1
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Zhan Z, Liu Y, Wang W, Du G, Cai S, Wang P. Atomic-level imaging of beam-sensitive COFs and MOFs by low-dose electron microscopy. NANOSCALE HORIZONS 2024; 9:900-933. [PMID: 38512352 DOI: 10.1039/d3nh00494e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Electron microscopy, an important technique that allows for the precise determination of structural information with high spatiotemporal resolution, has become indispensable in unravelling the complex relationships between material structure and properties ranging from mesoscale morphology to atomic arrangement. However, beam-sensitive materials, particularly those comprising organic components such as metal-organic frameworks (MOFs) and covalent organic frameworks (COFs), would suffer catastrophic damage from the high energy electrons, hindering the determination of atomic structures. A low-dose approach has arisen as a possible solution to this problem based on the integration of advancements in several aspects: electron optical system, detector, image processing, and specimen preservation. This article summarizes the transmission electron microscopy characterization of MOFs and COFs, including local structures, host-guest interactions, and interfaces at the atomic level. Revolutions in advanced direct electron detectors, algorithms in image acquisition and processing, and emerging methodology for high quality low-dose imaging are also reviewed. Finally, perspectives on the future development of electron microscopy methodology with the support of computer science are presented.
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Affiliation(s)
- Zhen Zhan
- Department of Applied Physics, The Hong Kong Polytechnic University, Kowloon 999077, Hong Kong SAR, China.
| | - Yuxin Liu
- Department of Applied Physics, The Hong Kong Polytechnic University, Kowloon 999077, Hong Kong SAR, China.
| | - Weizhen Wang
- Department of Applied Physics, The Hong Kong Polytechnic University, Kowloon 999077, Hong Kong SAR, China.
| | - Guangyu Du
- Department of Applied Physics, The Hong Kong Polytechnic University, Kowloon 999077, Hong Kong SAR, China.
| | - Songhua Cai
- Department of Applied Physics, The Hong Kong Polytechnic University, Kowloon 999077, Hong Kong SAR, China.
| | - Peng Wang
- Department of Physics, University of Warwick, CV4 7AL, Coventry, UK.
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2
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Ma Y, Shi J, Guzman R, Li A, Zhou W. Aberration Correction for Large-Angle Illumination Scanning Transmission Electron Microscopy by Using Iterative Electron Ptychography Algorithms. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2024; 30:226-235. [PMID: 38578297 DOI: 10.1093/mam/ozae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/21/2024] [Accepted: 01/24/2024] [Indexed: 04/06/2024]
Abstract
Modern aberration correctors in the scanning transmission electron microscope (STEM) have dramatically improved the attainable spatial resolution and enabled atomical structure and spectroscopic analysis even at low acceleration voltages (≤80 kV). For a large-angle illumination, achieving successful aberration correction to high angles is challenging with an aberration corrector, which limits further improvements in applications such as super-resolution, three-dimensional atomic depth resolution, or atomic surface morphology analyses. Electron ptychography based on four-dimensional STEM can provide a postprocessing strategy to overcome the current technological limitations. In this work, we have demonstrated that aberration correction for large-angle illumination is feasible by pushing the capabilities of regularized ptychographic iterative engine algorithms to reconstruct 4D data sets acquired using a relatively low-efficiency complementary metal oxide semiconductor camera. We report super resolution (0.71 Å) with large-angle illumination (50-60 mrad) and under 60 kV accelerating voltage.
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Affiliation(s)
- Yinhang Ma
- School of Physical Sciences and CAS Key Laboratory of Vacuum Physics, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Jinan Shi
- School of Physical Sciences and CAS Key Laboratory of Vacuum Physics, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Roger Guzman
- School of Physical Sciences and CAS Key Laboratory of Vacuum Physics, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Ang Li
- School of Physical Sciences and CAS Key Laboratory of Vacuum Physics, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Wu Zhou
- School of Physical Sciences and CAS Key Laboratory of Vacuum Physics, University of Chinese Academy of Sciences, Beijing 100190, China
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3
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Sun X, Zhang X, Cheng B, Liu C, Zhu J. Mixed-state ptychography for quantitative optical properties measurement of vector beam. OPTICS EXPRESS 2024; 32:7207-7219. [PMID: 38439408 DOI: 10.1364/oe.516428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/05/2024] [Indexed: 03/06/2024]
Abstract
Recent advances in ptychography have extended to anisotropic specimens, but vectorial reconstruction of probes owing to polarization aliasing remains a challenge. A polarization-sensitive ptychography that enables full optical property measurement of vector light is proposed. An optimized reconstruction strategy, first calibrating the propagation direction and then performing faithful retrieval, is established. This method avoids multiple image acquisitions with various polarizer configurations and significantly improves the measurement accuracy by correlating the intensity and position of different polarization components. The capability of the proposed method to quantify anisotropic parameters of optical materials and polarization properties of vector probe is demonstrated by experiment.
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4
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Nguyen KX, Jiang Y, Lee CH, Kharel P, Zhang Y, van der Zande AM, Huang PY. Achieving sub-0.5-angstrom-resolution ptychography in an uncorrected electron microscope. Science 2024; 383:865-870. [PMID: 38386746 DOI: 10.1126/science.adl2029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/19/2024] [Indexed: 02/24/2024]
Abstract
Subangstrom resolution has long been limited to aberration-corrected electron microscopy, where it is a powerful tool for understanding the atomic structure and properties of matter. Here, we demonstrate electron ptychography in an uncorrected scanning transmission electron microscope (STEM) with deep subangstrom spatial resolution down to 0.44 angstroms, exceeding the conventional resolution of aberration-corrected tools and rivaling their highest ptychographic resolutions. Our approach, which we demonstrate on twisted two-dimensional materials in a widely available commercial microscope, far surpasses prior ptychographic resolutions (1 to 5 angstroms) of uncorrected STEMs. We further show how geometric aberrations can create optimized, structured beams for dose-efficient electron ptychography. Our results demonstrate that expensive aberration correctors are no longer required for deep subangstrom resolution.
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Affiliation(s)
- Kayla X Nguyen
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Yi Jiang
- Advanced Photon Source Facility, Argonne National Laboratory, Lemont, IL, USA
| | - Chia-Hao Lee
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Priti Kharel
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Yue Zhang
- Department of Mechanical Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Arend M van der Zande
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Mechanical Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Materials Research Laboratory, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Pinshane Y Huang
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Materials Research Laboratory, University of Illinois Urbana-Champaign, Urbana, IL, USA
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5
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Zhang Z, Li J, Wang YG. Modeling Interfacial Dynamics on Single Atom Electrocatalysts: Explicit Solvation and Potential Dependence. Acc Chem Res 2024; 57:198-207. [PMID: 38166366 DOI: 10.1021/acs.accounts.3c00589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
ConspectusSingle atom electrocatalysts, with noble metal-free composition, maximal atom efficiency, and exceptional reactivity toward various energy and environmental applications, have become a research hot spot in the recent decade. Their simplicity and the isolated nature of the atomic structure of their active site have also made them an ideal model catalyst system for studying reaction mechanisms and activity trends. However, the state of the single atom active sites during electrochemical reactions may not be as simple as is usually assumed. To the contrary, the single atom electrocatalysts have been reported to be under greater influence from interfacial dynamics, with solvent and electrolyte ions perpetually interacting with the electrified active center under an applied electrode potential. These complexities render the activity trends and reaction mechanisms derived from simplistic models dubious.In this Account, with a few popular single atom electrocatalysis systems, we show how the change in electrochemical potential induces nontrivial variation in the free energy profile of elemental electrochemical reaction steps, demonstrate how the active centers with different electronic structure features can induce different solvation structures at the interface even for the same reaction intermediate of the simplest electrochemical reaction, and discuss the implication of the complexities on the kinetics and thermodynamics of the reaction system to better address the activity and selectivity trends. We also venture into more intriguing interfacial phenomena, such as alternative reaction pathways and intermediates that are favored and stabilized by solvation and polarization effects, long-range interfacial dynamics across the region far beyond the contact layer, and the dynamic activation or deactivation of single atom sites under operation conditions. We show the necessity of including realistic aspects (explicit solvent, electrolyte, and electrode potential) into the model to correctly capture the physics and chemistry at the electrochemical interface and to understand the reaction mechanisms and reactivity trends. We also demonstrate how the popular simplistic design principles fail and how they can be revised by including the kinetics and interfacial factors in the model. All of these rich dynamics and chemistry would remain hidden or overlooked otherwise. We believe that the complexity at an electrochemical interface is not a curse but a blessing in that it enables deeper understanding and finer control of the potential-dependent free energy landscape of electrochemical reactions, which opens up new dimensions for further design and optimization of single atom electrocatalysts and beyond. Limitations of current methods and challenges faced by the theoretical and experimental communities are discussed, along with the possible solutions awaiting development in the future.
