1
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Kusumi T, Katakami S, Ishikawa R, Kawahara K, Mullarkey T, Bekkevold JM, Peters JJP, Jones L, Shibata N, Okada M. New Poisson denoising method for pulse-count STEM imaging. Ultramicroscopy 2024; 264:113996. [PMID: 38885602 DOI: 10.1016/j.ultramic.2024.113996] [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: 02/19/2024] [Revised: 05/23/2024] [Accepted: 05/25/2024] [Indexed: 06/20/2024]
Abstract
With the recent progress in the development of detectors in electron microscopy, it has become possible to directly count the number of electrons per pixel, even with a scintillator-type detector, by incorporating a pulse-counting module. To optimize a denoising method for electron counting imaging, in this study, we propose a Poisson denoising method for atomic-resolution scanning transmission electron microscopy images. Our method is based on the Markov random field model and Bayesian inference, and we can reduce the electron dose by a factor of about 15 times or further below. Moreover, we showed that the method of reconstruction from multiple images without integrating them performs better than that from an integrated image.
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Affiliation(s)
- Taichi Kusumi
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5-1-5, Chiba 277-8561, Kashiwa, Japan
| | - Shun Katakami
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5-1-5, Chiba 277-8561, Kashiwa, Japan
| | - Ryo Ishikawa
- Institute of Engineering Innovation, The University of Tokyo, Hongo 7-3-1, Tokyo 113-8656, Bunkyo, Japan.
| | - Kazuaki Kawahara
- Institute of Engineering Innovation, The University of Tokyo, Hongo 7-3-1, Tokyo 113-8656, Bunkyo, Japan
| | - Tiarnan Mullarkey
- School of Physics, Trinity College Dublin, College Green, Dublin 2, D02 PN40, Dublin, Ireland
| | - Julie Marie Bekkevold
- School of Physics, Trinity College Dublin, College Green, Dublin 2, D02 PN40, Dublin, Ireland
| | - Jonathan J P Peters
- School of Physics, Trinity College Dublin, College Green, Dublin 2, D02 PN40, Dublin, Ireland
| | - Lewys Jones
- School of Physics, Trinity College Dublin, College Green, Dublin 2, D02 PN40, Dublin, Ireland
| | - Naoya Shibata
- Institute of Engineering Innovation, The University of Tokyo, Hongo 7-3-1, Tokyo 113-8656, Bunkyo, Japan; Nanostructures Research Laboratory, Japan Fine Ceramics Center, Atsuta Mutsuno 2-4-1, Aichi 456-8587, Nagoya, Japan
| | - Masato Okada
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5-1-5, Chiba 277-8561, Kashiwa, Japan.
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2
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Schwartz J, Di ZW, Jiang Y, Manassa J, Pietryga J, Qian Y, Cho MG, Rowell JL, Zheng H, Robinson RD, Gu J, Kirilin A, Rozeveld S, Ercius P, Fessler JA, Xu T, Scott M, Hovden R. Imaging 3D chemistry at 1 nm resolution with fused multi-modal electron tomography. Nat Commun 2024; 15:3555. [PMID: 38670945 PMCID: PMC11053043 DOI: 10.1038/s41467-024-47558-0] [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: 12/14/2023] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
Measuring the three-dimensional (3D) distribution of chemistry in nanoscale matter is a longstanding challenge for metrological science. The inelastic scattering events required for 3D chemical imaging are too rare, requiring high beam exposure that destroys the specimen before an experiment is completed. Even larger doses are required to achieve high resolution. Thus, chemical mapping in 3D has been unachievable except at lower resolution with the most radiation-hard materials. Here, high-resolution 3D chemical imaging is achieved near or below one-nanometer resolution in an Au-Fe3O4 metamaterial within an organic ligand matrix, Co3O4-Mn3O4 core-shell nanocrystals, and ZnS-Cu0.64S0.36 nanomaterial using fused multi-modal electron tomography. Multi-modal data fusion enables high-resolution chemical tomography often with 99% less dose by linking information encoded within both elastic (HAADF) and inelastic (EDX/EELS) signals. We thus demonstrate that sub-nanometer 3D resolution of chemistry is measurable for a broad class of geometrically and compositionally complex materials.
