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We show that unsupervised machine learning can be used to learn physical and chemical transformation pathways from the observational microscopic data, as demonstrated for atomically resolved images in Scanning Transmission Electron…

With the development of affordable aberration-correctors, analytical scanning transmission electron microscopy (STEM) studies of complex interfaces can now be conducted at high spatial resolution at laboratories worldwide. Energy-dispersive…

Materials Science · Physics 2017-04-10 Steven R. Spurgeon , Yingge Du , Scott A. Chambers

Quantitative analysis methods based on the usage of a scanning electron microscope (SEM), such as energy dispersive x-ray spectroscopy, often require specimens to have a flat surface oriented normal to the electron beam. In-situ procedures…

Mesoscale and Nanoscale Physics · Physics 2023-02-15 Clay Klein , Chunfei Li

Computed tomography is widely used to examine internal structures in a non-destructive manner. To obtain high-quality reconstructions, one typically has to acquire a densely sampled trajectory to avoid angular undersampling. However, many…

Image and Video Processing · Electrical Eng. & Systems 2020-12-10 Haoyu Wei , Florian Schiffers , Tobias Würfl , Daming Shen , Daniel Kim , Aggelos K. Katsaggelos , Oliver Cossairt

Quantum materials are driving a technology revolution in sensing, communication, and computing, while simultaneously testing many core theories of the past century. Materials such as topological insulators, complex oxides, quantum dots,…

Precise alignment of the electron beam is critical for successful application of scanning transmission electron microscopes (STEM) to understanding materials at atomic level. Despite the success of aberration correctors, aberration…

During the last few years, serial electron crystallography (Serial Electron Diffraction, SerialED) has been gaining attention for the structure determination of crystalline compounds that are sensitive to the irradiation of the electron…

Materials Science · Physics 2025-07-29 Sergi Plana-Ruiz , Penghan Lu , Govind Ummethala , Rafal Dunin-Borkowski

A sparse modeling approach is proposed for analyzing scanning tunneling microscopy topography data, which contains numerous peaks corresponding to surface atoms. The method, based on the relevance vector machine with $\mathrm{L}_1$…

Data Analysis, Statistics and Probability · Physics 2018-03-13 Masamichi J. Miyama , Koji Hukushima

4D-STEM-based orientation and phase mapping has enabled rapid microstructure quantification that can be directly combined with standard TEM- and STEM-based imaging modes. Typically, orientation mapping is coupled with beam precession (i.e.…

Materials Science · Physics 2026-04-01 Yichen Yang , Olivier Pierron , Josh Kacher , David Rowenhorst

Time resolution is one of the most severe limitations of scanning probe microscopies (SPMs), since the typical image acquisition times are in the order of several seconds or even few minutes. As a consequence, the characterization of…

The scanning electron microscope (SEM) delivers high resolution, high depth of focus and an image quality as if microscopic objects are seen by the naked eye. This makes it not only a powerful scientific instrument, but a tool inherently…

Applied Physics · Physics 2025-04-01 Casimir Kuzyk , Alexander Dimitrakopoulos , Alireza Nojeh

Scanning Electron Microscopy (SEM) is critical in nanotechnology, materials science, and biological imaging due to its high spatial resolution and depth of focus. Signal-to-noise ratio (SNR) is an essential parameter in SEM because it…

Machine Learning · Computer Science 2025-10-10 K. S. Sim , I. Bukhori , D. C. Y. Ong , K. B. Gan

Sparse autoencoders (SAEs) are used to analyze embeddings, but their role and practical value are debated. We propose a new perspective on SAEs by demonstrating that they can be naturally understood as topic models. We propose a continuous…

Computer Vision and Pattern Recognition · Computer Science 2026-05-19 Leander Girrbach , Zeynep Akata

Combinations of spectroscopic analysis and microscopic techniques are used across many disciplines of scientific research, including material science, chemistry and biology. X-ray spectromicroscopy, in particular, is a powerful tool used…

Medical Physics · Physics 2023-10-17 Oliver Townsend , Silvia Gazzola , Sergey Dolgov , Paul Quinn

Electron microscopy is a powerful tool for visualizing the shapes of sub-nanometer objects. However, contrast is not in proportional to density distribution, and therefore achieving a quantitative understanding of specimens is not…

Instrumentation and Detectors · Physics 2020-05-14 Masato Tomita , Yukinori Nagatani , Kazuyoshi Murata , Atsushi Momose

A universal challenge facing the development of electrochemical materials is our lack of understanding of physical and chemical processes at local length scales in 10-100 nm regime, and acquiring this understanding requires a new generation…

Mesoscale and Nanoscale Physics · Physics 2017-10-31 Ehsan Nasr Esfahani , Ahmad Eshghinejad , Yun Ou , Jinjin Zhao , Stuart Adler , Jiangyu Li

Over the last decade, scanning transmission electron microscopy (STEM) has emerged as a powerful tool for probing atomic structures of complex materials with picometer precision, opening the pathway toward exploring ferroelectric,…

Data Analysis, Statistics and Probability · Physics 2021-12-23 Ayana Ghosh , Christopher T. Nelson , Mark Oxley , Xiaohang Zhang , Maxim Ziatdinov , Ichiro Takeuchi , Sergei V. Kalinin

Cryo-electron microscopy (cryo-EM) enables the atomic-resolution visualization of biomolecules; however, modern direct detectors generate data volumes that far exceed the available storage and transfer bandwidth, thereby constraining…

Image and Video Processing · Electrical Eng. & Systems 2026-03-31 Zain Shabeeb , Daniel Saeedi , Darin Tsui , Vida Jamali , Amirali Aghazadeh

Accurate wave-optical simulation in electron microscopy is severely constrained by the extreme sampling requirements imposed by short wavelengths and relatively large convergence angles. Conventional implementations of the angular spectrum…

Optics · Physics 2026-03-18 Zdeněk Nekula , Jakub Bělín , Andrea Konečná

Compressed sensing is an image reconstruction technique to achieve high-quality results from limited amount of data. In order to achieve this, it utilizes prior knowledge about the samples that shall be reconstructed. Focusing on image…

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