Spatial-Frequency Learning for Scanning Transmission Electron Microscopy Image Enhancement

High-Resolution Transmission Electron Microscopy (HRTEM) enables atomic-scale observation of nucleation dynamics, which boosts the studies of advanced solid materials. Nonetheless, due to the millisecond-scale rapid change of nucleation, it requires short-exposure rapid imaging, leading to severe noise that obscures atomic positions. In this work, we propose a statistical characteristic-guided denoising network, which utilizes statistical characteristics to guide the denoising process in both spatial and frequency domains. In the spatial domain, we present spatial deviation-guided weighting to select appropriate convolution operations for each spatial position based on deviation characteristic. In the frequency domain, we present frequency band-guided weighting to enhance signals and suppress noise based on band characteristics. We also develop an HRTEM-specific noise calibration method and generate a dataset with disordered structures and realistic HRTEM image noises. It can ensure the denoising performance of models on real images for nucleation observation. Experiments on synthetic and real data show our method outperforms the state-of-the-art methods in HRTEM image denoising, with effectiveness in the localization downstream task. Code will be available at https://github.com/HeasonLee/SCGN.

Scanning Tunneling Microscopy (STM) is a widely used tool for characterizing surfaces of materials at the atomic scale, playing a crucial role in discoveries across condensed matter physics and materials science. Despite its extreme spatial resolution, STM is one of the most sensitive microscopy techniques and is highly prone to noise. While existing unsupervised denoising methods are very cheap to train, these are primarily focused on removing the noise with minimal recovery of key physical information. While supervised methods can offer superior performance, the major bottleneck is that a large amount of paired clean-noisy experimental images is required which are impractical to obtain. Thus, we developed a low-cost physics-driven digital toolkit to rapidly generate large volume of realistic STM images. Firstly, we simulate clean images from a chosen material system. Then, with prior knowledge of the physical characteristics of the artifacts and noise present in STM experiments, we formulate several artifact-noise functions such as Gaussian electronic noise, 1/f flicker noise, scan-line noise, background tilt and mechanical drift. These physically informed noise components are then added to the simulated clean images to generate realistic STM images. We demonstrated the capability of the proposed digital toolkit to generate AI-ready data for denoising images of the (111) surfaces of copper and lead, while preserving atoms, defects, and electron waves. We also validated the quality of the downstream image analysis of learning electron wave patterns induced by quantum interference from Cu(111) images. Results show that the supervised models trained on digitally generated AI-ready data can more effectively denoise and learn electron wave patterns on Cu(111) images than benchmarked unsupervised approaches, indicating that the proposed toolkit facilitate scientific discovery.

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.