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Affiliation(s)
- Zisheng Zhang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Jun Li
- Department of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China
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Diederichs B, Herdegen Z, Strauch A, Filbir F, Müller-Caspary K. Exact inversion of partially coherent dynamical electron scattering for picometric structure retrieval. Nat Commun 2024; 15:101. [PMID: 38168078 PMCID: PMC10762228 DOI: 10.1038/s41467-023-44268-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
The greatly nonlinear diffraction of high-energy electron probes focused to subatomic diameters frustrates the direct inversion of ptychographic data sets to decipher the atomic structure. Several iterative algorithms have been proposed to yield atomically-resolved phase distributions within slices of a 3D specimen, corresponding to the scattering centers of the electron wave. By pixelwise phase retrieval, current approaches do not only involve orders of magnitude more free parameters than necessary, but also neglect essential details of scattering physics such as the atomistic nature of the specimen and thermal effects. Here, we introduce a parametrized, fully differentiable scheme employing neural network concepts which allows the inversion of ptychographic data by means of entirely physical quantities. Omnipresent thermal diffuse scattering in thick specimens is treated accurately using frozen phonons, and atom types, positions and partial coherence are accounted for in the inverse model as relativistic scattering theory demands. Our approach exploits 4D experimental data collected in an aberration-corrected momentum-resolved scanning transmission electron microscopy setup. Atom positions in a 20 nm thick PbZr0.2Ti0.8O3 ferroelectric are measured with picometer precision, including the discrimination of different atom types and positions in mixed columns.
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Affiliation(s)
- Benedikt Diederichs
- Department of Chemistry and Centre for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
- Institute of Biological and Medical Imaging, Helmholtz Zentrum München, Neuherberg, Germany
| | - Ziria Herdegen
- Department of Chemistry and Centre for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Achim Strauch
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons, Forschungszentrum Jülich, Jülich, Germany
| | - Frank Filbir
- Institute of Biological and Medical Imaging, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Mathematics, TUM School of Computation, Information and Technology, Technische Universität München, Garching, Germany
| | - Knut Müller-Caspary
- Department of Chemistry and Centre for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany.
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons, Forschungszentrum Jülich, Jülich, Germany.
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7
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Chen Y, Chou TC, Fang CH, Lu CY, Hsiao CN, Hsu WT, Chen CC. Direct observation of single-atom defects in monolayer two-dimensional materials by using electron ptychography at 200 kV acceleration voltage. Sci Rep 2024; 14:277. [PMID: 38167628 PMCID: PMC10761697 DOI: 10.1038/s41598-023-50784-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 12/25/2023] [Indexed: 01/05/2024] Open
Abstract
Electron ptychography has emerged as a popular technology for high-resolution imaging by combining the high coherence of electron sources with the ultra-fast scanning electron coil. However, the limitations of conventional pixelated detectors, including poor dynamic range and slow data readout speeds, have posed restrictions in the past on conducting electron ptychography experiments. We used the Gatan STELA pixelated detector to capture sequential diffraction data of monolayer two-dimensional (2D) materials for ptychographic reconstruction. By using the pixelated detector and electron ptychography, we demonstrate the observation of the radiation damage at atomic resolution in Transition Metal Dichalcogenides (TMDs).
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Affiliation(s)
- Ying Chen
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Tzu-Chieh Chou
- Department of Physics, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Ching-Hsing Fang
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Cheng-Yi Lu
- Department of Physics, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Chien-Nan Hsiao
- Taiwan Instrument Research Institute, National Applied Research Laboratories, Hsinchu, 300092, Taiwan
| | - Wei-Ting Hsu
- Department of Physics, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Chien-Chun Chen
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu, 300044, Taiwan.
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8
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Liu T, Ren X, Fang J, Yu Z, Wang X. Multiomics Sequencing and AlphaFold2 Analysis of the Stereoselective Behavior of Mefentrifluconazole for Bioactivity Improvement and Risk Reduction. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:21348-21357. [PMID: 38051155 DOI: 10.1021/acs.est.3c05327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
As the first isopropanol chiral triazole fungicide, mefentrifluconazole has broad prospects for application. In this study, the stereoselective stability, bioactivity, fate, and biotoxicity were systematically investigated. Our results indicated that the stability of mefentrifluconazole enantiomers differed between environmental media, and they were stable in water and sediment in the dark. The bactericidal activity of R-mefentrifluconazole against the four target pathogens was 4.6-43 times higher than that of S-mefentrifluconazole. In the water-sediment system, S-mefentrifluconazole dissipated faster than R-mefentrifluconazole in water; however, its accumulation capacity was higher than that of R-mefentrifluconazole in sediment and zebrafish. S-Mefentrifluconazole induced more differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) in zebrafish than did R-mefentrifluconazole. Multiomics sequencing results showed that S-mefentrifluconazole enhanced the antioxidant, detoxification, immune, and metabolic functions of zebrafish by interacting with related proteins. Based on AlphaFold2 modeling and molecular docking, mefentrifluconazole enantiomers had different binding modes with key target proteins in pathogens and zebrafish, which may be the main reason for the stereoselective differences in bioactivity and biotoxicity. Based on its excellent bioactivity and low biotoxicity, the R-enantiomer can be developed to improve the bioactivity and reduce the risk of mefentrifluconazole.
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Affiliation(s)
- Tong Liu
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Xiangyu Ren
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Jianwei Fang
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Zihan Yu
- College of Plant Science, Jilin University, Changchun 130062, P.R. China
| | - Xiuguo Wang
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
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9
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Pan X, Wang S, Zhou Z, Zhou L, Liu P, Li C, Wang W, Zhang C, Dong Y, Zhang Y. An efficient ptychography reconstruction strategy through fine-tuning of large pre-trained deep learning model. iScience 2023; 26:108420. [PMID: 38034346 PMCID: PMC10687283 DOI: 10.1016/j.isci.2023.108420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/24/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023] Open
Abstract
With pre-trained large models and their associated fine-tuning paradigms being constantly applied in deep learning, the performance of large models achieves a dramatic boost, mostly owing to the improvements on both data quantity and quality. Next-generation synchrotron light sources offer ultra-bright and highly coherent X-rays, which are becoming one of the largest data sources for scientific experiments. As one of the most data-intensive scanning-based imaging methodologies, ptychography produces an immense amount of data, making the adoption of large deep learning models possible. Here, we introduce and refine the architecture of a neural network model to improve the reconstruction performance, through fine-tuning large pre-trained model using a variety of datasets. The pre-trained model exhibits remarkable generalization capability, while the fine-tuning strategy enhances the reconstruction quality. We anticipate this work will contribute to the advancement of deep learning methods in ptychography, as well as in broader coherent diffraction imaging methodologies in future.
