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Yeo J, Daurer BJ, Kimanius D, Balakrishnan D, Bepler T, Tan YZ, Loh ND. Ghostbuster: A phase retrieval diffraction tomography algorithm for cryo-EM. Ultramicroscopy 2024; 262:113962. [PMID: 38642481 DOI: 10.1016/j.ultramic.2024.113962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/16/2024] [Accepted: 04/01/2024] [Indexed: 04/22/2024]
Abstract
Ewald sphere curvature correction, which extends beyond the projection approximation, stretches the shallow depth of field in cryo-EM reconstructions of thick particles. Here we show that even for previously assumed thin particles, reconstruction artifacts which we refer to as ghosts can appear. By retrieving the lost phases of the electron exitwaves and accounting for the first Born approximation scattering within the particle, we show that these ghosts can be effectively eliminated. Our simulations demonstrate how such ghostbusting can improve reconstructions as compared to existing state-of-the-art software. Like ptychographic cryo-EM, our Ghostbuster algorithm uses phase retrieval to improve reconstructions, but unlike the former, we do not need to modify the existing data acquisition pipelines.
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Affiliation(s)
- Joel Yeo
- NUS Graduate School for Integrative Sciences and Engineering Programme, National University of Singapore, 119077 Singapore, Singapore; Department of Physics, National University of Singapore, 117551 Singapore, Singapore; Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, 138634 Singapore, Singapore
| | - Benedikt J Daurer
- Center for Bio-Imaging Sciences, National University of Singapore, 117557 Singapore, Singapore; Diamond Light Source, Harwell Campus, Didcot, OX11 0DE, UK
| | - Dari Kimanius
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK; CZ Imaging Institute, 3400 Bridge Parkway, Redwood City, CA 94065, USA
| | - Deepan Balakrishnan
- Department of Biological Sciences, National University of Singapore, 117558 Singapore, Singapore; Center for Bio-Imaging Sciences, National University of Singapore, 117557 Singapore, Singapore
| | - Tristan Bepler
- Simons Machine Learning Center, New York Structural Biology Center, New York, NY, USA
| | - Yong Zi Tan
- Department of Biological Sciences, National University of Singapore, 117558 Singapore, Singapore; Center for Bio-Imaging Sciences, National University of Singapore, 117557 Singapore, Singapore; Disease Intervention Technology Laboratory (DITL), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, 138648 Singapore, Singapore; Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, 138673 Singapore, Singapore
| | - N Duane Loh
- NUS Graduate School for Integrative Sciences and Engineering Programme, National University of Singapore, 119077 Singapore, Singapore; Department of Physics, National University of Singapore, 117551 Singapore, Singapore; Department of Biological Sciences, National University of Singapore, 117558 Singapore, Singapore; Center for Bio-Imaging Sciences, National University of Singapore, 117557 Singapore, Singapore.
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2
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Zheng W, Kang J, Niu K, Ophus C, Chan EM, Ercius P, Wang LW, Wu J, Zheng H. Reversible phase transformations between Pb nanocrystals and a viscous liquid-like phase. SCIENCE ADVANCES 2024; 10:eadn6426. [PMID: 38896628 PMCID: PMC11186508 DOI: 10.1126/sciadv.adn6426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/14/2024] [Indexed: 06/21/2024]
Abstract
Phase transformations have been a prominent topic of study for both fundamental and applied science. Solid-liquid reaction-induced phase transformations can be hard to characterize, and the transformation mechanisms are often not fully understood. Here, we report reversible phase transformations between a metal (Pb) nanocrystal and a viscous liquid-like phase unveiled by in situ liquid cell transmission electron microscopy. The reversible phase transformations are obtained by modulating the electron current density (between 1000 and 3000 electrons Å-2 s-1). The metal-organic viscous liquid-like phase exhibits short-range ordering with a preferred Pb-Pb distance of 0.5 nm. Assisted by density functional theory and molecular dynamics calculations, we show that the viscous liquid-like phase results from the reactions of Pb with the CH3O fragments from the triethylene glycol solution under electron beam irradiation. Such reversible phase transformations may find broad implementations.
