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Ohsuna T, Oh-Ishi K. Model-based deconvolution for particle analysis applied to a through-focus series of HAADF-STEM images. Microscopy (Oxf) 2023; 72:368-380. [PMID: 36537122 DOI: 10.1093/jmicro/dfac070] [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: 06/01/2022] [Revised: 11/06/2022] [Accepted: 12/19/2022] [Indexed: 08/05/2023] Open
Abstract
This paper presents an approach for determining the sizes and three-dimensional (3D) positions of nanoparticles from a through-focus series of high-angle annular dark-field scanning transmission electron microscopy images. By assuming spherical particles with uniform density, the sizes and 3D positions can be derived via Wiener deconvolution using a series of kernels prepared by the convolution of the 3D point spread function of the electron beam and the 3D density distribution of spheres with different radii. This process is referred to as a model-based deconvolution. Four 3D datasets with a volume size of 148 × 148 × 560 nm3 were obtained from the four sets of 256 high-angle annular dark-field scanning transmission electron microscopy images of 256 × 256 pixels taken from the same field of view under the through-focus condition. The 3D positions and radii of 14 particles in each 3D dataset were derived using the model-based deconvolution for ∼8 min. The observation errors of the 3D position were estimated as σx ≅ σy ≅ 0.3 nm and σz < 1.6 nm.
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Affiliation(s)
- Tetsu Ohsuna
- Materials Analysis & Evaluation Research-Domain, Toyota Central R&D Labs., Co. Ltd, 41-1, Yokomichi, Nagakute, Aichi 480-1192, Japan
| | - Keiichiro Oh-Ishi
- Materials Analysis & Evaluation Research-Domain, Toyota Central R&D Labs., Co. Ltd, 41-1, Yokomichi, Nagakute, Aichi 480-1192, Japan
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2
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Imaging biological samples by integrated differential phase contrast (iDPC) STEM technique. J Struct Biol 2022; 214:107837. [DOI: 10.1016/j.jsb.2022.107837] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 11/19/2022]
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3
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Prasai B, Haber GJ, Strub MP, Ahn R, Ciemniecki JA, Sochacki KA, Taraska JW. The nanoscale molecular morphology of docked exocytic dense-core vesicles in neuroendocrine cells. Nat Commun 2021; 12:3970. [PMID: 34172739 PMCID: PMC8233335 DOI: 10.1038/s41467-021-24167-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 06/04/2021] [Indexed: 12/31/2022] Open
Abstract
Rab-GTPases and their interacting partners are key regulators of secretory vesicle trafficking, docking, and fusion to the plasma membrane in neurons and neuroendocrine cells. Where and how these proteins are positioned and organized with respect to the vesicle and plasma membrane are unknown. Here, we use correlative super-resolution light and platinum replica electron microscopy to map Rab-GTPases (Rab27a and Rab3a) and their effectors (Granuphilin-a, Rabphilin3a, and Rim2) at the nanoscale in 2D. Next, we apply a targetable genetically-encoded electron microscopy labeling method that uses histidine based affinity-tags and metal-binding gold-nanoparticles to determine the 3D axial location of these exocytic proteins and two SNARE proteins (Syntaxin1A and SNAP25) using electron tomography. Rab proteins are distributed across the entire surface and t-SNARE proteins at the base of docked vesicles. We propose that the circumferential distribution of Rabs and Rab-effectors could aid in the efficient transport, capture, docking, and rapid fusion of calcium-triggered exocytic vesicles in excitable cells.
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Affiliation(s)
- Bijeta Prasai
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gideon J Haber
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marie-Paule Strub
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Regina Ahn
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - John A Ciemniecki
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kem A Sochacki
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Justin W Taraska
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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4
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Insight into long-period pattern by depth sectioning using aberration-corrected scanning transmission electron microscope. Ultramicroscopy 2019; 209:112885. [PMID: 31722280 DOI: 10.1016/j.ultramic.2019.112885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/28/2019] [Accepted: 11/03/2019] [Indexed: 11/23/2022]
Abstract
Long-period patterns (LPPs) are widely observed by transmission electron microscopy (TEM) in the study of nanoscale materials. Identifying the origin of LPPs is of significant importance when interpreting TEM images, and for an in-depth understanding of material characteristics. However, the two most common LPP categories, modulated structure and moiré patterns, are not easily differentiated by conventional TEM (CTEM). In this work, an LPP was observed in Cu2-xSe nanoplates by CTEM. And then the depth sectioning with an aberration-corrected scanning transmission electron microscope (AC STEM) has been performed to determine the LPP type. Two misorientated layers were recognized from the depth-series of atomic resolution images of an LPP region, confirming the LPP is a moiré pattern caused by two twisted stacked crystal flakes which commonly exists in nanosized materials. This depth sectioning method is generally applicable for structural characterization of layered systems, and is a powerful approach for the in-situ structural probe of nanomaterials. It is promising to be extended to fast three-dimensional (3D) reconstruction.
