Neuron SWC Editor

A free, browser-based online tool for visualizing and editing morphological neuron .swc files — no installation required.

Features

• 📊 Dual Visualization: View, edit, import, and export .swc files in both 2D and 3D interactive canvases
• 🖼️ Export Options: Generate transparent PNG images perfect for figures or presentations
• 🔬 Simulation Ready: Edited .swc files are compatible with simulation tools like NEURON and BRIAN
• 🔍 NeuroMorpho Integration: Search and load neurons directly from NeuroMorpho.Org using their public API
• ✂️ Branch Editing: Remove or modify specific branches in the neuronal tree structure
• 🎨 Color Customization: Change segment colors for better visualization and analysis
• 💻 No Installation: Works entirely in your browser with modern Chrome, Firefox, Safari, or Edge

Getting Started

Quick Start (Online)

1. Visit deangeckt.github.io/swc_editor
2. Upload your .swc file or search for neurons from NeuroMorpho.Org
3. Edit your neuron using the 2D or 3D canvas
4. Export your modified .swc file or save as PNG

Demos

Browse for online neurons available at NeuroMorpho.Org

demo.mp4

Remove a specific branch in the tree via the 2D editor, save for later analysis

demo.mp4

Upload your own neuron and change segments color

demo.mp4

MICrONS Skeletons Example

To use a skeleton from MICrONS, which can be loaded via skeleton_plot or Meshparty run:

Loading the skeleton:

import skeleton_plot.skel_io as skel_io
skel_path = "s3://bossdb-open-data/iarpa_microns/minnie/minnie65/skeletons/v661/skeletons/"
nucleus_id = 256609
segment_id = 864691135404231406
skel_filename = f"{segment_id}_{nucleus_id}.swc"
sk = skel_io.read_skeleton(skel_path, skel_filename)

Exporting the skeleton to SWC:

import numpy as np
sk.export_to_swc(
    f'{nucleus_id}.swc',
    node_labels=sk.vertex_properties["compartment"],
    radius=np.array(sk.vertex_properties["radius"]),
    xyz_scaling=1
)

Local Development

To run the editor locally:

# Clone the repository
git clone https://github.com/deangeckt/swc_editor.git
cd swc_editor

# Install dependencies
npm install

# Start development server
npm start

The app will open at http://localhost:3000

Build for Production

npm run build

Citation

If you use the Neuron SWC Editor in your research, please cite it as:

@software{swc_editor,
  author = {Dean Geckt},
  title = {Neuron SWC Editor: A Browser-Based Tool for Visualizing and Editing Neuronal Morphology},
  year = {2024},
  url = {https://github.com/deangeckt/swc_editor},
  note = {Available at: https://deangeckt.github.io/swc_editor/}
}

Contributing

Contributions are welcome! Feel free to fork the repository, make your improvements, and submit a pull request. Whether it's bug fixes, new features, or documentation improvements, all contributions help make this tool better for the neuroscience community.

Acknowledgments

• NeuroMorpho.Org for providing public access to neuronal reconstructions
• MICrONS Project for cortical neuron data

---