1
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Nonappa. Seeing the Supracolloidal Assemblies in 3D: Unraveling High-Resolution Structures Using Electron Tomography. ACS MATERIALS AU 2024; 4:238-257. [PMID: 38737122 PMCID: PMC11083119 DOI: 10.1021/acsmaterialsau.3c00067] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/19/2023] [Accepted: 10/19/2023] [Indexed: 05/14/2024]
Abstract
Transmission electron microscopy (TEM) imaging has revolutionized modern materials science, nanotechnology, and structural biology. Its ability to provide information about materials' structure, composition, and properties at atomic-level resolution has enabled groundbreaking discoveries and the development of innovative materials with precision and accuracy. Electron tomography, single particle reconstruction, and microcrystal electron diffraction techniques have paved the way for the three-dimensional (3D) reconstruction of biological samples, synthetic materials, and hybrid nanostructures at near atomic-level resolution. TEM tomography using a series of two-dimensional (2D) projections has been used extensively in biological science, but in recent years it has become an important method in synthetic nanomaterials and soft matter research. TEM tomography offers unprecedented morphological details of 3D objects, internal structures, packing patterns, growth mechanisms, and self-assembly pathways of self-assembled colloidal systems. It complements other analytical tools, including small-angle X-ray scattering, and provides valuable data for computational simulations for predictive design and reverse engineering of nanomaterials with the desired structure and properties. In this perspective, I will discuss the importance of TEM tomography in the structural understanding and engineering of self-assembled nanostructures with specific emphasis on colloidal capsids, composite cages, biohybrid superlattices with complex geometries, polymer assemblies, and self-assembled protein-based superstructures.
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Affiliation(s)
- Nonappa
- Faculty of Engineering and Natural
Sciences, Tampere University, FI-33720 Tampere, Finland
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2
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Hata S, Ihara S, Saito H, Murayama M. In-situ heating-and-electron tomography for materials research: from 3D (in-situ 2D) to 4D (in-situ 3D). Microscopy (Oxf) 2024; 73:133-144. [PMID: 38462986 PMCID: PMC11000667 DOI: 10.1093/jmicro/dfae008] [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: 08/16/2023] [Revised: 12/06/2023] [Accepted: 02/07/2024] [Indexed: 03/12/2024] Open
Abstract
In-situ observation has expanded the application of transmission electron microscopy (TEM) and has made a significant contribution to materials research and development for energy, biomedical, quantum, etc. Recent technological developments related to in-situ TEM have empowered the incorporation of three-dimensional observation, which was previously considered incompatible. In this review article, we take up heating as the most commonly used external stimulus for in-situ TEM observation and overview recent in-situ TEM studies. Then, we focus on the electron tomography (ET) and in-situ heating combined observation by introducing the authors' recent research as an example. Assuming that in-situ heating observation is expanded from two dimensions to three dimensions using a conventional TEM apparatus and a commercially available in-situ heating specimen holder, the following in-situ heating-and-ET observation procedure is proposed: (i) use a rapid heating-and-cooling function of a micro-electro-mechanical system holder; (ii) heat and cool the specimen intermittently and (iii) acquire a tilt-series dataset when the specimen heating is stopped. This procedure is not too technically challenging and can have a wide range of applications. Essential technical points for a successful 4D (space and time) observation will be discussed through reviewing the authors' example application.
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Affiliation(s)
- Satoshi Hata
- Faculty of Engineering Sciences, Kyushu University, 6-1 Kasugakoen, Kasuga, Fukuoka 816-8580, Japan
- The Ultramicroscopy Research Center, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Shiro Ihara
- Institute for Materials Chemistry and Engineering, Kyushu University, 6-1 Kasugakoen, Kasuga, Fukuoka 816-8580, Japan
| | - Hikaru Saito
- Institute for Materials Chemistry and Engineering, Kyushu University, 6-1 Kasugakoen, Kasuga, Fukuoka 816-8580, Japan
- Pan-Omics Data-Driven Research Innovation Center, Kyushu University, 6-1 Kasugakoen, Kasuga, Fukuoka 816-8580, Japan
| | - Mitsuhiro Murayama
- Institute for Materials Chemistry and Engineering, Kyushu University, 6-1 Kasugakoen, Kasuga, Fukuoka 816-8580, Japan
- Department of Materials Science and Engineering, Virginia Tech, 445 Old Turner St., Blacksburg, VA 24060, USA
- Reactor Materials and Mechanical Design Group, Energy and Environmental Directorate, Pacific Northwest National Laboratory, PO Box 999, Richland, WA 99352, USA
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3
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DeRonja J, Nowell M, Wright S, Kacher J. Generational assessment of EBSD detectors for cross-correlation-based analysis: From scintillators to direct detection. Ultramicroscopy 2024; 257:113913. [PMID: 38141535 DOI: 10.1016/j.ultramic.2023.113913] [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: 06/20/2023] [Revised: 11/17/2023] [Accepted: 12/19/2023] [Indexed: 12/25/2023]
Abstract
Introduced over ten years ago, cross-correlation-based electron backscatter diffraction has enabled high precision measurements of crystallographic rotations and elastic strain gradients at high spatial resolution. Since that time, there have been remarkable improvements in electron detector technology, including the advent of ultra-high speed detectors and the commercialization of direct detectors. In this study, we assess the efficacy of multiple generations of electron detectors for cross-correlation-based analysis using a single crystal Si sample as a reference. We show that, while improvements in precision are modest, there have been significant gains in the rate at which high-quality diffraction patterns can be collected. This has important implications in the size of datasets that can be collected and reduces the impact of drift and sample contamination.
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Affiliation(s)
| | | | | | - Josh Kacher
- Georgia Institute of Technology, Atlanta, GA 30332, United States.
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4
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Weisbord I, Segal-Peretz T. Revealing the 3D Structure of Block Copolymers with Electron Microscopy: Current Status and Future Directions. ACS APPLIED MATERIALS & INTERFACES 2023; 15:58003-58022. [PMID: 37338172 DOI: 10.1021/acsami.3c02956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Block copolymers (BCPs) are considered model systems for understanding and utilizing self-assembly in soft matter. Their tunable nanometric structure and composition enable comprehensive studies of self-assembly processes as well as make them relevant materials in diverse applications. A key step in developing and controlling BCP nanostructures is a full understanding of their three-dimensional (3D) structure and how this structure is affected by the BCP chemistry, confinement, boundary conditions, and the self-assembly evolution and dynamics. Electron microscopy (EM) is a leading method in BCP 3D characterization owing to its high resolution in imaging nanosized structures. Here we discuss the two main 3D EM methods: namely, transmission EM tomography and slice and view scanning EM tomography. We present each method's principles, examine their strengths and weaknesses, and discuss ways researchers have devised to overcome some of the challenges in BCP 3D characterization with EM- from specimen preparation to imaging radiation-sensitive materials. Importantly, we review current and new cutting-edge EM methods such as direct electron detectors, energy dispersive X-ray spectroscopy of soft matter, high temporal rate imaging, and single-particle analysis that have great potential for expanding the BCP understanding through EM in the future.
