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:

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

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.

Distributed under the terms of the BSD-3 license, "napari-swc-reader" is free and open source software

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

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