The FFT Analysis tool is useful for a wide variety of purposes, ranging from evaluating bias frames to focusing electron microscopes. An explanation of the theory and usage of FFT analysis is beyond the scope of this manual; however, many sources are available on the web.
The FFT requires a power-of-two analysis window. The analysis window must be equal to or less than the size of your image in both X and Y. Select the desired Analysis Region Size and a square window of that size will appear on your image. You can reposition that window using the mouse.
When you are ready to perform the analysis, click OK. The image window will be adjusted if necessary to match the Analysis Region Size, and the results of the FFT analysis will be displayed. Any patterns in the FFT image illustrate periodic structure in the original image.