1
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Xu Z, Li H, Wan X, Fernández JJ, Sun F, Zhang F, Han R. Markerauto2: A fast and robust fully automatic fiducial marker-based tilt series alignment software for electron tomography. Structure 2024; 32:1507-1518.e5. [PMID: 38936367 DOI: 10.1016/j.str.2024.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/21/2024] [Accepted: 05/31/2024] [Indexed: 06/29/2024]
Abstract
Cryoelectron tomography (cryo-ET) has become an indispensable technology for visualizing in situ biological ultrastructures, where the tilt series alignment is the key step to obtain a high-resolution three-dimensional reconstruction. Specifically, with the advent of high-throughput cryo-ET data collection, there is an increasing demand for high-accuracy and fully automatic tilt series alignment, to enable efficient data processing. Here, we propose Markerauto2, a fast and robust fully automatic software that enables accurate fiducial marker-based tilt series alignment. Markerauto2 implements the following novel pipelines: (1) an accelerated high-precision fiducial marker detection with wavelet multiscale template, (2) an ultra-fast and robust fiducial marker tracking supported by hashed geometric features, (3) a high-angle fiducial marker supplementation strategy to produce more complete tracks, and (4) a precise and robust calibration of projection parameters with group-weighted parameter optimization. Comprehensive experiments conducted on both simulated and real-world datasets demonstrate the robustness, efficiency, and effectiveness of the proposed software.
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Affiliation(s)
- Zihe Xu
- Frontiers Science Center for Nonlinear Expectations (Ministry of Education), Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao 266237, China; School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Hongjia Li
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Xiaohua Wan
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Jose-Jesus Fernández
- Spanish National Research Council, Health Research Institute of Asturias, Avenue Hospital Universitario s/n, 33011 Oviedo, Spain
| | - Fei Sun
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Fa Zhang
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China.
| | - Renmin Han
- Frontiers Science Center for Nonlinear Expectations (Ministry of Education), Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao 266237, China; Shanghai YueXin Life-science Infomation Technology Co. Ltd, Shanghai 200235, China.
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2
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Arenas Esteban D, Wang D, Kadu A, Olluyn N, Sánchez-Iglesias A, Gomez-Perez A, González-Casablanca J, Nicolopoulos S, Liz-Marzán LM, Bals S. Quantitative 3D structural analysis of small colloidal assemblies under native conditions by liquid-cell fast electron tomography. Nat Commun 2024; 15:6399. [PMID: 39080248 PMCID: PMC11289127 DOI: 10.1038/s41467-024-50652-y] [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: 11/23/2023] [Accepted: 07/16/2024] [Indexed: 08/02/2024] Open
Abstract
Electron tomography has become a commonly used tool to investigate the three-dimensional (3D) structure of nanomaterials, including colloidal nanoparticle assemblies. However, electron microscopy is typically done under high-vacuum conditions, requiring sample preparation for assemblies obtained by wet colloid chemistry methods. This involves solvent evaporation and deposition on a solid support, which consistently alters the nanoparticle organization. Here, we suggest using electron tomography to study nanoparticle assemblies in their original colloidal liquid environment. To address the challenges related to electron tomography in liquid, we devise a method that combines fast data acquisition in a commercial liquid-cell with a dedicated alignment and reconstruction workflow. We present the advantages of this methodology in accurately characterizing two different systems. 3D reconstructions of assemblies comprising polystyrene-capped Au nanoparticles encapsulated in polymeric shells reveal less compact and more distorted configurations for experiments performed in a liquid medium compared to their dried counterparts. A similar expansion can be observed in quantitative analysis of the surface-to-surface distances of self-assembled Au nanorods in water rather than in a vacuum, in agreement with bulk measurements. This study, therefore, emphasizes the importance of developing high-resolution characterization tools that preserve the native environment of colloidal nanostructures.
