CellPilot: an agentic framework that pilots small language models through autonomous single-cell annotation

Large language models can annotate cell types from marker gene lists, but they typically operate after preprocessing and clustering are complete, treating annotation as a terminal labeling step rather than controlling the analytical decisions that produce the evidence for cell identity. We present CellPilot, an agentic framework that guides a locally deployable small language model through the full single-cell analysis workflow, from raw count matrices to cluster-level annotation. CellPilot combines standard single-cell analysis tools with structured workflow control and observation-guided reasoning, allowing the model to plan analyses, execute tools, inspect intermediate results and revise decisions within a traceable session. On GTEx, structured workflow orchestration raised the same 8B model from 0.39 in a prompt-only setting to 0.89, closing most of the gap to GPT-4o (0.92) within the same framework; the framework gain was substantially larger for the smaller backbone across datasets (+0.35 versus +0.19). Across GTEx, Tabula Sapiens, and Mouse Cell Atlas, CellPilot achieves cluster-level annotation accuracies of 0.891, 0.750, and 0.773, outperforming representative reference-based, marker-based, and LLM-based methods. CellPilot confidence scores were associated with annotation correctness and supported post hoc filtering, while complete execution traces were retained for each analysis. These results suggest that structured workflow orchestration can be a critical determinant of performance in multi-step single-cell analysis, enabling locally deployable small language models to approach larger proprietary models while preserving transparency and practical usability.