I’m learning how to use Fourier transforms for image analysis. While Fiji has functions to easily do things like selecting a circular area or torus and filtering based on that, or filtering horizontal or vertical lines, other types of filtering can be useful too. There’s a video from MIPAR on FFT (search Mipar TUTORIAL: FFT Filtering) that illustrates the kind of techniques I’d like to learn how apply.

The two main techniques I’d like to be able to apply are using an FFT to remove image artifacts NOT horizontal or vertical (e.g. 45° to vertical), and keeping specific ‘zones’ of the FFT to enhance a repeating lattice.

I see the workflow as something like the following:

There doesn’t seem to be much help at all on how to manually create a binary mask and apply it to an image. Ideally, I’d like to be able to draw overlaid on the FFT, to ensure I’m retaining and erasing the correct parts of the FFT pattern.

Any advice/tutorials/links to applicable modules is greatly appreciated.