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

See docs/3d_visualizer_example.png And docs/2d_visualizer_example.png

Installation

Install SWC Visualizer from PyPI:

pip install swc-visualizer

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")

Command Line

SWC Visualizer can also be used directly from the command line. Provide the path to an individual SWC file or a directory containing SWC files, and a visualization type using --visualization. For example:

swc-visualizer my/neuron.swc --visualization 2d

or

swc-visualizer my/neuron_folder --visualization both

Example SWC Files

Example SWC files are included with the package and can be accessed using "examples":

from swc_visualizer import visualize_swc

visualize_swc("examples", visualization="3d")

From the command line, use the --examples flag:

swc-visualizer --examples

Acknowledgements

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

License

This project is licensed under the MIT License

Project links

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Credits

Author: Daniel Moreno

GitHub Statistics

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License expression

MIT
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Requires

Python >=3.11

Tags

morphology neuron neurons neuroscience visualizer plotly swc tree

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