Abstract: The present invention relates to systems and methods for real time, rapid detection, identification, and enumeration of a wide variety of analytes, which include but are not limited to, cells (Eukarya, Eubacteria, Archaea), microorganisms, organelles, viruses, proteins (recombinant or natural proteins), nucleic acids, prionss, and any chemical, metabolites, or biological markers. The systems and methods, which include the laser/optic/electronic units, the analytic software, the assay methods and reagents, and the high throughput automation, are particularly adapted to detection, identification, and enumeration of pathogens and non-pathogens in contaminated foods, clinical samples, and environmental samples. Other microorganisms that can be detected with the present invention include clinical pathogens, protozoa and, viruses.