SIMBA: an agentic AI platform for single-molecule multi-dimensional imaging

Abstract

Advances in multi-dimensional imaging method and probe developments have brought super-resolution fluorescence microscopy into a functional era. They capture additional single-molecule fluorescence information concurrently with spatial localization, enabling simultaneous identification of molecular species and interrogation of nanoscale environments with rich, high-dimensional imaging information. However, the adoption of multi-dimensional imaging has been hindered by fragmented analysis workflows, complex parameter tuning, and limited integration of advanced computational methods. Here, we introduce an agentic single-molecule multi-dimensional bioimaging AI, referred to as SIMBA, an AI-driven platform that unifies single-molecule localization, spectral processing and deep learning-based denoising within a single agentic and interactive framework. SIMBA incorporates large language model-based agents capable of interpreting user intent, orchestrating analysis pipelines, and dynamically selecting computational tools for automated data processing. We demonstrate that SIMBA enables supports standard single-molecule localization workflow, functional mapping of nanoscale environmental heterogeneity through single-molecule spectral analysis and denoising using developed supervised learning methods. By integrating extensible tool architectures with human language-guided workflows, SIMBA establishes a new paradigm for intelligent microscopy analysis, lowering barriers to multi-dimensional imaging adoption while enabling scalable, reproducible, and adaptive analysis of complex imaging datasets.