📄️ Outputs
This document describes the outputs generated by the main module of the Aegle pipeline. The outputs are organized into the following files and directories:
📄️ Preprocess
This document describes the preprocessing pipeline for CODEX images in Aegle. The preprocessing consists of two main stages: Full Image Preprocessing and Patched Image Preprocessing, as implemented in aegle/pipeline.py under the run_pipeline function.
📄️ Segmentation Analysis
This document describes the segmentation analysis module implemented in the Aegle pipeline. The segmentation analysis provides comprehensive evaluation of cell and nucleus segmentation results, intensity distributions across cellular compartments, and spatial density metrics.