A high-throughput optofluidic device for detecting fluorescent droplets is disclosed. The device uses time-domain encoded optofluidics to detect a high rate of droplets passing through parallel microfluidic channels. A light source modulated with a minimally correlating maximum length sequences is used to illuminate the droplets as they pass through the microfluidic device. By correlating the resulting signal with the expected pattern, each pattern formed by passing droplets can be resolved to identify individual droplets.