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Affiliation(s)
- Xinyu Pan
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuo Wang
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongzheng Zhou
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liang Zhou
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Liu
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chun Li
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
- Spallation Neutron Source Science Center, Dongguan, Guangdong 523803, China
| | - Wenhui Wang
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
- Spallation Neutron Source Science Center, Dongguan, Guangdong 523803, China
| | - Chenglong Zhang
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhui Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Zhang
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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10
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Pelz PM, Griffin SM, Stonemeyer S, Popple D, DeVyldere H, Ercius P, Zettl A, Scott MC, Ophus C. Solving complex nanostructures with ptychographic atomic electron tomography. Nat Commun 2023; 14:7906. [PMID: 38036516 PMCID: PMC10689721 DOI: 10.1038/s41467-023-43634-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 11/15/2023] [Indexed: 12/02/2023] Open
Abstract
Transmission electron microscopy (TEM) is essential for determining atomic scale structures in structural biology and materials science. In structural biology, three-dimensional structures of proteins are routinely determined from thousands of identical particles using phase-contrast TEM. In materials science, three-dimensional atomic structures of complex nanomaterials have been determined using atomic electron tomography (AET). However, neither of these methods can determine the three-dimensional atomic structure of heterogeneous nanomaterials containing light elements. Here, we perform ptychographic electron tomography from 34.5 million diffraction patterns to reconstruct an atomic resolution tilt series of a double wall-carbon nanotube (DW-CNT) encapsulating a complex ZrTe sandwich structure. Class averaging the resulting tilt series images and subpixel localization of the atomic peaks reveals a Zr11Te50 structure containing a previously unobserved ZrTe2 phase in the core. The experimental realization of atomic resolution ptychographic electron tomography will allow for the structural determination of a wide range of beam-sensitive nanomaterials containing light elements.
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Affiliation(s)
- Philipp M Pelz
- Institute of Micro- and Nanostructure Research (IMN) & Center for Nanoanalysis and Electron Microscopy (CENEM), Friedrich Alexander-Universität Erlangen-Nürnberg, IZNF, 91058, Erlangen, Germany.
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, 94720, USA.
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Sinéad M Griffin
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Scott Stonemeyer
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Kavli Energy NanoSciences Institute at the University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Chemistry, University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Physics, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Derek Popple
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Kavli Energy NanoSciences Institute at the University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Chemistry, University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Physics, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Hannah DeVyldere
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Peter Ercius
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alex Zettl
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Kavli Energy NanoSciences Institute at the University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Physics, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Mary C Scott
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, 94720, USA
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Colin Ophus
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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11
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Seifert J, Shao Y, van Dam R, Bouchet D, van Leeuwen T, Mosk AP. Maximum-likelihood estimation in ptychography in the presence of Poisson-Gaussian noise statistics. OPTICS LETTERS 2023; 48:6027-6030. [PMID: 37966780 DOI: 10.1364/ol.502344] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/21/2023] [Indexed: 11/16/2023]
Abstract
Optical measurements often exhibit mixed Poisson-Gaussian noise statistics, which hampers the image quality, particularly under low signal-to-noise ratio (SNR) conditions. Computational imaging falls short in such situations when solely Poissonian noise statistics are assumed. In response to this challenge, we define a loss function that explicitly incorporates this mixed noise nature. By using a maximum-likelihood estimation, we devise a practical method to account for a camera readout noise in gradient-based ptychography optimization. Our results, based on both experimental and numerical data, demonstrate that this approach outperforms the conventional one, enabling enhanced image reconstruction quality under challenging noise conditions through a straightforward methodological adjustment.
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12
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Zhao H, Lv X, Wang Y. Realistic Modeling of the Electrocatalytic Process at Complex Solid-Liquid Interface. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303677. [PMID: 37749877 PMCID: PMC10646274 DOI: 10.1002/advs.202303677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/02/2023] [Indexed: 09/27/2023]
Abstract
The rational design of electrocatalysis has emerged as one of the most thriving means for mitigating energy and environmental crises. The key to this effort is the understanding of the complex electrochemical interface, wherein the electrode potential as well as various internal factors such as H-bond network, adsorbate coverage, and dynamic behavior of the interface collectively contribute to the electrocatalytic activity and selectivity. In this context, the authors have reviewed recent theoretical advances, and especially, the contributions to modeling the realistic electrocatalytic processes at complex electrochemical interfaces, and illustrated the challenges and fundamental problems in this field. Specifically, the significance of the inclusion of explicit solvation and electrode potential as well as the strategies toward the design of highly efficient electrocatalysts are discussed. The structure-activity relationships and their dynamic responses to the environment and catalytic functionality under working conditions are illustrated to be crucial factors for understanding the complexed interface and the electrocatalytic activities. It is hoped that this review can help spark new research passion and ultimately bring a step closer to a realistic and systematic modeling method for electrocatalysis.
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Affiliation(s)
- Hongyan Zhao
- Department of Chemistry and Guangdong Provincial Key Laboratory of CatalysisSouthern University of Science and TechnologyShenzhenGuangdong518055China
| | - Xinmao Lv
- Department of Chemistry and Guangdong Provincial Key Laboratory of CatalysisSouthern University of Science and TechnologyShenzhenGuangdong518055China
| | - Yang‐Gang Wang
- Department of Chemistry and Guangdong Provincial Key Laboratory of CatalysisSouthern University of Science and TechnologyShenzhenGuangdong518055China
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13
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Kim NY, Cao S, More KL, Lupini AR, Miao J, Chi M. Hollow Ptychography: Toward Simultaneous 4D Scanning Transmission Electron Microscopy and Electron Energy Loss Spectroscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2208162. [PMID: 37203310 DOI: 10.1002/smll.202208162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 04/13/2023] [Indexed: 05/20/2023]
Abstract
With the recent development of high-acquisition-speed pixelated detectors, 4D scanning transmission electron microscopy (4D-STEM) is becoming routinely available in high-resolution electron microscopy. 4D-STEM acts as a "universal" method that provides local information on materials that is challenging to extract from bulk techniques. It extends conventional STEM imaging to include super-resolution techniques and to provide quantitative phase-based information, such as differential phase contrast, ptychography, or Bloch wave phase retrieval. However, an important missing factor is the chemical and bonding information provided by electron energy loss spectroscopy (EELS). 4D-STEM and EELS cannot currently be acquired simultaneously due to the overlapping geometry of the detectors. Here, the feasibility of modifying the detector geometry to overcome this challenge for bulk specimens is demonstrated, and the use of a partial or defective detector for ptycholgaphic structural imaging is explored. Results show that structural information beyond the diffraction-limit and chemical information from the material can be extracted together, resulting in simultaneous multi-modal measurements, adding the additional dimensions of spectral information to 4D datasets.
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Affiliation(s)
- Na Yeon Kim
- Department of Physics and Astronomy and California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
| | - Shaohong Cao
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Karren L More
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Andrew R Lupini
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jianwei Miao
- Department of Physics and Astronomy and California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
| | - Miaofang Chi
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
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14
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Jiang Y, Cao MC, Chen Z, Han Y. Optimizing Parameters for High-resolution and Low-dose Electron Ptychography. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:284-285. [PMID: 37613141 DOI: 10.1093/micmic/ozad067.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Yi Jiang
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL, United States
| | - Michael C Cao
- Department of Materials Science and NanoEngineering, Rice University, Houston, TX, United States
| | - Zhen Chen
- School of Materials Science and Engineering, Tsinghua University, Beijing, China
| | - Yimo Han
- Department of Materials Science and NanoEngineering, Rice University, Houston, TX, United States
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15
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Huang J, Kang K, Schleife A, Huang PY. Electron Ptychography Simulations for Atomic-resolution Magnetic Imaging. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:282-283. [PMID: 37613144 DOI: 10.1093/micmic/ozad067.130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Jeffrey Huang
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Kisung Kang
- NOMAD Laboratory at Fritz-Haber-Institut der Max-Planck-Gesellschaft and IRIS-Adlershof of the Humboldt-Universität zu Berlin, Berlin, Germany
| | - André Schleife
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Pinshane Y Huang
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL, United States
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16
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Pei X, Zhou L, Huang C, Boyce M, Kim JS, Liberti E, Hu Y, Sasaki T, Nellist PD, Zhang P, Stuart DI, Kirkland AI, Wang P. Cryogenic electron ptychographic single particle analysis with wide bandwidth information transfer. Nat Commun 2023; 14:3027. [PMID: 37230988 PMCID: PMC10212999 DOI: 10.1038/s41467-023-38268-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 04/22/2023] [Indexed: 05/27/2023] Open
Abstract
Advances in cryogenic transmission electron microscopy have revolutionised the determination of many macromolecular structures at atomic or near-atomic resolution. This method is based on conventional defocused phase contrast imaging. However, it has limitations of weaker contrast for small biological molecules embedded in vitreous ice, in comparison with cryo-ptychography, which shows increased contrast. Here we report a single-particle analysis based on the use of ptychographic reconstruction data, demonstrating that three dimensional reconstructions with a wide information transfer bandwidth can be recovered by Fourier domain synthesis. Our work suggests future applications in otherwise challenging single particle analyses, including small macromolecules and heterogeneous or flexible particles. In addition structure determination in situ within cells without the requirement for protein purification and expression may be possible.