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Affiliation(s)
- Daniel Arenas Esteban
- Electron Microscopy for Materials Science (EMAT) and NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Da Wang
- Electron Microscopy for Materials Science (EMAT) and NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
- Guangdong Provincial Key Laboratory of Optical Information Materials and Technology, Institute of Electronic Paper Displays, South China Academy of Advanced Optoelectronics, South China Normal University, Guangzhou, 510006, China
| | - Ajinkya Kadu
- Electron Microscopy for Materials Science (EMAT) and NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
- Centrum Wiskunde & Informatica (CWI), Amsterdam, The Netherlands
| | - Noa Olluyn
- Electron Microscopy for Materials Science (EMAT) and NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Ana Sánchez-Iglesias
- CIC biomaGUNE, Paseo de Miramon 182, 20009, Donostia-San Sebastián, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Paseo de Miramon 182, 20009, Donostia-San Sebastián, Spain
- Materials Physics Center, CSIC-UPV/EHU, Paseo Manuel de Lardizabal 5, 20018, Donostia-San Sebastián, Spain
| | | | | | | | - Luis M Liz-Marzán
- CIC biomaGUNE, Paseo de Miramon 182, 20009, Donostia-San Sebastián, Spain.
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Paseo de Miramon 182, 20009, Donostia-San Sebastián, Spain.
- Ikerbasque, Basque Foundation for Science, 48013, Bilbao, Spain.
- Cinbio, Universidade de Vigo, 36310, Vigo, Spain.
| | - Sara Bals
- Electron Microscopy for Materials Science (EMAT) and NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium.
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3
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Seifer S, Elbaum M. ClusterAlign: A fiducial tracking and tilt series alignment tool for thick sample tomography. BIOLOGICAL IMAGING 2022; 2:e7. [PMID: 38486831 PMCID: PMC10936405 DOI: 10.1017/s2633903x22000071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/04/2022] [Accepted: 07/18/2022] [Indexed: 03/17/2024]
Abstract
Thick specimens, as encountered in cryo-scanning transmission electron tomography, offer special challenges to conventional reconstruction workflows. The visibility of features, including gold nanoparticles introduced as fiducial markers, varies strongly through the tilt series. As a result, tedious manual refinement may be required in order to produce a successful alignment. Information from highly tilted views must often be excluded to the detriment of axial resolution in the reconstruction. We introduce here an approach to tilt series alignment based on identification of fiducial particle clusters that transform coherently in rotation, essentially those that lie at similar depth. Clusters are identified by comparison of tilted views with a single untilted reference, rather than with adjacent tilts. The software, called ClusterAlign, proves robust to poor signal to noise ratio and varying visibility of the individual fiducials and is successful in carrying the alignment to the ends of the tilt series where other methods tend to fail. ClusterAlign may be used to generate a list of tracked fiducials, to align a tilt series, or to perform a complete 3D reconstruction. Tools to evaluate alignment error by projection matching are included. Execution involves no manual intervention, and adherence to standard file formats facilitates an interface with other software, particularly IMOD/etomo, tomo3d, and tomoalign.
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Affiliation(s)
- Shahar Seifer
- Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Elbaum
- Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
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4
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Bian T, Gardin A, Gemen J, Houben L, Perego C, Lee B, Elad N, Chu Z, Pavan GM, Klajn R. Electrostatic co-assembly of nanoparticles with oppositely charged small molecules into static and dynamic superstructures. Nat Chem 2021; 13:940-949. [PMID: 34489564 PMCID: PMC7611764 DOI: 10.1038/s41557-021-00752-9] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 06/14/2021] [Indexed: 02/08/2023]
Abstract
Coulombic interactions can be used to assemble charged nanoparticles into higher-order structures, but the process requires oppositely charged partners that are similarly sized. The ability to mediate the assembly of such charged nanoparticles using structurally simple small molecules would greatly facilitate the fabrication of nanostructured materials and harnessing their applications in catalysis, sensing and photonics. Here we show that small molecules with as few as three electric charges can effectively induce attractive interactions between oppositely charged nanoparticles in water. These interactions can guide the assembly of charged nanoparticles into colloidal crystals of a quality previously only thought to result from their co-crystallization with oppositely charged nanoparticles of a similar size. Transient nanoparticle assemblies can be generated using positively charged nanoparticles and multiply charged anions that are enzymatically hydrolysed into mono- and/or dianions. Our findings demonstrate an approach for the facile fabrication, manipulation and further investigation of static and dynamic nanostructured materials in aqueous environments.
