The provided is a method that can automatically align image frames in recorded video clips. Individual frames in video may shift and rotate due to shaking or vibration of a video camera. Unaligned frames make some imaging processing techniques difficult or infeasible. One example of image processing techniques is to isolate, recognize, and/or quantitatively analyze vapor plume images captured by an Infrared (IR) camera. Such techniques have a great potential to be used to automatically detect volatile organic compounds (VOC) leaked from process equipment at refineries and chemical plants. This invention is a technique for various subsequent image processing techniques. The invention uses spatially based Fast Fourier Transforms (FFT) to determine amount of shift, rotation, and scaling to align image frames, and uses a digital filtering technique to improve the alignment.