Micrograph movie alignment: align micrograph movies with Unblur. http://grigoriefflab.janelia.org/unblur

Usage in command line

sxunblur.py  --input_micrograph_list_file unblur  input_mrc_micrograph  output --nr_threads=NR_THREADS  --nr_frames=nr_frames  --pixel_size=pixel_size  --skip_dose_filter  --exposure_per_frame=exposure_per_frame  --voltage=voltage  --pre_exposure=pre_exposure  --save_frames  --expert_mode  --shift_initial=shift_initial  --shift_radius=shift_radius  --b_factor=b_factor  --fourier_vertical=fourier_vertical  --fourier_horizontal=fourier_horizontal  --shift_threshold=shift_threshold  --iterations=iterations  --dont_restore_noise --verbose

Just shift data with dose filter.

sxunblur.py directory_to_unblur directory/prefix*suffix.mrc output_directory --nr_frames=25 --pixel_size=1.19 --exposure_per_frame=1.0 --voltage=300.0 --pre_exposure=0.0

Shift data with aligned sum files, and aligned frames without dose filter.

sxunblur.py directory_to_unblur directory/prefix*suffix.mrc output_directory --nr_frames=25 --pixel_size=1.19 --skip_dose_filter --save_frames --nr_threads=2

Dose filter and Expert Options and aligned frames

sxunblur.py directory_to_unblur directory/prefix*suffix.mrc output_directory --nr_frames=25 --pixel_size=1.19 --exposure_per_frame=1.0 --voltage=300.0 --pre_exposure=0.0 --save_frames --expert_mode --shift_initial=2.0 --shift_radius=200.0 --b_factor=1500.0 --fourier_vertical=1 --fourier_horizontal=1 --shift_threshold=0.1 --iterations=10 --verbose --nr_threads=1

input_micrograph_list_file

Input micrograph list file: Not an unblur option, extension of input micrograph list file must be '.txt'. If this is not provided, all files matched with the micrograph name pattern will be processed. (default none)

unblur

Path to unblur executable: (default required string)

input_mrc_micrograph

Input micrographs: You can use the wild cards (e.g. *) to specify a list of micrographs. (default required string)

output

Output directory: The results will be written here. This directory will be created automatically and it must not exist previously. (default required string)

nr_threads

Number of threads: Not an unblur option, number of threads unblur is allowed to use. The higher the faster, but it also needs a higher amount of memory. (default 1)

nr_frames

Number of frames: (default 3)

pixel_size

Pixel size [A]: (default required -1.0)

exposure_per_frame

Per frame exposure [e/A^2]: (default 1.0)

voltage

Microscope voltage [kV]: (default 300.0)

pre_exposure

Pre exposure [e/A^2]: (default 0.0)

save_frames

Save aligned frames: save aligned frames. This is only neccessary if one wants to perform movie refinement and will slow down the process. (default False)

skip_dose_filter

Skip the dose filter step: If yes, exposure per frame, voltage, and pre exposure will be ignored. (default False)

expert_mode

Set expert mode: Requires the options initial shift, shift radius, b-factor, fourier_vertical, fourier_horizontal, shift threshold, iterations, restore noise, and verbosity. (default False)

shift_initial

*EXPERT* Minimum shift for initial search [A]: (default 2.0)

shift_radius

*EXPERT* Outer radius shift limit [A]: (default 200.0)

b_factor

*EXPERT* Apply B-factor to images [A^2]: (default 1500.0)

fourier_vertical

*EXPERT* Half-width of central vertical line of fourier mask: (default 1)

fourier_horizontal

*EXPERT* Half-width of central horizontal line of fourier mask: (default 1)

shift_threshold

*EXPERT* Termination shift threshold: (default 0.1)

iterations

*EXPERT* Maximum iterations: (default 10)

dont_restore_noise

*EXPERT* Do not restore noise power: (default False)

verbose

*EXPERT* Verbose: (default False)

The program creates the directory automatically in the chosen output directory. (default required string)

Without dosefilter: Sum files will be written to the “corrsum” folder. Log files will be written to the “logfiles” folder Aligned frames will be written to the “corrsum” folder. Shift files will be written to the “shift” folder. FRC files will be written to the “frc” folder.

With dosefilter: As without dosefilter plus: Dose filtered sum files will be written to the “corrsum_dose_filtered” folder. Log files will be written to the “logfiles” folder Dose filtered aligned frames will be written to the “corrsum_dose_filtered” folder. Shift files will be written to the “shift” folder. FRC files will be written to the “frc” folder.

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Markus Stabrin

Category 1:: APPLICATIONS

sxunblur.py

sxgui_unblur.py

No bugs known so far.