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Affiliation(s)
- Inbal Weisbord
- Chemical Engineering Department, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Tamar Segal-Peretz
- Chemical Engineering Department, Technion-Israel Institute of Technology, Haifa 3200003, Israel
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5
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Wang HF, Marubayashi H, Jinnai H. Kinetic Pathway of the Order–Order Transition from Hexagonally Packed Cylinder to Hexagonally Perforated Layer in Polystyrene- block-Poly(2-vinylpyridine) Using Time-Resolved 3D Transmission Electron Microtomography. Macromolecules 2023. [DOI: 10.1021/acs.macromol.2c01849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Affiliation(s)
- Hsiao-Fang Wang
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Hironori Marubayashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Hiroshi Jinnai
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
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6
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De Wael A, De Backer A, Yu CP, Sentürk DG, Lobato I, Faes C, Van Aert S. Three Approaches for Representing the Statistical Uncertainty on Atom-Counting Results in Quantitative ADF STEM. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 29:1-9. [PMID: 36117265 DOI: 10.1017/s1431927622012284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A decade ago, a statistics-based method was introduced to count the number of atoms from annular dark-field scanning transmission electron microscopy (ADF STEM) images. In the past years, this method was successfully applied to nanocrystals of arbitrary shape, size, and composition (and its high accuracy and precision has been demonstrated). However, the counting results obtained from this statistical framework are so far presented without a visualization of the actual uncertainty about this estimate. In this paper, we present three approaches that can be used to represent counting results together with their statistical error, and discuss which approach is most suited for further use based on simulations and an experimental ADF STEM image.
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Affiliation(s)
- Annelies De Wael
- EMAT, University of Antwerp, Antwerp, Belgium
- NANOlab Center of Excellence, University of Antwerp, Antwerp, Belgium
| | - Annick De Backer
- EMAT, University of Antwerp, Antwerp, Belgium
- NANOlab Center of Excellence, University of Antwerp, Antwerp, Belgium
| | - Chu-Ping Yu
- EMAT, University of Antwerp, Antwerp, Belgium
- NANOlab Center of Excellence, University of Antwerp, Antwerp, Belgium
| | - Duygu Gizem Sentürk
- EMAT, University of Antwerp, Antwerp, Belgium
- NANOlab Center of Excellence, University of Antwerp, Antwerp, Belgium
| | - Ivan Lobato
- EMAT, University of Antwerp, Antwerp, Belgium
- NANOlab Center of Excellence, University of Antwerp, Antwerp, Belgium
| | - Christel Faes
- I-BioStat, Data Science Institute, Hasselt University, Hasselt, Belgium
| | - Sandra Van Aert
- EMAT, University of Antwerp, Antwerp, Belgium
- NANOlab Center of Excellence, University of Antwerp, Antwerp, Belgium
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7
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Jenkinson K, Liz-Marzán LM, Bals S. Multimode Electron Tomography Sheds Light on Synthesis, Structure, and Properties of Complex Metal-Based Nanoparticles. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2110394. [PMID: 35438805 DOI: 10.1002/adma.202110394] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/24/2022] [Indexed: 06/14/2023]
Abstract
Electron tomography has become a cornerstone technique for the visualization of nanoparticle morphology in three dimensions. However, to obtain in-depth information about a nanoparticle beyond surface faceting and morphology, different electron microscopy signals must be combined. The most notable examples of these combined signals include annular dark-field scanning transmission electron microscopy (ADF-STEM) with different collection angles and the combination of ADF-STEM with energy-dispersive X-ray or electron energy loss spectroscopies. Here, the experimental and computational development of various multimode tomography techniques in connection to the fundamental materials science challenges that multimode tomography has been instrumental to overcoming are summarized. Although the techniques can be applied to a wide variety of compositions, the study is restricted to metal and metal oxide nanoparticles for the sake of simplicity. Current challenges and future directions of multimode tomography are additionally discussed.
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Affiliation(s)
- Kellie Jenkinson
- EMAT and NANOlab Center of Excellence, University of Antwerp, Antwerp, 2020, Belgium
| | - Luis M Liz-Marzán
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, 20014, Spain
- Centro de Investigación Biomédica en Red de Bioingeniería Biomateriales, y Nanomedicina (CIBER-BBN), Donostia-San Sebastián, 20014, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, 48009, Spain
| | - Sara Bals
- EMAT and NANOlab Center of Excellence, University of Antwerp, Antwerp, 2020, Belgium
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8
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Jonaid GM, Casasanta MA, Dearnaley WJ, Berry S, Kaylor L, Dressel-Dukes MJ, Spilman MS, Gray JL, Kelly DF. Automated Tools to Advance High-Resolution Imaging in Liquid. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-10. [PMID: 35048845 DOI: 10.1017/s1431927621013921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Liquid-electron microscopy (EM), the room-temperature correlate to cryo-EM, is a rapidly growing field providing high-resolution insights of macromolecules in solution. Here, we describe how liquid-EM experiments can incorporate automated tools to propel the field to new heights. We demonstrate fresh workflows for specimen preparation, data collection, and computing processes to assess biological structures in liquid. Adeno-associated virus (AAV) and the SARS-CoV-2 nucleocapsid (N) were used as model systems to highlight the technical advances. These complexes were selected based on their major differences in size and natural symmetry. AAV is a highly symmetric, icosahedral assembly with a particle diameter of ~25 nm. At the other end of the spectrum, N protein is an asymmetric monomer or dimer with dimensions of approximately 5–7 nm, depending upon its oligomerization state. Equally important, both AAV and N protein are popular subjects in biomedical research due to their high value in vaccine development and therapeutic efforts against COVID-19. Overall, we demonstrate how automated practices in liquid-EM can be used to decode molecules of interest for human health and disease.
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Affiliation(s)
- G M Jonaid
- Bioinformatics and Genomics Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA16802, USA
| | - Michael A Casasanta
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA16802, USA
| | - William J Dearnaley
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA16802, USA
| | - Samantha Berry
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA16802, USA
| | - Liam Kaylor
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA16802, USA
- Molecular, Cellular, and Integrative Biosciences Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA16802, USA
| | | | | | - Jennifer L Gray
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
| | - Deborah F Kelly
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA16802, USA
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9
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He Y, Ming W, Shen R, Chen J. IDART: An Improved Discrete Tomography Algorithm for Reconstructing Images With Multiple Gray Levels. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2022; 31:2608-2619. [PMID: 35316179 DOI: 10.1109/tip.2022.3152632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The discrete algebraic reconstruction technique has many advantages in computed tomography and electron tomography. However, the number of gray levels and the absolute gray values that should be known in advance are typically not available in experiments especially when there are many gray levels in the image. In this paper, we report an automatic discrete tomography reconstruction algorithm to improve its feasibility in practice, without needing to know these two parameters. In our algorithm, the number of gray levels is estimated by labeling the connected components in the tomogram and the absolute values of them are determined by the modal value of each domain. The proposed algorithm was extensively validated on both simulated and experimental datasets. The results show that our algorithm can accurately recover not only the morphology but also the gray levels of the interested objects, even in the images with multiple gray levels. It is demonstrated that the presented algorithm is robust for eliminating missing wedge artifacts and tolerable for noisy data.
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10
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Five-second STEM dislocation tomography for 300 nm thick specimen assisted by deep-learning-based noise filtering. Sci Rep 2021; 11:20720. [PMID: 34702955 PMCID: PMC8548491 DOI: 10.1038/s41598-021-99914-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/30/2021] [Indexed: 11/22/2022] Open
Abstract
Scanning transmission electron microscopy (STEM) is suitable for visualizing the inside of a relatively thick specimen than the conventional transmission electron microscopy, whose resolution is limited by the chromatic aberration of image forming lenses, and thus, the STEM mode has been employed frequently for computed electron tomography based three-dimensional (3D) structural characterization and combined with analytical methods such as annular dark field imaging or spectroscopies. However, the image quality of STEM is severely suffered by noise or artifacts especially when rapid imaging, in the order of millisecond per frame or faster, is pursued. Here we demonstrate a deep-learning-assisted rapid STEM tomography, which visualizes 3D dislocation arrangement only within five-second acquisition of all the tilt-series images even in a 300 nm thick steel specimen. The developed method offers a new platform for various in situ or operando 3D microanalyses in which dealing with relatively thick specimens or covering media like liquid cells are required.