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Affiliation(s)
- Wenjing Zheng
- School of Energy and Power Engineering, North University of China, Taiyuan 030051, China
| | - Jun Kang
- Beijing Computational Science Research Center, Beijing 100193, China
- Department of Physics, Beijing Normal University, Beijing 100875, China
| | - Kaiyang Niu
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Colin Ophus
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Emory M. Chan
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Peter Ercius
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lin-Wang Wang
- Institute of Semiconductors, University of Chinese Academy of Sciences, Beijing 100083, China
| | - Junqiao Wu
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Haimei Zheng
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
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3
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Pelz PM, Griffin SM, Stonemeyer S, Popple D, DeVyldere H, Ercius P, Zettl A, Scott MC, Ophus C. Solving complex nanostructures with ptychographic atomic electron tomography. Nat Commun 2023; 14:7906. [PMID: 38036516 PMCID: PMC10689721 DOI: 10.1038/s41467-023-43634-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 11/15/2023] [Indexed: 12/02/2023] Open
Abstract
Transmission electron microscopy (TEM) is essential for determining atomic scale structures in structural biology and materials science. In structural biology, three-dimensional structures of proteins are routinely determined from thousands of identical particles using phase-contrast TEM. In materials science, three-dimensional atomic structures of complex nanomaterials have been determined using atomic electron tomography (AET). However, neither of these methods can determine the three-dimensional atomic structure of heterogeneous nanomaterials containing light elements. Here, we perform ptychographic electron tomography from 34.5 million diffraction patterns to reconstruct an atomic resolution tilt series of a double wall-carbon nanotube (DW-CNT) encapsulating a complex ZrTe sandwich structure. Class averaging the resulting tilt series images and subpixel localization of the atomic peaks reveals a Zr11Te50 structure containing a previously unobserved ZrTe2 phase in the core. The experimental realization of atomic resolution ptychographic electron tomography will allow for the structural determination of a wide range of beam-sensitive nanomaterials containing light elements.
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Affiliation(s)
- Philipp M Pelz
- Institute of Micro- and Nanostructure Research (IMN) & Center for Nanoanalysis and Electron Microscopy (CENEM), Friedrich Alexander-Universität Erlangen-Nürnberg, IZNF, 91058, Erlangen, Germany.
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, 94720, USA.
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Sinéad M Griffin
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Scott Stonemeyer
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Kavli Energy NanoSciences Institute at the University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Chemistry, University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Physics, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Derek Popple
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Kavli Energy NanoSciences Institute at the University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Chemistry, University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Physics, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Hannah DeVyldere
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Peter Ercius
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alex Zettl
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Kavli Energy NanoSciences Institute at the University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Physics, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Mary C Scott
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, 94720, USA
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Colin Ophus
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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Terzoudis-Lumsden EWC, Petersen TC, Brown HG, Pelz PM, Ophus C, Findlay SD. Resolution of Virtual Depth Sectioning from Four-Dimensional Scanning Transmission Electron Microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1409-1421. [PMID: 37488824 DOI: 10.1093/micmic/ozad068] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/15/2023] [Accepted: 05/25/2023] [Indexed: 07/26/2023]
Abstract
One approach to three-dimensional structure determination using the wealth of scattering data in four-dimensional (4D) scanning transmission electron microscopy (STEM) is the parallax method proposed by Ophus et al. (2019. Advanced phase reconstruction methods enabled by 4D scanning transmission electron microscopy, Microsc Microanal25, 10-11), which determines the scattering matrix and uses it to synthesize a virtual depth-sectioning reconstruction of the sample structure. Drawing on an equivalence with a hypothetical confocal imaging mode, we derive contrast transfer and point spread functions for this parallax method applied to weakly scattering objects, showing them identical to earlier depth-sectioning STEM modes when only bright field signal is used, but that improved depth resolution is possible if dark field signal can be used. Through a simulation-based study of doped Si, we show that this depth resolution is preserved for thicker samples, explore the impact of shot noise on the parallax reconstructions, discuss challenges to making use of dark field signal, and identify cases where the interpretation of the parallax reconstruction breaks down.
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Affiliation(s)
| | - T C Petersen
- School of Physics and Astronomy, Monash University, Melbourne, VIC 3800, Australia
- Monash Centre for Electron Microscopy, Monash University, Melbourne, VIC 3800, Australia
| | - H G Brown
- Ian Holmes Imaging Center, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3052, Australia
| | - P M Pelz
- Institute of Micro- and Nanostructure Research and Center for Nanoanalysis and Electron Microscopy, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Bavaria 91058, Germany
| | - C Ophus
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - S D Findlay
- School of Physics and Astronomy, Monash University, Melbourne, VIC 3800, Australia
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5
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Sadri A, Findlay SD. Determining the Projected Crystal Structure from Four-dimensional Scanning Transmission Electron Microscopy via the Scattering Matrix. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:967-982. [PMID: 37749695 DOI: 10.1093/micmic/ozad018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/15/2023] [Accepted: 02/05/2023] [Indexed: 09/27/2023]
Abstract
We present a gradient-descent-based approach to determining the projected electrostatic potential from four-dimensional scanning transmission electron microscopy measurements of a periodic, crystalline material even when dynamical scattering occurs. The method solves for the scattering matrix as an intermediate step, but overcomes the so-called truncation problem that limited previous scattering-matrix-based projected structure determination methods. Gradient descent is made efficient by using analytic expressions for the gradients. Through simulated case studies, we show that iteratively improving the scattering matrix determination can significantly improve the accuracy of the projected structure determination.