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Affiliation(s)
- Jonathan Schwartz
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Zichao Wendy Di
- Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, IL, USA
| | - Yi Jiang
- Advanced Photon Source Facility, Argonne National Laboratory, Lemont, IL, USA
| | - Jason Manassa
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Jacob Pietryga
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI, USA
- Department of Material Science and Engineering, Northwestern University, Evanston, IL, USA
| | - Yiwen Qian
- Department of Materials Science and Engineering, University of California at Berkeley, Berkeley, CA, USA
| | - Min Gee Cho
- Department of Materials Science and Engineering, University of California at Berkeley, Berkeley, CA, USA
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jonathan L Rowell
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Huihuo Zheng
- Argonne Leadership Computing Facility, Argonne National Laboratory, Lemont, IL, USA
| | - Richard D Robinson
- Department of Material Science and Engineering, Cornell University, Ithaca, NY, USA
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY, USA
| | - Junsi Gu
- Dow Chemical Co., Collegeville, PA, USA
| | | | | | - Peter Ercius
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeffrey A Fessler
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, USA
| | - Ting Xu
- Department of Materials Science and Engineering, University of California at Berkeley, Berkeley, CA, USA
- Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mary Scott
- Department of Materials Science and Engineering, University of California at Berkeley, Berkeley, CA, USA.
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Robert Hovden
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI, USA.
- Applied Physics Program, University of Michigan, Ann Arbor, MI, USA.
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3
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Optimal experiment design for element specific atom counting using multiple annular dark field scanning transmission electron microscopy detectors. Ultramicroscopy 2022; 242:113626. [DOI: 10.1016/j.ultramic.2022.113626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 11/19/2022]
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4
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Kharel P, Janicek BE, Bae SH, Loutris AL, Carmichael PT, Huang PY. Atomic-Resolution Imaging of Small Organic Molecules on Graphene. NANO LETTERS 2022; 22:3628-3635. [PMID: 35413204 DOI: 10.1021/acs.nanolett.2c00213] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Here, we demonstrate atomic-resolution scanning transmission electron microscopy (STEM) imaging of light elements in small organic molecules on graphene. We use low-dose, room-temperature, aberration-corrected STEM to image 2D monolayer and bilayer molecular crystals, followed by advanced image processing methods to create high-quality composite images from ∼102-104 individual molecules. In metalated porphyrin and phthalocyanine derivatives, these images contain an elementally sensitive contrast with up to 1.3 Å resolution─sufficient to distinguish individual carbon and nitrogen atoms. Importantly, our methods can be applied to molecules with low masses (∼0.6 kDa) and nanocrystalline domains containing just a few hundred molecules, making it possible to study systems for which large crystals cannot easily be grown. Our approach is enabled by low-background graphene substrates, which we show increase the molecules' critical dose by 2-7×. These results indicate a new route for low-dose, atomic-resolution electron microscopy imaging to solve the structures of small organic molecules.
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Affiliation(s)
- Priti Kharel
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Blanka E Janicek
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Sang Hyun Bae
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Amanda L Loutris
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Patrick T Carmichael
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pinshane Y Huang
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Materials Research Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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5
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Mawson T, Taplin DJ, Brown HG, Clark L, Ishikawa R, Seki T, Ikuhara Y, Shibata N, Paganin DM, Morgan MJ, Weyland M, Petersen TC, Findlay SD. Factors limiting quantitative phase retrieval in atomic-resolution differential phase contrast scanning transmission electron microscopy using a segmented detector. Ultramicroscopy 2022; 233:113457. [PMID: 35016130 DOI: 10.1016/j.ultramic.2021.113457] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/30/2021] [Accepted: 12/05/2021] [Indexed: 11/17/2022]
Abstract
Quantitative differential phase contrast imaging of materials in atomic-resolution scanning transmission electron microscopy using segmented detectors is limited by various factors, including coherent and incoherent aberrations, detector positioning and uniformity, and scan-distortion. By comparing experimental case studies of monolayer and few-layer graphene with image simulations, we explore which parameters require the most precise characterisation for reliable and quantitative interpretation of the reconstructed phases. Coherent and incoherent lens aberrations are found to have the most significant impact. For images over a large field of view, the impact of noise and non-periodic boundary conditions are appreciable, but in this case study have less of an impact than artefacts introduced by beam deflections coupling to beam scanning (imperfect tilt-shift purity).
