METHODS.md

Methodology

This document will describe the image processing pipeline and algorithms used by FociPy. Fill in each section as you implement the corresponding module. Include final parameter values, algorithm choices, and references to relevant literature.

1. Data Loading & Metadata Extraction

2. Image Preprocessing

3. Nuclear Segmentation

4. ROI Tracking & Drift Correction

5. Intensity Measurement & Normalization

6. Quantification Metrics

7. Output & Reproducibility

8. Libraries & Environment