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Affiliation(s)
- Alireza Sadri
- School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia
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6
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Gureyev TE, Brown HG, Quiney HM, Allen LJ. Unified fast reconstruction algorithm for conventional, phase-contrast, and diffraction tomography. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2022; 39:C143-C155. [PMID: 36520754 DOI: 10.1364/josaa.468350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
A unified method for three-dimensional reconstruction of objects from transmission images collected at multiple illumination directions is described. The method may be applicable to experimental conditions relevant to absorption-based, phase-contrast, or diffraction imaging using x rays, electrons, and other forms of penetrating radiation or matter waves. Both the phase retrieval (also known as contrast transfer function correction) and the effect of Ewald sphere curvature (in the cases with a shallow depth of field and significant in-object diffraction) are incorporated in the proposed algorithm and can be taken into account. Multiple scattering is not treated explicitly but can be mitigated as a result of angular averaging that constitutes an essential feature of the method. The corresponding numerical algorithm is based on three-dimensional gridding which allows for fast computational implementation, including a straightforward parallelization. The algorithm can be used with any scanning geometry involving plane-wave illumination. A software code implementing the proposed algorithm has been developed, tested on simulated and experimental image data, and made publicly available.
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7
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Xue Y, Ren D, Waller L. Three-dimensional bi-functional refractive index and fluorescence microscopy (BRIEF). BIOMEDICAL OPTICS EXPRESS 2022; 13:5900-5908. [PMID: 36733730 PMCID: PMC9872885 DOI: 10.1364/boe.456621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 09/19/2022] [Accepted: 10/01/2022] [Indexed: 06/18/2023]
Abstract
Fluorescence microscopy is a powerful tool for imaging biological samples with molecular specificity. In contrast, phase microscopy provides label-free measurement of the sample's refractive index (RI), which is an intrinsic optical property that quantitatively relates to cell morphology, mass, and stiffness. Conventional imaging techniques measure either the labeled fluorescence (functional) information or the label-free RI (structural) information, though it may be valuable to have both. For example, biological tissues have heterogeneous RI distributions, causing sample-induced scattering that degrades the fluorescence image quality. When both fluorescence and 3D RI are measured, one can use the RI information to digitally correct multiple-scattering effects in the fluorescence image. Here, we develop a new computational multi-modal imaging method based on epi-mode microscopy that reconstructs both 3D fluorescence and 3D RI from a single dataset. We acquire dozens of fluorescence images, each 'illuminated' by a single fluorophore, then solve an inverse problem with a multiple-scattering forward model. We experimentally demonstrate our method for epi-mode 3D RI imaging and digital correction of multiple-scattering effects in fluorescence images.
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Affiliation(s)
- Yi Xue
- Department of Biomedical Engineering, University of California, Davis, CA 95616, USA
| | - David Ren
- Department of Electrical Engineering & Computer Sciences, University of California, Berkeley, CA 94720, USA
| | - Laura Waller
- Department of Electrical Engineering & Computer Sciences, University of California, Berkeley, CA 94720, USA
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8
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Three-dimensional electron ptychography of organic-inorganic hybrid nanostructures. Nat Commun 2022; 13:4787. [PMID: 35970924 PMCID: PMC9378626 DOI: 10.1038/s41467-022-32548-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/04/2022] [Indexed: 11/22/2022] Open
Abstract
Three dimensional scaffolded DNA origami with inorganic nanoparticles has been used to create tailored multidimensional nanostructures. However, the image contrast of DNA is poorer than those of the heavy nanoparticles in conventional transmission electron microscopy at high defocus so that the biological and non-biological components in 3D scaffolds cannot be simultaneously resolved using tomography of samples in a native state. We demonstrate the use of electron ptychography to recover high contrast phase information from all components in a DNA origami scaffold without staining. We further quantitatively evaluate the enhancement of contrast in comparison with conventional transmission electron microscopy. In addition, We show that for ptychography post-reconstruction focusing simplifies the workflow and reduces electron dose and beam damage. The authors demonstrate electron ptychographic computed tomography by simultaneously recording high contrast data from both the organic- and inorganic components in a 3D DNA-origami framework hybrid nanostructure.
