SWC Visualizer

SWC Visualizer is a Python tool for validating, summarizing, and visualizing neuronal morphology stored in SWC files.

It is designed for people who are new to neuronal morphology and/or programming, who want to explore SWC files from databases such as NeuroMorpho.Org or other sources.

The tool can:

• Validate SWC morphology data.
• Provide basic summary information about neuronal morphology.
• Generate 2D visualizations of neuronal morphology.
• Generate interactive 3D visualizations of neuronal morphology.
• Process SWC files individually or. process all SWC files in a directory sequentially.

Example

Basic Usage

After installing the package, import and call visualize_swc

from swc_visualizer import visualize_swc

visualize_swc("my/neuron/folder", visualization="3d")

The visualization argument accepts:

• "2d" — generate a 2D visualization.
• "3d" — generate a 3D visualization.
• "both" — generate both 2D and 3D visualizations.

You can provide either an individual SWC file or a directory containing multiple SWC files:

from swc_visualizer import visualize_swc

# Process a single SWC file
visualize_swc("my/neuron.swc", visualization="2d")

# Process all SWC files in a directory
visualize_swc("my/neuron_folder", visualization="both")

Example SWC files from NeuroMorpho are provided in the morphology directory.

Acknowledgements

Special thanks to Marieke Westendorp for her guidance throughout this project.

License

This project is licensed under the MIT License