RIA-J: Ratio Imaging Analyzer (Java)

The native ImageJ/Fiji counterpart to the RIA (Python) project.

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📖 Overview

RIA-J is a lightweight, publication-grade tool designed to bring the rigorous workflow of ratiometric fluorescence analysis directly into the ImageJ/Fiji ecosystem.

It empowers researchers to perform Background Subtraction, Dynamic Masking, and Real-time Ratio Calculation through a modern, clutter-free dashboard. Featuring a "Silent Processing" engine, RIA-J handles multi-channel datasets entirely in memory, offering a fluid "Single-Window" experience without populating your workspace with unnecessary intermediate windows.

(The modern interface with streamlined inline controls)

✨ Key Features

• 🤫 Silent & Clean Workflow: Say goodbye to window clutter. RIA-J processes multi-channel composite images in memory. It intelligently splits channels and computes ratios without spawning "C1-" or "C2-" windows.
• 🎨 Compact Inline UI: The interface features a space-saving "Inline Layout" (Label-Slider-Input), ensuring a clean look and consistent experience across all operating systems and high-DPI screens.
• ⚡ Instant Preview System:
  • Real-time Tuning: Adjusting sliders (Background, Threshold) triggers a millisecond-level update of the current frame, allowing for lag-free parameter optimization.
  • Batch Recalculate: A dedicated button applies your finalized settings to the entire Time-lapse or Z-stack in one go.
• 📸 Publication-Ready Export:
  • RGB Stack: One-click export of your analysis as a high-quality RGB video/stack.
  • Auto-Sync: Ensures your current visualization settings (LUT, Contrast) are applied to every frame in the exported video.
  • AI-Friendly Legend: Generates a clean, independent color bar window (pure white background) for easy import into Adobe Illustrator.
• 🏷️ Smart Dynamic Naming: Result windows are automatically named based on active channels (e.g., RIA-C1_C2-Result...). If you swap channels, the filename updates dynamically to ensure data traceability.

📥 Installation

Method 1: Via Fiji Update Site (Recommended ⭐)

This is the easiest way to install RIA-J and keep it updated automatically.

1. Open Fiji / ImageJ.
2. Navigate to Help > Update...
3. Click the Manage update sites button.
4. Find RIA-J in the list and check the box.
   • If RIA-J is not in the list, click Add Unlisted Site and enter:
   • Name: RIA-J
   • URL: https://sites.imagej.net/RIA-J/
5. Click Apply and Close, then click Apply changes in the main updater window.
6. Restart Fiji. You will find it under Plugins > RIA-J (Ratio Processor).

Method 2: Manual Installation

If you prefer to install a specific version manually:

1. Download: Get the latest RIA_J-x.x.x.jar file from the Releases page.
2. Copy: Move the .jar file into your Fiji.app/plugins/ folder.
3. Restart: Restart ImageJ.
4. Run: Access the tool via Plugins > RIA-J (Ratio Processor).

🛠️ Usage Workflow

1. Open Images: Drag your raw data (Composite Stack or Split Files) into ImageJ.
2. Launch Plugin: Go to Plugins > RIA-J > Ratio Analyzer.
3. One-Click Import:
   • Click Import / Refresh.
   • The plugin silently detects channels in the background. No extra windows will appear.
4. Interactive Tuning:
   • Adjust Background and NaN Threshold.
   • Tune Min/Max Ratio sliders to optimize the dynamic range.
   • Changes are reflected immediately on the current frame only for maximum speed.
5. Process Stack:
   • Single Image: You are done!
   • Time-lapse/Z-Stack: Click the Recalculate button to apply your tuned parameters to the entire stack.
6. Export Results:
   • Data: The RIA-Result window contains the 32-bit raw data for quantification.
   • Publication: Click Save as RGB (Red Button) to export the Current Frame (Snapshot) or the Entire Stack (Movie).

📂 Output Files

RIA-J enforces a strict naming convention to keep your data organized:

File Type	Naming Convention	Bit-Depth	Purpose
Raw Result	RIA-[ChA_ChB]-Result...	32-bit Float	Measurement, Quantification, ROI Analysis
RGB Stack	RIA-RGB-Stack-[Name]	24-bit RGB	Video presentation, PowerPoint, Visual inspection
RGB Snap	RIA-RGB-Snap-[Name]	24-bit RGB	Figure creation (Adobe Illustrator/Inkscape)

⚙️ Build from Source

Prerequisites: JDK 8+ and Maven.

git clone [https://github.com/Epivitae/RIA-J.git](https://github.com/Epivitae/RIA-J.git)
cd RIA-J
mvn clean package

The compiled plugin will be generated in target/RIA_J-2.0.0.jar.

🤝 Contributing

Contributions are welcome! Please fork the repository and submit a Pull Request.

🖊️ Citation

If you use RIA-J in your research, please cite:

Wang, K. (2026). RIA-J: Ratio Imaging Analyzer (Java) - Publication-Grade Ratiometric Analysis for ImageJ/Fiji (v2.0.0). Zenodo. https://doi.org/10.5281/zenodo.18204761

📄 License

This project is licensed under the MIT License - see the LICENSE file for details.

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Developed by Kui Wang. Part of the RIA Project family.