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Affiliation(s)
- T Mawson
- School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia
| | - D J Taplin
- School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia
| | - H G Brown
- Ian Holmes Imaging Center, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - L Clark
- School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, UK
| | - R Ishikawa
- Institute of Engineering Innovation, University of Tokyo, Tokyo 113-8656, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 3320012, Japan
| | - T Seki
- Institute of Engineering Innovation, University of Tokyo, Tokyo 113-8656, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 3320012, Japan
| | - Y Ikuhara
- Institute of Engineering Innovation, University of Tokyo, Tokyo 113-8656, Japan
| | - N Shibata
- Institute of Engineering Innovation, University of Tokyo, Tokyo 113-8656, Japan
| | - D M Paganin
- School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia
| | - M J Morgan
- School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia
| | - M Weyland
- Monash Centre for Electron Microscopy, Monash University, Clayton, Victoria 3800, Australia; Department of Materials Science and Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - T C Petersen
- School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia; Monash Centre for Electron Microscopy, Monash University, Clayton, Victoria 3800, Australia
| | - S D Findlay
- School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia.
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6
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Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nat Commun 2020; 11:2994. [PMID: 32533001 PMCID: PMC7293311 DOI: 10.1038/s41467-020-16688-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 05/13/2020] [Indexed: 11/08/2022] Open
Abstract
Both high resolution and high precision are required to quantitatively determine the atomic structure of complex nanostructured materials. However, for conventional imaging methods in scanning transmission electron microscopy (STEM), atomic resolution with picometer precision cannot usually be achieved for weakly-scattering samples or radiation-sensitive materials, such as 2D materials. Here, we demonstrate low-dose, sub-angstrom resolution imaging with picometer precision using mixed-state electron ptychography. We show that correctly accounting for the partial coherence of the electron beam is a prerequisite for high-quality structural reconstructions due to the intrinsic partial coherence of the electron beam. The mixed-state reconstruction gains importance especially when simultaneously pursuing high resolution, high precision and large field-of-view imaging. Compared with conventional atomic-resolution STEM imaging techniques, the mixed-state ptychographic approach simultaneously provides a four-times-faster acquisition, with double the information limit at the same dose, or up to a fifty-fold reduction in dose at the same resolution. With conventional scanning transmission electron microscopy, some sensitive materials are difficult to image with atomic resolution. The authors present a method of mixed-state electron ptychography that enables picometer precision with fast acquisition and low dosage.
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7
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Hovden R, Liu P, Schnitzer N, Tsen AW, Liu Y, Lu W, Sun Y, Kourkoutis LF. Thickness and Stacking Sequence Determination of Exfoliated Dichalcogenides (1T-TaS2, 2H-MoS2) Using Scanning Transmission Electron Microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2018; 24:387-395. [PMID: 30175707 DOI: 10.1017/s1431927618012436] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Layered transition metal dichalcogenides (TMDs) have attracted interest due to their promise for future electronic and optoelectronic technologies. As one approaches the two-dimensional (2D) limit, thickness and local topology can greatly influence the macroscopic properties of a material. To understand the unique behavior of TMDs it is therefore important to identify the number of atomic layers and their stacking in a sample. The goal of this work is to extract the thickness and stacking sequence of TMDs directly by matching experimentally recorded high-angle annular dark-field scanning transmission electron microscope images and convergent-beam electron diffraction (CBED) patterns to quantum mechanical, multislice scattering simulations. Advantageously, CBED approaches do not require a resolved lattice in real space and are capable of neglecting the thickness contribution of amorphous surface layers. Here we demonstrate the crystal thickness can be determined from CBED in exfoliated 1T-TaS2 and 2H-MoS2 to within a single layer for ultrathin ≲9 layers and ±1 atomic layer (or better) in thicker specimens while also revealing information about stacking order-even when the crystal structure is unresolved in real space.