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5
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Bosch EGT, Lazić I. Analysis of depth-sectioning STEM for thick samples and 3D imaging. Ultramicroscopy 2019; 207:112831. [PMID: 31491735 DOI: 10.1016/j.ultramic.2019.112831] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 08/19/2019] [Accepted: 08/22/2019] [Indexed: 12/01/2022]
Abstract
We derive a model that describes 3D volume imaging in depth-sectioning STEM that is valid for all STEM techniques under three well-defined conditions: linearity, undisturbed probe and elastic scattering. The resulting undisturbed probe model generalizes the widely used idea that the undisturbed probe intensity in three dimensions can be used as the point spread function for depth-sectioning ADF-STEM to all STEM techniques including (A)BF- and iDPC-STEM. The model provides closed expressions for depth-sectioning STEM, which follow directly from the 2D expressions for thin samples, and thereby enables analysis of the 3D resolution. Using the model we explore the consequences of the resulting 3D contrast transfer function (CTF) for the z-resolution at different length scales and illustrate this with experiments. We investigate the validity and limitations of the model using multi-slice simulations showing that it is valid and quantitatively accurate for relatively thick amorphous samples but not for crystalline samples in zone-axis due to channeling. We compare depth-sectioning in iDPC- and ADF-STEM and show that iDPC-STEM can extract information from deeper into the sample, all the way till the bottom of the sample, thereby effectively allowing a thickness measurement. Also the difference in optimal focus conditions between iDPC- and ADF-STEM is explained. Finally, we propose practical criteria for deciding whether a sample is thin or thick.
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Affiliation(s)
- Eric G T Bosch
- Thermo Fisher Scientific, Achtseweg, Noord 5, 5651GG Eindhoven, NOORD-BRABANT, the Netherlands
| | - Ivan Lazić
- Thermo Fisher Scientific, Achtseweg, Noord 5, 5651GG Eindhoven, NOORD-BRABANT, the Netherlands.
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6
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4D-Data Acquisition in Scanning Confocal Electron Microscopy for Depth-Sectioned Imaging. E-JOURNAL OF SURFACE SCIENCE AND NANOTECHNOLOGY 2018. [DOI: 10.1380/ejssnt.2018.247] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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7
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Hamaoka T, Jao CY, Takeguchi M. Annular dark-field scanning confocal electron microscopy studied using multislice simulations. Microscopy (Oxf) 2018; 67:4995666. [PMID: 29762753 DOI: 10.1093/jmicro/dfy023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 04/25/2018] [Indexed: 11/13/2022] Open
Abstract
Annular dark-field scanning confocal electron microscopy (ADF-SCEM) has been studied using multislice simulations. Thermal diffuse scattering was considered in the calculations. Geometric aberrations of the lenses were introduced. A finite-sized pinhole was taken into consideration, in addition to an ideal point pinhole. ADF-SCEM images of Al crystals aligned along a zone-axis exhibit elongated contrast along the optic axis. Results of simulations suggest that if geometric aberrations of an imaging lens are corrected, depth resolution in ADF-SCEM can be improved by employing a large collection semi-angle of an annular aperture, even with a finite pinhole.
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Affiliation(s)
- Takumi Hamaoka
- Transmission Electron Microscopy Station, National Institute for Materials Science, Tsukuba 305-0047, Japan
| | - Chih-Yu Jao
- Transmission Electron Microscopy Station, National Institute for Materials Science, Tsukuba 305-0047, Japan
| | - Masaki Takeguchi
- Transmission Electron Microscopy Station, National Institute for Materials Science, Tsukuba 305-0047, Japan
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8
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Gnanasekaran K, de With G, Friedrich H. Quantification and optimization of ADF-STEM image contrast for beam-sensitive materials. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171838. [PMID: 29892376 PMCID: PMC5990820 DOI: 10.1098/rsos.171838] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/27/2018] [Indexed: 05/29/2023]
Abstract
Many functional materials are difficult to analyse by scanning transmission electron microscopy (STEM) on account of their beam sensitivity and low contrast between different phases. The problem becomes even more severe when thick specimens need to be investigated, a situation that is common for materials that are ordered from the nanometre to micrometre length scales or when performing dynamic experiments in a TEM liquid cell. Here we report a method to optimize annular dark-field (ADF) STEM imaging conditions and detector geometries for a thick and beam-sensitive low-contrast specimen using the example of a carbon nanotube/polymer nanocomposite. We carried out Monte Carlo simulations as well as quantitative ADF-STEM imaging experiments to predict and verify optimum contrast conditions. The presented method is general, can be easily adapted to other beam-sensitive and/or low-contrast materials, as shown for a polymer vesicle within a TEM liquid cell, and can act as an expert guide on whether an experiment is feasible and to determine the best imaging conditions.
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Affiliation(s)
- Karthikeyan Gnanasekaran
- Laboratory of Materials and Interface Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Gijsbertus de With
- Laboratory of Materials and Interface Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Heiner Friedrich
- Laboratory of Materials and Interface Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex and Molecular System, Eindhoven University of Technology, Eindhoven, The Netherlands
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9
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Comparison of 3D cellular imaging techniques based on scanned electron probes: Serial block face SEM vs. Axial bright-field STEM tomography. J Struct Biol 2018; 202:216-228. [PMID: 29408702 DOI: 10.1016/j.jsb.2018.01.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 01/26/2018] [Accepted: 01/30/2018] [Indexed: 11/22/2022]
Abstract
Microscopies based on focused electron probes allow the cell biologist to image the 3D ultrastructure of eukaryotic cells and tissues extending over large volumes, thus providing new insight into the relationship between cellular architecture and function of organelles. Here we compare two such techniques: electron tomography in conjunction with axial bright-field scanning transmission electron microscopy (BF-STEM), and serial block face scanning electron microscopy (SBF-SEM). The advantages and limitations of each technique are illustrated by their application to determining the 3D ultrastructure of human blood platelets, by considering specimen geometry, specimen preparation, beam damage and image processing methods. Many features of the complex membranes composing the platelet organelles can be determined from both approaches, although STEM tomography offers a higher ∼3 nm isotropic pixel size, compared with ∼5 nm for SBF-SEM in the plane of the block face and ∼30 nm in the perpendicular direction. In this regard, we demonstrate that STEM tomography is advantageous for visualizing the platelet canalicular system, which consists of an interconnected network of narrow (∼50-100 nm) membranous cisternae. In contrast, SBF-SEM enables visualization of complete platelets, each of which extends ∼2 µm in minimum dimension, whereas BF-STEM tomography can typically only visualize approximately half of the platelet volume due to a rapid non-linear loss of signal in specimens of thickness greater than ∼1.5 µm. We also show that the limitations of each approach can be ameliorated by combining 3D and 2D measurements using a stereological approach.
