📄️ Overview
This document provides detailed information about the core components of the Main analysis pipeline. The pipeline transforms raw multiplex imaging data into quantified single-cell profiles through a series of carefully orchestrated processing stages.
📄️ Usage Guide
This guide provides comprehensive instructions for running the Main pipeline, from single experiment execution to large-scale batch processing. The template for running the Main pipeline is launcher/runmaintemplate.sh. You can make a copy of the template (e.g. launcher/runmainft.sh) and modify it to run the Main pipeline for your experiment set and data. Put the copy in the launcher/ directory. Usually you need to change the EXPSETNAME and the EXPERIMENTS array, which are marked with TODO in the bash script. Then call bash launcher/runmainft.sh to run with your data.
📄️ Outputs
This document provides a comprehensive guide to all outputs generated by the Main pipeline. Understanding these outputs is essential for downstream analysis and quality assessment.
📄️ Configuration Reference
This document provides a comprehensive reference for all configuration parameters used in the Main pipeline. Configuration files use YAML format and are typically generated using the Experiment Configuration system.
📄️ Segmentation Details
This document provides detailed information about the segmentation process, which is the implmenetation of runcellsegmentation in segment.py.
📄️ Evaluation Details
This step is the automated segmentation quality assessment using the runsegevaluation function implemented in evaluation.py. This evaluation system provides comprehensive metrics to assess the quality of cell segmentation results.
📄️ Optional Cell Level QC Filtering
Overview
📄️ Mask Analysis Details
This document describes the quality control (QC) metrics calculated by the mask analysis module to assess sample quality in PhenoCycler scans. More technical details beyond this document are written in Overleaf upon request.