STEMGym: Benchmarking Sequential Decision-Making under Dose Budgets in Autonomous Electron Microscopy

The transmission electron microscope facilitates the highest-resolution imaging of any instrument ever created, and its limiting factor is no longer spatial resolution but dose efficiency. Low electron doses avoid sample damage but produce noisy images for which, unlike in classical computer vision, there is no ground truth. Autonomous materials experimentation poses a related problem, since closed-loop instruments need representations grounded in the microscope state at acquisition. Both demand representations grounded in how an image was acquired. We release 7,330 paired high-angle annular dark-field scanning-TEM (HAADF-STEM) images and their seven-dimensional acquisition metadata, and propose Contrastive Image-Metadata Pre-training (CIMP), a CLIP-style encoder that aligns the two modalities and reaches 84.4% Top-1 cross-modal retrieval on a held-out split. All seven parameters are individually recoverable from the frozen visual embedding through a linear probe, and we use the embedding to condition a metadata-conditioned style-transfer model that re-renders experimental images under different acquisition parameters. Virtually scaling dwell time and beam current of low-dose images turns this model into a physics-informed denoiser; in a blind user study, experimental microscopists prefer it over the current state-of-the-art denoiser for STEM imagery on 70.2% of trials.

Large language model agents are increasingly being developed to control a wide range of scientific characterization tools including microscopes and synchrotron beamlines. Research into agentic control of physical infrastructure is nascent and there are few well-established paradigms for how to engineer an agentic system. There are many choices to make when designing a microscopy agent, including the choice of LLM, the number of agents to use, agent responsibilities and delegation rules, retrieval-augmented generation parameters, and more. When designing and optimizing an agentic microscope controller, researchers not only want to ensure that the agent can correctly perform known tasks but also that the agent can generalize to new tasks that it has not encountered before. In this study, we develop a benchmark and trace-logging framework that reveals a) how different choices of agent architecture impact performance at microscopy tasks and b) the limitations of benchmarks for predicting if a particular agent will perform well on unseen microscopy tasks. The framework was used to evaluate one-, two-, and three-agent graph topologies, five LLMs, RAG and context parameters, and operational constraints across 53 microscopy benchmark tests. In total, 105 agent configurations, 1,949 individual test runs, and 49,109 RAG retrievals were recorded. Direct comparisons showed clear differences in latency, token use, cost, and failure mode between configurations. However, surrogate models trained on agent architecture and test results did not reliably predict an agent's performance on new, unseen tasks. These results show that these benchmarks are useful for qualification, regression testing, diagnosis, and direct comparison, but the current heterogeneous test suite does not support a task-independent global configuration model.

Advanced semiconductor nodes drastically increased demand for Transmission Electron Microscopy (TEM), yet destructive sample preparation, slow imaging and high costs severely limit the availability of diverse datasets needed for downstream machine learning (ML). Synthetic data generation is becoming essential, but current generative models often miss TEM-specific noise, structural detail, and stochastic variability crucial for evaluation. We present a Denoising Diffusion Probabilistic Model (DDPM) framework for synthetic TEM image generation under extreme data scarcity. A progressive patch-based training strategy scales from low-resolution patches to full images, enabling from-scratch training with only 15 samples. We integrate a custom TrivialAugment adaptation, cross-process domain transfer, classifier guidance, and RePaint-style inpainting, culminating in full-image generation that preserves global structural and spatial relationships in compliance with FAB metrology requirements. Beyond synthesis, we repurpose DDPM feature representations for segmentation, partitioning encoder feature maps to obtain coherent region masks. Our synthetic images achieve up to MS-SSIM > 0.98 and qualitative expert assessment consistent with structural similarity results, facilitating downstream ML training for defect detection, segmentation, and metrology while preserving statistical and physical realism.