The present invention provides systems, methods and apparatuses that perform digital detection for use in optical tomography. Methods and systems are provided in which digital lock-in detection is performed using an algorithm that employs a phase-independent quadrature technique. Methods and systems are provided in which a unique manipulation of an ordinary averaging filter optimized for sources discrimination and the consequent sampling constraints is presented as a novel filtering scheme for the lock-in detection. Systems and apparatuses are provided which include a digital signal processor which performs digital lock-in detection and an integrated complex programmable logic device for timing control. Apparatuses are provided which include an instrument having an integrated digital signal processor for performing digital processing and detection for use in optical tomography.