In order to design a microfluidic device that can produce monodispersed encapsulated enzymes as droplets, it is essential to be able to evaluate the system during its development. An automated method to determine the size of the droplets as well as a method to tag and track droplets as they move in the system is desirable for system evaluation. We apply the Hough transform for circles to determine droplet size. Most of the droplets in the images are detected, and the best results are obtained at 20x magnification. We also test the ability of the ImageJ 'particle tracker' plugin to determine the behaviour of the droplets as they move in microfluidic systems. It is effective in tracking droplets that travel less than 50 pixels between frames.