Proposal of low cost, submicrometer, and fast fluorescence microscopy Microarray scanners are now reaching submicron details for fast scan speeds on large surfaces such as microscope slides. Reading times depend on the required resolution. However, specific applications in food security tend to bring closer to the source the measurements necessary to decision making. For the development of salmonella and listeria on pig carcasses, the measurements taken directly at slaughter need to be interpreted within less than an hour, so that the decision of meat usage in a fresh/cooking circuit does not have significant economic consequence. We developed a method for marking immediately after impacting carcass, which makes it possible to read fluorescence signals 30 minutes after sampling. However, the sampling method leaves the sample some organic residues, whose irregularities in the thickness and the surface can cause problems in reading and interpretation with conventional scanners. We propose a method of packaging and reading for the automatic counting of salmonella with fast scanning, adapted to the environment of the slaughterhouse. Detection is carried out by a 488nm excitation and a conventional 520 nm fluorescence detection using a photomultiplier. The assembly proposed uses optical fibers. It provides a resolution close to 0.5 µm, the diffraction limit at 488nm.