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Here is one of the nifty things you may use fft filtering for.

The laser scanning confocal microscope scans along the X axis.  If there is noise in the laser, then this shows up most dramatically in adjacent X axis scans.   Filtering the frequency of the alternating X axis intensities cleans up the image.

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The original image.  Reflectance mode of the confocal using the 458 nm line of an Ar laser.  Note the horizontal lines. The power spectrum calculated by ImageJ 1.32h with contrast enhanced to show the bright spots that represent the X axis fluctuation. The power spectrum with masks drawn on it. The inverse transform applying the masks.

The Image Processing Toolkit also does this in Photoshop.

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