AreTomo (w)rapper for rln4
Project description
lil_aretomo
im not a (w)rapper
see the script in example directory for the kind of input script you need to run this.
To install, type: pip install lil_aretomo
Parameters
----------
tilt_series_file: file containing tilt-series images
tilt_angles: nominal stage tilt-angles from the microscope.
pixel_size: pixel size of the tilt-series in angstroms-per-pixel
output_directory: tilt-series directory for IMOD.
aretomo_executable: path to the AreTomo executable file
(optional) local_align: carry out local tilt series alignments? Yes or no, default is no
(optional) target_pixel_size: the ideal pixel size at which TSA is carried out. Default is 10A
(optional) nominal_rotation_angle: initial estimate for the rotation angle of the tilt
axis. AreTomo does not need this information but it might help.
(optional) n_patches_xy: if local_align is True, AreTomo will carry out patch tracking.
Specify the number of patches in X and Y here as tuple. Default is 5 (in X) and 4 (in Y).
(optional) correct_tilt_angle_offset: Apply tilt angle offset correction, yes or no.
Default is no. See AreTomo manual for full explanation: yes adds the -TiltCor 1 argument.
(optional) thickness_for_alignment: Specify AlignZ value. Default is 800.
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