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9
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Whittaker ML, Ren D, Ophus C, Zhang Y, Waller L, Gilbert B, Banfield JF. Ion complexation waves emerge at the curved interfaces of layered minerals. Nat Commun 2022; 13:3382. [PMID: 35697675 PMCID: PMC9192655 DOI: 10.1038/s41467-022-31004-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/30/2022] [Indexed: 11/11/2022] Open
Abstract
Visualizing hydrated interfaces is of widespread interest across the physical sciences and is a particularly acute need for layered minerals, whose properties are governed by the structure of the electric double layer (EDL) where mineral and solution meet. Here, we show that cryo electron microscopy and tomography enable direct imaging of the EDL at montmorillonite interfaces in monovalent electrolytes with ångstrom resolution over micron length scales. A learning-based multiple-scattering reconstruction method for cryo electron tomography reveals ions bound asymmetrically on opposite sides of curved, exfoliated layers. We observe conserved ion-density asymmetry across stacks of interacting layers in cryo electron microscopy that is associated with configurations of inner- and outer-sphere ion-water-mineral complexes that we term complexation waves. Coherent X-ray scattering confirms that complexation waves propagate at room-temperature via a competition between ion dehydration and charge interactions that are coupled across opposing sides of a layer, driving dynamic transitions between stacked and aggregated states via layer exfoliation. The structure of hydrated interfaces is essential for understanding of geochemical processes and behavior of layered minerals. The authors show that waves of hydrated ions emerge at curved aqueous interfaces and couple mineral deformation to the chemistry of the solution.
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Affiliation(s)
- Michael L Whittaker
- Energy Geosciences Division, Lawrence Berkeley National Laboratory, 94720, Berkeley, CA, USA. .,Department of Earth and Planetary Science, University of California, 94720, Berkeley, CA, USA.
| | - David Ren
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, 94720, USA
| | - Colin Ophus
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 94720, Berkeley, CA, USA
| | - Yugang Zhang
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Laura Waller
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, 94720, USA
| | - Benjamin Gilbert
- Energy Geosciences Division, Lawrence Berkeley National Laboratory, 94720, Berkeley, CA, USA.,Department of Earth and Planetary Science, University of California, 94720, Berkeley, CA, USA
| | - Jillian F Banfield
- Energy Geosciences Division, Lawrence Berkeley National Laboratory, 94720, Berkeley, CA, USA.,Department of Earth and Planetary Science, University of California, 94720, Berkeley, CA, USA
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10
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Gureyev TE, Quiney HM, Allen LJ. Method for virtual optical sectioning and tomography utilizing shallow depth of field. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2022; 39:936-947. [PMID: 36215455 DOI: 10.1364/josaa.455682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/10/2022] [Indexed: 06/16/2023]
Abstract
A method is proposed for high-resolution, three-dimensional reconstruction of internal structures of objects from planar transmission images. The described approach can be used with any form of radiation or matter waves, in principle, provided that the depth of field is smaller than the thickness of the sample. The physical optics basis for the method is elucidated, and the reconstruction algorithm is presented in detail. A simulated example demonstrates an application of the method to three-dimensional electron transmission imaging of a nanoparticle under realistic radiation dose and spatial resolution constraints. It is envisaged that the method can be applicable in high-resolution transmission electron microscopy, soft x-ray microscopy, ultrasound imaging, and other areas.
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11
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Gureyev TE, Paganin DM, Brown HG, Quiney HM, Allen LJ. A Method for High-Resolution Three-Dimensional Reconstruction with Ewald Sphere Curvature Correction from Transmission Electron Images. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-17. [PMID: 35485646 DOI: 10.1017/s1431927622000630] [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
A method for three-dimensional reconstruction of objects from defocused images collected at multiple illumination directions in high-resolution transmission electron microscopy is presented. The method effectively corrects for the Ewald sphere curvature by taking into account the in-particle propagation of the electron beam. Numerical simulations demonstrate that the proposed method is capable of accurately reconstructing biological molecules or nanoparticles from high-resolution defocused images under conditions achievable in single-particle electron cryo-microscopy or electron tomography with realistic radiation doses, non-trivial aberrations, multiple scattering, and other experimentally relevant factors. The physics of the method is based on the well-known Diffraction Tomography formalism, but with the phase-retrieval step modified to include a conjugation of the phase (i.e., multiplication of the phase by a negative constant). At each illumination direction, numerically backpropagating the beam with the conjugated phase produces maximum contrast at the location of individual atoms in the molecule or nanoparticle. The resultant algorithm, Conjugated Holographic Reconstruction, can potentially be incorporated into established software tools for single-particle analysis, such as, for example, RELION or FREALIGN, in place of the conventional contrast transfer function correction procedure, in order to account for the Ewald sphere curvature and improve the spatial resolution of the three-dimensional reconstruction.