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11
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Albrecht W, Van Aert S, Bals S. Three-Dimensional Nanoparticle Transformations Captured by an Electron Microscope. Acc Chem Res 2021; 54:1189-1199. [PMID: 33566587 DOI: 10.1021/acs.accounts.0c00711] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
ConspectusThree-dimensional (3D) morphology and composition govern the properties of nanoparticles (NPs). However, due to their high surface-to-volume ratio, the morphology and composition of nanomaterials are not as static as those for their bulk counterparts. One major influence is the increase in relative contribution of surface diffusion, which underlines rapid reshaping of NPs in response to changes in their environment. If not accounted for, these effects might affect the robustness of prospective NPs in practically relevant conditions, such as elevated temperatures, intense light illumination, or changing chemical environments. In situ techniques are promising tools to study NP transformations under relevant conditions. Among those tools, in situ transmission electron microscopy (TEM) provides an elegant platform to directly visualize NP changes down to the atomic scale. By the use of specialized holders or microscopes, external stimuli, such as heat, or environments, such as gas and liquids, can be controllably introduced inside the TEM. In addition, TEM is also a valuable tool to determine NP transformations upon ex situ stimuli such as laser excitation. However, standard TEM yields two-dimensional (2D) projection images of 3D objects. With the growing complexity of NP shapes and compositions, the information that is obtained in this manner is often insufficient to understand intricate diffusion dynamics.In this Account, we describe recent progress on measuring NP transformations in 3D inside the electron microscope. First, we discuss existing possibilities to obtain 3D information using either tomographic methods or the so-called atom counting technique, which utilizes single projection images. Next, we show how these techniques can be combined with in situ holders to quantify diffusion processes on a single nanoparticle level. Specifically, we focus on anisotropic metal NPs at elevated temperatures and in varying gas environments. Anisotropic metal NPs are important for plasmonic applications, because sharp tips and edges result in strong electromagnetic field enhancements. By electron tomography, surface diffusion as well as elemental diffusion can be tracked in monometallic and bimetallic NPs, which can then be directly related to changes in plasmonic properties of these systems. By atom counting, it has furthermore become possible to monitor the evolution of crystalline facets of metal NPs under gas and heat treatments, a change that influences catalytic properties. Next to in situ processes, we also demonstrate the value of electron tomography to assess external laser-induced NP transformations, making it viable to detect structural changes with atomic resolution. The application of the proposed methodologies is by far not limited to metal nanoparticles. In the final section, we therefore outline future material research that can benefit from tracking NP transformations from 3D techniques.
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Affiliation(s)
- Wiebke Albrecht
- EMAT and NANOlab Center of Excellence, University of Antwerp, B-2020 Antwerp, Belgium
| | - Sandra Van Aert
- EMAT and NANOlab Center of Excellence, University of Antwerp, B-2020 Antwerp, Belgium
| | - Sara Bals
- EMAT and NANOlab Center of Excellence, University of Antwerp, B-2020 Antwerp, Belgium
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12
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Ohma A, Furuya Y, Mashio T, Ito M, Nomura K, Nagao T, Nishihara H, Jinnai H, Kyotani T. Elucidation of oxygen reduction reaction and nanostructure of platinum-loaded graphene mesosponge for polymer electrolyte fuel cell electrocatalyst. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2020.137705] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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13
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Casar JR, McLellan CA, Siefe C, Dionne JA. Lanthanide-Based Nanosensors: Refining Nanoparticle Responsiveness for Single Particle Imaging of Stimuli. ACS PHOTONICS 2021; 8:3-17. [PMID: 34307765 PMCID: PMC8297747 DOI: 10.1021/acsphotonics.0c00894] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Lanthanide nanoparticles (LNPs) are promising sensors of chemical, mechanical, and temperature changes; they combine the narrow-spectral emission and long-lived excited states of individual lanthanide ions with the high spatial resolution and controlled energy transfer of nanocrystalline architectures. Despite considerable progress in optimizing LNP brightness and responsiveness for dynamic sensing, detection of stimuli with a spatial resolution approaching that of individual nanoparticles remains an outstanding challenge. Here, we highlight the existing capabilities and outstanding challenges of LNP sensors, en-route to nanometer-scale, single particle sensor resolution. First, we summarize LNP sensor read-outs, including changes in emission wavelength, lifetime, intensity, and spectral ratiometric values that arise from modified energy transfer networks within nanoparticles. Then, we describe the origins of LNP sensor imprecision, including sensitivity to competing conditions, interparticle heterogeneities, such as the concentration and distribution of dopant ions, and measurement noise. Motivated by these sources of signal variance, we describe synthesis characterization feedback loops to inform and improve sensor precision, and introduce noise-equivalent sensitivity as a figure of merit of LNP sensors. Finally, we project the magnitudes of chemical and pressure stimulus resolution achievable with single LNPs at nanoscale resolution. Our perspective provides a roadmap for translating ensemble LNP sensing capabilities to the single particle level, enabling nanometer-scale sensing in biology, medicine, and sustainability.
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Affiliation(s)
- Jason R Casar
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
| | - Claire A McLellan
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
| | - Chris Siefe
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
| | - Jennifer A Dionne
- Department of Materials Science and Engineering and Department of Radiology, Molecular Imaging Program, Stanford University, Stanford, California 94305, United States
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14
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Vanrompay H, Skorikov A, Bladt E, Béché A, Freitag B, Verbeeck J, Bals S. Fast versus conventional HAADF-STEM tomography of nanoparticles: advantages and challenges. Ultramicroscopy 2020; 221:113191. [PMID: 33321424 DOI: 10.1016/j.ultramic.2020.113191] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/30/2020] [Accepted: 12/06/2020] [Indexed: 11/24/2022]
Abstract
HAADF-STEM tomography is a widely used experimental technique for analyzing nanometer-scale structures of a large variety of materials in three dimensions. It is especially useful for studying crystalline nanoparticles, where conventional TEM tomography suffers from diffraction-related artefacts. Unfortunately, the acquisition of a HAADF-STEM tilt series can easily take up one hour or more, depending on the complexity of the experiment. It is therefore challenging to investigate samples that do not withstand long electron beam illumination or to acquire a large number of tilt series during a single TEM experiment. The latter would facilitate obtaining more statistically representative 3D data, and enable performing dynamic in situ 3D characterizations with a finer time resolution. Various HAADF-STEM acquisition strategies have been proposed to accelerate the tomographic acquisition and reduce the required electron dose. These methods include tilting the holder continuously while acquiring a projection "movie" and a hybrid, incremental, methodology which combines the benefits of the conventional and continuous technique. However, until now an experimental evaluation of these techniques has been lacking. In this paper, the different acquisition strategies will be experimentally compared in terms of speed, resolution and electron dose. This evaluation will be performed based on experimental tilt series, acquired for various metallic nanoparticles with different shapes and sizes. We discuss the necessary data processing and provide a general guideline that can be used to determine the most optimal acquisition strategy for specific electron tomography experiments.
