A spectrally encoded flow cytometry (SEFC) technique for imaging blood in the microcirculation. Since the dependency of one of the axes of the image on time prevents effective quantification of essential clinical parameters, the optical path in an SEFC system is split into two parallel imaging lines, followed by data analysis for recovering the flow speed from the multiplexed data. The data analysis may be auto-correlation of a pair of images obtained from a sequence of images of the imaged blood vessel.