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Affiliation(s)
- Robert Hovden
- 1School of Applied and Engineering Physics,Cornell University,Ithaca,NY 14853,USA
| | - Pengzi Liu
- 1School of Applied and Engineering Physics,Cornell University,Ithaca,NY 14853,USA
| | - Noah Schnitzer
- 2Department of Materials Science & Engineering,University of Michigan,Ann Arbor,MI48109,USA
| | - Adam W Tsen
- 3Department of Chemistry,University of Waterloo,Waterloo,ON,Canada,N2L 3G1
| | - Yu Liu
- 4Key Laboratory of Materials Physics,Chinese Academy of Sciences,Hefei 230031,China
| | - Wenjian Lu
- 4Key Laboratory of Materials Physics,Chinese Academy of Sciences,Hefei 230031,China
| | - Yuping Sun
- 4Key Laboratory of Materials Physics,Chinese Academy of Sciences,Hefei 230031,China
| | - Lena F Kourkoutis
- 1School of Applied and Engineering Physics,Cornell University,Ithaca,NY 14853,USA
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8
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Electron ptychography of 2D materials to deep sub-ångström resolution. Nature 2018; 559:343-349. [DOI: 10.1038/s41586-018-0298-5] [Citation(s) in RCA: 310] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 05/24/2018] [Indexed: 11/08/2022]
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9
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Martinez GT, van den Bos KHW, Alania M, Nellist PD, Van Aert S. Thickness dependence of scattering cross-sections in quantitative scanning transmission electron microscopy. Ultramicroscopy 2018; 187:84-92. [PMID: 29413416 DOI: 10.1016/j.ultramic.2018.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 01/16/2018] [Accepted: 01/17/2018] [Indexed: 11/16/2022]
Abstract
In quantitative scanning transmission electron microscopy (STEM), scattering cross-sections have been shown to be very sensitive to the number of atoms in a column and its composition. They correspond to the integrated intensity over the atomic column and they outperform other measures. As compared to atomic column peak intensities, which saturate at a given thickness, scattering cross-sections increase monotonically. A study of the electron wave propagation is presented to explain the sensitivity of the scattering cross-sections. Based on the multislice algorithm, we analyse the wave propagation inside the crystal and its link to the scattered signal for the different probe positions contained in the scattering cross-section for detector collection in the low-, middle- and high-angle regimes. The influence to the signal from scattering of neighbouring columns is also discussed.
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Affiliation(s)
- G T Martinez
- Electron Microscopy for Materials Science (EMAT), University of Antwerp, Gronenborgerlaan 171, 2020, Antwerp, Belgium
| | - K H W van den Bos
- Electron Microscopy for Materials Science (EMAT), University of Antwerp, Gronenborgerlaan 171, 2020, Antwerp, Belgium
| | - M Alania
- Electron Microscopy for Materials Science (EMAT), University of Antwerp, Gronenborgerlaan 171, 2020, Antwerp, Belgium
| | - P D Nellist
- Department of Materials, Oxford University, Parks Road, Oxford OX1 3PH, United Kingdom
| | - S Van Aert
- Electron Microscopy for Materials Science (EMAT), University of Antwerp, Gronenborgerlaan 171, 2020, Antwerp, Belgium.