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Affiliation(s)
- Timur E Gureyev
- ARC Centre in Advanced Molecular Imaging, School of Physics, The University of Melbourne, Parkville, VIC3010, Australia
- School of Physics and Astronomy, Monash University, Clayton, VIC3800, Australia
| | - David M Paganin
- School of Physics and Astronomy, Monash University, Clayton, VIC3800, Australia
| | - Hamish G Brown
- ARC Centre in Advanced Molecular Imaging, School of Physics, The University of Melbourne, Parkville, VIC3010, Australia
| | - Harry M Quiney
- ARC Centre in Advanced Molecular Imaging, School of Physics, The University of Melbourne, Parkville, VIC3010, Australia
| | - Leslie J Allen
- ARC Centre in Advanced Molecular Imaging, School of Physics, The University of Melbourne, Parkville, VIC3010, Australia
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12
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Petersen T, Zhao C, Bøjesen E, Broge N, Hata S, Liu Y, Etheridge J. Volume imaging by tracking sparse topological features in electron micrograph tilt series. Ultramicroscopy 2022; 236:113475. [DOI: 10.1016/j.ultramic.2022.113475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/17/2021] [Accepted: 01/24/2022] [Indexed: 10/19/2022]
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13
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Pelz PM, Groschner C, Bruefach A, Satariano A, Ophus C, Scott MC. Simultaneous Successive Twinning Captured by Atomic Electron Tomography. ACS NANO 2022; 16:588-596. [PMID: 34783237 DOI: 10.1021/acsnano.1c07772] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Shape-controlled synthesis of multiply twinned nanostructures is heavily emphasized in nanoscience, in large part due to the desire to control the size, shape, and terminating facets of metal nanoparticles for applications in catalysis. Direct control of the size and shape of solution-grown nanoparticles relies on an understanding of how synthetic parameters alter nanoparticle structures during synthesis. However, while outcome populations can be effectively studied with standard electron microscopy methods, transient structures that appear during some synthetic routes are difficult to study using conventional high resolution imaging methods due to the high complexity of the 3D nanostructures. Here, we have studied the prevalence of transient structures during growth of multiply twinned particles and employed atomic electron tomography to reveal the atomic-scale three-dimensional structure of a Pd nanoparticle undergoing a shape transition. By identifying over 20 000 atoms within the structure and classifying them according to their local crystallographic environment, we observe a multiply twinned structure consistent with a simultaneous successive twinning from a decahedral to icosahedral structure.
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Affiliation(s)
- Philipp M Pelz
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, California 94720, United States
- The National Center for Electron Microscopy, Molecular Foundry, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Catherine Groschner
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Alexandra Bruefach
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Adam Satariano
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Colin Ophus
- The National Center for Electron Microscopy, Molecular Foundry, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Mary C Scott
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, California 94720, United States
- The National Center for Electron Microscopy, Molecular Foundry, 1 Cyclotron Road, Berkeley, California 94720, United States
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14
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Perspective: Emerging strategies for determining atomic-resolution structures of macromolecular complexes within cells. J Struct Biol 2021; 214:107827. [PMID: 34915129 PMCID: PMC8978977 DOI: 10.1016/j.jsb.2021.107827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/05/2021] [Accepted: 12/08/2021] [Indexed: 11/28/2022]
Abstract
In principle, electron cryo-tomography (cryo-ET) of thin portions of cells provides high-resolution images of the three-dimensional spatial arrangement of all members of the proteome. In practice, however, radiation damage creates a tension between recording images at many different tilt angles, but at correspondingly reduced exposure levels, versus limiting the number of tilt angles in order to improve the signal-to-noise ratio (SNR). Either way, it is challenging to read the available information out at the level of atomic structure. Here, we first review work that explores the optimal strategy for data collection, which currently seems to favor the use of a limited angular range for tilting the sample or even the use of a single image to record the high-resolution information. Looking then to the future, we point to the alternative of so-called “deconvolution microscopy”, which may be applied to tilt-series or optically-sectioned, focal series data. Recording data as a focal series has the advantage that little or no translational alignment of frames might be needed, and a three-dimensional reconstruction might require only 2/3 the number of images as does standard tomography. We also point to the unexploited potential of phase plates to increase the contrast, and thus to reduce the electron exposure levels while retaining the ability align and merge the data. In turn, using much lower exposures per image could have the advantage that high-resolution information is retained throughout the full data-set, whether recorded as a tilt series or a focal series of images.