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Affiliation(s)
- Tong Bian
- Department of Organic Chemistry, Weizmann Institute of Science,
Rehovot 76100, Israel
| | - Andrea Gardin
- Department of Innovative Technologies, University of Applied
Sciences and Arts of Southern Switzerland, CH-6928 Manno, Switzerland,Department of Applied Science and Technology, Politecnico di Torino,
10129 Torino, Italy
| | - Julius Gemen
- Department of Organic Chemistry, Weizmann Institute of Science,
Rehovot 76100, Israel
| | - Lothar Houben
- Department of Chemical Research Support, Weizmann Institute of
Science, Rehovot 76100, Israel
| | - Claudio Perego
- Department of Innovative Technologies, University of Applied
Sciences and Arts of Southern Switzerland, CH-6928 Manno, Switzerland
| | - Byeongdu Lee
- X-ray Science Division, Advanced Photon Source, Argonne National
Laboratory, Lemont, IL 60439, USA
| | - Nadav Elad
- Department of Chemical Research Support, Weizmann Institute of
Science, Rehovot 76100, Israel
| | - Zonglin Chu
- Department of Organic Chemistry, Weizmann Institute of Science,
Rehovot 76100, Israel
| | - Giovanni M. Pavan
- Department of Innovative Technologies, University of Applied
Sciences and Arts of Southern Switzerland, CH-6928 Manno, Switzerland,Department of Applied Science and Technology, Politecnico di Torino,
10129 Torino, Italy
| | - Rafal Klajn
- Department of Organic Chemistry, Weizmann Institute of Science,
Rehovot 76100, Israel,
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5
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Mesoscale Anisotropy in Porous Media Made of Clay Minerals. A Numerical Study Constrained by Experimental Data. MATERIALS 2018; 11:ma11101972. [PMID: 30322150 PMCID: PMC6212813 DOI: 10.3390/ma11101972] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/11/2018] [Accepted: 10/12/2018] [Indexed: 11/16/2022]
Abstract
The anisotropic properties of clay-rich porous media have significant impact on the directional dependence of fluids migration in environmental and engineering sciences. This anisotropy, linked to the preferential orientation of flat anisometric clay minerals particles, is studied here on the basis of the simulation of three-dimensional packings of non-interacting disks, using a sequential deposition algorithm under a gravitational field. Simulations show that the obtained porosities fall onto a single master curve when plotted against the anisotropy value. This finding is consistent with results from sedimentation experiments using polytetrafluoroethylene (PTFE) disks and subsequent extraction of particle anisotropy through X-ray microtomography. Further geometrical analyses of computed porous media highlight that both particle orientation and particle aggregation are responsible of the evolution of porosity as a function of anisotropy. Moreover, morphological analysis of the porous media using chord length measurements shows that the anisotropy of the pore and solid networks can be correlated with particle orientation. These results indicate that computed porous media, mimicking the organization of clay minerals, can be used to shed light on the anisotropic properties of fluid transfer in clay-based materials.
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6
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Ranjan P, Kaplan-Ashiri I, Popovitz-Biro R, Cohen SR, Houben L, Tenne R, Lahav M, van der Boom ME. Metallic Nanocrystal Ripening on Inorganic Surfaces. ACS OMEGA 2018; 3:6533-6539. [PMID: 31458829 PMCID: PMC6644818 DOI: 10.1021/acsomega.8b00779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 05/22/2018] [Indexed: 06/10/2023]
Abstract
In this paper, we demonstrate the formation of hybrid nanostructures consisting of two distinctive components mainly in a one-to-one ratio. Thermolysis of inorganic nanotubes (INT) and closed-cage, inorganic fullerene-like (IF) nanoparticles decorated with a dense coating of metallic nanoparticles (M = Au, Ag, Pd) results in migration of relatively small NPs or surface-enhanced diffusion of atoms or clusters, generating larger particles (ripening). AuNP growth on the surface of INTs has been captured in real time using in situ electron microscopy measurements. Reaction of the AuNP-decorated INTs with an alkylthiol results in a chemically induced NP fusion process at room temperature. The NPs do not dissociate from the surfaces of the INTs and IFs, but for proximate IFs we observed fusion between AuNPs originating from different IFs.
