tracer-workspace

Webknossos Segment Renamer

A Tampermonkey userscript that adds quick semantic renaming to Webknossos segments via context menus.

Features

✨ Two Ways to Rename Segments:

• 🖱️ Right-click segments in the segment list for instant renaming
• 🎯 Right-click segments in 2D viewports via integrated context menu

🎨 Pre-defined Semantic Categories:

• 🔴 Dendrite
• 🔵 Axon
• 🟡 Soma
• 🟣 Nucleus
• 🟠 Glia
• ⚪ Extracellular Space
• 🟤 Myelin
• ❤️ Blood Vessel
• 🔀 Merge Between Classes
• ❓ Uncertain

⚡ Smart Features:

• Automatic edit mode activation
• Smart submenu positioning (never goes off-screen!)
• Works with Webknossos’s native context menus
• Visual feedback with emoji icons

Installation

Prerequisites

1. Install Tampermonkey extension for your browser:
   • Chrome/Brave
   • Firefox
   • Edge

Install the Script

Option 1: Direct Install (Recommended)

1. Click on the raw script file: webknossos-segment-renamer.user.js
2. Tampermonkey will automatically detect it and show an installation prompt
3. Click Install

Option 2: Manual Install

1. Copy the contents of webknossos-segment-renamer.user.js
2. Open Tampermonkey Dashboard
3. Click ”+” to create a new script
4. Paste the code
5. Save (Ctrl+S / Cmd+S)

Usage

Renaming from Segment List

1. Open a Webknossos annotation
2. Right-click any segment in the segment list
3. Choose a semantic ID from the popup menu
4. ✅ Segment automatically renamed!

Renaming from 2D View

1. Open a Webknossos annotation
2. Right-click on a segment in any 2D viewport
3. Look for “🏷️ Rename Segment ▶” in the context menu
4. Hover to see submenu with semantic IDs
5. Click your choice
6. ✅ Segment automatically renamed!

Configuration

Custom Webknossos Domain

If your Webknossos instance is on a custom domain, update the @match directives:

// Add your domain to the script header
// @match        https://your-domain.com/*
// @match        http://your-domain.com:9000/*

Custom Semantic IDs

Edit the SEMANTIC_IDS array in the script:

const SEMANTIC_IDS = [
    { id: 'your-id', label: 'Your Label', emoji: '🎯' },
    { id: 'another', label: 'Another Type', emoji: '🌟' },
    // Add more...
];

Compatibility

• ✅ Webknossos (tested on wk.zetta.ai)
• ✅ Chrome/Brave/Edge (Chromium-based browsers)
• ✅ Firefox
• ✅ Tampermonkey 5.0+

Troubleshooting

Script not working?

1. Check Tampermonkey icon - should show the script is enabled
2. Open Console (F12) - look for “Webknossos Segment Renamer initialized”
3. Verify URL match - script only runs on configured domains

Menu not appearing in 2D view?

• Check console for [2D Menu] debug messages
• Ensure you’re right-clicking directly on a segment
• Webknossos should show segment ID in its context menu

Renaming not saving?

• The script automatically clicks the save button
• Check console for any error messages
• Verify you can rename manually (pencil icon → edit → enter)

Development

Debug Mode

The script logs detailed information to the console:

[2D Menu] Found segment context menu with ID: 23
[2D Menu] Injecting rename menu item for segment: 23
[2D Menu] Inserted menu item before divider

Open DevTools (F12) → Console to see these messages.

Project Structure

tampermonkey-scripts/
├── README.md                                    # This file
├── CHANGELOG.md                                 # Version history
├── LICENSE                                      # License information
├── QUICK_START.md                              # Quick reference guide
└── scripts/
    └── webknossos-segment-renamer.user.js      # Main script

Contributing

Contributions are welcome! To contribute:

1. Fork this repository
2. Create a feature branch (git checkout -b feature/amazing-feature)
3. Make your changes
4. Test thoroughly on your Webknossos instance
5. Commit your changes (git commit -m 'Add amazing feature')
6. Push to the branch (git push origin feature/amazing-feature)
7. Open a Pull Request

License

MIT License - see LICENSE file for details.

Free to use for research, personal, and commercial projects.

Acknowledgments

• Built for the neuroscience community
• Designed for Webknossos - open-source annotation tool
• Uses Ant Design context menu patterns

Changelog

See CHANGELOG.md for version history and updates.

Support

• 🐛 Report bugs: Open an issue
• 💡 Request features: Open an issue
• ❓ Questions: Check existing issues or open a new one

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Made with ❤️ for efficient connectomics annotation