Pub Date : 2025-12-21DOI: 10.1016/j.ultramic.2025.114303
Francisco Fernandez-Canizares , Javier Rodriguez-Vazquez , Rafael V. Ferreira , Isabel Tenreiro , Alberto Rivera-Calzada , Amalia Fernando-Saavedra , Miguel A. Sanchez-Garcia , Yong Xie , Andres Castellanos-Gomez , Maria Varela , Gabriel Sánchez-Santolino
Automated atomic column detection and identification constitutes an active open front in advanced scanning transmission electron microscopy techniques. In this work we use clustering algorithms in combination with dimensionality reduction techniques to identify specific columns in a series of very different cutting-edge materials, ranging from ultrathin 2D materials to bulk semiconductors or complex oxides, which include different types of columns (heavy and light), and thus pose a challenge towards automated detection. By implementing a three-stage cascaded clustering pipeline, we are able to automatically identify all atomic column sites of our test materials and resolve them from the background interatomic space. This approach could enable new data-driven in-depth analysis of materials, allowing the automatic detection of chemical and structural characteristics of materials.
{"title":"Automated atomic site determination by four-dimensional scanning transmission electron microscopy data analytics","authors":"Francisco Fernandez-Canizares , Javier Rodriguez-Vazquez , Rafael V. Ferreira , Isabel Tenreiro , Alberto Rivera-Calzada , Amalia Fernando-Saavedra , Miguel A. Sanchez-Garcia , Yong Xie , Andres Castellanos-Gomez , Maria Varela , Gabriel Sánchez-Santolino","doi":"10.1016/j.ultramic.2025.114303","DOIUrl":"10.1016/j.ultramic.2025.114303","url":null,"abstract":"<div><div>Automated atomic column detection and identification constitutes an active open front in advanced scanning transmission electron microscopy techniques. In this work we use clustering algorithms in combination with dimensionality reduction techniques to identify specific columns in a series of very different cutting-edge materials, ranging from ultrathin 2D materials to bulk semiconductors or complex oxides, which include different types of columns (heavy and light), and thus pose a challenge towards automated detection. By implementing a three-stage cascaded clustering pipeline, we are able to automatically identify all atomic column sites of our test materials and resolve them from the background interatomic space. This approach could enable new data-driven in-depth analysis of materials, allowing the automatic detection of chemical and structural characteristics of materials.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"281 ","pages":"Article 114303"},"PeriodicalIF":2.0,"publicationDate":"2025-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145884241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-19DOI: 10.1016/j.ultramic.2025.114291
Tom Fraysse, Robin Cours, Hugo Lourenço-Martins, Florent Houdellier
This paper explores the topologies of caustics observed in instruments that employ charged particles, such as electron and ion microscopes. These geometrical figures are studied here using catastrophe theory. The application of this geometrical theory to our optical situation has enabled us to analytically reproduce the behaviours of various caustics. The interest lies mainly in the universal nature of these results since our treatment requires no prior knowledge of the optical configuration, but only a smart definition of the control space. This universal approach has finally made it possible to extract mathematical relationships between the aberration coefficients of any optical system, which were hidden by the complexity of optical trajectories but revealed by the set of catastrophes in the control space. These results provide a glimpse for future applications of caustics in the development of new corrected optical systems, especially for ions-based devices.