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Affiliation(s)
- Hans Vanrompay
- Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Belgium
| | - Alexander Skorikov
- Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Belgium
| | - Eva Bladt
- Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Belgium
| | - Armand Béché
- Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Belgium
| | - Bert Freitag
- Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Johan Verbeeck
- Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Belgium
| | - Sara Bals
- Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Belgium.
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15
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Imaging how thermal capillary waves and anisotropic interfacial stiffness shape nanoparticle supracrystals. Nat Commun 2020; 11:4555. [PMID: 32917872 PMCID: PMC7486387 DOI: 10.1038/s41467-020-18363-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 08/07/2020] [Indexed: 01/18/2023] Open
Abstract
Development of the surface morphology and shape of crystalline nanostructures governs the functionality of various materials, ranging from phonon transport to biocompatibility. However, the kinetic pathways, following which such development occurs, have been largely unexplored due to the lack of real-space imaging at single particle resolution. Here, we use colloidal nanoparticles assembling into supracrystals as a model system, and pinpoint the key role of surface fluctuation in shaping supracrystals. Utilizing liquid-phase transmission electron microscopy, we map the spatiotemporal surface profiles of supracrystals, which follow a capillary wave theory. Based on this theory, we measure otherwise elusive interfacial properties such as interfacial stiffness and mobility, the former of which demonstrates a remarkable dependence on the exposed facet of the supracrystal. The facet of lower surface energy is favored, consistent with the Wulff construction rule. Our imaging–analysis framework can be applicable to other phenomena, such as electrodeposition, nucleation, and membrane deformation. Interfacial fluctuations at the nanoscale, such as shape evolution of a growing crystal, are prohibitively difficult to study experimentally. Here, the authors are able to map the kinetic and thermodynamic parameters involved in shaping of nanoparticle supracrystals by directly imaging the fluctuating crystal surface by liquid-phase TEM, and analyzing it in the context of capillary wave theory.
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Hata S, Furukawa H, Gondo T, Hirakami D, Horii N, Ikeda KI, Kawamoto K, Kimura K, Matsumura S, Mitsuhara M, Miyazaki H, Miyazaki S, Murayama MM, Nakashima H, Saito H, Sakamoto M, Yamasaki S. Electron tomography imaging methods with diffraction contrast for materials research. Microscopy (Oxf) 2020; 69:141-155. [PMID: 32115659 PMCID: PMC7240780 DOI: 10.1093/jmicro/dfaa002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 01/08/2020] [Accepted: 02/04/2020] [Indexed: 11/14/2022] Open
Abstract
Transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM) enable the visualization of three-dimensional (3D) microstructures ranging from atomic to micrometer scales using 3D reconstruction techniques based on computed tomography algorithms. This 3D microscopy method is called electron tomography (ET) and has been utilized in the fields of materials science and engineering for more than two decades. Although atomic resolution is one of the current topics in ET research, the development and deployment of intermediate-resolution (non-atomic-resolution) ET imaging methods have garnered considerable attention from researchers. This research trend is probably not irrelevant due to the fact that the spatial resolution and functionality of 3D imaging methods of scanning electron microscopy (SEM) and X-ray microscopy have come to overlap with those of ET. In other words, there may be multiple ways to carry out 3D visualization using different microscopy methods for nanometer-scale objects in materials. From the above standpoint, this review paper aims to (i) describe the current status and issues of intermediate-resolution ET with regard to enhancing the effectiveness of TEM/STEM imaging and (ii) discuss promising applications of state-of-the-art intermediate-resolution ET for materials research with a particular focus on diffraction contrast ET for crystalline microstructures (superlattice domains and dislocations) including a demonstration of in situ dislocation tomography.
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Affiliation(s)
- Satoshi Hata
- Department of Advanced Materials Science, Kyushu University, Fukuoka 816-8580, Japan
- The Ultramicroscopy Research Center, Kyushu University, Fukuoka 819-0395, Japan
| | - Hiromitsu Furukawa
- TEMography Division, System in Frontier Inc., Tachikawa-shi, Tokyo 190-0012, Japan
| | - Takashi Gondo
- Research Laboratory, Mel-Build Corporation, Fukuoka 819-0025, Japan
| | - Daisuke Hirakami
- Steel Research Laboratories, Nippon Steel Corporation, Chiba 293-8511, Japan
| | - Noritaka Horii
- TEMography Division, System in Frontier Inc., Tachikawa-shi, Tokyo 190-0012, Japan
| | - Ken-Ichi Ikeda
- Division of Materials Science and Engineering, Faculty of Engineering, Hokkaido University, Hokkaido 060-8628, Japan
| | - Katsumi Kawamoto
- TEMography Division, System in Frontier Inc., Tachikawa-shi, Tokyo 190-0012, Japan
| | - Kosuke Kimura
- Morphological Research Laboratory, Toray Research Center, Inc., Shiga 520-8567, Japan
| | - Syo Matsumura
- The Ultramicroscopy Research Center, Kyushu University, Fukuoka 819-0395, Japan
- Department of Applied Quantum Physics and Nuclear Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Masatoshi Mitsuhara
- Department of Advanced Materials Science, Kyushu University, Fukuoka 816-8580, Japan
| | - Hiroya Miyazaki
- Research Laboratory, Mel-Build Corporation, Fukuoka 819-0025, Japan
| | - Shinsuke Miyazaki
- Research Laboratory, Mel-Build Corporation, Fukuoka 819-0025, Japan
- Analytical Instruments, Materials and Structural Analysis, Thermo Fisher Scientific, Shinagawa-ku, Tokyo 140-0002, Japan
| | - Mitsu Mitsuhiro Murayama
- Department of Materials Science and Engineering, Virginia Tech, Blacksburg, VA 24061, USA
- Energy and Environmental Directorate, Pacific Northwest National Laboratory, WA 99352, USA
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 816-8580, Japan
| | - Hideharu Nakashima
- Department of Advanced Materials Science, Kyushu University, Fukuoka 816-8580, Japan
| | - Hikaru Saito
- Department of Advanced Materials Science, Kyushu University, Fukuoka 816-8580, Japan
| | - Masashi Sakamoto
- Steel Research Laboratories, Nippon Steel Corporation, Chiba 293-8511, Japan
| | - Shigeto Yamasaki
- Department of Advanced Materials Science, Kyushu University, Fukuoka 816-8580, Japan
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17
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Dearnaley WJ, Schleupner B, Varano AC, Alden NA, Gonzalez F, Casasanta MA, Scharf BE, Dukes MJ, Kelly DF. Liquid-Cell Electron Tomography of Biological Systems. NANO LETTERS 2019; 19:6734-6741. [PMID: 31244227 PMCID: PMC6786937 DOI: 10.1021/acs.nanolett.9b01309] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Liquid-cell electron microscopy is a rapidly growing field in the imaging domain. While real-time observations are readily available to analyze materials and biological systems, these measurementshave been limited to the two-dimensional (2-D) image plane. Here, we introduce an exciting technical advance to image materials in 3-D while enclosed in liquid. The development of liquid-cell electron tomography permitted us to observe and quantify host-pathogen interactions in solution while contained in the vacuum system of the electron microscope. In doing so, we demonstrate new insights for the rules of engagement involving a unique bacteriophage and its host bacterium. A deeper analysis of the genetic content of the phage pathogens revealed structural features of the infectious units while introducing a new paradigm for host interactions. Overall, we demonstrate a technological opportunity to elevate research efforts for in situ imaging while providing a new level of dimensionality beyond the current state of the field.
