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:

• slice alignment using constrained SIFT
• two charge artifact suppression filters
  • directional fourier bandapass filter
  • line-by-line filter function optimiser and subtraction (requires charge artifact labels) - uses chafer
• fourier ring correlation (FRC) resolution estimation - uses quoll

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, clone this package then navigate 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 launch 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.