{"title":"Morphologies of caustics studied by catastrophe charged-particle optics","authors":"Tom Fraysse, Robin Cours, Hugo Lourenço-Martins, Florent Houdellier","doi":"10.1016/j.ultramic.2025.114291","DOIUrl":"10.1016/j.ultramic.2025.114291","url":null,"abstract":"<div><div>This paper explores the topologies of caustics observed in instruments that employ charged particles, such as electron and ion microscopes. These geometrical figures are studied here using catastrophe theory. The application of this geometrical theory to our optical situation has enabled us to analytically reproduce the behaviours of various caustics. The interest lies mainly in the universal nature of these results since our treatment requires no prior knowledge of the optical configuration, but only a smart definition of the control space. This universal approach has finally made it possible to extract mathematical relationships between the aberration coefficients of any optical system, which were hidden by the complexity of optical trajectories but revealed by the set of catastrophes in the control space. These results provide a glimpse for future applications of caustics in the development of new corrected optical systems, especially for ions-based devices.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"282 ","pages":"Article 114291"},"PeriodicalIF":2.0,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145928659","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-18DOI: 10.1016/j.ultramic.2025.114301
Nicolò M. Della Ventura , Kalani Moore , McLean P. Echlin , Matthew R. Begley , Tresa M. Pollock , Marc De Graef , Daniel S. Gianola
Accurate quantification of the energy distribution of backscattered electrons (BSEs) contributing to electron backscatter diffraction (EBSD) patterns remains as an active challenge. This study introduces an energy-resolved EBSD methodology based on a monolithic active pixel sensor direct electron detector and an electron-counting algorithm to enable the energy quantification of individual BSEs, providing direct measurements of electron energy spectra within diffraction patterns. Following detector calibration of the detector signal as a function of primary beam energy, measurements using a 12 keV primary beam on Si(100) reveal a broad BSE energy distribution across the diffraction pattern, extending down to 3 keV. Furthermore, an angular dependence in the weighted average BSE energy is observed, closely matching predictions from Monte Carlo simulations. Pixel-resolved energy maps reveal subtle modulations at Kikuchi band edges, offering insights into the backscattering process. By applying energy filtering within spectral windows as narrow as 2 keV centered on the primary beam energy, significant enhancement in pattern clarity and high-frequency detail is observed. Notably, BSEs in the 9–10 keV range dominate Kikuchi pattern formation, while BSEs in the 2–8 keV range, despite having undergone substantial energy loss, still produce Kikuchi patterns. By enabling energy determination at the single-electron level, this approach introduces a versatile tool-set for expanding the quantitative capabilities of EBSD, thereby offering the potential to deepen the understanding of diffraction contrast mechanisms and to advance the precision of crystallographic measurements.
{"title":"Energy-resolved EBSD using a monolithic direct electron detector","authors":"Nicolò M. Della Ventura , Kalani Moore , McLean P. Echlin , Matthew R. Begley , Tresa M. Pollock , Marc De Graef , Daniel S. Gianola","doi":"10.1016/j.ultramic.2025.114301","DOIUrl":"10.1016/j.ultramic.2025.114301","url":null,"abstract":"<div><div>Accurate quantification of the energy distribution of backscattered electrons (BSEs) contributing to electron backscatter diffraction (EBSD) patterns remains as an active challenge. This study introduces an energy-resolved EBSD methodology based on a monolithic active pixel sensor direct electron detector and an electron-counting algorithm to enable the energy quantification of individual BSEs, providing direct measurements of electron energy spectra within diffraction patterns. Following detector calibration of the detector signal as a function of primary beam energy, measurements using a 12 keV primary beam on Si(100) reveal a broad BSE energy distribution across the diffraction pattern, extending down to 3 keV. Furthermore, an angular dependence in the weighted average BSE energy is observed, closely matching predictions from Monte Carlo simulations. Pixel-resolved energy maps reveal subtle modulations at Kikuchi band edges, offering insights into the backscattering process. By applying energy filtering within spectral windows as narrow as 2 keV centered on the primary beam energy, significant enhancement in pattern clarity and high-frequency detail is observed. Notably, BSEs in the 9–10 keV range dominate Kikuchi pattern formation, while BSEs in the 2–8 keV range, despite having undergone substantial energy loss, still produce Kikuchi patterns. By enabling energy determination at the single-electron level, this approach introduces a versatile tool-set for expanding the quantitative capabilities of EBSD, thereby offering the potential to deepen the understanding of diffraction contrast mechanisms and to advance the precision of crystallographic measurements.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"281 ","pages":"Article 114301"},"PeriodicalIF":2.0,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145791018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-18DOI: 10.1016/j.ultramic.2025.114302
Johann Brenner , Jürgen M. Plitzko , Sven Klumpe
Focused ion beams (FIB) are widely used instruments in transmission electron microscopy (TEM) sample preparation across scientific disciplines. Generally, site-specific ablation of material is achieved by scanning a highly focused probe across a selected area, leading to the removal of material. However, the geometries of TEM lamellae milled with the FIB are usually highly non-isometric, with their thickness generally being orders of magnitude smaller than their width and length. Here, we explore a changed probe shape for milling. Instead of using an ion beam with the standard, Gaussian-like probe, we characterize the use of the stigmator as quasi-cylindrical lens to create a highly astigmatic probe that we term ‘ion knife’. Using the ion knife allows for material removal by spreading the current over a larger area and changes the dimension of the probe as observed in spot burn cross-sections. To allow for rapid alignment of parameters in beam shaping, we demonstrate a method to approximate the shapes of our probes by imaging. Finally, exploring shaped probes in cryogenic lamella preparation, we demonstrate the feasibility of cellular lamella milling and sectioning of cryo-lift-out volumes with the ion knife.