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10
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Sekine R, Moore KL, Matzke M, Vallotton P, Jiang H, Hughes GM, Kirby JK, Donner E, Grovenor CRM, Svendsen C, Lombi E. Complementary Imaging of Silver Nanoparticle Interactions with Green Algae: Dark-Field Microscopy, Electron Microscopy, and Nanoscale Secondary Ion Mass Spectrometry. ACS NANO 2017; 11:10894-10902. [PMID: 29061049 DOI: 10.1021/acsnano.7b04556] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Increasing consumer use of engineered nanomaterials has led to significantly increased efforts to understand their potential impact on the environment and living organisms. Currently, no individual technique can provide all the necessary information such as their size, distribution, and chemistry in complex biological systems. Consequently, there is a need to develop complementary instrumental imaging approaches that provide enhanced understanding of these "bio-nano" interactions to overcome the limitations of individual techniques. Here we used a multimodal imaging approach incorporating dark-field light microscopy, high-resolution electron microscopy, and nanoscale secondary ion mass spectrometry (NanoSIMS). The aim was to gain insight into the bio-nano interactions of surface-functionalized silver nanoparticles (Ag-NPs) with the green algae Raphidocelis subcapitata, by combining the fidelity, spatial resolution, and elemental identification offered by the three techniques, respectively. Each technique revealed that Ag-NPs interact with the green algae with a dependence on the size (10 nm vs 60 nm) and surface functionality (tannic acid vs branched polyethylenimine, bPEI) of the NPs. Dark-field light microscopy revealed the presence of strong light scatterers on the algal cell surface, and SEM imaging confirmed their nanoparticulate nature and localization at nanoscale resolution. NanoSIMS imaging confirmed their chemical identity as Ag, with the majority of signal concentrated at the cell surface. Furthermore, SEM and NanoSIMS provided evidence of 10 nm bPEI Ag-NP internalization at higher concentrations (40 μg/L), correlating with the highest toxicity observed from these NPs. This multimodal approach thus demonstrated an effective approach to complement dose-response studies in nano-(eco)-toxicological investigations.
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Affiliation(s)
- Ryo Sekine
- Future Industries Institute, University of South Australia , Building X, Mawson Lakes Campus, Adelaide, SA 5095, Australia
- Centre for Ecology and Hydrology , Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire OX10 8BB, United Kingdom
| | - Katie L Moore
- Department of Materials, The University of Oxford , Parks Road, Oxford, OX1 3PH, United Kingdom
- School of Materials, The University of Manchester , Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Marianne Matzke
- Centre for Ecology and Hydrology , Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire OX10 8BB, United Kingdom
| | - Pascal Vallotton
- Institute für Biochemie, ETH Zurich , Otto-Stern-Weg 3, 8093 Zürich, Switzerland
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia , 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Haibo Jiang
- Department of Materials, The University of Oxford , Parks Road, Oxford, OX1 3PH, United Kingdom
- CSIRO Land and Water, Environmental Contaminant Mitigation and Biotechnology Program , Waite Campus, Waite Road, Perth, SA 5064, Australia
| | - Gareth M Hughes
- Department of Materials, The University of Oxford , Parks Road, Oxford, OX1 3PH, United Kingdom
| | - Jason K Kirby
- CSIRO Land and Water, Environmental Contaminant Mitigation and Biotechnology Program , Waite Campus, Waite Road, Perth, SA 5064, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia , Building X, Mawson Lakes Campus, Adelaide, SA 5095, Australia
| | - Chris R M Grovenor
- Department of Materials, The University of Oxford , Parks Road, Oxford, OX1 3PH, United Kingdom
| | - Claus Svendsen
- Centre for Ecology and Hydrology , Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire OX10 8BB, United Kingdom
| | - Enzo Lombi
- Future Industries Institute, University of South Australia , Building X, Mawson Lakes Campus, Adelaide, SA 5095, Australia
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11
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Wan X, Katchalski T, Churas C, Ghosh S, Phan S, Lawrence A, Hao Y, Zhou Z, Chen R, Chen Y, Zhang F, Ellisman MH. Electron tomography simulator with realistic 3D phantom for evaluation of acquisition, alignment and reconstruction methods. J Struct Biol 2017; 198:103-115. [PMID: 28392451 DOI: 10.1016/j.jsb.2017.04.002] [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: 08/24/2016] [Revised: 12/22/2016] [Accepted: 04/03/2017] [Indexed: 11/16/2022]
Abstract
Because of the significance of electron microscope tomography in the investigation of biological structure at nanometer scales, ongoing improvement efforts have been continuous over recent years. This is particularly true in the case of software developments. Nevertheless, verification of improvements delivered by new algorithms and software remains difficult. Current analysis tools do not provide adaptable and consistent methods for quality assessment. This is particularly true with images of biological samples, due to image complexity, variability, low contrast and noise. We report an electron tomography (ET) simulator with accurate ray optics modeling of image formation that includes curvilinear trajectories through the sample, warping of the sample and noise. As a demonstration of the utility of our approach, we have concentrated on providing verification of the class of reconstruction methods applicable to wide field images of stained plastic-embedded samples. Accordingly, we have also constructed digital phantoms derived from serial block face scanning electron microscope images. These phantoms are also easily modified to include alignment features to test alignment algorithms. The combination of more realistic phantoms with more faithful simulations facilitates objective comparison of acquisition parameters, alignment and reconstruction algorithms and their range of applicability. With proper phantoms, this approach can also be modified to include more complex optical models, including distance-dependent blurring and phase contrast functions, such as may occur in cryotomography.
