https://github.com/favreau/metabrain
https://github.com/favreau/metabrain
Last synced: 5 months ago
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- Host: GitHub
- URL: https://github.com/favreau/metabrain
- Owner: favreau
- License: apache-2.0
- Created: 2024-10-05T21:34:47.000Z (almost 2 years ago)
- Default Branch: main
- Last Pushed: 2024-11-07T15:12:45.000Z (over 1 year ago)
- Last Synced: 2025-09-10T23:49:13.086Z (11 months ago)
- Language: Jupyter Notebook
- Size: 22.5 KB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Neuroscience Visualization Tools
Welcome to the Neuroscience Visualization Tools project! This project is a collection of simple yet powerful tools designed to make the lives of neuroscientists easier. Whether you are trying to visualize single neurons or entire networks, these tools aim to provide clear, interactive visualizations that help you understand the underlying data.
## Tools Overview
1. **Single Neuron Visualizer**
- Visualize neurons using SWC files, which are standard formats in neuroscience research.
- Offers an interactive 3D view, allowing users to rotate, zoom, and inspect neuron structures using a web browser.
- Smooth visual representation of neuron structures, complete with dendrites, axons, and the soma.
2. **Multi-Neuron Network Viewer** (Coming Soon)
- A tool to visualize multiple neurons within a network.
- Supports connectivity analysis and dynamic simulation.
3. **Data Import and Formatting Helper**
- Simple tools to help neuroscientists import SWC data and other formats into a standardized structure for visualization.
## Single Neuron Visualizer
The **Single Neuron Visualizer** is a web-based tool designed to help neuroscientists explore the 3D structure of individual neurons. This tool reads SWC files and generates a smooth, interactive 3D representation of the neuron, including features such as dendrites, axons, and soma.
### How to Use the Single Neuron Visualizer
1. **Open the Visualizer in a Web Browser**
- Simply open the `index.html` file in any modern web browser.
2. **Specify the SWC File URL**
- To specify the SWC file to be visualized, you can add the SWC URL as a parameter in the main URL of the page.
- For example: https://single-neuron.scientific-visualization.org/?swc=your_neuron_file.swc
- Replace `your_neuron_file.swc` with the actual path or URL of your SWC file.
3. **Interact with the Visualization**
- Use your mouse to rotate and zoom into the neuron to examine the dendrites and axon structures more closely.
- The soma is highlighted in red, axons in blue, and dendrites in green for easy identification.
## Getting Started
- Clone or download the repository.
- Open `index.html` in your favorite browser.
- Use the URL parameter method to load your neuron SWC files and start exploring!
## Requirements
- A modern web browser (e.g., Chrome, Firefox, Safari).
- Internet connection for accessing dependencies hosted online.
## Future Enhancements
- Adding support for network visualization with connectivity data.
- Tools for dynamic simulation of neural activity.
## Contributing
We welcome contributions from the community! Feel free to submit issues, feature requests, or pull requests.
## License
This project is licensed under the Apache 2.0 License. See the LICENSE file for more details.
## Contact
If you have any questions, please reach out via GitHub or email us at [cyrille.favreau@gmail.com](mailto\:cyrille.favreau@gmail.com).
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With these tools, we hope to make the journey of exploring the complex structure of neurons more intuitive and effective for all neuroscientists.