AI and the World's Hard Problems · Life sciences · arXiv · 2026-10-19
Harness-Driven Agentic Operation of Optical Pooled Screen Analysis
Optical pooled screens link genetic perturbations to cell morphology, but turning the microscopy data into results takes complex, multi-day analyses that require manual parameter tuning and troubleshooting. The authors built Brieflow-auto, a Claude Code plugin that lets a coding LLM operate the open-source Brieflow pipeline, tuning parameters, validating configurations, recovering from failures, and checking output quality. In five previously analyzed screens it assigned more cells to a single gene with confidence than the original hand analyses, and on a new screen it turned failures into reviewed upstream fixes.