1. System Overview This document outlines requirements for a next-generation system for processing, analyzing, and managing high-throughput microscopy data from image-based profiling experiments, in particular, pooled optical screens. The system will orchestrate complex image processing workflows, manage computational resources efficiently, and provide mechanisms for both automated and manual intervention during the processing pipeline. 2. Core Requirements 2.1 Image Processing Capabilities Must support automated execution of CellProfiler pipelines for all stages of image processing:Illumination correction calculation and application Cell segmentation and validation Image stitching and cropping Channel alignment across imaging cycles Barcode identification and calling

This guide provides documentation for the starrynight image processing system for optical pooled screening. The system consists of 10 different modules, and this document currently shows how to use the illumination correction module alone. One-Time Setup Steps These steps are performed once regardless of which module you're using. Creating a Test Dataset First, create a test fixture with a single plate of Cell Painting images: Copy sample files from S3:​​​mkdir -p scratch