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Affiliation(s)
- Priyadarshi Ranjan
- Department
of Organic Chemistry, Department of Materials and Interfaces, and Department of
Chemical Research Support, The Weizmann
Institute of Science, Rehovot 7610001, Israel
| | - Ifat Kaplan-Ashiri
- Department
of Organic Chemistry, Department of Materials and Interfaces, and Department of
Chemical Research Support, The Weizmann
Institute of Science, Rehovot 7610001, Israel
| | - Ronit Popovitz-Biro
- Department
of Organic Chemistry, Department of Materials and Interfaces, and Department of
Chemical Research Support, The Weizmann
Institute of Science, Rehovot 7610001, Israel
| | - Sidney R. Cohen
- Department
of Organic Chemistry, Department of Materials and Interfaces, and Department of
Chemical Research Support, The Weizmann
Institute of Science, Rehovot 7610001, Israel
| | - Lothar Houben
- Department
of Organic Chemistry, Department of Materials and Interfaces, and Department of
Chemical Research Support, The Weizmann
Institute of Science, Rehovot 7610001, Israel
| | - Reshef Tenne
- Department
of Organic Chemistry, Department of Materials and Interfaces, and Department of
Chemical Research Support, The Weizmann
Institute of Science, Rehovot 7610001, Israel
| | - Michal Lahav
- Department
of Organic Chemistry, Department of Materials and Interfaces, and Department of
Chemical Research Support, The Weizmann
Institute of Science, Rehovot 7610001, Israel
| | - Milko E. van der Boom
- Department
of Organic Chemistry, Department of Materials and Interfaces, and Department of
Chemical Research Support, The Weizmann
Institute of Science, Rehovot 7610001, Israel
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7
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Sanders T, Arslan I. Improved Three-Dimensional (3D) Resolution of Electron Tomograms Using Robust Mathematical Data-Processing Techniques. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2017; 23:1121-1129. [PMID: 29143700 DOI: 10.1017/s1431927617012636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Electron tomography has become an essential tool for three-dimensional (3D) characterization of nanomaterials. In recent years, advances have been made in specimen preparation and mounting, acquisition geometries, and reconstruction algorithms. All of these components work together to optimize the resolution and clarity of an electron tomogram. However, one important component of the data-processing has received less attention: the 2D tilt series alignment. This is challenging for a number of reasons, namely because the nature of the data sets and the need to be coherently aligned over the full range of angles. An inaccurate alignment may be difficult to identify, yet can significantly limit the final 3D resolution. In this work, we present an improved center-of-mass alignment model that allows us to overcome discrepancies from unwanted objects that enter the imaging area throughout the tilt series. In particular, we develop an approach to overcome changes in the total mass upon rotation of the imaging area. We apply our approach to accurately recover small Pt nanoparticles embedded in a zeolite that may otherwise go undetected both in the 2D microscopy images and the 3D reconstruction. In addition to this, we highlight the particular effectiveness of the compressed sensing methods with this data set.
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Affiliation(s)
- Toby Sanders
- 1School of Mathematical and Statistical Sciences,Arizona State University,PO Box 871804,Tempe,AZ 85287-1804,USA
| | - Ilke Arslan
- 2Physical Sciences Division,Pacific Northwest National Laboratory,Richland,WA 99352,USA
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8
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Ramos T, Jørgensen JS, Andreasen JW. Automated angular and translational tomographic alignment and application to phase-contrast imaging. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2017; 34:1830-1843. [PMID: 29036054 DOI: 10.1364/josaa.34.001830] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 08/12/2017] [Indexed: 06/07/2023]
Abstract
X-ray computerized tomography (CT) is a 3D imaging technique that makes use of x-ray illumination and image reconstruction techniques to reproduce the internal cross-sections of a sample. Tomographic projection data usually require an initial relative alignment or knowledge of the exact object position and orientation with respect to the detector. As tomographic imaging reaches increasingly better resolution, thermal drifts, mechanical instabilities, and equipment limitations are becoming the main dominant factors contributing to sample positioning uncertainties that will further introduce reconstruction artifacts and limit the attained resolution in the final tomographic reconstruction. Alignment algorithms that require manual interaction impede data analysis with ever-increasing data acquisition rates, supplied by more brilliant sources. We present in this paper an iterative reconstruction algorithm for wrapped phase projection data and an alignment algorithm that automatically takes 5 degrees of freedom, including the possible linear and angular motion errors, into consideration. The presented concepts are applied to simulated and real measured phase-contrast data, exhibiting a possible improvement in the reconstruction resolution. A MATLAB implementation is made publicly available and will allow robust analysis of large volumes of phase-contrast tomography data.