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Affiliation(s)
- William J. Dearnaley
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Center for Structural Oncology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, Virginia 24016, United States
| | - Beatrice Schleupner
- Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, Virginia 24016, United States
| | - A. Cameron Varano
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Center for Structural Oncology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, Virginia 24016, United States
| | - Nick A. Alden
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, Virginia 24016, United States
| | - Floricel Gonzalez
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Michael A. Casasanta
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Center for Structural Oncology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Birgit E. Scharf
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Madeline J. Dukes
- Applications Science, Protochips Inc., Morrisville, North Carolina 27560, United States
| | - Deborah F. Kelly
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Center for Structural Oncology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, Virginia 24016, United States
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18
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Reed BW, Moghadam AA, Bloom RS, Park ST, Monterrosa AM, Price PM, Barr CM, Briggs SA, Hattar K, McKeown JT, Masiel DJ. Electrostatic subframing and compressive-sensing video in transmission electron microscopy. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:054303. [PMID: 31559318 PMCID: PMC6756919 DOI: 10.1063/1.5115162] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/28/2019] [Indexed: 05/30/2023]
Abstract
We present kilohertz-scale video capture rates in a transmission electron microscope, using a camera normally limited to hertz-scale acquisition. An electrostatic deflector rasters a discrete array of images over a large camera, decoupling the acquisition time per subframe from the camera readout time. Total-variation regularization allows features in overlapping subframes to be correctly placed in each frame. Moreover, the system can be operated in a compressive-sensing video mode, whereby the deflections are performed in a known pseudorandom sequence. Compressive sensing in effect performs data compression before the readout, such that the video resulting from the reconstruction can have substantially more total pixels than that were read from the camera. This allows, for example, 100 frames of video to be encoded and reconstructed using only 15 captured subframes in a single camera exposure. We demonstrate experimental tests including laser-driven melting/dewetting, sintering, and grain coarsening of nanostructured gold, with reconstructed video rates up to 10 kHz. The results exemplify the power of the technique by showing that it can be used to study the fundamentally different temporal behavior for the three different physical processes. Both sintering and coarsening exhibited self-limiting behavior, whereby the process essentially stopped even while the heating laser continued to strike the material. We attribute this to changes in laser absorption and to processes inherent to thin-film coarsening. In contrast, the dewetting proceeded at a relatively uniform rate after an initial incubation time consistent with the establishment of a steady-state temperature profile.
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Affiliation(s)
- B W Reed
- Integrated Dynamic Electron Solutions, Inc., Pleasanton, California 94588, USA
| | - A A Moghadam
- Integrated Dynamic Electron Solutions, Inc., Pleasanton, California 94588, USA
| | - R S Bloom
- Integrated Dynamic Electron Solutions, Inc., Pleasanton, California 94588, USA
| | - S T Park
- Integrated Dynamic Electron Solutions, Inc., Pleasanton, California 94588, USA
| | - A M Monterrosa
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - P M Price
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - C M Barr
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | | | - K Hattar
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - J T McKeown
- Lawrence Livermore National Laboratory, Livermore, California 94551, USA
| | - D J Masiel
- Integrated Dynamic Electron Solutions, Inc., Pleasanton, California 94588, USA
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19
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Danev R, Yanagisawa H, Kikkawa M. Cryo-Electron Microscopy Methodology: Current Aspects and Future Directions. Trends Biochem Sci 2019; 44:837-848. [PMID: 31078399 DOI: 10.1016/j.tibs.2019.04.008] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/08/2019] [Accepted: 04/12/2019] [Indexed: 01/01/2023]
Abstract
Cryo-electron microscopy (cryo-EM) has emerged as a powerful structure determination technique. Its most prolific branch is single particle analysis (SPA), a method being used in a growing number of laboratories worldwide to determine high-resolution protein structures. Cryo-electron tomography (cryo-ET) is another powerful approach that enables visualization of protein complexes in their native cellular environment. Despite the wide-ranging success of cryo-EM, there are many methodological aspects that could be improved. Those include sample preparation, sample screening, data acquisition, image processing, and structure validation. Future developments will increase the reliability and throughput of the technique and reduce the cost and skill level barrier for its adoption.
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Affiliation(s)
- Radostin Danev
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Haruaki Yanagisawa
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Masahide Kikkawa
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.
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20
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Ede JM, Beanland R. Improving electron micrograph signal-to-noise with an atrous convolutional encoder-decoder. Ultramicroscopy 2019; 202:18-25. [PMID: 30928639 DOI: 10.1016/j.ultramic.2019.03.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/19/2019] [Accepted: 03/25/2019] [Indexed: 11/20/2022]
Abstract
We present an atrous convolutional encoder-decoder trained to denoise electron micrographs. It consists of a modified Xception backbone, atrous convoltional spatial pyramid pooling module and a multi-stage decoder. Our neural network was trained end-to-end using 512 × 512 micrographs created from a large dataset of high-dose ( > 2500 counts per pixel) micrographs with added Poisson noise to emulate low-dose ( ≪ 300 counts per pixel) data. It was then fine-tuned for high dose data (200-2500 counts per pixel). Its performance is benchmarked against bilateral, Gaussian, median, total variation, wavelet, and Wiener restoration methods with their default parameters. Our network outperforms their best mean squared error and structural similarity index performances by 24.6% and 9.6% for low doses and by 43.7% and 5.5% for high doses. In both cases, our network's mean squared error has the lowest variance. Source code and links to our high-quality dataset and pre-trained models are available at https://github.com/Jeffrey-Ede/Electron-Micrograph-Denoiser.
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Affiliation(s)
- Jeffrey M Ede
- Department of Physics, University of Warwick, Coventry, England CV4 7AL, United Kingdom.
| | - Richard Beanland
- Department of Physics, University of Warwick, Coventry, England CV4 7AL, United Kingdom.
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21
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Melo LGA, Hitchcock AP. Electron beam damage of perfluorosulfonic acid studied by soft X-ray spectromicroscopy. Micron 2019; 121:8-20. [PMID: 30875488 DOI: 10.1016/j.micron.2019.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/08/2019] [Accepted: 02/19/2019] [Indexed: 10/27/2022]
Abstract
Scanning transmission X-ray microscopy (STXM) was used to study chemical changes to perfluorosulfonic acid (PFSA) spun cast thin films as a function of dose imparted by exposure of a 200 kV electron beam in a Transmission Electron Microscope (TEM). The relationship between electron beam fluence and absorbed dose was calibrated using a modified version of a protocol based on the positive to negative lithography transition in PMMA [Leontowich et al, J. Synchrotron Rad. 19 (2012) 976]. STXM was used to characterize and quantify the chemical changes caused by electron irradiation of PFSA under several different conditions. The critical dose for CF2-CF2 amorphization was used to explore the effects of the sample environment on electron beam damage. Use of a silicon nitride substrate was found to increase the CF2-CF2 amorphization critical dose by ∼x2 from that for free-standing PFSA films. Freestanding PFSA and PMMA films were damaged by 200 kV electrons at ∼100 K and then the damage was measured by STXM at 300 K (RT). The lithography cross-over dose for PMMA was found to be ∼2x higher when the PMMA thin film was electron irradiated at 120 K rather than at 300 K. The critical dose for CF2-CF2 amorphization in PFSA irradiated at 120 K followed by warming and delayed measurement by STXM at 300 K was found to be ∼2x larger than at 300 K. To place these results in the context of the use of electron microscopy to study PFSA ionomer in fuel cell systems, an exposure of 300 e-/nm2 at 300 K (which corresponds to an absorbed dose of ∼20 MGy) amorphizes ∼10% of the CF2-CF2 bonds in PFSA. At this dose level, the spatial resolution for TEM imaging of PFSA is limited to 3.5 nm by radiation damage, if one is using a direct electron detector with DQE = 1. This work recommends caution about 2D and 3D morphological information of PFSA materials based on TEM studies which use fluences higher than 300 e-/nm2.