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Affiliation(s)
- Xiaohua Wan
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China; National Center for Microscopy and Imaging Research, University of California, San Diego, USA
| | - Tsvi Katchalski
- National Center for Microscopy and Imaging Research, University of California, San Diego, USA
| | - Christopher Churas
- National Center for Microscopy and Imaging Research, University of California, San Diego, USA
| | - Sreya Ghosh
- National Center for Microscopy and Imaging Research, University of California, San Diego, USA
| | - Sebastien Phan
- National Center for Microscopy and Imaging Research, University of California, San Diego, USA
| | - Albert Lawrence
- National Center for Microscopy and Imaging Research, University of California, San Diego, USA.
| | - Yu Hao
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Ziying Zhou
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China; Beijing Institute of Technology, Beijing, China
| | - Ruijuan Chen
- School of Electronic and Information Engineering, Tianjin Polytechnic University, Tianjin, China; National Center for Microscopy and Imaging Research, University of California, San Diego, USA
| | - Yu Chen
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Fa Zhang
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, University of California, San Diego, USA; Departments of Neurosciences and Bioengineering, University of California, San Diego, USA
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12
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Hamaoka T, Jao CY, Zhang X, Oshima Y, Takeguchi M. Three-dimensional characterization of Guinier-Preston zones in an Al-Cu alloy using depth-sectioning technique. Microscopy (Oxf) 2017; 66:78-88. [PMID: 27927875 DOI: 10.1093/jmicro/dfw104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/04/2016] [Indexed: 11/14/2022] Open
Abstract
Guinier-Preston (GP) zones formed as nanometer-sized Cu-rich monolayers in α-Al matrix phase during aging process have been investigated using depth-sectioning technique, where through-focal high-angle annular dark-field (HAADF) images were recorded along a <001> zone axis of the α-Al phase using aberration-corrected scanning transmission electron microscopy (STEM). HAADF intensities of the GP zones in the through-focal series vary with defocus settings, depending on the depths of the GP zones in the sample. Determination of the depth of a GP zone is not straightforward because the electron wave function of the STEM probe in the aligned crystalline material is affected by electron channeling. The depths of GP zones were then estimated via comparison with multislice simulations where GP zones were arranged at various depths in a supercell, and HAADF intensities were simulated with various defocus values. We show that the depth-sectioning technique can be used to investigate three-dimensional configurations of GP zones in the sample.
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Affiliation(s)
- Takumi Hamaoka
- Transmission Electron Microscopy Station, National Institute for Materials Science, Tsukuba 305-0047, Japan
| | - Chih-Yu Jao
- Transmission Electron Microscopy Station, National Institute for Materials Science, Tsukuba 305-0047, Japan
| | - Xiaobin Zhang
- School of Materials Science, Japan Advanced Institute of Science and Technology, Nomi 923-1292, Japan
| | - Yoshifumi Oshima
- School of Materials Science, Japan Advanced Institute of Science and Technology, Nomi 923-1292, Japan
| | - Masaki Takeguchi
- Transmission Electron Microscopy Station, National Institute for Materials Science, Tsukuba 305-0047, Japan
- In-situ Characterization Technique Development Group, Research Center for Advanced Measurement and Characterization, National Institute for Materials Science, Tsukuba 305-0047, Japan
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13
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Dahmen T, Engstler M, Pauly C, Trampert P, de Jonge N, Mücklich F, Slusallek P. Feature Adaptive Sampling for Scanning Electron Microscopy. Sci Rep 2016; 6:25350. [PMID: 27150131 PMCID: PMC4858653 DOI: 10.1038/srep25350] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 04/12/2016] [Indexed: 11/09/2022] Open
Abstract
A new method for the image acquisition in scanning electron microscopy (SEM) was introduced. The method used adaptively increased pixel-dwell times to improve the signal-to-noise ratio (SNR) in areas of high detail. In areas of low detail, the electron dose was reduced on a per pixel basis, and a-posteriori image processing techniques were applied to remove the resulting noise. The technique was realized by scanning the sample twice. The first, quick scan used small pixel-dwell times to generate a first, noisy image using a low electron dose. This image was analyzed automatically, and a software algorithm generated a sparse pattern of regions of the image that require additional sampling. A second scan generated a sparse image of only these regions, but using a highly increased electron dose. By applying a selective low-pass filter and combining both datasets, a single image was generated. The resulting image exhibited a factor of ≈3 better SNR than an image acquired with uniform sampling on a Cartesian grid and the same total acquisition time. This result implies that the required electron dose (or acquisition time) for the adaptive scanning method is a factor of ten lower than for uniform scanning.