{"title":"Exploring shaped focused ion beams for lamella preparation","authors":"Johann Brenner , Jürgen M. Plitzko , Sven Klumpe","doi":"10.1016/j.ultramic.2025.114302","DOIUrl":"10.1016/j.ultramic.2025.114302","url":null,"abstract":"<div><div>Focused ion beams (FIB) are widely used instruments in transmission electron microscopy (TEM) sample preparation across scientific disciplines. Generally, site-specific ablation of material is achieved by scanning a highly focused probe across a selected area, leading to the removal of material. However, the geometries of TEM lamellae milled with the FIB are usually highly non-isometric, with their thickness generally being orders of magnitude smaller than their width and length. Here, we explore a changed probe shape for milling. Instead of using an ion beam with the standard, Gaussian-like probe, we characterize the use of the stigmator as quasi-cylindrical lens to create a highly astigmatic probe that we term ‘ion knife’. Using the ion knife allows for material removal by spreading the current over a larger area and changes the dimension of the probe as observed in spot burn cross-sections. To allow for rapid alignment of parameters in beam shaping, we demonstrate a method to approximate the shapes of our probes by imaging. Finally, exploring shaped probes in cryogenic lamella preparation, we demonstrate the feasibility of cellular lamella milling and sectioning of cryo-lift-out volumes with the ion knife.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"282 ","pages":"Article 114302"},"PeriodicalIF":2.0,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145967105","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-11DOI: 10.1016/j.ultramic.2025.114298
S. Matinyan , P. Filipcik , D.G. Waterman , C.D. Owen , J.P. Abrahams
Scientific data in structural biology are being produced faster and in larger volumes than can be comfortably stored, processed, or shared. To address this challenge, we introduced the next generation TERSE/PROLIX (TRPX) algorithm for efficient, fast, and lossless compression of integer greyscale data, implemented in C++20. Here, we report a multithreaded extension with additional options for compressing low-intensity integer images and for lossless or lossy compression of greyscale float data. This new implementation is accessible through a dedicated, multithreaded Python library (pyterse) and as an HDF5 filter (terse), allowing seamless integration into existing scientific workflows.
Benchmarks show that TRPXv2.0 is at least 2.5 times faster than existing compression schemes for diffraction data, without increasing file sizes, and often with better compression ratios.
By combining speed, flexibility, and interoperability, TRPXv2.0 provides a practical and scalable solution for high-throughput data handling in modern structural biology.
{"title":"TRPXv2.0: superfast, parallel compression of diffraction patterns and images, with native Python and HDF5 support","authors":"S. Matinyan , P. Filipcik , D.G. Waterman , C.D. Owen , J.P. Abrahams","doi":"10.1016/j.ultramic.2025.114298","DOIUrl":"10.1016/j.ultramic.2025.114298","url":null,"abstract":"<div><div>Scientific data in structural biology are being produced faster and in larger volumes than can be comfortably stored, processed, or shared. To address this challenge, we introduced the next generation TERSE/PROLIX (TRPX) algorithm for efficient, fast, and lossless compression of integer greyscale data, implemented in <em>C</em>++20. Here, we report a multithreaded extension with additional options for compressing low-intensity integer images and for lossless or lossy compression of greyscale float data. This new implementation is accessible through a dedicated, multithreaded Python library (pyterse) and as an HDF5 filter (terse), allowing seamless integration into existing scientific workflows.</div><div>Benchmarks show that TRPXv2.0 is at least 2.5 times faster than existing compression schemes for diffraction data, without increasing file sizes, and often with better compression ratios.</div><div>By combining speed, flexibility, and interoperability, TRPXv2.0 provides a practical and scalable solution for high-throughput data handling in modern structural biology.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"281 ","pages":"Article 114298"},"PeriodicalIF":2.0,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145820900","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-09DOI: 10.1016/j.ultramic.2025.114297
M.J. Adriaans, J.P. Hoogenboom, A. Mohammadi-Gheidari
Monochromators are essential components in electron microscopy and spectroscopy for improving spatial and energy resolution. Their use in scanning electron microscopes (SEMs), however, remains limited due to high cost and operational complexity. Using a thin-deflector analysis of a homogeneous electrostatic deflector, we show that conventional monochromators exhibit extreme sensitivity to power-supply drift and mechanical imperfections. Meeting these stringent tolerances typically requires additional correction elements, which further increase system complexity and cost.
