okapi-em

https://github.com/rosalindfranklininstitute/okapi-em

A napari plugin for processing serial-FIB-SEM data.

Powered by chafer and quoll.

This napari plugin contains the following tools:

• Two charge artifact suppression filter
  • directional fourier bandapass filter
  • line-by-line filter function optimiser and subtraction (requires charge artifact labels)
• slice alignment using constrained SIFT
• FRC estimation

This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

Installation

You can install okapi-em via pip:

pip install okapi-em

For development mode it can be installed by navigating to the cloned okapi-em folder and run:

pip install -e .

This should install in any machine, however ...

Currently the FRC calculation provided by the quoll package which is optional because of its stringent environmemt requirements from miplib package. These currently are:

• python 3.7
• linux OS

This issue will be addressed in future version.

To install okapi-em with quoll included:

pip install okapi-em[all]

Note that to run napari in python 3.7 you will need to use the command:

python -m napari

Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the Apache Software License 2.0 license, "okapi-em" is free and open source software

Issues

If you encounter any problems, please [file an issue] along with a detailed description.