Fluorescence Image Aligner (FIA): Robust Motion Correction with Dense Flow for ImageJ/Fiji

FIA (Fluorescence Image Aligner) is a professional ImageJ/Fiji plugin designed to correct motion artifacts (drift, jitter, rotation) in time-lapse fluorescence microscopy data. Unlike conventional center-of-mass methods, FIA utilizes the OpenCV ECC (Enhanced Correlation Coefficient) algorithm, making it highly robust against fluctuating signals common in functional imaging (e.g., calcium/voltage imaging). v1.0.0 Initial Release: This version introduces a fully non-destructive workflow and a modern Swing-based controller, providing precise sub-pixel registration without altering original raw data. Key Features: 🛡️ Non-Destructive Workflow: Prioritizes data integrity by generating a new aligned stack (FIA-Result) instead of modifying the input file, ensuring the raw data remains untouched. 🧠 Intensity-Invariant Algorithm: Uses the ECC metric to align images based on correlation rather than simple intensity features, ensuring stable registration even when neurons flash on and off. 🚀 Warm Start Strategy: Implements a smart state-tracking mechanism where the transformation matrix of the previous frame serves as the initial guess for the next, preventing alignment loss during rapid movement. 🌈 Smart Multi-Channel Support: Automatically detects the channel with the best signal-to-noise ratio (highest mean intensity) to calculate the motion vector, then applies the correction to all channels synchronously. 📊 Quantitative Output: Offers an option to export the precise geometric transformation matrix to a .csv file for post-hoc trajectory analysis.