Access to clean drinking water is necessary to maintain healthy populations. Remote locations often do not have the equipment or the means to test water quality. A rapid, affordable, user friendly, portable system that can detect and analyze pathogens in water is discussed in this thesis. The system is designed to optically quantify pathogens by digital droplet PCR (Polymerase Chain Reaction) using fluorescence detection and Lab-on-a-Disk technology. A sample microfluidic disk is inserted into the system. The system uses centrifugal forces to break apart cells within the sample, mix reagents with the sample, and generate droplets. Infrared heating is then used to amplify DNA within the sample. Fluorescent images of the droplets within the microfluidic disk are captured. The system functions as designed.