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9
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Gürsoy D, Hong YP, He K, Hujsak K, Yoo S, Chen S, Li Y, Ge M, Miller LM, Chu YS, De Andrade V, He K, Cossairt O, Katsaggelos AK, Jacobsen C. Rapid alignment of nanotomography data using joint iterative reconstruction and reprojection. Sci Rep 2017; 7:11818. [PMID: 28924196 PMCID: PMC5603591 DOI: 10.1038/s41598-017-12141-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/22/2017] [Indexed: 11/16/2022] Open
Abstract
As x-ray and electron tomography is pushed further into the nanoscale, the limitations of rotation stages become more apparent, leading to challenges in the alignment of the acquired projection images. Here we present an approach for rapid post-acquisition alignment of these projections to obtain high quality three-dimensional images. Our approach is based on a joint estimation of alignment errors, and the object, using an iterative refinement procedure. With simulated data where we know the alignment error of each projection image, our approach shows a residual alignment error that is a factor of a thousand smaller, and it reaches the same error level in the reconstructed image in less than half the number of iterations. We then show its application to experimental data in x-ray and electron nanotomography.
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Affiliation(s)
- Doğa Gürsoy
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL, 60439, USA.
- Department of Electrical Engineering and Computer Science, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA.
| | - Young P Hong
- Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Kuan He
- Department of Electrical Engineering and Computer Science, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Karl Hujsak
- Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, IL, 60208, USA
| | - Seunghwan Yoo
- Department of Electrical Engineering and Computer Science, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Si Chen
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL, 60439, USA
| | - Yue Li
- Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Mingyuan Ge
- National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, NY, 11967, USA
| | - Lisa M Miller
- National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, NY, 11967, USA
| | - Yong S Chu
- National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, NY, 11967, USA
| | - Vincent De Andrade
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL, 60439, USA
| | - Kai He
- Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, IL, 60208, USA
| | - Oliver Cossairt
- Department of Electrical Engineering and Computer Science, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Aggelos K Katsaggelos
- Department of Electrical Engineering and Computer Science, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Chris Jacobsen
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL, 60439, USA
- Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
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10
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Reichel V, Kovács A, Kumari M, Bereczk-Tompa É, Schneck E, Diehle P, Pósfai M, Hirt AM, Duchamp M, Dunin-Borkowski RE, Faivre D. Single crystalline superstructured stable single domain magnetite nanoparticles. Sci Rep 2017; 7:45484. [PMID: 28358051 PMCID: PMC5371993 DOI: 10.1038/srep45484] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 02/27/2017] [Indexed: 11/09/2022] Open
Abstract
Magnetite nanoparticles exhibit magnetic properties that are size and organization dependent and, for applications that rely on their magnetic state, they usually have to be monodisperse. Forming such particles, however, has remained a challenge. Here, we synthesize 40 nm particles of magnetite in the presence of polyarginine and show that they are composed of 10 nm building blocks, yet diffract like single crystals. We use both bulk magnetic measurements and magnetic induction maps recorded from individual particles using off-axis electron holography to show that each 40 nm particle typically contains a single magnetic domain. The magnetic state is therefore determined primarily by the size of the superstructure and not by the sizes of the constituent sub-units. Our results fundamentally demonstrate the structure – property relationship in a magnetic mesoparticle.
