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We describe a fluorescent detection technique for a lab-on-a-chip flow cytometer. Fluorescent emission is encoded into a time-dependent signal as a fluorescent cell or bead traverses a waveguide array with integrated spatial filters and color filters. Different from conventional colored filters with well-defined transmission spectral window, the integrated color filters are designed to have broad transmission characteristics, similar to the red-green-blue photoreceptors in the retina of human eye. This unique design allows us to detect multiple fluorescent colors with only three color filters based on the technique of color-space-time coding using only one single photomultiplier tube or avalanche photodetector.