napari-swc-reader

A minimal napari plugin to load swc file to napari viewer.

---

This napari plugin was generated with copier using the napari-plugin-template.

Features

• Load swc file(s) to napari viewer
• Display swc file(s) in napari viewer as points layers and lines layers
• Size of points and lines are using the radius of the swc file
• You can load an example swc from https://neuromorpho.org/dableFiles/jacobs/CNG%20version/204-2-6nj.CNG.swc or load it under File -> Open Sample -> napari-swc-reader

Limitations:

• Only support swc file(s) following specs http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html 7 columns
• Cannot write swc file(s) to disk but you can access the raw swc data from the napari layers from metadata attribute with key raw_swc

Roadmap:

• Switch to use napari.layers.Graph when it is available

Installation

You can install napari-swc-reader via pip:

pip install napari-swc-reader

To install latest development version :

pip install git+https://github.com/LaboratoryOpticsBiosciences/napari-swc-reader.git

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 BSD-3 license, "napari-swc-reader" is free and open source software

Issues

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

Other Resources

Checkout this cool other ressources working with swc files and napari:

• https://skeleton-analysis.org/stable/index.html
• https://www.napari-hub.org/plugins/napari-tracing