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Affiliation(s)
- Xudong Pei
- National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, College of Engineering and Applied Sciences and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, China
| | - Liqi Zhou
- National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, College of Engineering and Applied Sciences and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, China
- Department of Physics, University of Warwick, Coventry, UK
| | - Chen Huang
- The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, UK
| | - Mark Boyce
- Division of Structural Biology, Welcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Judy S Kim
- The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, UK
- Department of Materials, University of Oxford, Oxford, UK
| | - Emanuela Liberti
- The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, UK
| | - Yiming Hu
- National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, College of Engineering and Applied Sciences and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, China
| | | | | | - Peijun Zhang
- Division of Structural Biology, Welcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - David I Stuart
- Division of Structural Biology, Welcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Angus I Kirkland
- The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, UK.
- Department of Materials, University of Oxford, Oxford, UK.
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
| | - Peng Wang
- National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, College of Engineering and Applied Sciences and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, China.
- Department of Physics, University of Warwick, Coventry, UK.
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17
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Hu Z, Zhang Y, Li P, Batey D, Maiden A. Near-field multi-slice ptychography: quantitative phase imaging of optically thick samples with visible light and X-rays. OPTICS EXPRESS 2023; 31:15791-15809. [PMID: 37157672 DOI: 10.1364/oe.487002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Ptychography is a form of lens-free coherent diffractive imaging now used extensively in electron and synchrotron-based X-ray microscopy. In its near-field implementation, it offers a route to quantitative phase imaging at an accuracy and resolution competitive with holography, with the added advantages of extended field of view and blind deconvolution of the illumination beam profile from the sample image. In this paper we show how near-field ptychography can be combined with a multi-slice model, adding to this list of advantages the unique ability to recover high-resolution phase images of larger samples, whose thickness places them beyond the depth of field of alternative methods.
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18
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Zhou Y, Tang Y, Liao C, Su M, Shih K. Recent advances toward structural incorporation for stabilizing heavy metal contaminants: A critical review. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130977. [PMID: 36860053 DOI: 10.1016/j.jhazmat.2023.130977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/27/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Heavy metal pollution has resulted in serious environmental damage and raised significant public health concerns. One potential solution in terminal waste treatment is to structurally incorporate and immobilize heavy metals in some robust frameworks. Yet extant research offers a limited perspective on how metal incorporation behavior and stabilization mechanisms can effectively manage heavy metal-laden waste. This review sets forth detailed research on the feasibility of treatment strategies to incorporate heavy metals into structural frameworks; this paper also compares common methods and advanced characterization techniques for identifying metal stabilization mechanisms. Furthermore, this review analyses the typical hosting structures for heavy metal contaminants and metal incorporation behavior, highlighting the importance of structural features on metal speciation and immobilization efficiency. Lastly, this paper systematically summarizes key factors (i.e., intrinsic properties and external conditions) affecting metal incorporation behavior. Drawing on these impactful findings, the paper discusses future directions in the design of waste forms that efficiently, effectively treat heavy metal contaminants. By examining tailored composition-structure-property relationships in metal immobilization strategies, this review reveals possible solutions for crucial challenges in waste treatment and enhances the development of structural incorporation strategies for heavy metal immobilization in environmental applications.
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Affiliation(s)
- Ying Zhou
- Center for Water Research, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai 519087, China; Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region of China
| | - Yuanyuan Tang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Changzhong Liao
- State Key Laboratory of Featured Metal Materials and Life-cycle Safety for Composite Structures, School of Resources, Environment and Materials, Guangxi University, Nanning 530004, China
| | - Minhua Su
- Guangdong Provincial Key Laboratory of Radionuclides Pollution Control and Resources, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Kaimin Shih
- Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region of China.
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19
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Ning S, Xu W, Loh L, Lu Z, Bosman M, Zhang F, He Q. An integrated constrained gradient descent (iCGD) protocol to correct scan-positional errors for electron ptychography with high accuracy and precision. Ultramicroscopy 2023; 248:113716. [PMID: 36958156 DOI: 10.1016/j.ultramic.2023.113716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 02/11/2023] [Accepted: 03/10/2023] [Indexed: 03/13/2023]
Abstract
Correcting scan-positional errors is critical in achieving electron ptychography with both high resolution and high precision. This is a demanding and challenging task due to the sheer number of parameters that need to be optimized. For atomic-resolution ptychographic reconstructions, we found classical refining methods for scan positions not satisfactory due to the inherent entanglement between the object and scan positions, which can produce systematic errors in the results. Here, we propose a new protocol consisting of a series of constrained gradient descent (CGD) methods to achieve better recovery of scan positions. The central idea of these CGD methods is to utilize a priori knowledge about the nature of STEM experiments and add necessary constraints to isolate different types of scan positional errors during the iterative reconstruction process. Each constraint will be introduced with the help of simulated 4D-STEM datasets with known positional errors. Then the integrated constrained gradient decent (iCGD) protocol will be demonstrated using an experimental 4D-STEM dataset of the 1H-MoS2 monolayer. We will show that the iCGD protocol can effectively address the errors of scan positions across the spectrum and help to achieve electron ptychography with high accuracy and precision.
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Affiliation(s)
- Shoucong Ning
- Department of Materials Science and Engineering, National University of Singapore, 117575, Singapore
| | - Wenhui Xu
- Department of Electrical and Electronic Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Harbin Institute of Technology, Harbin 150001, China
| | - Leyi Loh
- Department of Materials Science and Engineering, National University of Singapore, 117575, Singapore
| | - Zhen Lu
- Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Michel Bosman
- Department of Materials Science and Engineering, National University of Singapore, 117575, Singapore
| | - Fucai Zhang
- Department of Electrical and Electronic Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Qian He
- Department of Materials Science and Engineering, National University of Singapore, 117575, Singapore.
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20
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Dong Z, Zhang E, Jiang Y, Zhang Q, Mayoral A, Jiang H, Ma Y. Atomic-Level Imaging of Zeolite Local Structures Using Electron Ptychography. J Am Chem Soc 2023; 145:6628-6632. [PMID: 36877580 DOI: 10.1021/jacs.2c12673] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Zeolites are among the most important heterogeneous catalysts, widely employed in separation reaction, fine chemical production, and petroleum refining. Through rational design of the frameworks, zeolites with versatile functions can be synthesized. Local imaging of zeolite structures at the atomic scale, including the basic framework atoms (Si, Al, and O) and extra-framework cations, is necessary to understand the structure-function relationship of zeolites. Herein, we implemented electron ptychography into direct imaging of local structures of two zeolites, Na-LTA and ZSM-5. Not only all the framework atoms but also extra-framework Na+ cations with only 1/4 occupation probabilities in Na-LTA were directly observed. Local structures of ZSM-5 zeolites having guest molecules among channels with different orientations were also unraveled using different reconstruction algorithms. The approach presented here provides a new way to locally image zeolites structure, and it is expected to be an essential key for further studying and tuning zeolites active sites at the atomic level.
