napari-filament-annotator 0.1.2

Annotation of filaments / curvilinear structures in 3D

3D Filament Annotator

3D Filament Annotator is a tool for annotating filaments and other curvilinear structures in 3D. The 3D annotation is done by annotating the filament in two different projections, calculating intersection, and refining the filament position with active contours.

Installation

Install napari

pip install napari[all]

Install the filament annotator

pip install git+https://github.com/amedyukhina/napari-filament-annotator.git

Usage

For detailed usage instructions, please refer to the usage tutorial.

Contributing

Contributions are very welcome both with regard to plugin functionality, and tips on using it and setting parameters.

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, "napari-filament-annotator" is free and open source software

Dependencies

• napari
• scikit-image
• scikit-learn
• NetworkX
• Geometry3D

Issues

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

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