Abstract: An embedded data acquisition and control system for a precision instruments, such as a non-invasive glucose prediction instrument is disclosed. One feature of the invention provides synchronization of stepper motor position and analog-to-digital converters. An embedded controller is provided that controls the stepper motor driver directly to minimize the wavelength shift error due to the asynchronous condition. The controller synchronizes the event of reading the A/D converters with each stepper motor position. Because the stepper motor controls the wavelength of the monochromator optical output, the net result is that each A/D conversion recorded by the embedded controller is precisely tracked to a specific wavelength. Another feature of the invention provides closed loop motor position control for enhanced system performance. In the closed loop system, a position encoder is coupled to the stepper motor shaft.