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Affiliation(s)
- Tim Dahmen
- German Research Center for Artificial Intelligence GmbH (DFKI), 66123 Saarbrücken, Germany
| | | | | | - Patrick Trampert
- German Research Center for Artificial Intelligence GmbH (DFKI), 66123 Saarbrücken, Germany
- Saarland University, 66123 Saarbrücken, Germany
| | - Niels de Jonge
- Saarland University, 66123 Saarbrücken, Germany
- INM-Leibniz Institute for New Materials, 66123 Saarbrücken, Germany
| | | | - Philipp Slusallek
- German Research Center for Artificial Intelligence GmbH (DFKI), 66123 Saarbrücken, Germany
- Saarland University, 66123 Saarbrücken, Germany
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14
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Niclis JC, Murphy SV, Parkinson DY, Zedan A, Sathananthan AH, Cram DS, Heraud P. Three-dimensional imaging of human stem cells using soft X-ray tomography. J R Soc Interface 2016; 12:20150252. [PMID: 26063819 DOI: 10.1098/rsif.2015.0252] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Three-dimensional imaging of human stem cells using transmission soft X-ray tomography (SXT) is presented for the first time. Major organelle types--nuclei, nucleoli, mitochondria, lysosomes and vesicles--were discriminated at approximately 50 nm spatial resolution without the use of contrast agents, on the basis of measured linear X-ray absorption coefficients and comparison of the size and shape of structures to transmission electron microscopy (TEM) images. In addition, SXT was used to visualize the distribution of a cell surface protein using gold-labelled antibody staining. We present the strengths of SXT, which include excellent spatial resolution (intermediate between that of TEM and light microscopy), the lack of the requirement for fixative or contrast agent that might perturb cellular morphology or produce imaging artefacts, and the ability to produce three-dimensional images of cells without microtome sectioning. Possible applications to studying the differentiation of human stem cells are discussed.
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Affiliation(s)
- J C Niclis
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria 3800, Australia The Florey Institute of Neuroscience and Mental Health, Melbourne University, Parkville, Victoria 3052, Australia
| | - S V Murphy
- The Ritchie Centre, Monash Institute of Medical Research, Monash University, Clayton, Victoria 3800, Australia Wake Forest Baptist Medical Center, Wake Forest Institute for Regenerative Medicine, Winston-Salem, NC, USA
| | - D Y Parkinson
- Advanced Light Source, Lawrence Berkeley National Laboratory, US Department of Energy, Berkeley, CA, USA
| | - A Zedan
- Advanced Light Source, Lawrence Berkeley National Laboratory, US Department of Energy, Berkeley, CA, USA
| | - A H Sathananthan
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria 3800, Australia
| | - D S Cram
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria 3800, Australia
| | - P Heraud
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria 3800, Australia Centre for Biospectroscopy, School of Chemistry, Monash University, Melbourne, Victoria, Australia
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15
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Park J, Park H, Ercius P, Pegoraro AF, Xu C, Kim JW, Han SH, Weitz DA. Direct Observation of Wet Biological Samples by Graphene Liquid Cell Transmission Electron Microscopy. NANO LETTERS 2015; 15:4737-4744. [PMID: 26065925 DOI: 10.1021/acs.nanolett.5b01636] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Recent development of liquid phase transmission electron microscopy (TEM) enables the study of specimens in wet ambient conditions within a liquid cell; however, direct structural observation of biological samples in their native solution using TEM is challenging since low-mass biomaterials embedded in a thick liquid layer of the host cell demonstrate low contrast. Furthermore, the integrity of delicate wet samples is easily compromised during typical sample preparation and TEM imaging. To overcome these limitations, we introduce a graphene liquid cell (GLC) using multilayer graphene sheets to reliably encapsulate and preserve biological samples in a liquid for TEM observation. We achieve nanometer scale spatial resolution with high contrast using low-dose TEM at room temperature, and we use the GLC to directly observe the structure of influenza viruses in their native buffer solution at room temperature. The GLC is further extended to investigate whole cells in wet conditions using TEM. We also demonstrate the potential of the GLC for correlative studies by TEM and fluorescence light microscopy imaging.
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Affiliation(s)
- Jungwon Park
- †Department of Applied Physics, Harvard University, Cambridge, Massachusetts 02138, United States
- ‡School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Hyesung Park
- §School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 689-798, South Korea
| | - Peter Ercius
- ∥The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Adrian F Pegoraro
- †Department of Applied Physics, Harvard University, Cambridge, Massachusetts 02138, United States
- ‡School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Chen Xu
- ⊥Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454, United States
| | - Jin Woong Kim
- #Department of Applied Chemistry, Hanyang University, Ansan 426-791, South Korea
- ∇Department of Bionano Technology, Hanyang University, Ansan 426-791, South Korea
| | | | - David A Weitz
- †Department of Applied Physics, Harvard University, Cambridge, Massachusetts 02138, United States
- ‡School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
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16
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Dahmen T, Kohr H, de Jonge N, Slusallek P. Matched Backprojection Operator for Combined Scanning Transmission Electron Microscopy Tilt- and Focal Series. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2015; 21:725-738. [PMID: 26046398 DOI: 10.1017/s1431927615000525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Combined tilt- and focal series scanning transmission electron microscopy is a recently developed method to obtain nanoscale three-dimensional (3D) information of thin specimens. In this study, we formulate the forward projection in this acquisition scheme as a linear operator and prove that it is a generalization of the Ray transform for parallel illumination. We analytically derive the corresponding backprojection operator as the adjoint of the forward projection. We further demonstrate that the matched backprojection operator drastically improves the convergence rate of iterative 3D reconstruction compared to the case where a backprojection based on heuristic weighting is used. In addition, we show that the 3D reconstruction is of better quality.
