Nikola L. Kolev

Utkarsh Pratiush, Austin Houston, Kamyar Barakati et al.

Microscopy is a primary source of information on materials structure and functionality at nanometer and atomic scales. The data generated is often well-structured, enriched with metadata and sample histories, though not always consistent in detail or format. The adoption of Data Management Plans (DMPs) by major funding agencies promotes preservation and access. However, deriving insights remains difficult due to the lack of standardized code ecosystems, benchmarks, and integration strategies. As a result, data usage is inefficient and analysis time is extensive. In addition to post-acquisition analysis, new APIs from major microscope manufacturers enable real-time, ML-based analytics for automated decision-making and ML-agent-controlled microscope operation. Yet, a gap remains between the ML and microscopy communities, limiting the impact of these methods on physics, materials discovery, and optimization. Hackathons help bridge this divide by fostering collaboration between ML researchers and microscopy experts. They encourage the development of novel solutions that apply ML to microscopy, while preparing a future workforce for instrumentation, materials science, and applied ML. This hackathon produced benchmark datasets and digital twins of microscopes to support community growth and standardized workflows. All related code is available at GitHub: https://github.com/KalininGroup/Mic-hackathon-2024-codes-publication/tree/1.0.0.1

Nikola L. Kolev, Tommaso Rodani, Neil J. Curson et al.

Scanning tunnelling microscopy (STM) enables atomic-resolution imaging and atom manipulation, but its utility is often limited by tip degradation and slow serial data acquisition. Fabrication adds another layer of complexity since the tip is often subjected to large voltages, which may alter the shape of its apex, requiring it to be conditioned. Here, we propose a machine learning (ML) approach for image repair and super-resolution to alleviate both challenges. Using a dataset of only 36 pristine experimental images of Si(001):H, we demonstrate that a physics-informed synthetic data generation pipeline can be used to train several state-of-the-art flow-matching and diffusion models. Quantitative evaluation with metrics such as the CLIP Maximum Mean Discrepancy (CMMD) score and structural similarity demonstrates that our models are able to effectively restore images and offer a two- to fourfold reduction in image acquisition time by accurately reconstructing images from sparsely sampled data. Our framework has the potential to significantly increase STM experimental throughput by offering a route to reducing the frequency of tip-conditioning procedures and to enhancing frame rates in existing high-speed STM systems.

Nikola L. Kolev, Max Trouton, Filippo Federici Canova et al.

Scanning tunnelling microscopy (STM) is a powerful technique for imaging surfaces with atomic resolution, providing insight into physical and chemical processes at the level of single atoms and molecules. A regular task of STM image analysis is the identification and labelling of features of interest against a uniform background. Performing this manually is a labour-intensive task, requiring significant human effort. To reduce this burden, we propose an automated approach to the segmentation of STM images that uses both few-shot learning and unsupervised learning. Our technique offers greater flexibility compared to previous supervised methods; it removes the requirement for large manually annotated datasets and is thus easier to adapt to an unseen surface while still maintaining a high accuracy. We demonstrate the effectiveness of our approach by using it to recognise atomic features on three distinct surfaces: Si(001), Ge(001), and TiO$_2$(110), including adsorbed AsH$_3$ molecules on the silicon and germanium surfaces. Our model exhibits strong generalisation capabilities, and following initial training, can be adapted to unseen surfaces with as few as one additional labelled data point. This work is a significant step towards efficient and material-agnostic, automatic segmentation of STM images.