This package provides a pure python implementation of the optical flow component of the motion correction algorithm described in Chen*, Hermans* et al., Nature Communications, 2018.
This package can be installed using pip.
Navigate to this directory in the command line using cd and enter the flowing command:
pip install -e .
The preferred way to use ofco is via the command line or in a python script.
It can be launched in the command line with the following command.
ofco stack1.tif stack2.tif output
where stack1.tif is the path to the stack used for motion estimation and stack2.tif
is the path to a second stack that is warped with the same displacement vector field.
The output is saved in the directory output as files warped1.tif and warped2.tif.
For more command line options see the output of ofco -h.
Alternatively, ofco can be incorporated in a python analysis pipeline as follows.
from skimage import io
from ofco import motion_compensate
from ofco.utils import default_parameters
stack1 = io.imread("path_to_stack1.tif")
stack2 = io.imread("path_to_stack2.tif")
param = default_parameters()
frames = range(2)
motion_compensate(stack1, stack2, 'warped1.tif', 'warped2.tif', frames, param)
For more information check the documentation.
The last possibility is to run the main python file directly with the following command:
python -m ofco.main stack1.tif stack2.tif output
This provides the same options as the command line interface mentioned above.