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Affiliation(s)
- Tim Dahmen
- 1German Research Center for Artificial Intelligence GmbH (DFKI),66123 Saarbrücken,Germany
| | - Holger Kohr
- 2Department of Mathematics,KTH Royal Institute of Technology,Lindstedtsvägen 25,Stockholm,SE 100 44,Sweden
| | - Niels de Jonge
- 3INM Leibniz Institute for New Materials,66123 Saarbrücken,Germany
| | - Philipp Slusallek
- 1German Research Center for Artificial Intelligence GmbH (DFKI),66123 Saarbrücken,Germany
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17
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Sohlberg K, Pennycook TJ, Zhou W, Pennycook SJ. Insights into the physical chemistry of materials from advances in HAADF-STEM. Phys Chem Chem Phys 2015; 17:3982-4006. [DOI: 10.1039/c4cp04232h] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
HAADF-STEM provides atomic-resolution real space imaging. Here an image of a single Si dopant atom in a graphene lattice is shown adjacent to a schematic of the instrument. Simultaneous EELS on electrons scattered to low angles can provide chemical identification of the species preset. Differences between the Si L-edge spectra reveal differences in atomic bonding and hybridization for different configurations of Si atoms in graphene.
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Affiliation(s)
- Karl Sohlberg
- Department of Chemistry
- Drexel University
- Philadelphia
- USA
| | | | - Wu Zhou
- Materials Science & Technology Division
- Oak Ridge National Laboratory
- Oak Ridge
- USA
| | - Stephen J. Pennycook
- Department of Materials Science and Engineering
- University of Tennessee
- Knoxville
- USA
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18
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Dahmen T, Baudoin JP, Lupini AR, Kübel C, Slusallek P, de Jonge N. Combined scanning transmission electron microscopy tilt- and focal series. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2014; 20:548-560. [PMID: 24548618 DOI: 10.1017/s1431927614000075] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In this study, a combined tilt- and focal series is proposed as a new recording scheme for high-angle annular dark-field scanning transmission electron microscopy (STEM) tomography. Three-dimensional (3D) data were acquired by mechanically tilting the specimen, and recording a through-focal series at each tilt direction. The sample was a whole-mount macrophage cell with embedded gold nanoparticles. The tilt-focal algebraic reconstruction technique (TF-ART) is introduced as a new algorithm to reconstruct tomograms from such combined tilt- and focal series. The feasibility of TF-ART was demonstrated by 3D reconstruction of the experimental 3D data. The results were compared with a conventional STEM tilt series of a similar sample. The combined tilt- and focal series led to smaller "missing wedge" artifacts, and a higher axial resolution than obtained for the STEM tilt series, thus improving on one of the main issues of tilt series-based electron tomography.
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Affiliation(s)
- Tim Dahmen
- 1 German Research Center for Artificial Intelligence GmbH (DFKI), 66123 Saarbrücken, Germany
| | - Jean-Pierre Baudoin
- 2 Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232-0615, USA
| | - Andrew R Lupini
- 4 Karlsruhe Institute for Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Christian Kübel
- 4 Karlsruhe Institute for Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Philipp Slusallek
- 1 German Research Center for Artificial Intelligence GmbH (DFKI), 66123 Saarbrücken, Germany
| | - Niels de Jonge
- 2 Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232-0615, USA
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19
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Baudoin JP, Jinschek JR, Boothroyd CB, Dunin-Borkowski RE, de Jonge N. Chromatic aberration-corrected tilt series transmission electron microscopy of nanoparticles in a whole mount macrophage cell. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2013; 19:814-820. [PMID: 23659678 DOI: 10.1017/s1431927613001475] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Transmission electron microscopy (TEM) in combination with electron tomography is widely used to obtain nanometer scale three-dimensional (3D) structural information about biological samples. However, studies of whole eukaryotic cells are limited in resolution and/or contrast on account of the effect of chromatic aberration of the TEM objective lens on electrons that have been scattered inelastically in the specimen. As a result, 3D information is usually obtained from sections and not from whole cells. Here, we use chromatic aberration-corrected TEM to record bright-field TEM images of nanoparticles in a whole mount macrophage cell. Tilt series of images are used to generate electron tomograms, which are analyzed to assess the spatial resolution that can be achieved for different vertical positions in the specimen. The uptake of gold nanoparticles coated with low-density lipoprotein (LDL) is studied. The LDL is found to assemble in clusters. The clusters contain nanoparticles taken up on different days, which are joined without mixing their nanoparticle cargo.
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Affiliation(s)
- Jean-Pierre Baudoin
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232-0615, USA
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20
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Ramachandra R, Demers H, de Jonge N. The influence of the sample thickness on the lateral and axial resolution of aberration-corrected scanning transmission electron microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2013; 19:93-101. [PMID: 23290505 DOI: 10.1017/s143192761201392x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The lateral and axial resolution of three-dimensional (3D) focal series aberration-corrected scanning transmission electron microscopy was studied for samples of different thicknesses. The samples consisted of gold nanoparticles placed on the top and at the bottom of silicon nitride membranes of thickness between 50 and 500 nm. Atomic resolution was obtained for nanoparticles on top of 50-, 100-, and 200-nm-thick membranes with respect to the electron beam traveling downward. Atomic resolution was also achieved for nanoparticles placed below 50-, 100-, and 200-nm-thick membranes but with a lower contrast at the larger thicknesses. Beam broadening led to a reduced resolution for a 500-nm-thick membrane. The influence of the beam broadening on the axial resolution was also studied using Monte Carlo simulations with a 3D sample geometry.
