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Corrêa LM, Ortega E, Ponce A, Cotta MA, Ugarte D. High precision orientation mapping from 4D-STEM precession electron diffraction data through quantitative analysis of diffracted intensities. Ultramicroscopy 2024; 259:113927. [PMID: 38330596 DOI: 10.1016/j.ultramic.2024.113927] [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: 08/02/2023] [Revised: 01/09/2024] [Accepted: 01/21/2024] [Indexed: 02/10/2024]
Abstract
The association of scanning transmission electron microscopy (STEM) and detection of a diffraction pattern at each probe position (so-called 4D-STEM) represents one of the most promising approaches to analyze structural properties of materials with nanometric resolution and low irradiation levels. This is widely used for texture analysis of materials using automated crystal orientation mapping (ACOM). Herein, we perform orientation mapping in InP nanowires exploiting precession electron diffraction (PED) patterns acquired by an axial CMOS camera. Crystal orientation is determined at each probe position by the quantitative analysis of diffracted intensities minimizing a residue comparing experiments and simulations in analogy to x-ray structural refinement. Our simulations are based on the two-beam dynamical diffraction approximation and yield a high angular precision (∼0.03°), much lower than the traditional ACOM based on pattern matching algorithms (∼1°). We anticipate that simultaneous exploration of both spot positions and high precision crystal misorientation will allow the exploration of the whole potentiality provided by PED-based 4D-STEM for the characterization of deformation fields in nanomaterials.
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Affiliation(s)
- Leonardo M Corrêa
- Instituto de Fisica "Gleb Wataghin", Universidade Estadual de Campinas-UNICAMP, 13083-859 Campinas, SP, Brazil
| | - Eduardo Ortega
- Department of Physics and Astronomy, University of Texas, San Antonio, TX 78249, United States
| | - Arturo Ponce
- Department of Physics and Astronomy, University of Texas, San Antonio, TX 78249, United States
| | - Mônica A Cotta
- Instituto de Fisica "Gleb Wataghin", Universidade Estadual de Campinas-UNICAMP, 13083-859 Campinas, SP, Brazil
| | - Daniel Ugarte
- Instituto de Fisica "Gleb Wataghin", Universidade Estadual de Campinas-UNICAMP, 13083-859 Campinas, SP, Brazil.
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Lim S, Nam H, Shin H, Jeong S, Kim K, Lee Y. Noise Reduction for a Virtual Grid Using a Generative Adversarial Network in Breast X-ray Images. J Imaging 2023; 9:272. [PMID: 38132690 PMCID: PMC10744184 DOI: 10.3390/jimaging9120272] [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: 10/23/2023] [Revised: 11/27/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
In this study, we aimed to address the issue of noise amplification after scatter correction when using a virtual grid in breast X-ray images. To achieve this, we suggested an algorithm for estimating noise level and developed a noise reduction algorithm based on generative adversarial networks (GANs). Synthetic scatter in breast X-ray images were collected using Sizgraphy equipment and scatter correction was performed using dedicated software. After scatter correction, we determined the level of noise using noise-level function plots and trained a GAN using 42 noise combinations. Subsequently, we obtained the resulting images and quantitatively evaluated their quality by measuring the contrast-to-noise ratio (CNR), coefficient of variance (COV), and normalized noise-power spectrum (NNPS). The evaluation revealed an improvement in the CNR by approximately 2.80%, an enhancement in the COV by 12.50%, and an overall improvement in the NNPS across all frequency ranges. In conclusion, the application of our GAN-based noise reduction algorithm effectively reduced noise and demonstrated the acquisition of improved-quality breast X-ray images.
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Affiliation(s)
- Sewon Lim
- Department of Health Science, General Graduate School of Gachon University, 191, Hambakmoe-ro, Yeonsu-gu, Incheon 21936, Republic of Korea;
| | - Hayun Nam
- Department of Radiological Science, Gachon University, 191, Hambakmoe-ro, Yeonsu-gu, Incheon 21936, Republic of Korea; (H.N.); (H.S.); (S.J.)
| | - Hyemin Shin
- Department of Radiological Science, Gachon University, 191, Hambakmoe-ro, Yeonsu-gu, Incheon 21936, Republic of Korea; (H.N.); (H.S.); (S.J.)
| | - Sein Jeong
- Department of Radiological Science, Gachon University, 191, Hambakmoe-ro, Yeonsu-gu, Incheon 21936, Republic of Korea; (H.N.); (H.S.); (S.J.)
| | - Kyuseok Kim
- Department of Biomedical Engineering, Eulji University, 533, Sanseong-daero, Sujung-gu, Seongnam-si 13135, Republic of Korea
| | - Youngjin Lee
- Department of Radiological Science, Gachon University, 191, Hambakmoe-ro, Yeonsu-gu, Incheon 21936, Republic of Korea; (H.N.); (H.S.); (S.J.)
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Chari A, Stark H. Prospects and Limitations of High-Resolution Single-Particle Cryo-Electron Microscopy. Annu Rev Biophys 2023; 52:391-411. [PMID: 37159297 DOI: 10.1146/annurev-biophys-111622-091300] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Single particle cryo-electron microscopy (cryo-EM) has matured into a robust method for the determination of biological macromolecule structures in the past decade, complementing X-ray crystallography and nuclear magnetic resonance. Constant methodological improvements in both cryo-EM hardware and image processing software continue to contribute to an exponential growth in the number of structures solved annually. In this review, we provide a historical view of the many steps that were required to make cryo-EM a successful method for the determination of high-resolution protein complex structures. We further discuss aspects of cryo-EM methodology that are the greatest pitfalls challenging successful structure determination to date. Lastly, we highlight and propose potential future developments that would improve the method even further in the near future.