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Affiliation(s)
- Lis G A Melo
- Dept. Chemistry and Chemical Biology, McMaster University, Hamilton, ON, L8S4M1, Canada.
| | - Adam P Hitchcock
- Dept. Chemistry and Chemical Biology, McMaster University, Hamilton, ON, L8S4M1, Canada
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22
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Higuchi T, Gondo T, Miyazaki H, Kumagai A, Akutagawa K, Jinnai H. Development of a three-dimensional tomography holder for in situ tensile deformation for soft materials. Microscopy (Oxf) 2018; 67:296-300. [PMID: 29893959 DOI: 10.1093/jmicro/dfy027] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 05/16/2018] [Indexed: 11/13/2022] Open
Abstract
An in situ straining holder capable of tensile deformation and high-angle tilt for electron tomography was developed for polymeric materials. The holder has a dedicated sample cartridge, on which a variety of polymeric materials, such as microtomed thin sections of bulk specimens and solvent-cast thin films, can be mounted. Fine, stable control of the deformation process with nanoscale magnification was achieved. The holder allows large tensile deformation (≃800 μm) with a large field of view (800 × 200 μm before the deformation), and a high tilt angle (±75°) during in situ observations. With the large tensile deformation, the strain on the specimen can be as large as 26, at least one order of magnitude larger than the holder's predecessor. We expect that meso- and microscopic insights into the dynamic mechanical deformation and fracture processes of polymeric materials can be obtained by combining the holder with a transmission electron microscope equipped with an energy filter. The filter allows zero-loss imaging to improve the resolution and image contrast for thick specimens. We used this technique to study the deformation process in a silica nanoparticle-filled isoprene rubber.
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Affiliation(s)
- Takeshi Higuchi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Japan
| | - Takashi Gondo
- Mel-Build Corporation, 2-11-36 Ishimaru, Nishi-ku, Fukuoka, Japan
| | - Hiroya Miyazaki
- Mel-Build Corporation, 2-11-36 Ishimaru, Nishi-ku, Fukuoka, Japan
| | - Akemi Kumagai
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Japan
| | - Keizo Akutagawa
- Bridgestone Corporation, 3-1-1 Ogawahigashi-Cho, Kodaira-Shi, Tokyo, Japan
| | - Hiroshi Jinnai
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Japan
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24
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Evaluation of noise and blur effects with SIRT-FISTA-TV reconstruction algorithm: Application to fast environmental transmission electron tomography. Ultramicroscopy 2018; 189:109-123. [DOI: 10.1016/j.ultramic.2018.03.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/21/2018] [Accepted: 03/28/2018] [Indexed: 11/21/2022]
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26
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Murata K, Wolf M. Cryo-electron microscopy for structural analysis of dynamic biological macromolecules. Biochim Biophys Acta Gen Subj 2017; 1862:324-334. [PMID: 28756276 DOI: 10.1016/j.bbagen.2017.07.020] [Citation(s) in RCA: 181] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 07/22/2017] [Accepted: 07/25/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND Since the introduction of what became today's standard for cryo-embedding of biological macromolecules at native conditions more than 30years ago, techniques and equipment have been drastically improved and the structure of biomolecules can now be studied at near atomic resolution by cryo-electron microscopy (cryo-EM) while capturing multiple dynamic states. Here we review the recent progress in cryo-EM for structural studies of dynamic biological macromolecules. SCOPE OF REVIEW We provide an overview of the cryo-EM method and introduce contemporary studies to investigate biomolecular structure and dynamics, including examples from the recent literature. MAJOR CONCLUSIONS Cryo-EM is a powerful tool for the investigation of biological macromolecular structures including analysis of their dynamics by using advanced image-processing algorithms. The method has become even more widely applicable with present-day single particle analysis and electron tomography. GENERAL SIGNIFICANCE The cryo-EM method can be used to determine the three-dimensional structure of biomacromolecules in near native condition at close to atomic resolution, and has the potential to reveal conformations of dynamic molecular complexes. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Kazuyoshi Murata
- National Institute for Physiological Sciences, 38 Myodaiji, Okazaki, Aichi 444-8585, Japan.
| | - Matthias Wolf
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology, 7542 Onna, Onna-Son, Kunigami, Okinawa 904-0411, Japan.
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27
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Müller-Caspary K, Krause FF, Grieb T, Löffler S, Schowalter M, Béché A, Galioit V, Marquardt D, Zweck J, Schattschneider P, Verbeeck J, Rosenauer A. Measurement of atomic electric fields and charge densities from average momentum transfers using scanning transmission electron microscopy. Ultramicroscopy 2017; 178:62-80. [PMID: 27217350 DOI: 10.1016/j.ultramic.2016.05.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/04/2016] [Accepted: 05/07/2016] [Indexed: 10/21/2022]
Abstract
This study sheds light on the prerequisites, possibilities, limitations and interpretation of high-resolution differential phase contrast (DPC) imaging in scanning transmission electron microscopy (STEM). We draw particular attention to the well-established DPC technique based on segmented annular detectors and its relation to recent developments based on pixelated detectors. These employ the expectation value of the momentum transfer as a reliable measure of the angular deflection of the STEM beam induced by an electric field in the specimen. The influence of scattering and propagation of electrons within the specimen is initially discussed separately and then treated in terms of a two-state channeling theory. A detailed simulation study of GaN is presented as a function of specimen thickness and bonding. It is found that bonding effects are rather detectable implicitly, e.g., by characteristics of the momentum flux in areas between the atoms than by directly mapping electric fields and charge densities. For strontium titanate, experimental charge densities are compared with simulations and discussed with respect to experimental artifacts such as scan noise. Finally, we consider practical issues such as figures of merit for spatial and momentum resolution, minimum electron dose, and the mapping of larger-scale, built-in electric fields by virtue of data averaged over a crystal unit cell. We find that the latter is possible for crystals with an inversion center. Concerning the optimal detector design, this study indicates that a sampling of 5mrad per pixel is sufficient in typical applications, corresponding to approximately 10×10 available pixels.
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Affiliation(s)
- Knut Müller-Caspary
- Institut für Festkörperphysik, Universität Bremen, Otto-Hahn-Allee 1, 28359 Bremen, Germany.
| | - Florian F Krause
- Institut für Festkörperphysik, Universität Bremen, Otto-Hahn-Allee 1, 28359 Bremen, Germany.