We demonstrate that fringe-field deflectors are inherently less sensitive to these limitations. Based on this insight, we propose a simple and cost-effective monochromator architecture relying solely on fringe fields. The design achieves optimal energy resolution by incorporating short-range deceleration lenses surrounding the main deflector, eliminating the need for auxiliary correction elements. Such a fully electrostatic configuration is compatible with MEMS fabrication, offering a compact, robust, and accessible pathway for high-performance energy filtering in SEMs.
{"title":"Basic considerations in the design of an electrostatic electron monochromator","authors":"M.J. Adriaans, J.P. Hoogenboom, A. Mohammadi-Gheidari","doi":"10.1016/j.ultramic.2025.114297","DOIUrl":"10.1016/j.ultramic.2025.114297","url":null,"abstract":"<div><div>Monochromators are essential components in electron microscopy and spectroscopy for improving spatial and energy resolution. Their use in scanning electron microscopes (SEMs), however, remains limited due to high cost and operational complexity. Using a thin-deflector analysis of a homogeneous electrostatic deflector, we show that conventional monochromators exhibit extreme sensitivity to power-supply drift and mechanical imperfections. Meeting these stringent tolerances typically requires additional correction elements, which further increase system complexity and cost.</div><div>We demonstrate that fringe-field deflectors are inherently less sensitive to these limitations. Based on this insight, we propose a simple and cost-effective monochromator architecture relying solely on fringe fields. The design achieves optimal energy resolution by incorporating short-range deceleration lenses surrounding the main deflector, eliminating the need for auxiliary correction elements. Such a fully electrostatic configuration is compatible with MEMS fabrication, offering a compact, robust, and accessible pathway for high-performance energy filtering in SEMs.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"281 ","pages":"Article 114297"},"PeriodicalIF":2.0,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145775870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-08DOI: 10.1016/j.ultramic.2025.114299
Harry J. Whitlow , Rattanaporn Norarat , Robert J.W. Frost , Aishee Ghosh , Donruedee Toyen , Deepanwita Bose , Aaron McLaughlin , Francois Villinger
Fourier optics provides a powerful and objective approach to handling Poissonian statistics in images. Fourier optics has been used to develop an approach to segment microbeam images into tissue and void (non-tissue) areas (e.g. villi, crypts, blood vessels and lymph canals etc.). Image segmentation is important in order to accurately measure the major element composition and thickness of biological sections. The method is based on comparing the spatial frequency of non-zero pixels in a reference void with tissue regions using a convolution method. The method automatically and conservatively segments tissue areas and uses no free-parameters. Since the method is based on spatial frequencies it can be used over a wide span of image counting statistics.
{"title":"A Fourier-optical approach for segmentation of ion microprobe images into tissue and non-tissue covered areas","authors":"Harry J. Whitlow , Rattanaporn Norarat , Robert J.W. Frost , Aishee Ghosh , Donruedee Toyen , Deepanwita Bose , Aaron McLaughlin , Francois Villinger","doi":"10.1016/j.ultramic.2025.114299","DOIUrl":"10.1016/j.ultramic.2025.114299","url":null,"abstract":"<div><div>Fourier optics provides a powerful and objective approach to handling Poissonian statistics in images. Fourier optics has been used to develop an approach to segment microbeam images into tissue and void (non-tissue) areas (e.g. villi, crypts, blood vessels and lymph canals etc.). Image segmentation is important in order to accurately measure the major element composition and thickness of biological sections. The method is based on comparing the spatial frequency of non-zero pixels in a reference void with tissue regions using a convolution method. The method automatically and conservatively segments tissue areas and uses no free-parameters. Since the method is based on spatial frequencies it can be used over a wide span of image counting statistics.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"281 ","pages":"Article 114299"},"PeriodicalIF":2.0,"publicationDate":"2025-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145769267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-07DOI: 10.1016/j.ultramic.2025.114295
Sangjun Kang , Hyeyoung Cho , Maximilian Töllner , Vanessa Wollersen , Di Wang , Hionsuck Baik , Marie Joëlle Perera , Omar Adjaoud , Karsten Albe , Christian Kübel , Xiaoke Mu
Electron pair distribution function (ePDF), combined with four-dimensional scanning transmission electron microscopy (4D-STEM), provides a powerful approach for uncovering detailed information about the local atomic structure and structural variations in disordered materials. However, achieving high accuracy in ePDF analysis requires careful control of experimental and instrumental parameters. In this study, we systematically investigate the effect of key electron optical, measurement and processing parameters on ePDF analysis using simulations as the primary tool, complemented by experimental validation. Specifically, we examine the influence of diffraction angle range, beam convergence semi-angle, detector pixel resolution, sample thickness (multiple scattering effect), noise, and electron beam precession on the resulting ePDF. By integrating multi-slice electron diffraction simulations with experimental diffraction data, we identify optimal conditions for accurate ePDF extraction and provide practical guidelines to improve analysis precision and reliability. These insights contribute to refining ePDF techniques, particularly for applications involving amorphous and nanostructured materials.
