Metadata-Version: 2.1
Name: lil-aretomo
Version: 0.0.2
Summary: AreTomo (w)rapper for rln4
Home-page: https://github.com/EuanPyle/lil_aretomo
Author: Euan Pyle
Author-email: euanpyle@gmail.com
License: BSD license
Project-URL: Source Code, https://github.com/EuanPyle/lil_aretomo
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Provides-Extra: testing
Provides-Extra: dev
License-File: LICENSE

# 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_x: if local_align is True, AreTomo will carry out patch tracking.
    Specify the number of patches in X here. Default is 5.
    (optional) n_patches_y: same as above, but in Y. Default is 4.
    (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.
