📄️ Introduction
The experiment configuration system provides automated generation and management of configuration files for the PhenoCycler data analysis pipeline. This system enables researchers to efficiently manage multiple experiments through CSV-based design tables and YAML templates.
📄️ Usage Guide
This guide walks you through the process of using the experiment configuration system to generate and manage configurations for your CODEX analysis experiments.
📄️ Outputs
The configuration generator produces configuration files and also prints an experiment list for downstream batch execution.
📄️ Templates and Design Tables
This section covers both YAML configuration templates and CSV experiment design tables, which work together to generate experiment-specific configurations. The templates define the structure and defaults, while the design tables specify experiment-specific parameters.