A real-time monitoring system based on the dual slit methodology for the characterization of the red blood cell velocity at the level of microcirculation has been developed. The analog photometric signals are acquired and processed using a hybrid hardware-software system that exploits a A/D conversion and an optimized correlation algorithm on an embedded system. It is implemented exploiting the resources of a general purpose board capable to extract the useful information from the noisy photometric signals, to process them, to show and save the results and, therefore, to make the experiments reproducible. Two different approaches to the crosscorrelation algorithm have been tested and their performances have been compared to each. The system has been tested in in vivo experiments on anaesthetized hamsters. Several microvessels have been observed and the results have been compared to the output of an analog crosscorrelator to verify their coherence.