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10
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Detection of isolated protein-bound metal ions by single-particle cryo-STEM. Proc Natl Acad Sci U S A 2017; 114:11139-11144. [PMID: 28973937 DOI: 10.1073/pnas.1708609114] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Metal ions play essential roles in many aspects of biological chemistry. Detecting their presence and location in proteins and cells is important for understanding biological function. Conventional structural methods such as X-ray crystallography and cryo-transmission electron microscopy can identify metal atoms on protein only if the protein structure is solved to atomic resolution. We demonstrate here the detection of isolated atoms of Zn and Fe on ferritin, using cryogenic annular dark-field scanning transmission electron microscopy (cryo-STEM) coupled with single-particle 3D reconstructions. Zn atoms are found in a pattern that matches precisely their location at the ferroxidase sites determined earlier by X-ray crystallography. By contrast, the Fe distribution is smeared along an arc corresponding to the proposed path from the ferroxidase sites to the mineral nucleation sites along the twofold axes. In this case the single-particle reconstruction is interpreted as a probability distribution function based on the average of individual locations. These results establish conditions for detection of isolated metal atoms in the broader context of electron cryo-microscopy and tomography.
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11
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Kramberger C, Meyer J. Progress in structure recovery from low dose exposures: Mixed molecular adsorption, exploitation of symmetry and reconstruction from the minimum signal level. Ultramicroscopy 2016; 170:60-68. [DOI: 10.1016/j.ultramic.2016.08.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 08/03/2016] [Accepted: 08/05/2016] [Indexed: 11/25/2022]
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12
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Ophus C, Ciston J, Pierce J, Harvey TR, Chess J, McMorran BJ, Czarnik C, Rose HH, Ercius P. Efficient linear phase contrast in scanning transmission electron microscopy with matched illumination and detector interferometry. Nat Commun 2016; 7:10719. [PMID: 26923483 PMCID: PMC4773450 DOI: 10.1038/ncomms10719] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 01/15/2016] [Indexed: 11/17/2022] Open
Abstract
The ability to image light elements in soft matter at atomic resolution enables unprecedented insight into the structure and properties of molecular heterostructures and beam-sensitive nanomaterials. In this study, we introduce a scanning transmission electron microscopy technique combining a pre-specimen phase plate designed to produce a probe with structured phase with a high-speed direct electron detector to generate nearly linear contrast images with high efficiency. We demonstrate this method by using both experiment and simulation to simultaneously image the atomic-scale structure of weakly scattering amorphous carbon and strongly scattering gold nanoparticles. Our method demonstrates strong contrast for both materials, making it a promising candidate for structural determination of heterogeneous soft/hard matter samples even at low electron doses comparable to traditional phase-contrast transmission electron microscopy. Simulated images demonstrate the extension of this technique to the challenging problem of structural determination of biological material at the surface of inorganic crystals. Scanning transmission electron microscopy is a powerful material probe, but constrained to large atomic number samples due to the issues of beam damage and weak scattering. Here, Ophus et al. propose a method that produces linear phase contrast in a focused electron beam to image dose-sensitive objects.
