http://imagej.273.s1.nabble.com/FFT-on-a-stack-automatization-tp3693511p3693513.html
You might also try the FFT Bandpass filter.
> Hi Guenther,
>
> Process>FFT>Custom filter works on stacks.
>
> Take our FFT, make a mask from it that is 255 where wou want to pass
> the frequencies and 0 where you want to block it (essentially the
> same as you would do for normal filtering, but you have to change the
> values both inside *and* outside of your roi). Then smooth it
> slightly (3 times 'smooth' or Gaussian Blur with a small radius to
> aviod ringing artifacts).
>
> In contrast to normal 'Inverse FFT', for 'Custom Filter' you have to
> take care about creating a symmetric filter, it won't be made
> symmetric with respect to the origin.
>
> Michael
> ________________________________________________________________
>
> On 2 Mar 2009, at 07:45, Guenter Giese wrote:
>
> > Dear list members,
> >
> > I have stacks of images with darkened regions (shadow-like stripes)
> > running
> > through (two main directions with angles only some degrees to
> > orthogonal
> > directions). On a single image, I run FFT, edit the power spectrum
> > (clearing
> > of a polygonal ROI), and then do inverse FFT.
> >
> > Is it possible to do automated FFT/ROI clearing/inverse FFT on a
> > whole stack
> > using a polygonal (predefined?) ROI for editing the power spectrum?
> > Perhaps
> > as a macro?
> >
> > Best,
> >
> > Guenter
> >
> > ------------------------------------------
> > Dr. Guenter Giese
> > Light Microscopy Facility Manager
> > Dept. of Biomedical Optics
> > MPI fuer Medizinische Forschung Jahnstr. 29
> > D-69120 Heidelberg, Germany
> > Phone (+49) 6221-486-360 (Fax: -325)
> > e-mail:
[hidden email]
Joel B. Sheffield, Ph.D