Dave Mitchell's DigitalMicrograph™ Scripting Website

A script to compute the phase image from either a single defocused image or a pair of images at differing foci.

This script can compute a phase image from a single defocused image (non-quantitatively), by approximating the zero focus image as a flat field image of intensity equal to the background in the image. In the case of a pair of defocused images, the phase is computed quantitatively by subtracting one defocused image from another. The Tikhonov parameter correction is used to overcome the singularity problem at zero radius in the FFT of this difference image arising from the the 1/q term.

The script will operate on either one or two defocused images. In the case of a single image, a region of representative background intensity is selected and the phase computed. In the case of two images, they must be aligned and where the defocus difference between them is large, they must be corrected for the accompanying magnification changes. The script will scale and align the two images and then compute the phase.

The Tikhonov correction is carried out by specifying a radius (a parameter) from the centre of the FFT as the peak in the Tikhonov function (which becomes zero at zero radius, and also declines at higher radii). The script allows a series of phase images to be calculated by specifying the number and size of the steps in the a parameter. At higher a parameter values, the function selects higher frequency information from the FFT and so the frequency and resolution of each image will vary with the a parameter. The range of a parameter values should be chosen to span the frequencies of interest.

This filter may be of use in image processing of biological micrographs, as a way of enhancing weak contrast. The cited Micron paper by Verguet et al. shows several applications.

A detailed description of the controls of the script is provided in the script header and can be printed to the Output window by clicking the tools button in the dialog.

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