| | - Tim Grieb
- Institut für Festkörperphysik, Universität Bremen, Otto-Hahn-Allee 1, 28359 Bremen, Germany
| | - Stefan Löffler
- Institute of Solid State Physics, Vienna University of Technology, Wiedner Hauptstraße 8-10/E138, A-1040 Vienna, Austria; University Service Centre for Transmission Electron Microscopy, Wiedner Hauptstraße 8-10/E052, A-1040 Vienna, Austria
| | - Marco Schowalter
- Institut für Festkörperphysik, Universität Bremen, Otto-Hahn-Allee 1, 28359 Bremen, Germany
| | - Armand Béché
- EMAT, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerpen, Belgium
| | - Vincent Galioit
- Institut für Experimentelle und Angewandte Physik, Universität Regensburg, Universitätsstraße 31, 93040 Regensburg, Germany
| | - Dennis Marquardt
- Institut für Festkörperphysik, Universität Bremen, Otto-Hahn-Allee 1, 28359 Bremen, Germany
| | - Josef Zweck
- Institut für Experimentelle und Angewandte Physik, Universität Regensburg, Universitätsstraße 31, 93040 Regensburg, Germany
| | - Peter Schattschneider
- Institute of Solid State Physics, Vienna University of Technology, Wiedner Hauptstraße 8-10/E138, A-1040 Vienna, Austria; University Service Centre for Transmission Electron Microscopy, Wiedner Hauptstraße 8-10/E052, A-1040 Vienna, Austria
| | - Johan Verbeeck
- EMAT, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerpen, Belgium
| | - Andreas Rosenauer
- Institut für Festkörperphysik, Universität Bremen, Otto-Hahn-Allee 1, 28359 Bremen, Germany
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Jinnai H, Higuchi T, Zhuge X, Kumamoto A, Batenburg KJ, Ikuhara Y. Three-Dimensional Visualization and Characterization of Polymeric Self-Assemblies by Transmission Electron Microtomography. Acc Chem Res 2017; 50:1293-1302. [PMID: 28525260 DOI: 10.1021/acs.accounts.7b00103] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Self-assembling structures and their dynamical processes in polymeric systems have been investigated using three-dimensional transmission electron microscopy (3D-TEM). Block copolymers (BCPs) self-assemble into nanoscale periodic structures called microphase-separated structures, a deep understanding of which is important for creating nanomaterials with superior physical properties, such as high-performance membranes with well-defined pore size and high-density data storage media. Because microphase-separated structures have become increasingly complicated with advances in precision polymerization, characterizing these complex morphologies is becoming increasingly difficult. Thus, microscopes capable of obtaining 3D images are required. In this article, we demonstrate that 3D-TEM is an essential tool for studying BCP nanostructures, especially those self-assembled during dynamical processes and under confined conditions. The first example is a dynamical process called order-order transitions (OOTs). Upon changing temperature or pressure or applying an external field, such as a shear flow or electric field, BCP nanostructures transform from one type of structure to another. The OOTs are examined by freezing the specimens in the middle of the OOT and then observing the boundary structures between the preexisting and newly formed nanostructures in three-dimensions. In an OOT between the bicontinuous double gyroid and hexagonally packed cylindrical structures, two different types of epitaxial phase transition paths are found. Interestingly, the paths depend on the direction of the OOT. The second example is BCP self-assemblies under confinement that have been examined by 3D-TEM. A variety of intriguing and very complicated 3D morphologies can be formed even from the BCPs that self-assemble into simple nanostructures, such as lamellar and cylindrical structures in the bulk (in free space). Although 3D-TEM is becoming more frequently used for detailed morphological investigations, it is generally used to study static nanostructures. Although OOTs are dynamical processes, the actual experiment is done in the static state, through a detailed morphological study of a snapshot taken during the OOT. Developing time-dependent nanoscale 3D imaging has become a hot topic. Here, the two main problems preventing the development of in situ electron tomography for polymer materials are addressed. First, the staining protocol often used to enhance contrast for electrons is replaced by a new contrast enhancement based on chemical differences between polymers. In this case, no staining is necessary. Second, a new 3D reconstruction algorithm allows us to obtain a high-contrast, quantitative 3D image from fewer projections than is required for the conventional algorithm to achieve similar contrast, reducing the number of projections and thus the electron beam dose. Combining these two new developments is expected to open new doors to 3D in situ real-time structural observation of polymer materials.
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Affiliation(s)
- Hiroshi Jinnai
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1
Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Takeshi Higuchi
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1
Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Xiaodong Zhuge
- Centrum Wiskunde and Informatica, Amsterdam 1098 XG, The Netherlands
| | - Akihito Kumamoto
- Institute
of Engineering Innovation, School of Engineering, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kees Joost Batenburg
- Centrum Wiskunde and Informatica, Amsterdam 1098 XG, The Netherlands
- Mathematical
Institute, Leiden University, RA Leiden 2300, The Netherlands
| | - Yuichi Ikuhara
- Institute
of Engineering Innovation, School of Engineering, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-8656, Japan
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29
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ROIBAN L, LI S, AOUINE M, TUEL A, FARRUSSENG D, EPICIER T. Fast ‘Operando
’ electron nanotomography. J Microsc 2017; 269:117-126. [DOI: 10.1111/jmi.12557] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 02/21/2017] [Indexed: 11/30/2022]
Affiliation(s)
- L. ROIBAN
- Univ Lyon, INSA-Lyon; Université Claude Bernard Lyon I; MATEIS, UMR5510 CNRS Villeurbanne Cedex France
| | - S. LI
- Univ Lyon; Université Claude Bernard Lyon I; Ircelyon, UMR5256 CNRS Villeurbanne France
| | - M. AOUINE
- Univ Lyon; Université Claude Bernard Lyon I; Ircelyon, UMR5256 CNRS Villeurbanne France
| | - A. TUEL
- Univ Lyon; Université Claude Bernard Lyon I; Ircelyon, UMR5256 CNRS Villeurbanne France
| | - D. FARRUSSENG
- Univ Lyon; Université Claude Bernard Lyon I; Ircelyon, UMR5256 CNRS Villeurbanne France
| | - T. EPICIER
- Univ Lyon, INSA-Lyon; Université Claude Bernard Lyon I; MATEIS, UMR5510 CNRS Villeurbanne Cedex France
- Univ Lyon; Université Claude Bernard Lyon I; Ircelyon, UMR5256 CNRS Villeurbanne France
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30
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Hata S, Miyazaki S, Gondo T, Kawamoto K, Horii N, Sato K, Furukawa H, Kudo H, Miyazaki H, Murayama M. In-situ straining and time-resolved electron tomography data acquisition in a transmission electron microscope. Microscopy (Oxf) 2017; 66:143-153. [PMID: 27993950 DOI: 10.1093/jmicro/dfw109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 11/23/2016] [Indexed: 11/13/2022] Open
Abstract
This paper reports the preliminary results of a new in-situ three-dimensional (3D) imaging system for observing plastic deformation behavior in a transmission electron microscope (TEM) as a directly relevant development of the recently reported straining-and-tomography holder [Sato K et al. (2015) Development of a novel straining holder for transmission electron microscopy compatible with single tilt-axis electron tomography. Microsc. 64: 369-375]. We designed an integrated system using the holder and newly developed straining and image-acquisition software and then developed an experimental procedure for in-situ straining and time-resolved electron tomography (ET) data acquisition. The software for image acquisition and 3D visualization was developed based on the commercially available ET software TEMographyTM. We achieved time-resolved 3D visualization of nanometer-scale plastic deformation behavior in a Pb-Sn alloy sample, thus demonstrating the capability of this system for potential applications in materials science.
