svs-to-ometiff-gui 0.1.0

Flask GUI for converting SVS whole-slide images to OME-TIFF.

svs-to-ometiff GUI

A web-based graphical user interface for converting SVS whole-slide images to OME-TIFF format using the svs_to_ometiff library.

Experimental: This GUI is experimental and not yet thoroughly tested. Use with caution on production data. Always verify outputs.

Requirements

• Python 3.9+
• pip

Installation

Install from the project directory:

cd /path/to/svs-to-ometiff-gui
pip install -e .

This installs the GUI package and its runtime dependencies:

• svs-to-ometiff>=0.2.0
• flask>=2.3

Usage

Run the GUI with the console script:

svs-to-ometiff-gui

Or run it as a Python module:

python -m svs_to_ometiff_gui

This will:

1. Print an experimental warning banner.
2. Automatically open http://127.0.0.1:8765 in your default browser.
3. Start the Flask development server.

Web Interface

1. Drag & drop an .svs file onto the drop zone, or click the drop zone to use a file dialog.
2. The Input SVS Path field will be populated automatically.
3. The Output Path is auto-derived (same directory, .ome.tiff extension). You may edit it manually.
4. (Optional) Click the gear icon to expand Advanced Settings and adjust:
   • Tile Size (default: 512)
   • Compression (default: lzw; options: lzw, zlib, deflate, none)
   • Levels (default: 6)
   • Downsample Factor (default: 2)
5. Click Convert to start the conversion.
6. Monitor progress via the progress bar and status text.
7. When complete, click Open Output Folder to reveal the output file.

Project Structure

svs-to-ometiff-gui/
├── svs_to_ometiff_gui/
│   ├── __init__.py
│   ├── __main__.py           # python -m svs_to_ometiff_gui entry point
│   ├── serve.py              # Flask app with SSE progress
│   └── templates/
│       └── index.html         # Single-page GUI (inline CSS/JS)
├── pyproject.toml
├── requirements.txt
└── README.md

License

Same as the svs_to_ometiff project.