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Affiliation(s)
- Zhuoya Dong
- School of Physical Science and Technology & Shanghai Key Laboratory of High-resolution Electron Microscopy, ShanghaiTech University, Shanghai 201210, P. R. China.,Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain
| | - Enci Zhang
- School of Physical Science and Technology & Shanghai Key Laboratory of High-resolution Electron Microscopy, ShanghaiTech University, Shanghai 201210, P. R. China
| | - Yilan Jiang
- School of Physical Science and Technology & Shanghai Key Laboratory of High-resolution Electron Microscopy, ShanghaiTech University, Shanghai 201210, P. R. China
| | - Qing Zhang
- School of Physical Science and Technology & Shanghai Key Laboratory of High-resolution Electron Microscopy, ShanghaiTech University, Shanghai 201210, P. R. China
| | - Alvaro Mayoral
- School of Physical Science and Technology & Shanghai Key Laboratory of High-resolution Electron Microscopy, ShanghaiTech University, Shanghai 201210, P. R. China.,Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain
| | - Huaidong Jiang
- School of Physical Science and Technology & Shanghai Key Laboratory of High-resolution Electron Microscopy, ShanghaiTech University, Shanghai 201210, P. R. China.,Center for Transformative Science, ShanghaiTech University, Shanghai 201210, P. R. China
| | - Yanhang Ma
- School of Physical Science and Technology & Shanghai Key Laboratory of High-resolution Electron Microscopy, ShanghaiTech University, Shanghai 201210, P. R. China
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21
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Assalauova D, Vartanyants IA. The structure of tick-borne encephalitis virus determined at X-ray free-electron lasers. Simulations. JOURNAL OF SYNCHROTRON RADIATION 2023; 30:24-34. [PMID: 36601923 PMCID: PMC9814066 DOI: 10.1107/s1600577522011341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
The study of virus structures by X-ray free-electron lasers (XFELs) has attracted increased attention in recent decades. Such experiments are based on the collection of 2D diffraction patterns measured at the detector following the application of femtosecond X-ray pulses to biological samples. To prepare an experiment at the European XFEL, the diffraction data for the tick-borne encephalitis virus (TBEV) was simulated with different parameters and the optimal values were identified. Following the necessary steps of a well established data-processing pipeline, the structure of TBEV was obtained. In the structure determination presented, a priori knowledge of the simulated virus orientations was used. The efficiency of the proposed pipeline was demonstrated.
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Affiliation(s)
- Dameli Assalauova
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Ivan A. Vartanyants
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
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22
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Li G, Zhang H, Han Y. 4D-STEM Ptychography for Electron-Beam-Sensitive Materials. ACS CENTRAL SCIENCE 2022; 8:1579-1588. [PMID: 36589892 PMCID: PMC9801507 DOI: 10.1021/acscentsci.2c01137] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Indexed: 05/26/2023]
Abstract
Recent advances in high-speed pixelated electron detectors have substantially facilitated the implementation of four-dimensional scanning transmission electron microscopy (4D-STEM). A critical application of 4D-STEM is electron ptychography, which reveals the atomic structure of a specimen by reconstructing its transmission function from redundant convergent-beam electron diffraction patterns. Although 4D-STEM ptychography offers many advantages over conventional imaging modes, this emerging technique has not been fully applied to materials highly sensitive to electron beams. In this Outlook, we introduce the fundamentals of 4D-STEM ptychography, focusing on data collection and processing methods, and present the current applications of 4D-STEM ptychography in various materials. Next, we discuss the potential advantages of imaging electron-beam-sensitive materials using 4D-STEM ptychography and explore its feasibility by performing simulations and experiments on a zeolite material. The preliminary results demonstrate that, at the low electron dose required to preserve the zeolite structure, 4D-STEM ptychography can reliably provide higher resolution and greater tolerance to the specimen thickness and probe defocus as compared to existing imaging techniques. In the final section, we discuss the challenges and possible strategies to further reduce the electron dose for 4D-STEM ptychography. If successful, it will be a game-changer for imaging extremely sensitive materials, such as metal-organic frameworks, hybrid halide perovskites, and supramolecular crystals.
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23
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Chen Z, Turgut E, Jiang Y, Nguyen KX, Stolt MJ, Jin S, Ralph DC, Fuchs GD, Muller DA. Lorentz electron ptychography for imaging magnetic textures beyond the diffraction limit. NATURE NANOTECHNOLOGY 2022; 17:1165-1170. [PMID: 36316543 DOI: 10.1038/s41565-022-01224-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Abstract
Nanoscale spin textures, especially magnetic skyrmions, have attracted intense interest as candidate high-density and power-efficient information carriers for spintronic devices1,2. Facilitating a deeper understanding of sub-hundred-nanometre to atomic-scale spin textures requires more advanced magnetic imaging techniques3-5. Here we demonstrate a Lorentz electron ptychography method that can enable high-resolution, high-sensitivity magnetic field imaging for widely available electron microscopes. The resolution of Lorentz electron ptychography is not limited by the usual diffraction limit of lens optics, but instead is determined by the maximum scattering angle at which a statistically meaningful dose can still be recorded-this can be an improvement of up to 2-6 times depending on the allowable dose. Using FeGe as the model system, we realize a more accurate magnetic field measurement of skyrmions with an improved spatial resolution and sensitivity by also correcting the probe-damping effect from the imaging optics via Lorentz electron ptychography. This allows us to directly resolve subtle internal structures of magnetic skyrmions near the skyrmion cores, boundaries and dislocations in an FeGe single crystal. Our study establishes a quantitative, high-resolution magnetic microscopy technique that can reveal nanoscale spin textures, especially magnetization discontinuities and topological defects in nanomagnets6. The technique's high-dose efficiency should also make it well suited for the exploration of magnetic textures in electron radiation-sensitive materials such as organic or molecular magnets7.
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Affiliation(s)
- Zhen Chen
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA.
- School of Materials Science and Engineering, Tsinghua University, Beijing, China.
| | - Emrah Turgut
- Department of Physics, Oklahoma State University, Stillwater, OK, USA
| | - Yi Jiang
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL, USA
| | - Kayla X Nguyen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Matthew J Stolt
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Daniel C Ralph
- Department of Physics, Cornell University, Ithaca, NY, USA
- Kavli Institute at Cornell for Nanoscale Science, Ithaca, NY, USA
| | - Gregory D Fuchs
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - David A Muller
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA.
- Kavli Institute at Cornell for Nanoscale Science, Ithaca, NY, USA.
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24
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Automatic parameter selection for electron ptychography via Bayesian optimization. Sci Rep 2022; 12:12284. [PMID: 35854039 PMCID: PMC9296498 DOI: 10.1038/s41598-022-16041-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/04/2022] [Indexed: 11/08/2022] Open
Abstract
Electron ptychography provides new opportunities to resolve atomic structures with deep sub-angstrom spatial resolution and to study electron-beam sensitive materials with high dose efficiency. In practice, obtaining accurate ptychography images requires simultaneously optimizing multiple parameters that are often selected based on trial-and-error, resulting in low-throughput experiments and preventing wider adoption. Here, we develop an automatic parameter selection framework to circumvent this problem using Bayesian optimization with Gaussian processes. With minimal prior knowledge, the workflow efficiently produces ptychographic reconstructions that are superior to those processed by experienced experts. The method also facilitates better experimental designs by exploring optimized experimental parameters from simulated data.
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25
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Wen X, Zhou X, Li Y, Ji Y, Zhou K, Liu S, Jia D, Liu W, Chi D, Liu Z. High-performance lensless diffraction imaging from diverse holograms by three-dimensional scanning. OPTICS LETTERS 2022; 47:3423-3426. [PMID: 35838695 DOI: 10.1364/ol.464864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
For lensless diffraction imaging, it is a challenging dilemma to achieve a large field of view (FOV) and high resolution with a small amount of data at the same time. Ptychography can reconstruct the high-resolution image and illumination light simultaneously. But the illumination is limited to a small size by a probe in typical ptychography. For large samples, it takes much time to collect abundant patterns and has strict requirements for the computing power of computers. Another widely applied method, multi-height measurement, can realize a wide FOV with several holograms. But, the recovered image is easily destroyed by the background noise. In this Letter, a lensless diffraction imaging method by three-dimensional scanning is proposed. All positions of the object are different in three directions instead of scanning schemes only on a plane or along the optic axis, so more diversity of diffraction information is obtained. We apply the illumination without the limit of a confined aperture, which means that the imaging FOV of a pattern is equal to the size of the utilized image sensor. In comparison with the multi-height method, our method can separate the illumination background noise from the retrieved object. Consequently, the proposed method realized high resolution and contrast, large FOV, and the removal of background noise simultaneously. Experimental validations and comparisons with other methods are presented.