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Affiliation(s)
- Colin Ophus
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Jim Ciston
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Jordan Pierce
- Department of Physics, University of Oregon, 1585 E 13th Avenue, Eugene, Oregon 97403, USA
| | - Tyler R Harvey
- Department of Physics, University of Oregon, 1585 E 13th Avenue, Eugene, Oregon 97403, USA
| | - Jordan Chess
- Department of Physics, University of Oregon, 1585 E 13th Avenue, Eugene, Oregon 97403, USA
| | - Benjamin J McMorran
- Department of Physics, University of Oregon, 1585 E 13th Avenue, Eugene, Oregon 97403, USA
| | - Cory Czarnik
- Gatan Inc., 5794 W Las Positas Boulevard, Pleasanton, California 94588, USA
| | - Harald H Rose
- Department of Physics, Center for Electron Microscopy, Ulm University, Albert-Einstein-Allee 11, 89069 Ulm, Germany
| | - Peter Ercius
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
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13
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14
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Van Aert S, De Backer A, Martinez GT, den Dekker AJ, Van Dyck D, Bals S, Van Tendeloo G. Advanced electron crystallography through model-based imaging. IUCRJ 2016; 3:71-83. [PMID: 26870383 PMCID: PMC4704081 DOI: 10.1107/s2052252515019727] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 10/19/2015] [Indexed: 05/30/2023]
Abstract
The increasing need for precise determination of the atomic arrangement of non-periodic structures in materials design and the control of nanostructures explains the growing interest in quantitative transmission electron microscopy. The aim is to extract precise and accurate numbers for unknown structure parameters including atomic positions, chemical concentrations and atomic numbers. For this purpose, statistical parameter estimation theory has been shown to provide reliable results. In this theory, observations are considered purely as data planes, from which structure parameters have to be determined using a parametric model describing the images. As such, the positions of atom columns can be measured with a precision of the order of a few picometres, even though the resolution of the electron microscope is still one or two orders of magnitude larger. Moreover, small differences in average atomic number, which cannot be distinguished visually, can be quantified using high-angle annular dark-field scanning transmission electron microscopy images. In addition, this theory allows one to measure compositional changes at interfaces, to count atoms with single-atom sensitivity, and to reconstruct atomic structures in three dimensions. This feature article brings the reader up to date, summarizing the underlying theory and highlighting some of the recent applications of quantitative model-based transmisson electron microscopy.
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Affiliation(s)
- Sandra Van Aert
- Electron Microscopy for Materials Research (EMAT), University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Annick De Backer
- Electron Microscopy for Materials Research (EMAT), University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Gerardo T. Martinez
- Electron Microscopy for Materials Research (EMAT), University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Arnold J. den Dekker
- iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
- Delft Center for Systems and Control (DCSC), Delft University of Technology, Mekelweg 2, 2628 CD Delft, The Netherlands
| | - Dirk Van Dyck
- Electron Microscopy for Materials Research (EMAT), University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Sara Bals
- Electron Microscopy for Materials Research (EMAT), University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Gustaaf Van Tendeloo
- Electron Microscopy for Materials Research (EMAT), University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
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15
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Efficient phase contrast imaging in STEM using a pixelated detector. Part II: Optimisation of imaging conditions. Ultramicroscopy 2015; 151:232-239. [DOI: 10.1016/j.ultramic.2014.10.013] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 10/17/2014] [Accepted: 10/17/2014] [Indexed: 11/18/2022]
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16
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Meyer JC, Kotakoski J, Mangler C. Atomic structure from large-area, low-dose exposures of materials: a new route to circumvent radiation damage. Ultramicroscopy 2013; 145:13-21. [PMID: 24315660 PMCID: PMC4153813 DOI: 10.1016/j.ultramic.2013.11.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 11/21/2013] [Accepted: 11/21/2013] [Indexed: 11/18/2022]
Abstract
Beam-induced structural modifications are a major nuisance in the study of materials by high-resolution electron microscopy. Here, we introduce a new approach to circumvent the radiation damage problem by a statistical treatment of large, noisy, low-dose data sets of non-periodic configurations (e.g. defects) in the material. We distribute the dose over a mixture of different defect structures at random positions and with random orientations, and recover representative model images via a maximum likelihood search. We demonstrate reconstructions from simulated images at such low doses that the location of individual entities is not possible. The approach may open a route to study currently inaccessible beam-sensitive configurations. A new approach to circumvent radiation damage. Statistical treatment of large noisy data sets. Analysis of radiation sensitive material defects.
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Affiliation(s)
- J C Meyer
- University of Vienna, Department of Physics, Vienna, Austria.
| | - J Kotakoski
- University of Vienna, Department of Physics, Vienna, Austria
| | - C Mangler
- University of Vienna, Department of Physics, Vienna, Austria
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den Dekker A, Gonnissen J, De Backer A, Sijbers J, Van Aert S. Estimation of unknown structure parameters from high-resolution (S)TEM images: What are the limits? Ultramicroscopy 2013; 134:34-43. [DOI: 10.1016/j.ultramic.2013.05.017] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/16/2013] [Accepted: 05/20/2013] [Indexed: 10/26/2022]
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