A microfluidic detection system is provided. The system comprises a device for illuminating a microfluidic sample comprising an analyte, wherein illumination from the illuminating device is modulated on and off at a determined frequency, a gated phase-sensitive detector that detects, one or more wavelengths emitting from the analyte, at a determined frequency, and a control device that coordinates the modulating frequency of the illumination and the detecting frequency of the detector.