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A microfluidic analyzer system and a cell detection algorithm were developed to analyze biomedical fluids. The obtained microfluidic device is based on the integration of different fluidic systems: the SensoNor glass/silicon/glass multilayer microchip and ThinXXS plastic slide. A hydrodynamic focuser was designed to sort and analyze cells/particles in a 100μm wide channel. The advantages of this Lab-On-a-Chip (LOC) structure are the easy interfaceability with electrodes and optical systems, biocompatibility and ability of optical analysis and morphologic recognition. The proposed CNN-based (Cellular Neural Network) algorithm is real-time and scalable. This constructed microfluidic and optical system is able to analyze and measure any biological liquid, which contain less than 10μm size particles or cells, and count the number of morphologically well-separated different elements in the focused liquid flow using real-time image processing algorithms.