New or reoccurring bacterial threats are a major challenge of this century, and a delayed response due to the lack of field-testing options risks human lives and causing an epidemic. Classical microbiology techniques are relatively slow, while cytometric methods allow the measurement of cell count, morphology etc. in an easy, reliable, and fast way. State of the art flow cytometers are high-throughput benchtop instruments that are neither portable nor cheap enough for field testing, causing logistic delays in bacterial testing in remote areas and conflict zones or where infrastructure is limited. The goal of this R&D activity is to create the proof of concept of and develop the methodology for low-cost, fully portable flow cytometers based on droplet microfluidics, which will not only allow field analysis of bacteria, but will have a single-cell resolution. Furthermore, through cognitive electronics, the system will be easy to use and fully automated from sample input to result output.