Add RIA-J ratiometric analysis plugin page

_pages/plugins/ria-j.md

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+---
+title: RIA-J
+name: RIA-J (Ratio Imaging Analyzer - Java Edition)
+description: A high-performance, interactive dashboard for real-time ratiometric fluorescence analysis and visualization.
+categories: [Analysis, Visualization, Image Characterization]
+authors: [Kui Wang]
+labels: [ratiometric, fluorescence, FRET, biosensor, kinetics, normalized-convolution]
+icon: /images/RIA-J.png
+project: https://github.com/Epivitae/RIA-J
+source: https://github.com/Epivitae/RIA-J/blob/main/src/main/java/com/mybiolab/RIA_J.java
+website: https://github.com/Epivitae/RIA-J
+dev-status: active
+support: https://github.com/Epivitae/RIA-J/issues
+doi: 10.5281/zenodo.18200078
+update-site: RIA-J
+---
+
+**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 `NaN` thresholding 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.
+
+1. Open **Fiji / ImageJ**.
+2. Navigate to **Help › Update...**
+3. Click **Manage update sites**.
+4. Check **RIA-J** from the list.
+5. Click **Apply and Close**, then restart Fiji.
+
+{% include notice icon="info" content="If the site is missing from the list, you can add it manually:<br>**Name:** `RIA-J`<br>**URL:** `https://sites.imagej.net/RIA-J/`" %}
+
+## Usage Workflow
+
+1. **Initialize**: Open your dual-channel image and click **"Import / Refresh Images"** in the RIA-J panel.
+2. **Tune**: Adjust the **Background** and **NaN Threshold** sliders while observing the real-time preview.
+3. **Refine**: (Optional) Apply **Normalized Convolution** for edge-aware smoothing.
+4. **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:
+
+{% include citation
+   text="Wang, K. (2026). RIA-J: Ratio Imaging Analyzer (Java) - Interactive Ratiometric Analysis for ImageJ/Fiji (Version v0.3.0). Zenodo."
+   doi="10.5281/zenodo.18200078"
+%}
+
+* **Repository**: [https://github.com/Epivitae/RIA-J](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.*