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26
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Egerton R, Watanabe M. Spatial Resolution in Transmission Electron Microscopy. Micron 2022; 160:103304. [DOI: 10.1016/j.micron.2022.103304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/05/2022] [Accepted: 05/19/2022] [Indexed: 10/18/2022]
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27
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Sha H, Cui J, Yu R. Deep sub-angstrom resolution imaging by electron ptychography with misorientation correction. SCIENCE ADVANCES 2022; 8:eabn2275. [PMID: 35559675 PMCID: PMC9106290 DOI: 10.1126/sciadv.abn2275] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/30/2022] [Indexed: 05/31/2023]
Abstract
Superresolution imaging of solids is essential to explore local symmetry breaking and derived material properties. Electron ptychography is one of the most promising schemes to realize superresolution imaging beyond aberration correction. However, to reach both deep sub-angstrom resolution imaging and accurate measurement of atomic structures, it is still required for the electron beam to be nearly parallel to the zone axis of crystals. Here, we report an efficient and robust method to correct the specimen misorientation in electron ptychography, giving deep sub-angstrom resolution for specimens with large misorientations. The method largely reduces the experimental difficulties of electron ptychography and paves the way for widespread applications of ptychographic deep sub-angstrom resolution imaging.
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Affiliation(s)
- Haozhi Sha
- National Center for Electron Microscopy in Beijing, Tsinghua University, Beijing 100084, China
- Key Laboratory of Advanced Materials of Ministry of Education of China, Tsinghua University, Beijing 100084, China
- State Key Laboratory of New Ceramics and Fine Processing, Tsinghua University, Beijing 100084, China
- School of Materials Science and Engineering, Tsinghua University, Beijing 100084, China
| | - Jizhe Cui
- National Center for Electron Microscopy in Beijing, Tsinghua University, Beijing 100084, China
- Key Laboratory of Advanced Materials of Ministry of Education of China, Tsinghua University, Beijing 100084, China
- State Key Laboratory of New Ceramics and Fine Processing, Tsinghua University, Beijing 100084, China
- School of Materials Science and Engineering, Tsinghua University, Beijing 100084, China
| | - Rong Yu
- National Center for Electron Microscopy in Beijing, Tsinghua University, Beijing 100084, China
- Key Laboratory of Advanced Materials of Ministry of Education of China, Tsinghua University, Beijing 100084, China
- State Key Laboratory of New Ceramics and Fine Processing, Tsinghua University, Beijing 100084, China
- School of Materials Science and Engineering, Tsinghua University, Beijing 100084, China
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28
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Levitan A, Comin R. Error metrics for partially coherent wave fields. OPTICS LETTERS 2022; 47:2322-2325. [PMID: 35486790 DOI: 10.1364/ol.455955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/04/2022] [Indexed: 06/14/2023]
Abstract
Lensless imaging methods that account for partial coherence have become very common in the past decade. However, there are no metrics in use for comparing partially coherent light fields, despite the widespread use of such metrics to compare fully coherent objects and wave fields. Here, we show how reformulating the mean squared error and Fourier ring correlation in terms of quantum state fidelity naturally generalizes them to partially coherent wave fields. These results fill an important gap in the lensless imaging literature and will enable quantitative assessments of the reliability and resolution of reconstructed partially coherent wave fields.
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29
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Ning S, Xu W, Ma Y, Loh L, Pennycook TJ, Zhou W, Zhang F, Bosman M, Pennycook SJ, He Q, Loh ND. Accurate and Robust Calibration of the Uniform Affine Transformation Between Scan-Camera Coordinates for Atom-Resolved In-Focus 4D-STEM Datasets. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-11. [PMID: 35260221 DOI: 10.1017/s1431927622000320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Accurate geometrical calibration between the scan coordinates and the camera coordinates is critical in four-dimensional scanning transmission electron microscopy (4D-STEM) for both quantitative imaging and ptychographic reconstructions. For atomic-resolved, in-focus 4D-STEM datasets, we propose a hybrid method incorporating two sub-routines, namely a J-matrix method and a Fourier method, which can calibrate the uniform affine transformation between the scan-camera coordinates using raw data, without a priori knowledge of the crystal structure of the specimen. The hybrid method is found robust against scan distortions and residual probe aberrations. It is also effective even when defects are present in the specimen, or the specimen becomes relatively thick. We will demonstrate that a successful geometrical calibration with the hybrid method will lead to a more reliable recovery of both the specimen and the electron probe in a ptychographic reconstruction. We will also show that, although the elimination of local scan position errors still requires an iterative approach, the rate of convergence can be improved, and the residual errors can be further reduced if the hybrid method can be firstly applied for initial calibration. The code is made available as a simple-to-use tool to correct affine transformations of the scan-camera coordinates in 4D-STEM experiments.
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Affiliation(s)
- Shoucong Ning
- Department of Materials Science and Engineering, National University of Singapore, Singapore117575, Singapore
- Center for Bio-Imaging Sciences, National University of Singapore, Singapore117557, Singapore
| | - Wenhui Xu
- Department of Electrical and Electronic Engineering, Southern University of Science and Technology, Shenzhen518055, China
- Harbin Institute of Technology, Harbin150001, China
| | - Yinhang Ma
- School of Physical Sciences and CAS Key Laboratory of Vacuum Physics, University of Chinese Academy of Sciences, Beijing100049, China
| | - Leyi Loh
- Department of Materials Science and Engineering, National University of Singapore, Singapore117575, Singapore
| | | | - Wu Zhou
- School of Physical Sciences and CAS Key Laboratory of Vacuum Physics, University of Chinese Academy of Sciences, Beijing100049, China
| | - Fucai Zhang
- Department of Electrical and Electronic Engineering, Southern University of Science and Technology, Shenzhen518055, China
| | - Michel Bosman
- Department of Materials Science and Engineering, National University of Singapore, Singapore117575, Singapore
| | - Stephen J Pennycook
- School of Physical Sciences and CAS Key Laboratory of Vacuum Physics, University of Chinese Academy of Sciences, Beijing100049, China
| | - Qian He
- Department of Materials Science and Engineering, National University of Singapore, Singapore117575, Singapore
| | - N Duane Loh
- Center for Bio-Imaging Sciences, National University of Singapore, Singapore117557, Singapore
- Department of Physics, National University of Singapore, Singapore117551, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore117557, Singapore
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30
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Philipp HT, Tate MW, Shanks KS, Mele L, Peemen M, Dona P, Hartong R, van Veen G, Shao YT, Chen Z, Thom-Levy J, Muller DA, Gruner SM. Very-High Dynamic Range, 10,000 Frames/Second Pixel Array Detector for Electron Microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-16. [PMID: 35249574 DOI: 10.1017/s1431927622000174] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Precision and accuracy of quantitative scanning transmission electron microscopy (STEM) methods such as ptychography, and the mapping of electric, magnetic, and strain fields depend on the dose. Reasonable acquisition time requires high beam current and the ability to quantitatively detect both large and minute changes in signal. A new hybrid pixel array detector (PAD), the second-generation Electron Microscope Pixel Array Detector (EMPAD-G2), addresses this challenge by advancing the technology of a previous generation PAD, the EMPAD. The EMPAD-G2 images continuously at a frame-rates up to 10 kHz with a dynamic range that spans from low-noise detection of single electrons to electron beam currents exceeding 180 pA per pixel, even at electron energies of 300 keV. The EMPAD-G2 enables rapid collection of high-quality STEM data that simultaneously contain full diffraction information from unsaturated bright-field disks to usable Kikuchi bands and higher-order Laue zones. Test results from 80 to 300 keV are presented, as are first experimental results demonstrating ptychographic reconstructions, strain and polarization maps. We introduce a new information metric, the maximum usable imaging speed (MUIS), to identify when a detector becomes electron-starved, saturated or its pixel count is mismatched with the beam current.