{"title":"Validating electron pair distribution function analysis: The role of multiple scattering, beam, measurement, and processing parameters","authors":"Sangjun Kang , Hyeyoung Cho , Maximilian Töllner , Vanessa Wollersen , Di Wang , Hionsuck Baik , Marie Joëlle Perera , Omar Adjaoud , Karsten Albe , Christian Kübel , Xiaoke Mu","doi":"10.1016/j.ultramic.2025.114295","DOIUrl":"10.1016/j.ultramic.2025.114295","url":null,"abstract":"<div><div>Electron pair distribution function (ePDF), combined with four-dimensional scanning transmission electron microscopy (4D-STEM), provides a powerful approach for uncovering detailed information about the local atomic structure and structural variations in disordered materials. However, achieving high accuracy in ePDF analysis requires careful control of experimental and instrumental parameters. In this study, we systematically investigate the effect of key electron optical, measurement and processing parameters on ePDF analysis using simulations as the primary tool, complemented by experimental validation. Specifically, we examine the influence of diffraction angle range, beam convergence semi-angle, detector pixel resolution, sample thickness (multiple scattering effect), noise, and electron beam precession on the resulting ePDF. By integrating multi-slice electron diffraction simulations with experimental diffraction data, we identify optimal conditions for accurate ePDF extraction and provide practical guidelines to improve analysis precision and reliability. These insights contribute to refining ePDF techniques, particularly for applications involving amorphous and nanostructured materials.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"281 ","pages":"Article 114295"},"PeriodicalIF":2.0,"publicationDate":"2025-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145737640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-07DOI: 10.1016/j.ultramic.2025.114296
Chang-Gi Lee , Byeong-Gyu Chae , I-Jun Ro , Kyuseon Jang , Nak-Kyoon Kim , Jae-Pyoung Ahn , Eric Woods , Jaemin Ahn , Seong Yong Park , Baptiste Gault , Se-Ho Kim
Atom probe tomography (APT) enables near-atomic-scale, three-dimensional elemental mapping through controlled field evaporation of surface atoms, triggered by the combined application of a DC voltage with either voltage or laser pulses. As selected laser wavelengths in atom probes transitioned from near-infrared (1050–1064 nm) toward shorter wavelengths, such as green (532 nm) and near-ultraviolet (NUV 355 nm), the quality of data improved and the range of analyzable materials expanded significantly. Recently, a new commercial atom probe (Invizo 6000) employing a deep ultraviolet (DUV) laser wavelength of 257.5 nm has been introduced. Invizo 6000 incorporates several new design elements, such as dual laser beam, einzel lens, and flat counter electrode. However, despite these substantial design modifications, systematic studies comparing its performance with conventional local electrode atom probe (LEAP) systems across different classes of materials remain scarce. In this study, various materials, including metals and oxides, were examined using commercial LEAP 5000 and Invizo 6000. The quality of the data obtained from both instruments was systematically evaluated using four key metrics: background levels, detection events, ion detection histograms, and mass-resolving power. Additionally, applying a thin coating to the prepared APT specimens was found to enhance data quality.
