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An experimental structured light projection system which includes a miniaturized projector is described. The system has been designed to be integrated in a fluorescence molecular tomography (FMT) prototype in order to reconstruct the surface of mice and phantom studies. A high-accuracy phase map is retrieved with phase-shifted sinusoidal fringes. Phase error due to the nonlinear gamma function of the pico-projector is calibrated and compensated. Robust phase unwrapping is performed with an additional Gray-code projection sequence. An automatic phase-to-height non-linear calibration scheme has been applied using objects located in the extremes of the field of view. The accuracy of the proposed method has been tested with a realistic mouse model and ray-tracing software.