Automated Colocalization Quantification Macro for Two-Protein Analysis in ImageJ/Fiji

This repository contains ImageJ/Fiji macros for automated analysis of protein colocalization in mammalian cells. The package includes two complementary tools:

1. Preprocessing Macro: Prepares fluorescence microscopy images for colocalization analysis through background subtraction, noise reduction, and channel alignment.
2. Colocalization Analysis Macro: Quantifies spatial overlap and correlation between two fluorescently-labeled proteins using comprehensive colocalization metrics including Pearson's correlation coefficient, Manders' M1/M2 coefficients, overlap coefficients, and Costes' automatic threshold determination.

These macros streamline the workflow from raw microscopy images to quantitative colocalization measurements, reducing manual processing time and improving reproducibility. The tools are designed for dual-channel fluorescence images of mammalian cells and output standardized metrics suitable for statistical analysis.

Requirements: ImageJ/Fiji Input: Dual-channel fluorescence microscopy images Output: Quantitative colocalization measurements (CSV format) and processed images