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Affiliation(s)
- Victoria Reichel
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
| | - András Kovács
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Monika Kumari
- Institute of Geophysics, ETH-Zürich, Sonneggstrasse 5, CH-8092 Zürich, Switzerland
| | - Éva Bereczk-Tompa
- Department of Earth and Environmental Sciences, University of Pannonia, Egyetem u. 10, H8200 Veszprém, Hungary
| | - Emanuel Schneck
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
| | - Patrick Diehle
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Mihály Pósfai
- Department of Earth and Environmental Sciences, University of Pannonia, Egyetem u. 10, H8200 Veszprém, Hungary
| | - Ann M Hirt
- Institute of Geophysics, ETH-Zürich, Sonneggstrasse 5, CH-8092 Zürich, Switzerland
| | - Martial Duchamp
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Rafal E Dunin-Borkowski
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Damien Faivre
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
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11
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Hayashida M, Malac M. Practical electron tomography guide: Recent progress and future opportunities. Micron 2016; 91:49-74. [PMID: 27728842 DOI: 10.1016/j.micron.2016.09.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 09/26/2016] [Accepted: 09/27/2016] [Indexed: 10/20/2022]
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12
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Yan R, Edwards TJ, Pankratz LM, Kuhn RJ, Lanman JK, Liu J, Jiang W. Simultaneous determination of sample thickness, tilt, and electron mean free path using tomographic tilt images based on Beer-Lambert law. J Struct Biol 2015; 192:287-96. [PMID: 26433027 DOI: 10.1016/j.jsb.2015.09.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 09/26/2015] [Accepted: 09/30/2015] [Indexed: 10/22/2022]
Abstract
Cryo-electron tomography (cryo-ET) is an emerging technique that can elucidate the architecture of macromolecular complexes and cellular ultrastructure in a near-native state. Some important sample parameters, such as thickness and tilt, are needed for 3-D reconstruction. However, these parameters can currently only be determined using trial 3-D reconstructions. Accurate electron mean free path plays a significant role in modeling image formation process essential for simulation of electron microscopy images and model-based iterative 3-D reconstruction methods; however, their values are voltage and sample dependent and have only been experimentally measured for a limited number of sample conditions. Here, we report a computational method, tomoThickness, based on the Beer-Lambert law, to simultaneously determine the sample thickness, tilt and electron inelastic mean free path by solving an overdetermined nonlinear least square optimization problem utilizing the strong constraints of tilt relationships. The method has been extensively tested with both stained and cryo datasets. The fitted electron mean free paths are consistent with reported experimental measurements. The accurate thickness estimation eliminates the need for a generous assignment of Z-dimension size of the tomogram. Interestingly, we have also found that nearly all samples are a few degrees tilted relative to the electron beam. Compensation of the intrinsic sample tilt can result in horizontal structure and reduced Z-dimension of tomograms. Our fast, pre-reconstruction method can thus provide important sample parameters that can help improve performance of tomographic reconstruction of a wide range of samples.
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Affiliation(s)
- Rui Yan
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Thomas J Edwards
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Logan M Pankratz
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Richard J Kuhn
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Jason K Lanman
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Jun Liu
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Wen Jiang
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
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13
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Migunov V, Ryll H, Zhuge X, Simson M, Strüder L, Batenburg KJ, Houben L, Dunin-Borkowski RE. Rapid low dose electron tomography using a direct electron detection camera. Sci Rep 2015; 5:14516. [PMID: 26434767 PMCID: PMC4592966 DOI: 10.1038/srep14516] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/02/2015] [Indexed: 01/26/2023] Open
Abstract
We demonstrate the ability to record a tomographic tilt series containing 3487 images in only 3.5 s by using a direct electron detector in a transmission electron microscope. The electron dose is lower by at least one order of magnitude when compared with that used to record a conventional tilt series of fewer than 100 images in 15-60 minutes and the overall signal-to-noise ratio is greater than 4. Our results, which are illustrated for an inorganic nanotube, are important for ultra-low-dose electron tomography of electron-beam-sensitive specimens and real-time dynamic electron tomography of nanoscale objects with sub-ms temporal resolution.
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Affiliation(s)
- Vadim Migunov
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Henning Ryll
- PNSensor GmbH, Otto-Hahn-Ring 6, 81739 München, Germany
| | - Xiaodong Zhuge
- Centrum Wiskunde & Informatica, P.O. Box 94079, NL-1090 GB Amsterdam, The Netherlands
| | - Martin Simson
