superimpose_psf can handle several of the steps of turning an image of
a single bead into a CTF file for the deconvolution
application; consult the "Measuring the CTF" section in the deconvolution documentation
for an outline of the procedure.
superimpose_psf performs the following actions:
- Can sum adjacent z sections to give a single section in the output. If
the extended header is one of the formats mentioned in the
IM library documentation, the
photosensor measurements are summed as well.
- Determines the location of the peak intensity and interpolates the
position of the peak by a quadratic fit to the pixel and its six
immediately adjacent neighbors. If the photosensor measurements are
available in the extended header, they are taken into account for the
interpolation of the peak's z coordinate. The reported coordinates are
zero-based.
- Can estimate the background (it does so by averaging the edge pixels
of the in-focus section and the section above and below the in-focus
section) and subtract that background estimate from the data.
To use superimpose_psf, invoke it from the command line. The expected form
of the command line is (optional parts are shown in brackets):
superimpose_psf input_dataset output_dataset \
[-nrepeat=n] [-no_background]
The meanings of the different entries on the command line are:
- input_dataset
- input_dataset is expected to be the name of a Priism image
stack.
- output_dataset
- output_dataset is the name of the Priism data set where the
output should be stored. output_dataset may not be the same
as input_dataset.
-nrepeat=n
- Specifies that n adjacent z sections should be summed to give
a single z section in the output. n must be greater than zero
and less than the z size of the input data set. If n does not
evenly divide the input's z size, the trailing sections are ignored. If
-nrepeat is not specified on the command line, superimpose_psf
does not sum adjacent z sections.
-no_background
- If specified on the command line,
-no_background suppresses
the estimation and subtraction of the background.
Related Priism Topics
Deconvolution |
Priism