yet another IMOD wrapper
Project description
yet-another-imod-wrapper
A simple Python API for aligning single axis tilt-series in IMOD.
from yet_another_imod_wrapper import (
align_tilt_series_using_fiducials,
align_tilt_series_using_patch_tracking
)
import mrcfile
import numpy as np
# load tilt series into (n, y, x) numpy array
tilt_series = mrcfile.read('my_tilt_series.mrc')
# align using fiducials
align_tilt_series_using_fiducials(
tilt_series=tilt_series,
tilt_angles=np.arange(-60, 63, 3),
pixel_size=1.35,
fiducial_size=10,
nominal_rotation_angle=85,
basename='my_tilt_series',
output_directory='fiducials',
skip_if_completed=False
)
# align using patch-tracking
align_tilt_series_using_patch_tracking(
tilt_series=tilt_series,
tilt_angles=np.arange(-60, 63, 3),
pixel_size=1.35,
patch_size=1000,
patch_overlap_percentage=33,
basename='my_tilt_series',
output_directory='patch_tracking',
skip_if_completed=False
)
Installation
This package requires that IMOD>=4.11.0 is installed and on the PATH.
yet-another-imod-wrapper can be installed using pip.
pip install yet-another-imod-wrapper
We recommend installing into a fresh virtual environment.
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