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15
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Ribet SM, Murthy AA, Roth EW, Dos Reis R, Dravid VP. Making the Most of your Electrons: Challenges and Opportunities in Characterizing Hybrid Interfaces with STEM. MATERIALS TODAY (KIDLINGTON, ENGLAND) 2021; 50:100-115. [PMID: 35241968 PMCID: PMC8887695 DOI: 10.1016/j.mattod.2021.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Inspired by the unique architectures composed of hard and soft materials in natural and biological systems, synthetic hybrid structures and associated soft-hard interfaces have recently evoked significant interest. Soft matter is typically dominated by fluctuations even at room temperature, while hard matter (which often serves as the substrate or anchor for the soft component) is governed by rigid mechanical behavior. This dichotomy offers considerable opportunities to leverage the disparate properties offered by these components across a wide spectrum spanning from basic science to engineering insights with significant technological overtones. Such hybrid structures, which include polymer nanocomposites, DNA functionalized nanoparticle superlattices and metal organic frameworks to name a few, have delivered promising insights into the areas of catalysis, environmental remediation, optoelectronics, medicine, and beyond. The interfacial structure between these hard and soft phases exists across a variety of length scales and often strongly influence the functionality of hybrid systems. While scanning/transmission electron microscopy (S/TEM) has proven to be a valuable tool for acquiring intricate molecular and nanoscale details of these interfaces, the unusual nature of hybrid composites presents a suite of challenges that make assessing or establishing the classical structure-property relationships especially difficult. These include challenges associated with preparing electron-transparent samples and obtaining sufficient contrast to resolve the interface between dissimilar materials given the dose sensitivity of soft materials. We discuss each of these challenges and supplement a review of recent developments in the field with additional experimental investigations and simulations to present solutions for attaining a nano or atomic-level understanding of these interfaces. These solutions present a host of opportunities for investigating and understanding the role interfaces play in this unique class of functional materials.
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Affiliation(s)
- Stephanie M Ribet
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL
| | - Akshay A Murthy
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL
- International Institute of Nanotechnology, Northwestern University, Evanston, IL
| | - Eric W Roth
- The NUANCE Center, Northwestern University, Evanston, IL
| | - Roberto Dos Reis
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL
- The NUANCE Center, Northwestern University, Evanston, IL
| | - Vinayak P Dravid
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL
- International Institute of Nanotechnology, Northwestern University, Evanston, IL
- The NUANCE Center, Northwestern University, Evanston, IL
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16
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Ronen R, Attias Y, Schechner YY, Jaffe JS, Orenstein E. Plankton reconstruction through robust statistical optical tomography. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2021; 38:1320-1331. [PMID: 34613139 DOI: 10.1364/josaa.423037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
Plankton interact with the environment according to their size and three-dimensional (3D) structure. To study them outdoors, these translucent specimens are imaged in situ. Light projects through a specimen in each image. The specimen has a random scale, drawn from the population's size distribution and random unknown pose. The specimen appears only once before drifting away. We achieve 3D tomography using such a random ensemble to statistically estimate an average volumetric distribution of the plankton type and specimen size. To counter errors due to non-rigid deformations, we weight the data, drawing from advanced models developed for cryo-electron microscopy. The weights convey the confidence in the quality of each datum. This confidence relies on a statistical error model. We demonstrate the approach on live plankton using an underwater field microscope.
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17
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Findlay SD, Brown HG, Pelz PM, Ophus C, Ciston J, Allen LJ. Scattering Matrix Determination in Crystalline Materials from 4D Scanning Transmission Electron Microscopy at a Single Defocus Value. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2021; 27:744-757. [PMID: 34311809 DOI: 10.1017/s1431927621000490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Recent work has revived interest in the scattering matrix formulation of electron scattering in transmission electron microscopy as a stepping stone toward atomic-resolution structure determination in the presence of multiple scattering. We discuss ways of visualizing the scattering matrix that make its properties clear. Through a simulation-based case study incorporating shot noise, we shown how regularizing on this continuity enables the scattering matrix to be reconstructed from 4D scanning transmission electron microscopy (STEM) measurements from a single defocus value. Intriguingly, for crystalline samples, this process also yields the sample thickness to nanometer accuracy with no a priori knowledge about the sample structure. The reconstruction quality is gauged by using the reconstructed scattering matrix to simulate STEM images at defocus values different from that of the data from which it was reconstructed.
