AtomDiffuser: Time-Aware Degradation Modeling for Drift and Beam Damage in STEM Imaging

Scanning transmission electron microscopy (STEM) plays a critical role in modern materials science, enabling direct imaging of atomic structures and their evolution under external interferences. However, interpreting time-resolved STEM data remains challenging due to two entangled degradation effects: spatial drift caused by mechanical and thermal instabilities, and beam-induced signal loss resulting from radiation damage. These factors distort both geometry and intensity in complex, temporally correlated ways, making it difficult for existing methods to explicitly separate their effects or model material dynamics at atomic resolution. In this work, we present AtomDiffuser, a time-aware degradation modeling framework that disentangles sample drift and radiometric attenuation by predicting an affine transformation and a spatially varying decay map between any two STEM frames. Unlike traditional denoising or registration pipelines, our method leverages degradation as a physically heuristic, temporally conditioned process, enabling interpretable structural evolutions across time. Trained on synthetic degradation processes, AtomDiffuser also generalizes well to real-world cryo-STEM data. It further supports high-resolution degradation inference and drift alignment, offering tools for visualizing and quantifying degradation patterns that correlate with radiation-induced atomic instabilities.