- PNDetector GmbH, Otto-Hahn-Ring 6, 81739 München, Germany
| | - Lothar Strüder
- PNSensor GmbH, Otto-Hahn-Ring 6, 81739 München, Germany
- University of Siegen, Walter Flex Str. 3, 57068 Siegen, Germany
| | - K. Joost Batenburg
- Centrum Wiskunde & Informatica, P.O. Box 94079, NL-1090 GB Amsterdam, The Netherlands
- Mathematical Institute, Leiden University, The Netherlands
- iMinds-Vision Lab, University of Antwerp, Belgium
| | - Lothar Houben
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Rafal E. Dunin-Borkowski
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, D-52425 Jülich, Germany
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14
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Printemps T, Mula G, Sette D, Bleuet P, Delaye V, Bernier N, Grenier A, Audoit G, Gambacorti N, Hervé L. Self-adapting denoising, alignment and reconstruction in electron tomography in materials science. Ultramicroscopy 2015; 160:23-34. [PMID: 26413937 DOI: 10.1016/j.ultramic.2015.09.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 09/09/2015] [Accepted: 09/16/2015] [Indexed: 11/28/2022]
Abstract
An automatic procedure for electron tomography is presented. This procedure is adapted for specimens that can be fashioned into a needle-shaped sample and has been evaluated on inorganic samples. It consists of self-adapting denoising, automatic and accurate alignment including detection and correction of tilt axis, and 3D reconstruction. We propose the exploitation of a large amount of information of an electron tomography acquisition to achieve robust and automatic mixed Poisson-Gaussian noise parameter estimation and denoising using undecimated wavelet transforms. The alignment is made by mixing three techniques, namely (i) cross-correlations between neighboring projections, (ii) common line algorithm to get a precise shift correction in the direction of the tilt axis and (iii) intermediate reconstructions to precisely determine the tilt axis and shift correction in the direction perpendicular to that axis. Mixing alignment techniques turns out to be very efficient and fast. Significant improvements are highlighted in both simulations and real data reconstructions of porous silicon in high angle annular dark field mode and agglomerated silver nanoparticles in incoherent bright field mode. 3D reconstructions obtained with minimal user-intervention present fewer artefacts and less noise, which permits easier and more reliable segmentation and quantitative analysis. After careful sample preparation and data acquisition, the denoising procedure, alignment and reconstruction can be achieved within an hour for a 3D volume of about a hundred million voxels, which is a step toward a more routine use of electron tomography.
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Affiliation(s)
- Tony Printemps
- Université Grenoble Alpes, F-38000 Grenoble, France; CEA, LETI, MINATEC Campus, F-38054 Grenoble, France.
| | - Guido Mula
- Dipartimento di Fisica, Università di Cagliari, Cittadella Universitaria, S.P. 8km 0.700, 09042 Monserrato (Ca), Italy
| | - Daniele Sette
- Université Grenoble Alpes, F-38000 Grenoble, France; CEA, LETI, MINATEC Campus, F-38054 Grenoble, France
| | - Pierre Bleuet
- Université Grenoble Alpes, F-38000 Grenoble, France; CEA, LETI, MINATEC Campus, F-38054 Grenoble, France
| | - Vincent Delaye
- Université Grenoble Alpes, F-38000 Grenoble, France; CEA, LETI, MINATEC Campus, F-38054 Grenoble, France
| | - Nicolas Bernier
- Université Grenoble Alpes, F-38000 Grenoble, France; CEA, LETI, MINATEC Campus, F-38054 Grenoble, France
| | - Adeline Grenier
- Université Grenoble Alpes, F-38000 Grenoble, France; CEA, LETI, MINATEC Campus, F-38054 Grenoble, France
| | - Guillaume Audoit
- Université Grenoble Alpes, F-38000 Grenoble, France; CEA, LETI, MINATEC Campus, F-38054 Grenoble, France
| | - Narciso Gambacorti
- Université Grenoble Alpes, F-38000 Grenoble, France; CEA, LETI, MINATEC Campus, F-38054 Grenoble, France
| | - Lionel Hervé
- Université Grenoble Alpes, F-38000 Grenoble, France; CEA, LETI, MINATEC Campus, F-38054 Grenoble, France
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15
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Sanders T, Prange M, Akatay C, Binev P. Physically motivated global alignment method for electron tomography. ACTA ACUST UNITED AC 2015. [DOI: 10.1186/s40679-015-0005-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
AbstractElectron tomography is widely used for nanoscale determination of 3-D structures in many areas of science. Determining the 3-D structure of a sample from electron tomography involves three major steps: acquisition of sequence of 2-D projection images of the sample with the electron microscope, alignment of the images to a common coordinate system, and 3-D reconstruction and segmentation of the sample from the aligned image data. The resolution of the 3-D reconstruction is directly influenced by the accuracy of the alignment, and therefore, it is crucial to have a robust and dependable alignment method. In this paper, we develop a new alignment method which avoids the use of markers and instead traces the computed paths of many identifiable ‘local’ center-of-mass points as the sample is rotated. Compared with traditional correlation schemes, the alignment method presented here is resistant to cumulative error observed from correlation techniques, has very rigorous mathematical justification, and is very robust since many points and paths are used, all of which inevitably improves the quality of the reconstruction and confidence in the scientific results.