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Affiliation(s)
- Hugh T Philipp
- Laboratory of Atomic and Solid-State Physics (LASSP), Cornell University, Ithaca, NY, USA
| | - Mark W Tate
- Laboratory of Atomic and Solid-State Physics (LASSP), Cornell University, Ithaca, NY, USA
| | - Katherine S Shanks
- Laboratory of Atomic and Solid-State Physics (LASSP), Cornell University, Ithaca, NY, USA
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY, USA
| | - Luigi Mele
- R&D Laboratory, Thermo-Fisher Scientific, Achtseweg Noord 5, 5651GGEindhoven, The Netherlands
| | - Maurice Peemen
- R&D Laboratory, Thermo-Fisher Scientific, Achtseweg Noord 5, 5651GGEindhoven, The Netherlands
| | - Pleun Dona
- R&D Laboratory, Thermo-Fisher Scientific, Achtseweg Noord 5, 5651GGEindhoven, The Netherlands
| | - Reinout Hartong
- R&D Laboratory, Thermo-Fisher Scientific, Achtseweg Noord 5, 5651GGEindhoven, The Netherlands
| | - Gerard van Veen
- R&D Laboratory, Thermo-Fisher Scientific, Achtseweg Noord 5, 5651GGEindhoven, The Netherlands
| | - Yu-Tsun Shao
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Zhen Chen
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Julia Thom-Levy
- Laboratory for Elementary-Particle Physics (LEPP), Cornell University, Ithaca, NY, USA
| | - David A Muller
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
- Kavli Institute at Cornell for Nanoscale Science, Ithaca, NY, USA
| | - Sol M Gruner
- Laboratory of Atomic and Solid-State Physics (LASSP), Cornell University, Ithaca, NY, USA
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY, USA
- Kavli Institute at Cornell for Nanoscale Science, Ithaca, NY, USA
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31
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Jannis D, Hofer C, Gao C, Xie X, Béché A, Pennycook TJ, Verbeeck J. Event driven 4D STEM acquisition with a Timepix3 detector: Microsecond dwell time and faster scans for high precision and low dose applications. Ultramicroscopy 2022; 233:113423. [PMID: 34837737 DOI: 10.1016/j.ultramic.2021.113423] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/11/2021] [Accepted: 10/31/2021] [Indexed: 10/19/2022]
Abstract
Four dimensional scanning transmission electron microscopy (4D STEM) records the scattering of electrons in a material in great detail. The benefits offered by 4D STEM are substantial, with the wealth of data it provides facilitating for instance high precision, high electron dose efficiency phase imaging via centre of mass or ptychography based analysis. However the requirement for a 2D image of the scattering to be recorded at each probe position has long placed a severe bottleneck on the speed at which 4D STEM can be performed. Recent advances in camera technology have greatly reduced this bottleneck, with the detection efficiency of direct electron detectors being especially well suited to the technique. However even the fastest frame driven pixelated detectors still significantly limit the scan speed which can be used in 4D STEM, making the resulting data susceptible to drift and hampering its use for low dose beam sensitive applications. Here we report the development of the use of an event driven Timepix3 direct electron camera that allows us to overcome this bottleneck and achieve 4D STEM dwell times down to 100 ns; orders of magnitude faster than what has been possible with frame based readout. We characterize the detector for different acceleration voltages and show that the method is especially well suited for low dose imaging and promises rich datasets without compromising dwell time when compared to conventional STEM imaging.
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Affiliation(s)
- D Jannis
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - C Hofer
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - C Gao
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - X Xie
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - A Béché
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - T J Pennycook
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - J Verbeeck
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium.
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32
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Keskinbora K, Levitan AL, Comin R. Maskless Fourier transform holography. OPTICS EXPRESS 2022; 30:403-413. [PMID: 35201217 DOI: 10.1364/oe.444455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
Fourier transform holography is a lensless imaging technique that retrieves an object's exit-wave function with high fidelity. It has been used to study nanoscale phenomena and spatio-temporal dynamics in solids, with sensitivity to the phase component of electronic and magnetic textures. However, the method requires an invasive and labor-intensive nanopatterning of a holography mask directly onto the sample, which can alter the sample properties, forces a fixed field-of-view, and leads to a low signal-to-noise ratio at high resolution. In this work, we propose using wavefront-shaping diffractive optics to create a structured probe with full control of its phase at the sample plane, circumventing the need for a mask. We demonstrate in silico that the method can image nanostructures and magnetic textures and validate our approach with a visible light-based experiment. The method enables investigation of a plethora of phenomena at the nanoscale including magnetic and electronic phase coexistence in solids, with further uses in soft and biological matter research.
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33
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Roitman D, Shiloh R, Lu PH, Dunin-Borkowski RE, Arie A. Shaping of Electron Beams Using Sculpted Thin Films. ACS PHOTONICS 2021; 8:3394-3405. [PMID: 34938823 PMCID: PMC8679091 DOI: 10.1021/acsphotonics.1c00951] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 10/31/2021] [Accepted: 11/04/2021] [Indexed: 05/04/2023]
Abstract
Electron beam shaping by sculpted thin films relies on electron-matter interactions and the wave nature of electrons. It can be used to study physical phenomena of special electron beams and to develop technological applications in electron microscopy that offer new and improved measurement techniques and increased resolution in different imaging modes. In this Perspective, we review recent applications of sculpted thin films for electron orbital angular momentum sorting, improvements in phase contrast transmission electron microscopy, and aberration correction. For the latter, we also present new results of our work toward correction of the spherical aberration of Lorentz scanning transmission electron microscopes and suggest a method to correct chromatic aberration using thin films. This review provides practical insight for researchers in the field and motivates future progress in electron microscopy.
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Affiliation(s)
- Dolev Roitman
- School
of Electrical Engineering, Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel
| | - Roy Shiloh
- Physics
Department, Friedrich-Alexander-Universität
Erlangen-Nürnberg, Erlangen 91058, Germany
| | - Peng-Han Lu
- Ernst
Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter
Grünberg Institute, Forschungszentrum
Jülich, Jülich 52428, Germany
- RWTH
Aachen University, Aachen 52062, Germany
| | - Rafal E. Dunin-Borkowski
- Ernst
Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter
Grünberg Institute, Forschungszentrum
Jülich, Jülich 52428, Germany
| | - Ady Arie
- School
of Electrical Engineering, Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel
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34
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Zhang Y, Lu PH, Rotunno E, Troiani F, van Schayck JP, Tavabi AH, Dunin-Borkowski RE, Grillo V, Peters PJ, Ravelli RBG. Single-particle cryo-EM: alternative schemes to improve dose efficiency. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:1343-1356. [PMID: 34475283 PMCID: PMC8415325 DOI: 10.1107/s1600577521007931] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Imaging of biomolecules by ionizing radiation, such as electrons, causes radiation damage which introduces structural and compositional changes of the specimen. The total number of high-energy electrons per surface area that can be used for imaging in cryogenic electron microscopy (cryo-EM) is severely restricted due to radiation damage, resulting in low signal-to-noise ratios (SNR). High resolution details are dampened by the transfer function of the microscope and detector, and are the first to be lost as radiation damage alters the individual molecules which are presumed to be identical during averaging. As a consequence, radiation damage puts a limit on the particle size and sample heterogeneity with which electron microscopy (EM) can deal. Since a transmission EM (TEM) image is formed from the scattering process of the electron by the specimen interaction potential, radiation damage is inevitable. However, we can aim to maximize the information transfer for a given dose and increase the SNR by finding alternatives to the conventional phase-contrast cryo-EM techniques. Here some alternative transmission electron microscopy techniques are reviewed, including phase plate, multi-pass transmission electron microscopy, off-axis holography, ptychography and a quantum sorter. Their prospects for providing more or complementary structural information within the limited lifetime of the sample are discussed.
