conclude with a detailed chapter describing how to interface the microcontroller to a wide variety of input and output devices.