napari okapi-em

okapi-em

napari plugin to deal with charging artifacts in tomography electron microscopy data


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    • Documentation
    • Support site
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    Source code:

    • Information not submitted

    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 filters
      • 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.

    Version:

    • 0.0.7

    Release date:

    • 08 December 2022

    First released:

    • 19 October 2022

    License:

    • Apache-2.0

    Supported data:

    • Information not submitted

    Plugin type:

    GitHub activity:

    • Stars: 0
    • Forks: 0
    • Issues + PRs: 0

    Python versions supported:

    Operating system:

    Requirements:

    • numpy
    • magicgui
    • qtpy
    • chafer
    • napari[all]
    • opencv-python

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