RIA-J: Ratio Imaging Analyzer (Java) - Publication-Grade Ratiometric Analysis for ImageJ/Fiji

RIA-J (Ratio Imaging Analyzer - Java Edition) is a publication-grade ImageJ/Fiji plugin designed to streamline the workflow of ratiometric fluorescence analysis. It brings the rigorous quantification capabilities of the standalone RIA (Python) project directly into the native ImageJ ecosystem. v1.0.0 Update: Now featuring a "Direct Stack" engine, RIA-J automatically processes high-dimensional time-lapse datasets in the background immediately upon import, offering a seamless "What You See Is What You Get" experience without manual batch application. Key Features: 🚀 Direct Stack Workflow: Eliminates manual batch steps. The plugin automatically computes the entire ratio stack upon import, allowing real-time parameter tuning that is instantly reflected across the dataset. 🧠 Smart Automation: Features global window scanning to detect open images, intelligently splitting composite files and auto-pairing numerator/denominator channels. ⚡ Publication-Ready Export: Includes a dedicated RGB Export engine that generates "burnt-in" RGB Snapshots or RGB Stacks (Videos). It automatically synchronizes visualization settings (LUTs, contrast) to all frames before export. 🎨 AI-Friendly Visualization: Generates independent, borderless Legend/Color Bar windows with pure white backgrounds, optimized for easy assembly in Adobe Illustrator or Inkscape. 🏷️ Standardized Data Management: Enforces a strict naming convention (e.g., RIA-Result, RIA-RGB-Stack) and includes a filename cleaner to strip technical prefixes, ensuring data traceability.