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Affiliation(s)
- Yue Zhang
- Maastricht Multimodal Molecular Imaging Institute, Division of Nanoscopy, Maastricht University, Universiteitssingel 50, Maastricht 6229 ER, The Netherlands
| | - Peng-Han Lu
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, Jülich 52425, Germany
| | - Enzo Rotunno
- CNR-Istituto Nanoscienze, Centro S3, Via G Campi 213/A, I-41125 Modena, Italy
| | - Filippo Troiani
- CNR-Istituto Nanoscienze, Centro S3, Via G Campi 213/A, I-41125 Modena, Italy
| | - J. Paul van Schayck
- Maastricht Multimodal Molecular Imaging Institute, Division of Nanoscopy, Maastricht University, Universiteitssingel 50, Maastricht 6229 ER, The Netherlands
| | - Amir H. Tavabi
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, Jülich 52425, Germany
| | - Rafal E. Dunin-Borkowski
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, Jülich 52425, Germany
| | - Vincenzo Grillo
- CNR-Istituto Nanoscienze, Centro S3, Via G Campi 213/A, I-41125 Modena, Italy
| | - Peter J. Peters
- Maastricht Multimodal Molecular Imaging Institute, Division of Nanoscopy, Maastricht University, Universiteitssingel 50, Maastricht 6229 ER, The Netherlands
| | - Raimond B. G. Ravelli
- Maastricht Multimodal Molecular Imaging Institute, Division of Nanoscopy, Maastricht University, Universiteitssingel 50, Maastricht 6229 ER, The Netherlands
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35
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Liu JJ. Advances and Applications of Atomic-Resolution Scanning Transmission Electron Microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2021; 27:1-53. [PMID: 34414878 DOI: 10.1017/s1431927621012125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Although scanning transmission electron microscopy (STEM) images of individual heavy atoms were reported 50 years ago, the applications of atomic-resolution STEM imaging became wide spread only after the practical realization of aberration correctors on field-emission STEM/TEM instruments to form sub-Ångstrom electron probes. The innovative designs and advances of electron optical systems, the fundamental understanding of electron–specimen interaction processes, and the advances in detector technology all played a major role in achieving the goal of atomic-resolution STEM imaging of practical materials. It is clear that tremendous advances in computer technology and electronics, image acquisition and processing algorithms, image simulations, and precision machining synergistically made atomic-resolution STEM imaging routinely accessible. It is anticipated that further hardware/software development is needed to achieve three-dimensional atomic-resolution STEM imaging with single-atom chemical sensitivity, even for electron-beam-sensitive materials. Artificial intelligence, machine learning, and big-data science are expected to significantly enhance the impact of STEM and associated techniques on many research fields such as materials science and engineering, quantum and nanoscale science, physics and chemistry, and biology and medicine. This review focuses on advances of STEM imaging from the invention of the field-emission electron gun to the realization of aberration-corrected and monochromated atomic-resolution STEM and its broad applications.
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Affiliation(s)
- Jingyue Jimmy Liu
- Department of Physics, Arizona State University, Tempe, AZ85287, USA
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36
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Chen Z, Jiang Y, Shao YT, Holtz ME, Odstrčil M, Guizar-Sicairos M, Hanke I, Ganschow S, Schlom DG, Muller DA. Electron ptychography achieves atomic-resolution limits set by lattice vibrations. Science 2021; 372:826-831. [DOI: 10.1126/science.abg2533] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/13/2021] [Indexed: 01/30/2023]
Affiliation(s)
- Zhen Chen
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Yi Jiang
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Yu-Tsun Shao
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Megan E. Holtz
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, USA
| | | | | | - Isabelle Hanke
- Leibniz-Institut für Kristallzüchtung, Max-Born-Str. 2, 12489 Berlin, Germany
| | - Steffen Ganschow
- Leibniz-Institut für Kristallzüchtung, Max-Born-Str. 2, 12489 Berlin, Germany
| | - Darrell G. Schlom
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, USA
- Leibniz-Institut für Kristallzüchtung, Max-Born-Str. 2, 12489 Berlin, Germany
- Kavli Institute at Cornell for Nanoscale Science, Ithaca, NY, USA
| | - David A. Muller
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
- Kavli Institute at Cornell for Nanoscale Science, Ithaca, NY, USA
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37
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ab initio description of bonding for transmission electron microscopy. Ultramicroscopy 2021; 231:113253. [PMID: 33773844 DOI: 10.1016/j.ultramic.2021.113253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 02/12/2021] [Accepted: 02/20/2021] [Indexed: 01/10/2023]
Abstract
The simulation of transmission electron microscopy (TEM) images or diffraction patterns is often required to interpret their contrast and extract specimen features. This is especially true for high-resolution phase-contrast imaging of materials, but electron scattering simulations based on atomistic models are widely used in materials science and structural biology. Since electron scattering is dominated by the nuclear cores, the scattering potential is typically described by the widely applied independent atom model. This approximation is fast and fairly accurate, especially for scanning TEM (STEM) annular dark-field contrast, but it completely neglects valence bonding and its effect on the transmitting electrons. However, an emerging trend in electron microscopy is to use new instrumentation and methods to extract the maximum amount of information from each electron. This is evident in the increasing popularity of techniques such as 4D-STEM combined with ptychography in materials science, and cryogenic microcrystal electron diffraction in structural biology, where subtle differences in the scattering potential may be both measurable and contain additional insights. Thus, there is increasing interest in electron scattering simulations based on electrostatic potentials obtained from first principles, mainly via density functional theory, which was previously mainly required for holography. In this Review, we discuss the motivation and basis for these developments, survey the pioneering work that has been published thus far, and give our outlook for the future. We argue that a physically better justified ab initio description of the scattering potential is both useful and viable for an increasing number of systems, and we expect such simulations to steadily gain in popularity and importance.
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38
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Biological Applications of Short Wavelength Microscopy Based on Compact, Laser-Produced Gas-Puff Plasma Source. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10238338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Over the last decades, remarkable efforts have been made to improve the resolution in photon-based microscopes. The employment of compact sources based on table-top laser-produced soft X-ray (SXR) in the “water window” spectral range (λ = 2.3–4.4 nm) and extreme ultraviolet (EUV) plasma allowed to overcome the limitations imposed by large facilities, such as synchrotrons and X-ray free electron lasers (XFEL), because of their high complexity, costs, and limited user access. A laser-plasma double stream gas-puff target source represents a powerful tool for microscopy operating in transmission mode, significantly improving the spatial resolution into the nanometric scale, comparing to the traditional visible light (optical) microscopes. Such an approach allows generating the plasma efficiently, without debris, providing a high flux of EUV and SXR photons. In this review, we present the development and optimization of desktop imaging systems: a EUV and an SXR full field microscope, allowing to achieve a sub-50 nm spatial resolution with short exposure time and an SXR contact microscope, capable to resolve internal structures in a thin layer of sensitive photoresist. Details about the source, as well as imaging results for biological applications, will be presented and discussed.
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39
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Schloz M, Pekin TC, Chen Z, Van den Broek W, Muller DA, Koch CT. Overcoming information reduced data and experimentally uncertain parameters in ptychography with regularized optimization. OPTICS EXPRESS 2020; 28:28306-28323. [PMID: 32988105 DOI: 10.1364/oe.396925] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
The overdetermination of the mathematical problem underlying ptychography is reduced by a host of experimentally more desirable settings. Furthermore, reconstruction of the sample-induced phase shift is typically limited by uncertainty in the experimental parameters and finite sample thicknesses. Presented is a conjugate gradient descent algorithm, regularized optimization for ptychography (ROP), that recovers the partially known experimental parameters along with the phase shift, improves resolution by incorporating the multislice formalism to treat finite sample thicknesses, and includes regularization in the optimization process, thus achieving reliable results from noisy data with severely reduced and underdetermined information.
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