RIA-J (Ratio Imaging Analyzer - Java Edition) is a lightweight, high-performance ImageJ/Fiji plugin designed for interactive ratiometric fluorescence analysis. Developed by Kui Wang at the Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Chinese Academy of Sciences, it serves as the native Java counterpart to the Python-based RIA software.
Key Features
- Interactive Swing Dashboard: A non-modal control panel that allows for real-time parameter tuning (background subtraction, thresholding) without blocking the image view.
- Smart Masking: Implements dynamic
NaNthresholding in the denominator channel to eliminate noise and division artifacts. - Scientific-Grade Processing: Supports Normalized Convolution, a technique used to smooth signals while correctly handling boundaries, avoiding the “dark halo” artifacts common with standard Gaussian blurs.
- Batch Engine: Efficient “Apply to Stack” functionality for processing high-dimensional time-lapse (T-series) or Z-stack data.
- Integrated Visualization: Automated scientific LUT application (Fire, Ice, Spectrum) and calibration bar generation.
Installation & Update
RIA-J is distributed via an official Fiji Update Site.
- Open Fiji / ImageJ.
- Navigate to Help › Update…
- Click Manage update sites.
- Check RIA-J from the list.
- Click Apply and Close, then restart Fiji.
If the site is missing from the list, you can add it manually:
Name: RIA-J
URL: https://sites.imagej.net/RIA-J/
Usage Workflow
- Initialize: Open your dual-channel image and click “Import / Refresh Images” in the RIA-J panel.
- Tune: Adjust the Background and NaN Threshold sliders while observing the real-time preview.
- Refine: (Optional) Apply Normalized Convolution for edge-aware smoothing.
- Export: Click “Apply to Stack” to generate the final ratiometric result.
Citation & DOI
If you use this software in your research, please cite the permanent Zenodo record:
- Repository: https://github.com/Epivitae/RIA-J
Developed by Kui Wang © 2026. Part of the development for genetically encoded indicators, including GEM-CPPU1.0 and phosphate (Pi) probes.