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16
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Meiron OE, Houben L, Bar-Sadan M. Understanding the formation mechanism and the 3D structure of Mo(SxSe1−x)2 nanoflowers. RSC Adv 2015. [DOI: 10.1039/c5ra16853h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Colloidal synthesis of MoS2, MoSe2 and their alloys produces fine nanoflowers with tunable composition. Their reaction mechanism produces homogeneous solid solutions, beneficial for designing specific properties.
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Affiliation(s)
- O. E. Meiron
- Ben-Gurion University of The Negev
- Department of Chemistry
- Beer Sheva
- Israel
| | - L. Houben
- Chemical Research Support
- Weizmann Institute of Science
- Rehovot
- Israel
| | - M. Bar-Sadan
- Ben-Gurion University of The Negev
- Department of Chemistry
- Beer Sheva
- Israel
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17
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Ben-Moshe A, Wolf SG, Sadan MB, Houben L, Fan Z, Govorov AO, Markovich G. Enantioselective control of lattice and shape chirality in inorganic nanostructures using chiral biomolecules. Nat Commun 2014; 5:4302. [DOI: 10.1038/ncomms5302] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 06/04/2014] [Indexed: 12/23/2022] Open
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18
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Van Tendeloo G, Bals S, Van Aert S, Verbeeck J, Van Dyck D. Advanced electron microscopy for advanced materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2012; 24:5655-5675. [PMID: 22907862 DOI: 10.1002/adma.201202107] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Indexed: 06/01/2023]
Abstract
The idea of this Review is to introduce newly developed possibilities of advanced electron microscopy to the materials science community. Over the last decade, electron microscopy has evolved into a full analytical tool, able to provide atomic scale information on the position, nature, and even the valency atoms. This information is classically obtained in two dimensions (2D), but can now also be obtained in 3D. We show examples of applications in the field of nanoparticles and interfaces.
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19
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Chuntonov L, Bar-Sadan M, Houben L, Haran G. Correlating electron tomography and plasmon spectroscopy of single noble metal core-shell nanoparticles. NANO LETTERS 2012; 12:145-150. [PMID: 22168793 DOI: 10.1021/nl204125d] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The 3D structure reconstruction of gold core-silver shell nanoparticles by electron tomography is combined with optical dark-field spectroscopy. Electron tomography allows segmentation of the particles into core and shell subvolumes and facilitates avoiding Bragg diffraction artifacts inherent in 2D images. This advantage proves essential for accurate correlation of plasmon spectra and structure. We find that for the nanoparticles of near-spherical shape studied here the plasmon resonances depend on the relative size of the core and shell, rather than on their exact shapes and concentricity. A remarkable dependence of the spectral shape on the permittivity of the surrounding medium is also demonstrated, suggesting that core-shell nanoparticles can be used as ratiometric sensors with a very high dynamic range.
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Affiliation(s)
- Lev Chuntonov
- Department of Chemical Physics, Weizmann Institute of Science, 76100, Rehovot, Israel
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20
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Parkinson DY, Knoechel C, Yang C, Larabell CA, Le Gros MA. Automatic alignment and reconstruction of images for soft X-ray tomography. J Struct Biol 2011; 177:259-66. [PMID: 22155289 DOI: 10.1016/j.jsb.2011.11.027] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 11/17/2011] [Accepted: 11/23/2011] [Indexed: 01/23/2023]
Abstract
Soft X-ray tomography (SXT) is a powerful imaging technique that generates quantitative, 3D images of the structural organization of whole cells in a near-native state. SXT is also a high-throughput imaging technique. At the National Center for X-ray Tomography (NCXT), specimen preparation and image collection for tomographic reconstruction of a whole cell require only minutes. Aligning and reconstructing the data, however, take significantly longer. Here we describe a new component of the high throughput computational pipeline used for processing data at the NCXT. We have developed a new method for automatic alignment of projection images that does not require fiducial markers or manual interaction with the software. This method has been optimized for SXT data sets, which routinely involve full rotation of the specimen. This software gives users of the NCXT SXT instrument a new capability - virtually real-time initial 3D results during an imaging experiment, which can later be further refined. The new code, Automatic Reconstruction 3D (AREC3D), is also fast, reliable, and robust. The fundamental architecture of the code is also adaptable to high performance GPU processing, which enables significant improvements in speed and fidelity.
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Affiliation(s)
- Dilworth Y Parkinson
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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