Embodied Intelligence Unlocks Autonomous Microscopy

Advanced microscopy is a cornerstone of modern science, yet its potential is constrained by a reliance on manual operation, which struggles with the complexity and reproducibility of long-term experiments protocols. While scripting offers a degree of automation, it lacks the generalizability to adapt to new samples or dynamic biological events. A fundamental challenge is the absence of an intelligent system that can interpret high-level scientific intent and ground it in the physical actions of the microscope. To bridge this gap, we introduce an Embodied Intelligent Microscope System (EIMS) with hierarchical reasoning structure that reimagines the microscope autonomous control. This system leverages the advanced reasoning of large models to interpret complex user commands and decompose them into actionable steps. To solve the critical grounding problem, we constrain the model’s output to the feasible action space, effectively serving as the model’s “hands and eyes” in the physical world. We demonstrate that our system achieves zero-shot generalization on complex, multi-step protocols and successfully automates challenging biological missions requiring expert-level judgment, such as capturing the sparse spatiotemporal events of cell mitosis and locating scatteredly distributed organoids. This work establishes a new paradigm for scientific instrumentation—fusing high-level intent understanding with grounded, dynamic execution—and provides a generalizable framework for deploying embodied intelligence to accelerate autonomous scientific discovery.