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Affiliation(s)
- Ranjan Ramachandra
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232-0615, USA
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21
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Immuno EM–OM correlative microscopy in solution by atmospheric scanning electron microscopy (ASEM). J Struct Biol 2012; 180:259-70. [DOI: 10.1016/j.jsb.2012.08.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Revised: 08/01/2012] [Accepted: 08/07/2012] [Indexed: 12/12/2022]
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22
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Zhang X, Takeguchi M, Hashimoto A, Mitsuishi K, Wang P, Nellist PD, Kirkland AI, Tezuka M, Shimojo M. Three-dimensional observation of SiO2 hollow spheres with a double-shell structure using aberration-corrected scanning confocal electron microscopy. Microscopy (Oxf) 2012; 61:159-69. [DOI: 10.1093/jmicro/dfs039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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23
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Ramachandra R, de Jonge N. Optimized deconvolution for maximum axial resolution in three-dimensional aberration-corrected scanning transmission electron microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2012; 18:218-228. [PMID: 22152090 PMCID: PMC3387366 DOI: 10.1017/s1431927611012347] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Three-dimensional (3D) datasets were recorded of gold nanoparticles placed on both sides of silicon nitride membranes using focal series aberration-corrected scanning transmission electron microscopy (STEM). Deconvolution of the 3D datasets was applied to obtain the highest possible axial resolution. The deconvolution involved two different point spread functions, each calculated iteratively via blind deconvolution. Supporting membranes of different thicknesses were tested to study the effect of beam broadening on the deconvolution. It was found that several iterations of deconvolution was efficient in reducing the imaging noise. With an increasing number of iterations, the axial resolution was increased, and most of the structural information was preserved. Additional iterations improved the axial resolution by maximal a factor of 4 to 6, depending on the particular dataset, and up to 8 nm maximal, but also led to a reduction of the lateral size of the nanoparticles in the image. Thus, the deconvolution procedure optimized for the highest axial resolution is best suited for applications where one is interested in the 3D locations of nanoparticles only.
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Affiliation(s)
- Ranjan Ramachandra
- Vanderbilt University School of Medicine, Department of Molecular Physiology and Biophysics, TN, Nashville, 37232-0615, USA
| | - Niels de Jonge
- Vanderbilt University School of Medicine, Department of Molecular Physiology and Biophysics, TN, Nashville, 37232-0615, USA
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24
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Lupini AR, de Jonge N. The three-dimensional point spread function of aberration-corrected scanning transmission electron microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2011; 17:817-26. [PMID: 21878149 PMCID: PMC3390684 DOI: 10.1017/s1431927611011913] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Aberration correction reduces the depth of field in scanning transmission electron microscopy (STEM) and thus allows three-dimensional (3D) imaging by depth sectioning. This imaging mode offers the potential for sub-Ångstrom lateral resolution and nanometer-scale depth sensitivity. For biological samples, which may be many microns across and where high lateral resolution may not always be needed, optimizing the depth resolution even at the expense of lateral resolution may be desired, aiming to image through thick specimens. Although there has been extensive work examining and optimizing the probe formation in two dimensions, there is less known about the probe shape along the optical axis. Here the probe shape is examined in three dimensions in an attempt to better understand the depth resolution in this mode. Examples are presented of how aberrations change the probe shape in three dimensions, and it is found that off-axial aberrations may need to be considered for focal series of large areas. It is shown that oversized or annular apertures theoretically improve the vertical resolution for 3D imaging of nanoparticles. When imaging nanoparticles of several nanometer size, regular STEM can thereby be optimized such that the vertical full-width at half-maximum approaches that of the aberration-corrected STEM with a standard aperture.
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Affiliation(s)
- Andrew R Lupini
- Oak Ridge National Laboratory, Materials Science and Technology Division, Oak Ridge, TN 37831-6064, USA
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25
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Wang F, Cao M, Zhang HB, Nishi R, Takaoka A. Note: direct measurement of the point-to-point resolution for microns-thick specimens in the ultrahigh-voltage electron microscope. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2011; 82:066101. [PMID: 21721736 DOI: 10.1063/1.3597672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We report on a direct measurement method and results of the point-to-point resolution for microns-thick amorphous specimens in the ultrahigh-voltage electron microscope (ultra-HVEM). We first obtain the ultra-HVEM images of nanometer gold particles with different sizes on the top surfaces of the thick epoxy-resin specimens. Based on the Rayleigh criterion, the point-to-point resolution is then determined as the minimum distance between centers of two resolvable tangent gold particles. Some values of resolution are accordingly acquired for the specimens with different thicknesses at the accelerating voltage of 2 MV, for example, 18.5 nm and 28.4 nm for the 5 μm and 8 μm thick epoxy-resin specimens, respectively. The presented method and results provide a reliable and useful approach to quantifying and comparing the achievable spatial resolution for the thick specimens imaged in the mode of transmission electron including the scanning transmission electron microscope.
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Affiliation(s)
- Fang Wang
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Department of Electronic Science and Technology, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
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26
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Hashimoto A, Mitsuishi K, Shimojo M, Zhu Y, Takeguchi M. Experimental examination of the characteristics of bright-field scanning confocal electron microscopy images. JOURNAL OF ELECTRON MICROSCOPY 2011; 60:227-234. [PMID: 21486860 DOI: 10.1093/jmicro/dfr013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We experimentally examined the characteristics of bright-field (BF) scanning confocal electron microscopy (SCEM) images by changing the observation conditions and comparing the images with those obtained by BF transmission electron microscopy (TEM) and BF scanning TEM (STEM) modes. The observation of 5-nm-diameter Au nanoparticles demonstrated that BF-SCEM produces object elongation of more than 2000 nm along the optical axis, as do BF-TEM and BF-STEM. We demonstrated the relationship between elongation length and geometric effects such as convergence and collection angles of a probe and the lateral size of an object; the relationship is consistent with previous theoretical prediction. Further, we observed interesting features that are seen only in the BF-SCEM images; the film contrast was strongly enhanced, compared with that of BF-STEM. In addition, a bright contrast appeared around the object position in the elongated images. Using this characteristic, we could determine the object position and structure.
