ria-gui 1.8.1.4

RIA: Ratio Imaging Analyzer for biological quantification

Ratio Imaging Analyzer (RIA / 莉丫)

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Meet RIA (or as we affectionately call her, "Li Ya / 莉丫").

RIA is an open-source tool built to solve a simple but annoying problem: Ratiometric analysis shouldn't be stuck on the microscope computer.

Ratiometric imaging (like FRET or sensors for Tryptophan/pH/Ca²⁺) is amazing for normalizing data, but analyzing it usually requires expensive commercial software (like MetaMorph or NIS-Elements) that is locked to a specific workstation with a dongle.

We built RIA so you can take your TIFF stacks, go to a coffee shop (or just your desk), and run rigorous analysis on your own laptop—no coding required.

[Image of fluorescence ratiometric imaging process diagram]

💡 Why use RIA?

• Analysis Unchained: Stop queuing for the lab workstation. RIA is a standalone executable that runs on standard PCs.
• Math Done Right: Calculating ratios isn't just A / B. Biological images have edges and noise. We implemented a normalized convolution algorithm that handles NaN (Not a Number) values correctly. This means your data doesn't get eroded or corrupted at cell boundaries—a common issue in simple script-based analysis.
• Zero Coding Needed: We know not everyone loves Python. RIA has a full GUI for background subtraction, thresholding, and dragging-and-dropping ROIs.
• Trust Your Data: We don't hide the numbers. You get the visual stacks, but you also get the raw float32 ratio data and time-series CSVs. You can take these straight to Prism, Origin, or Excel.

📁 Project Structure

RatioImagingAnalyzer/
├── data/               # Sample TIFFs so you can try it out immediately
├── paper/              # JOSS submission files
├── src/ria_gui         # The actual code
│   ├── main.py         # Start here
│   ├── gui.py          # The frontend logic
│   ├── processing.py   # The math/algorithm heavy lifting
│   └── components.py   # UI Widgets
├── tests/              # Automated tests to keep bugs away
└── requirements.txt    # Dependencies

🚀 Installation

Option 1: Install via PyPI (Recommended for Pythoners)

RIA is available on the Python Package Index. Open your terminal and run:

pip install ria-gui

Once installed, simply type the following command to launch the software:

ria

Option 2: Running from Source (Recommended for Developers/Reviewers)

1. Clone the repository:

   git clone https://github.com/Epivitae/RatioImagingAnalyzer.git
   cd RatioImagingAnalyzer
   

2. Install dependencies: It is recommended to use a virtual environment.

   pip install -r requirements.txt
   

3. Run the application: The source code is located in the src directory:

   python src/ria_gui/main.py
   

Option 3: Standalone Executable (For End Users)

Check the Releases page to download the latest compiled .exe file for Windows. No Python installation is required.

📖 Usage Workflow

1. Load Files:
   • Supports both Single-Channel (Intensity) and Multi-Channel (Ratio) Tiff stacks.
   • Drag & drop or browse files. RIA automatically detects the channel structure.
2. Preprocessing:
   • Motion Correction: Align shaky time-lapse data using the built-in ECC algorithm.
   • Background: Set a global background subtraction (Percentile) or use a custom ROI.
3. Visualization:
   • Switch views between Ratio, Ch1, Ch2, or Aux channels using the toolbar.
4. Analyze:
   • Draw ROIs (Rectangle, Circle, Polygon).
   • Click Plot Curve to see real-time intensity/ratio changes.
5. Save & Export:
   • Save Project: Save your session as a .ria file.
   • Export Data: Copy data to clipboard or save processed images as Tiff stacks.

🧪 Automated Testing

RIA v1.8.0 introduces a "Ghost Pilot" automated testing script powered by rich to ensure stability.

To run the visual E2E test demo:

python tests/auto_drive_rich.py

🤝 Contributing

Contributions are welcome! Please check the Issue Tracker or submit a Pull Request.

📄 License

Distributed under the MIT License. See LICENSE for more information.

Citation

If you use RIA in your research, please cite:

Wang, K. (2025). Ratio Imaging Analyzer (RIA): A Lightweight, Standalone Python Tool for Portable Fluorescence Analysis (v1.8.0). Zenodo. https://doi.org/10.5281/zenodo.18107966

Or use the BibTeX entry:

@software{Wang_RIA_2025,
  author = {Wang, Kui},
  title = {{Ratio Imaging Analyzer (RIA): A Lightweight, Standalone Python Tool for Portable Fluorescence Analysis}},
  month = dec,
  year = {2025},
  publisher = {Zenodo},
  version = {v1.8.0},
  doi = {10.5281/zenodo.18107966},
  url = {https://doi.org/10.5281/zenodo.18107966}
}