In the past few decades, many kinds of UAS for image acquisition have been developed. But software for image aligning and correcting is mostly high-cost commercial. This problem caused the cost-problem in using UAS. Nowadays, a variety of software, not only commercial but also open-source, provides powerful image processing tool. There are a number of software to support image processing. In this study,five popular programs are tested for comparison. The goal of this study is to compare popular open-source software based on the ease use, overall accuracy and processing time for chunk of images from UAS.