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Affiliation(s)
- S Hata
- Department of Electrical and Materials Science and Engineering and The Ultramicroscopy Research Center, Kyushu University, 6-1 Kasugakoen, Kasuga-shi, Fukuoka 816-8580, Japan
| | - S Miyazaki
- FEI Company Japan Ltd. (Currently, Materials and Structural Analysis, Thermo Fisher Scientific), 4-12-2 Higashi-Shinagawa, Shinagawa-ku, Tokyo 140-0002, Japan.,Mel-Build Corporation, 3-1-15, Shimoyamato, Nishi-ku, Fukuoka 819-0052, Japan
| | - T Gondo
- Mel-Build Corporation, 3-1-15, Shimoyamato, Nishi-ku, Fukuoka 819-0052, Japan
| | - K Kawamoto
- Engineering Department, System in Frontier Inc., 2-8-3, Shinsuzuharu bldg. 4F, Akebono-cho, Tachikawa-shi, Tokyo 190-0012, Japan
| | - N Horii
- Engineering Department, System in Frontier Inc., 2-8-3, Shinsuzuharu bldg. 4F, Akebono-cho, Tachikawa-shi, Tokyo 190-0012, Japan
| | - K Sato
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, 7-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - H Furukawa
- System in Frontier Inc., 2-8-3, Shinsuzuharu bldg. 4F, Akebono-cho, Tachikawa-shi, Tokyo 190-0012, Japan
| | - H Kudo
- Faculty of Engineering, Information and Systems, University of Tsukuba, Tennoudai 1-1-1, Tsukuba 305-8573, Japan.,JST-ERATO, Momose Quantum-Beam Phase Imaging Project, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - H Miyazaki
- Mel-Build Corporation, 3-1-15, Shimoyamato, Nishi-ku, Fukuoka 819-0052, Japan
| | - M Murayama
- Department of Materials Science and Engineering, Virginia Tech, 134 Randolph Hall (MC 0286), 460 Old Turner Street, Blacksburg, VA 24061, USA
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31
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Zhuge X, Jinnai H, Dunin-Borkowski RE, Migunov V, Bals S, Cool P, Bons AJ, Batenburg KJ. Automated discrete electron tomography – Towards routine high-fidelity reconstruction of nanomaterials. Ultramicroscopy 2017; 175:87-96. [DOI: 10.1016/j.ultramic.2017.01.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 12/29/2016] [Accepted: 01/21/2017] [Indexed: 11/27/2022]
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32
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Hayashida M, Malac M. Practical electron tomography guide: Recent progress and future opportunities. Micron 2016; 91:49-74. [PMID: 27728842 DOI: 10.1016/j.micron.2016.09.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 09/26/2016] [Accepted: 09/27/2016] [Indexed: 10/20/2022]
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33
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Materials characterisation by angle-resolved scanning transmission electron microscopy. Sci Rep 2016; 6:37146. [PMID: 27849001 PMCID: PMC5111052 DOI: 10.1038/srep37146] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 10/25/2016] [Indexed: 11/08/2022] Open
Abstract
Solid-state properties such as strain or chemical composition often leave characteristic fingerprints in the angular dependence of electron scattering. Scanning transmission electron microscopy (STEM) is dedicated to probe scattered intensity with atomic resolution, but it drastically lacks angular resolution. Here we report both a setup to exploit the explicit angular dependence of scattered intensity and applications of angle-resolved STEM to semiconductor nanostructures. Our method is applied to measure nitrogen content and specimen thickness in a GaNxAs1-x layer independently at atomic resolution by evaluating two dedicated angular intervals. We demonstrate contrast formation due to strain and composition in a Si- based metal-oxide semiconductor field effect transistor (MOSFET) with GexSi1-x stressors as a function of the angles used for imaging. To shed light on the validity of current theoretical approaches this data is compared with theory, namely the Rutherford approach and contemporary multislice simulations. Inconsistency is found for the Rutherford model in the whole angular range of 16-255 mrad. Contrary, the multislice simulations are applicable for angles larger than 35 mrad whereas a significant mismatch is observed at lower angles. This limitation of established simulations is discussed particularly on the basis of inelastic scattering.
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34
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Hata S. OM-II-5Issues of experimental apparatuses for electron tomography observation in crystalline materials. Microscopy (Oxf) 2016. [DOI: 10.1093/jmicro/dfw083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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35
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Attota RK, Liu EC. Volume determination of irregularly-shaped quasi-spherical nanoparticles. Anal Bioanal Chem 2016; 408:7897-7903. [PMID: 27659817 DOI: 10.1007/s00216-016-9909-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 08/22/2016] [Accepted: 08/26/2016] [Indexed: 10/21/2022]
Abstract
Nanoparticles (NPs) are widely used in diverse application areas, such as medicine, engineering, and cosmetics. The size (or volume) of NPs is one of the most important parameters for their successful application. It is relatively straightforward to determine the volume of regular NPs such as spheres and cubes from a one-dimensional or two-dimensional measurement. However, due to the three-dimensional nature of NPs, it is challenging to determine the proper physical size of many types of regularly and irregularly-shaped quasi-spherical NPs at high-throughput using a single tool. Here, we present a relatively simple method that determines a better volume estimate of NPs by combining measurements from their top-down projection areas and peak heights using two tools. The proposed method is significantly faster and more economical than the electron tomography method. We demonstrate the improved accuracy of the combined method over scanning electron microscopy (SEM) or atomic force microscopy (AFM) alone by using modeling, simulations, and measurements. This study also exposes the existence of inherent measurement biases for both SEM and AFM, which usually produce larger measured diameters with SEM than with AFM. However, in some cases SEM measured diameters appear to have less error compared to AFM measured diameters, especially for widely used IS-NPs such as of gold, and silver. The method provides a much needed, proper high-throughput volumetric measurement method useful for many applications. Graphical Abstract The combined method for volume determination of irregularly-shaped quasi-spherical nanoparticles.
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Affiliation(s)
- Ravi Kiran Attota
- Engineering Physics Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA.
| | - Eileen Cherry Liu
- Engineering Physics Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
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36
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Biological application of Compressed Sensing Tomography in the Scanning Electron Microscope. Sci Rep 2016; 6:33354. [PMID: 27646194 PMCID: PMC5028842 DOI: 10.1038/srep33354] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 08/22/2016] [Indexed: 01/06/2023] Open
Abstract
The three-dimensional tomographic reconstruction of a biological sample, namely collagen fibrils in human dermal tissue, was obtained from a set of projection-images acquired in the Scanning Electron Microscope. A tailored strategy for the transmission imaging mode was implemented in the microscope and proved effective in acquiring the projections needed for the tomographic reconstruction. Suitable projection alignment and Compressed Sensing formulation were used to overcome the limitations arising from the experimental acquisition strategy and to improve the reconstruction of the sample. The undetermined problem of structure reconstruction from a set of projections, limited in number and angular range, was indeed supported by exploiting the sparsity of the object projected in the electron microscopy images. In particular, the proposed system was able to preserve the reconstruction accuracy even in presence of a significant reduction of experimental projections.
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37
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Furnival T, Leary RK, Midgley PA. Denoising time-resolved microscopy image sequences with singular value thresholding. Ultramicroscopy 2016; 178:112-124. [PMID: 27262768 DOI: 10.1016/j.ultramic.2016.05.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 04/20/2016] [Accepted: 05/07/2016] [Indexed: 10/21/2022]
Abstract
Time-resolved imaging in microscopy is important for the direct observation of a range of dynamic processes in both the physical and life sciences. However, the image sequences are often corrupted by noise, either as a result of high frame rates or a need to limit the radiation dose received by the sample. Here we exploit both spatial and temporal correlations using low-rank matrix recovery methods to denoise microscopy image sequences. We also make use of an unbiased risk estimator to address the issue of how much thresholding to apply in a robust and automated manner. The performance of the technique is demonstrated using simulated image sequences, as well as experimental scanning transmission electron microscopy data, where surface adatom motion and nanoparticle structural dynamics are recovered at rates of up to 32 frames per second.
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Affiliation(s)
- Tom Furnival
- Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge CB3 0FS, United Kingdom.
| | - Rowan K Leary
- Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge CB3 0FS, United Kingdom.
| | - Paul A Midgley
- Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge CB3 0FS, United Kingdom.
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