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Affiliation(s)
- Ayako Hashimoto
- Advanced Nano-characterization Center, National Institute for Materials Science, 3-13 Sakura, Tsukuba, Japan.
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27
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Dukes MJ, Ramachandra R, Baudoin JP, Gray Jerome W, de Jonge N. Three-dimensional locations of gold-labeled proteins in a whole mount eukaryotic cell obtained with 3nm precision using aberration-corrected scanning transmission electron microscopy. J Struct Biol 2011; 174:552-62. [PMID: 21440635 DOI: 10.1016/j.jsb.2011.03.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Revised: 03/17/2011] [Accepted: 03/18/2011] [Indexed: 01/23/2023]
Abstract
Three-dimensional (3D) maps of proteins within the context of whole cells are important for investigating cellular function. However, 3D reconstructions of whole cells are challenging to obtain using conventional transmission electron microscopy (TEM). We describe a methodology to determine the 3D locations of proteins labeled with gold nanoparticles on whole eukaryotic cells. The epidermal growth factor receptors on COS7 cells were labeled with gold nanoparticles, and critical-point dried whole-mount cell samples were prepared. 3D focal series were obtained with aberration-corrected scanning transmission electron microscopy (STEM), without tilting the specimen. The axial resolution was improved with deconvolution. The vertical locations of the nanoparticles in a whole-mount cell were determined with a precision of 3nm. From the analysis of the variation of the axial positions of the labels we concluded that the cellular surface was ruffled. To achieve sufficient stability of the sample under electron beam irradiation during the recording of the focal series, the sample was carbon coated. A quantitative method was developed to analyze the stability of the ultrastructure after electron beam irradiation using TEM. The results of this study demonstrate the feasibility of using aberration-corrected STEM to study the 3D nanoparticle distribution in whole cells.
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Affiliation(s)
- Madeline J Dukes
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
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28
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Demers H, Poirier-Demers N, Drouin D, de Jonge N. Simulating STEM imaging of nanoparticles in micrometers-thick substrates. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2010; 16:795-804. [PMID: 20961483 PMCID: PMC3165039 DOI: 10.1017/s1431927610094080] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Scanning transmission electron microscope (STEM) images of three-dimensional (3D) samples were simulated. The samples consisted of a micrometer(s)-thick substrate and gold nanoparticles at various vertical positions. The atomic number (Z) contrast as obtained via the annular dark-field detector was generated. The simulations were carried out using the Monte Carlo method in the CASINO software (freeware). The software was adapted to include the STEM imaging modality, including the noise characteristics of the electron source, the conical shape of the beam, and 3D scanning. Simulated STEM images of nanoparticles on a carbon substrate revealed the influence of the electron dose on the visibility of the nanoparticles. The 3D datasets obtained by simulating focal series showed the effect of beam broadening on the spatial resolution and on the signal-to-noise ratio. Monte Carlo simulations of STEM imaging of nanoparticles on a thick water layer were compared with experimental data by programming the exact sample geometry. The simulated image corresponded to the experimental image, and the signal-to-noise levels were similar. The Monte Carlo simulation strategy described here can be used to calculate STEM images of objects of an arbitrary geometry and amorphous sample composition. This information can then be used, for example, to optimize the microscope settings for imaging sessions where a low electron dose is crucial for the design of equipment, or for the analysis of the composition of a certain specimen.
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Affiliation(s)
- H. Demers
- Universite de Sherbrooke, Electrical and Computer Engineering Department, Sherbrooke, Quebec, J1K 2R1, Canada
| | - N. Poirier-Demers
- Universite de Sherbrooke, Electrical and Computer Engineering Department, Sherbrooke, Quebec, J1K 2R1, Canada
| | - D. Drouin
- Universite de Sherbrooke, Electrical and Computer Engineering Department, Sherbrooke, Quebec, J1K 2R1, Canada
| | - N. de Jonge
- Vanderbilt University School of Medicine, Department of Molecular Physiology and Biophysics, TN, Nashville, 37232-0615, USA
- To whom correspondence should be addressed. Phone: 615-322-6036,
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29
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Demers H, Poirier-Demers N, Drouin D, de Jonge N. Simulating STEM imaging of nanoparticles in micrometers-thick substrates. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2010; 16:795-804. [PMID: 20961483 DOI: 10.1017/s1431927611005770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Scanning transmission electron microscope (STEM) images of three-dimensional (3D) samples were simulated. The samples consisted of a micrometer(s)-thick substrate and gold nanoparticles at various vertical positions. The atomic number (Z) contrast as obtained via the annular dark-field detector was generated. The simulations were carried out using the Monte Carlo method in the CASINO software (freeware). The software was adapted to include the STEM imaging modality, including the noise characteristics of the electron source, the conical shape of the beam, and 3D scanning. Simulated STEM images of nanoparticles on a carbon substrate revealed the influence of the electron dose on the visibility of the nanoparticles. The 3D datasets obtained by simulating focal series showed the effect of beam broadening on the spatial resolution and on the signal-to-noise ratio. Monte Carlo simulations of STEM imaging of nanoparticles on a thick water layer were compared with experimental data by programming the exact sample geometry. The simulated image corresponded to the experimental image, and the signal-to-noise levels were similar. The Monte Carlo simulation strategy described here can be used to calculate STEM images of objects of an arbitrary geometry and amorphous sample composition. This information can then be used, for example, to optimize the microscope settings for imaging sessions where a low electron dose is crucial for the design of equipment, or for the analysis of the composition of a certain specimen.
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Affiliation(s)
- H Demers
- Universite de Sherbrooke, Electrical and Computer Engineering Department, Sherbrooke, Quebec J1K 2R1, Canada
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