Xmipp

xmipp_xray_import (v3.0)

Usage

Imports X-ray micrographs with .spe extension

This program converts a single-axis tilt series coming from a X-ray microscope in SPE format into a MRC stack. Several corrections are applied during this conversion including correction by the beam current, the exposure time, and the slitwidth. The flatfield and a possible darkfield are also corrected. The exact formula applied is

                       (I-darkfield)/(expTime*beamCurrent*slitWidth)
Icorrected=log10 -----------------------------------------------------------
                 Avg{(Iflatfield-darkfield)/(expTime*beamCurrent*slitWidth)}

If the darkfield is not available, it is not used for the correction. The flatfields and the the tilt series may be in any directory. If the darkfield are available, they must be within the flatfield and the tilt series under a directory named darkfields (in small letters). For each SPE file there must be a positions file. For instance, the file myfile.spe must have in the same directory the file myfile-positions.txt. The exposure time, the beam current and the slit width are taken from this file.

The exposure time is the parameter xm:ccd:exp_time, the beam current is sr:current, and the slit width is xm:mono:slitwidth. The tilt angle xm:sample:rx.

Parameters

--data <inputDataDirectory>
Directory with SPE images, position files, and optionally, darkfields (in a directory called darkfields)
--oroot <outputRootname>
Rootname for output files The following files are created: rootname_darkfield.xmp: darkfield for the tilt series rootname_flatfields_darkfield.xmp: darkfield of the flatfields rootname_flatfields_avg.xmp: average flatfield corrected by its darkfield rootname.mrcs: MRC stack with tilt series fully corrected as described above rootname.sel: selfile with the images in the stack rootname.tlt: list of angles
--flat <inputFlatfieldDirectory=>
Directory with SPE images, position files, and optionally, darkfields (in a directory called darkfields)
--crop <size=0>
Number of pixels to crop from each side This is used to avoid some black pixels of some cameras
--thr <N=1>
Number of threads

Filters

--filterBadPixels, -f <mask=>
Apply a boundaries median filter to bad pixels given in mask.
--log, -l
Apply a log10 correction to normalized output images.

Examples and notes

The most standard call is
xmipp_xray_import --data 10s --flat flatfields --oroot ProcessedData/img --crop 7

User's comments

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