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Affiliation(s)
- Scott D Findlay
- School of Physics and Astronomy, Monash University, Clayton, VIC3800, Australia
| | - Hamish G Brown
- National Center for Electron Microscopy Facility, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA94720, USA
- Ian Holmes Imaging Center, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC3052, Australia
| | - Philipp M Pelz
- National Center for Electron Microscopy Facility, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA94720, USA
- Department of Materials Science and Engineering, University of California, Berkeley, CA94720, USA
| | - Colin Ophus
- National Center for Electron Microscopy Facility, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA94720, USA
| | - Jim Ciston
- National Center for Electron Microscopy Facility, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA94720, USA
| | - Leslie J Allen
- School of Physics, University of Melbourne, Parkville, VIC3010, Australia
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18
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Rizvi A, Mulvey JT, Carpenter BP, Talosig R, Patterson JP. A Close Look at Molecular Self-Assembly with the Transmission Electron Microscope. Chem Rev 2021; 121:14232-14280. [PMID: 34329552 DOI: 10.1021/acs.chemrev.1c00189] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Molecular self-assembly is pervasive in the formation of living and synthetic materials. Knowledge gained from research into the principles of molecular self-assembly drives innovation in the biological, chemical, and materials sciences. Self-assembly processes span a wide range of temporal and spatial domains and are often unintuitive and complex. Studying such complex processes requires an arsenal of analytical and computational tools. Within this arsenal, the transmission electron microscope stands out for its unique ability to visualize and quantify self-assembly structures and processes. This review describes the contribution that the transmission electron microscope has made to the field of molecular self-assembly. An emphasis is placed on which TEM methods are applicable to different structures and processes and how TEM can be used in combination with other experimental or computational methods. Finally, we provide an outlook on the current challenges to, and opportunities for, increasing the impact that the transmission electron microscope can have on molecular self-assembly.
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Affiliation(s)
- Aoon Rizvi
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Justin T Mulvey
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Brooke P Carpenter
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Rain Talosig
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Joseph P Patterson
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
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19
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Wu H, Li T, Maddala SP, Khalil ZJ, Joosten RRM, Mezari B, Hensen EJM, de With G, Friedrich H, van Bokhoven JA, Patterson JP. Studying Reaction Mechanisms in Solution Using a Distributed Electron Microscopy Method. ACS NANO 2021; 15:10296-10308. [PMID: 34077193 DOI: 10.1021/acsnano.1c02461] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Electron microscopy (EM) of materials undergoing chemical reactions provides knowledge of the underlying mechanisms. However, the mechanisms are often complex and cannot be fully resolved using a single method. Here, we present a distributed electron microscopy method for studying complex reactions. The method combines information from multiple stages of the reaction and from multiple EM methods, including liquid phase EM (LP-EM), cryogenic EM (cryo-EM), and cryo-electron tomography (cryo-ET). We demonstrate this method by studying the desilication mechanism of zeolite crystals. Collectively, our data reveal that the reaction proceeds via a two-step anisotropic etching process and that the defects in curved surfaces and between the subunits in the crystal control the desilication kinetics by directing mass transport.
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Affiliation(s)
- Hanglong Wu
- Laboratory of Physical Chemistry, Department of Chemical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Teng Li
- Department of Chemistry and Applied Bioscience, Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Sai P Maddala
- Laboratory of Physical Chemistry, Department of Chemical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Zafeiris J Khalil
- Laboratory of Physical Chemistry, Department of Chemical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Rick R M Joosten
- Center for Multiscale Electron Microscopy, Department of Chemical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Brahim Mezari
- Inorganic Materials & Catalysis Group, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Emiel J M Hensen
- Inorganic Materials & Catalysis Group, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Gijsbertus de With
- Laboratory of Physical Chemistry, Department of Chemical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Heiner Friedrich
- Laboratory of Physical Chemistry, Department of Chemical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Center for Multiscale Electron Microscopy, Department of Chemical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands
| | - Jeroen A van Bokhoven
- Department of Chemistry and Applied Bioscience, Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Joseph P Patterson
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
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20
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A new solution to the curved Ewald sphere problem for 3D image reconstruction in electron microscopy. Ultramicroscopy 2021; 224:113234. [DOI: 10.1016/j.ultramic.2021.113234] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 02/07/2021] [Accepted: 02/12/2021] [Indexed: 11/24/2022]
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21
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Du M, Di ZW, Gürsoy D, Xian RP, Kozorovitskiy Y, Jacobsen C. Upscaling X-ray nanoimaging to macroscopic specimens. J Appl Crystallogr 2021; 54:386-401. [PMID: 33953650 PMCID: PMC8056767 DOI: 10.1107/s1600576721000194] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 01/06/2021] [Indexed: 11/10/2022] Open
Abstract
Upscaling X-ray nanoimaging to macroscopic specimens has the potential for providing insights across multiple length scales, but its feasibility has long been an open question. By combining the imaging requirements and existing proof-of-principle examples in large-specimen preparation, data acquisition and reconstruction algorithms, the authors provide imaging time estimates for howX-ray nanoimaging can be scaled to macroscopic specimens. To arrive at this estimate, a phase contrast imaging model that includes plural scattering effects is used to calculate the required exposure and corresponding radiation dose. The coherent X-ray flux anticipated from upcoming diffraction-limited light sources is then considered. This imaging time estimation is in particular applied to the case of the connectomes of whole mouse brains. To image the connectome of the whole mouse brain, electron microscopy connectomics might require years, whereas optimized X-ray microscopy connectomics could reduce this to one week. Furthermore, this analysis points to challenges that need to be overcome (such as increased X-ray detector frame rate) and opportunities that advances in artificial-intelligence-based 'smart' scanning might provide. While the technical advances required are daunting, it is shown that X-ray microscopy is indeed potentially applicable to nanoimaging of millimetre- or even centimetre-size specimens.