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Affiliation(s)
- Ashwin Chari
- Research Group for Structural Biochemistry and Mechanisms, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany;
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Rizvi A, Mulvey JT, Carpenter BP, Talosig R, Patterson JP. A Close Look at Molecular Self-Assembly with the Transmission Electron Microscope. Chem Rev 2021; 121:14232-14280. [PMID: 34329552 DOI: 10.1021/acs.chemrev.1c00189] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Molecular self-assembly is pervasive in the formation of living and synthetic materials. Knowledge gained from research into the principles of molecular self-assembly drives innovation in the biological, chemical, and materials sciences. Self-assembly processes span a wide range of temporal and spatial domains and are often unintuitive and complex. Studying such complex processes requires an arsenal of analytical and computational tools. Within this arsenal, the transmission electron microscope stands out for its unique ability to visualize and quantify self-assembly structures and processes. This review describes the contribution that the transmission electron microscope has made to the field of molecular self-assembly. An emphasis is placed on which TEM methods are applicable to different structures and processes and how TEM can be used in combination with other experimental or computational methods. Finally, we provide an outlook on the current challenges to, and opportunities for, increasing the impact that the transmission electron microscope can have on molecular self-assembly.
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Affiliation(s)
- Aoon Rizvi
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Justin T Mulvey
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Brooke P Carpenter
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Rain Talosig
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Joseph P Patterson
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
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A data reduction and compression description for high throughput time-resolved electron microscopy. Nat Commun 2021; 12:664. [PMID: 33510168 PMCID: PMC7844242 DOI: 10.1038/s41467-020-20694-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 12/09/2020] [Indexed: 12/05/2022] Open
Abstract
Fast, direct electron detectors have significantly improved the spatio-temporal resolution of electron microscopy movies. Preserving both spatial and temporal resolution in extended observations, however, requires storing prohibitively large amounts of data. Here, we describe an efficient and flexible data reduction and compression scheme (ReCoDe) that retains both spatial and temporal resolution by preserving individual electron events. Running ReCoDe on a workstation we demonstrate on-the-fly reduction and compression of raw data streaming off a detector at 3 GB/s, for hours of uninterrupted data collection. The output was 100-fold smaller than the raw data and saved directly onto network-attached storage drives over a 10 GbE connection. We discuss calibration techniques that support electron detection and counting (e.g., estimate electron backscattering rates, false positive rates, and data compressibility), and novel data analysis methods enabled by ReCoDe (e.g., recalibration of data post acquisition, and accurate estimation of coincidence loss). The use of electron detectors with high spatio-temporal resolution is limited by the large amounts of data generated. Here, the authors describe ReCoDe, a data reduction and compression scheme, that preserves individual electron events, and enable on-the-fly reduction and compression of raw data.
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O'Leary CM, Martinez GT, Liberti E, Humphry MJ, Kirkland AI, Nellist PD. Contrast transfer and noise considerations in focused-probe electron ptychography. Ultramicroscopy 2020; 221:113189. [PMID: 33360480 DOI: 10.1016/j.ultramic.2020.113189] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/24/2020] [Accepted: 11/30/2020] [Indexed: 11/26/2022]
Abstract
Electron ptychography is a 4-D STEM phase-contrast imaging technique with applications to light-element and beam-sensitive materials. Although the electron dose (electrons incident per unit area on the sample) is the primary figure of merit for imaging beam-sensitive materials, it is also necessary to consider the contrast transfer properties of the imaging technique. Here, we explore the contrast transfer properties of electron ptychography. The contrast transfer of focused-probe, non-iterative electron ptychography using the single-side-band (SSB) method is demonstrated experimentally. The band-pass nature of the phase-contrast transfer function (PCTF) for SSB ptychography places strict limitations on the probe convergence semi-angles required to resolve specific sample features with high contrast. The PCTF of the extended ptychographic iterative engine (ePIE) is broader than that for SSB ptychography, although when both high and low spatial frequencies are transferred, band-pass filtering is required to remove image artefacts. Normalisation of the transfer function with respect to the noise level shows that the transfer window is increased while avoiding noise amplification. Avoiding algorithms containing deconvolution steps may also increase the dose-efficiency of ptychographic phase reconstructions.
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Affiliation(s)
- Colum M O'Leary
- Department of Materials, University of Oxford, Parks Rd, Oxford OX13PH, United Kingdom.
| | - Gerardo T Martinez
- Department of Materials, University of Oxford, Parks Rd, Oxford OX13PH, United Kingdom
| | - Emanuela Liberti
- Department of Materials, University of Oxford, Parks Rd, Oxford OX13PH, United Kingdom; electron Physical Science Imaging Centre (ePSIC), Diamond Light Source, Didcot OX11 0DE, United Kingdom
| | - Martin J Humphry
- Phase Focus Ltd, Electric Works, Sheffield Digital Campus, Sheffield S1 2BJ, United Kingdom
| | - Angus I Kirkland
- Department of Materials, University of Oxford, Parks Rd, Oxford OX13PH, United Kingdom; electron Physical Science Imaging Centre (ePSIC), Diamond Light Source, Didcot OX11 0DE, United Kingdom; The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
| | - Peter D Nellist
- Department of Materials, University of Oxford, Parks Rd, Oxford OX13PH, United Kingdom
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