OmicsNavigator: an LLM-driven multi-agent system for autonomous zero-shot biological analysis in spatial omics

Spatial omics provides unprecedented high-resolution insights into molecular tissue compositions but poses significant analytical challenges due to massive data volumes, complex hierarchical spatial structures, and domain-specific interpretive demands. To address these limitations, we introduce OmicsNavigator, an LLM-driven multi-agent system that autonomously distills expert-level biological insights from raw spatial omics data without domain-specific fine-tuning. OmicsNavigator encodes spatial data into concise natural language summaries, enabling zero-shot annotation of structural components, quantitative analysis of pathological relevance, and semantic search of regions of interest using free-form text queries. We evaluated OmicsNavigator on multiple spatial omics studies of kidney cohorts with different phenotypes and biomarker panels, where OmicsNavigator achieved outstanding performances in structural annotations, pathology assessments, and semantic search across studies. OmicsNavigator offers a scalable, interpretable, and modality-agnostic solution for spatial omics analysis.