{"title":"Performance evaluation of deep-ultraviolet laser-assisted Invizo 6000 and near-ultraviolet laser-assisted LEAP 5000 for a range of material systems","authors":"Chang-Gi Lee , Byeong-Gyu Chae , I-Jun Ro , Kyuseon Jang , Nak-Kyoon Kim , Jae-Pyoung Ahn , Eric Woods , Jaemin Ahn , Seong Yong Park , Baptiste Gault , Se-Ho Kim","doi":"10.1016/j.ultramic.2025.114296","DOIUrl":"10.1016/j.ultramic.2025.114296","url":null,"abstract":"<div><div>Atom probe tomography (APT) enables near-atomic-scale, three-dimensional elemental mapping through controlled field evaporation of surface atoms, triggered by the combined application of a DC voltage with either voltage or laser pulses. As selected laser wavelengths in atom probes transitioned from near-infrared (1050–1064 nm) toward shorter wavelengths, such as green (532 nm) and near-ultraviolet (NUV 355 nm), the quality of data improved and the range of analyzable materials expanded significantly. Recently, a new commercial atom probe (Invizo 6000) employing a deep ultraviolet (DUV) laser wavelength of 257.5 nm has been introduced. Invizo 6000 incorporates several new design elements, such as dual laser beam, einzel lens, and flat counter electrode. However, despite these substantial design modifications, systematic studies comparing its performance with conventional local electrode atom probe (LEAP) systems across different classes of materials remain scarce. In this study, various materials, including metals and oxides, were examined using commercial LEAP 5000 and Invizo 6000. The quality of the data obtained from both instruments was systematically evaluated using four key metrics: background levels, detection events, ion detection histograms, and mass-resolving power. Additionally, applying a thin coating to the prepared APT specimens was found to enhance data quality.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"281 ","pages":"Article 114296"},"PeriodicalIF":2.0,"publicationDate":"2025-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145737642","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-07DOI: 10.1016/j.ultramic.2025.114300
Yangfan Li , Yue Pan , Xincheng Lei , Weiwei Chen , Yang Shen , Mengshu Ge , Xiaozhi Liu , Dong Su
High-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) is a vital tool for characterizing single-atom catalysts (SACs). However, reliable elemental identification of different atoms remains challenging because the signal intensity of HAADF depends strongly on defocus and other imaging parameters, potentially ruining the Z-contrast of atoms at different depths. In this work, we investigated the influence of the vertical position of atoms (defocus), support thickness, interatomic height, convergence, and collection angles via multi-slice simulations on a model system of Fe/Pt atoms on amorphous carbon supports. Our calculation shows that at a convergence angle of 28 mrad, a defocus of 8.5 nm can cause Fe and Pt atoms to be indistinguishable. At a larger convergence angle, this critical indistinguishable defocus can be even shorter. To address this limitation, we propose a Multi-Defocus Fusion (MDF) method, retrieving the Z-contrast from serial images from multiple defocus. Experimental validation on a Fe/Pt SAC sample confirms the effectiveness of MDF, yielding clearly separated intensity histograms corresponding to Fe and Pt atoms. This work presents a robust, easy-to-implement strategy for accurate single-atom identification, offering valuable guidance for the accelerated screening and rational design of high-performance SACs.
{"title":"Differentiation of distinct single atoms via multi‑defocus fusion method","authors":"Yangfan Li , Yue Pan , Xincheng Lei , Weiwei Chen , Yang Shen , Mengshu Ge , Xiaozhi Liu , Dong Su","doi":"10.1016/j.ultramic.2025.114300","DOIUrl":"10.1016/j.ultramic.2025.114300","url":null,"abstract":"<div><div>High-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) is a vital tool for characterizing single-atom catalysts (SACs). However, reliable elemental identification of different atoms remains challenging because the signal intensity of HAADF depends strongly on defocus and other imaging parameters, potentially ruining the Z-contrast of atoms at different depths. In this work, we investigated the influence of the vertical position of atoms (defocus), support thickness, interatomic height, convergence, and collection angles via multi-slice simulations on a model system of Fe/Pt atoms on amorphous carbon supports. Our calculation shows that at a convergence angle of 28 mrad, a defocus of 8.5 nm can cause Fe and Pt atoms to be indistinguishable. At a larger convergence angle, this critical indistinguishable defocus can be even shorter. To address this limitation, we propose a Multi-Defocus Fusion (MDF) method, retrieving the Z-contrast from serial images from multiple defocus. Experimental validation on a Fe/Pt SAC sample confirms the effectiveness of MDF, yielding clearly separated intensity histograms corresponding to Fe and Pt atoms. This work presents a robust, easy-to-implement strategy for accurate single-atom identification, offering valuable guidance for the accelerated screening and rational design of high-performance SACs.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"281 ","pages":"Article 114300"},"PeriodicalIF":2.0,"publicationDate":"2025-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145737641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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