Ctrax is an open-source, freely available, machine vision program for estimating the positions and orientations of many walking flies, maintaining their individual identities over long periods of time. It was designed to allow high-throughput, quantitative analysis of behavior in freely moving flies. Our primary goal in this project is to provide quantitative behavior analysis tools to the neuroethology community, thus we've endeavored to make the system adaptable to other lab's setups. We have assessed the quality of the tracking results for our setup, and found that it can maintain fly identities indefinitely with minimal supervision, and on average for 1.5 fly-hours automatically.