Xmipp

xmipp_xray_psf_create (v3.0)

Usage

Create a volume with the 3D PSF of an X-ray microscope. A param file can be passed or directly setting the microscope parameters. The program generates a PSF volume file and its associated info file.

See also
xray_project

Parameters

-i, --input <psf_param_file>
XRay-Microscope parameters file.
-o, --output <output_name_file>
Name for output files. It creates a PSF volume file and a PSF parameters file.
--lambda <v=2.43>
X-ray wavelength (nm).
--out_width <deltaR=40>
Outermost zone width of the X-ray Fresnel lens (nm).
--zones <N=560>
Number of zones of the X-ray Fresnel lens.
--mag <Ms=2304>
Magnification of the X-ray microscope.
--sampling <dxy=10> <dz=dxy>
Sampling rate in X-Y plane and Z axis (nm).
--zshift <deltaZ=0>
Longitudinal displacement along Z axis in microns.
--size <x> <y=x> <z=x>
Size of the X-ray PSF volume.
--type <lens_type=ideal>
Lens type to generate the PSF.
where <lens_type> can be:
  • ideal Ideal phase Fresnel lens.
  • zp Fresnel Zone Plate lens.

Examples and notes

The parameters are in a file
xmipp_xray_psf_create -i psf560.xmd -o psf560.vol
The parameters are given in the command line
xmipp_xray_psf_create -o psf900.vol -lambda 2.5 -zones 900
In the following link you can find an example of X-ray microscope parameters file:

http://sourceforge.net/p/testxmipp/code/ci/3.0/tree/input/xray_psf.xmd

User's comments

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