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Affiliation(s)
- Ming Du
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Zichao Wendy Di
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA.,Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Doǧa Gürsoy
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA.,Department of Electrical Engineering and Computer Science, Northwestern University, Evanston, IL 60208, USA
| | - R Patrick Xian
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
| | - Yevgenia Kozorovitskiy
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA.,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Chris Jacobsen
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA.,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA.,Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
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22
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Hong X, Zeltmann SE, Savitzky BH, Rangel DaCosta L, Müller A, Minor AM, Bustillo KC, Ophus C. Multibeam Electron Diffraction. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2021; 27:129-139. [PMID: 33303043 DOI: 10.1017/s1431927620024770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
One of the primary uses for transmission electron microscopy (TEM) is to measure diffraction pattern images in order to determine a crystal structure and orientation. In nanobeam electron diffraction (NBED), we scan a moderately converged electron probe over the sample to acquire thousands or even millions of sequential diffraction images, a technique that is especially appropriate for polycrystalline samples. However, due to the large Ewald sphere of TEM, excitation of Bragg peaks can be extremely sensitive to sample tilt, varying strongly for even a few degrees of sample tilt for crystalline samples. In this paper, we present multibeam electron diffraction (MBED), where multiple probe-forming apertures are used to create multiple scanning transmission electron microscopy (STEM) probes, all of which interact with the sample simultaneously. We detail designs for MBED experiments, and a method for using a focused ion beam to produce MBED apertures. We show the efficacy of the MBED technique for crystalline orientation mapping using both simulations and proof-of-principle experiments. We also show how the angular information in MBED can be used to perform 3D tomographic reconstruction of samples without needing to tilt or scan the sample multiple times. Finally, we also discuss future opportunities for the MBED method.
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Affiliation(s)
- Xuhao Hong
- School of Physics, Nanjing University, Nanjing210093, PR China
| | - Steven E Zeltmann
- Department of Materials Science and Engineering, University of California, Berkeley, CA94720, USA
| | - Benjamin H Savitzky
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA94720, USA
| | - Luis Rangel DaCosta
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA94720, USA
| | - Alexander Müller
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA94720, USA
| | - Andrew M Minor
- Department of Materials Science and Engineering, University of California, Berkeley, CA94720, USA
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA94720, USA
| | - Karen C Bustillo
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA94720, USA
| | - Colin Ophus
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA94720, USA
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23
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Ali S, Du M, Adams MF, Smith B, Jacobsen C. Comparison of distributed memory algorithms for X-ray wave propagation in inhomogeneous media. OPTICS EXPRESS 2020; 28:29590-29618. [PMID: 33114856 PMCID: PMC7679186 DOI: 10.1364/oe.400240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Calculations of X-ray wave propagation in large objects are needed for modeling diffractive X-ray optics and for optimization-based approaches to image reconstruction for objects that extend beyond the depth of focus. We describe three methods for calculating wave propagation with large arrays on parallel computing systems with distributed memory: (1) a full-array Fresnel multislice approach, (2) a tiling-based short-distance Fresnel multislice approach, and (3) a finite difference approach. We find that the first approach suffers from internode communication delays when the transverse array size becomes large, while the second and third approaches have similar scaling to large array size problems (with the second approach offering about three times the compute speed).
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Affiliation(s)
- Sajid Ali
- Applied Physics Program, Northwestern University, Evanston, Illinois 60208, USA
| | - Ming Du
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Mark F. Adams
- Scalable Solvers Group, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Barry Smith
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Chris Jacobsen
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA
- Department of Physics & Astronomy, Northwestern University, Evanston, Illinois 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, USA
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