1
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Chan LM, Courteau BJ, Maker A, Wu M, Basanta B, Mehmood H, Bulkley D, Joyce D, Lee BC, Mick S, Czarnik C, Gulati S, Lander GC, Verba KA. High-resolution single-particle imaging at 100-200 keV with the Gatan Alpine direct electron detector. J Struct Biol 2024; 216:108108. [PMID: 38944401 DOI: 10.1016/j.jsb.2024.108108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/03/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Developments in direct electron detector technology have played a pivotal role in enabling high-resolution structural studies by cryo-EM at 200 and 300 keV. Yet, theory and recent experiments indicate advantages to imaging at 100 keV, energies for which the current detectors have not been optimized. In this study, we evaluated the Gatan Alpine detector, designed for operation at 100 and 200 keV. Compared to the Gatan K3, Alpine demonstrated a significant DQE improvement at these energies, specifically a ∼ 4-fold improvement at Nyquist at 100 keV. In single-particle cryo-EM experiments, Alpine datasets yielded better than 2 Å resolution reconstructions of apoferritin at 120 and 200 keV on a ThermoFisher Scientific (TFS) Glacios microscope fitted with a non-standard SP-Twin lens. We also achieved a ∼ 3.2 Å resolution reconstruction of a 115 kDa asymmetric protein complex, proving Alpine's effectiveness with complex biological samples. In-depth analysis revealed that Alpine reconstructions are comparable to K3 reconstructions at 200 keV, and remarkably, reconstruction from Alpine at 120 keV on a TFS Glacios surpassed all but the 300 keV data from a TFS Titan Krios with GIF/K3. Additionally, we show Alpine's capability for high-resolution data acquisition and screening on lower-end systems by obtaining ∼ 3 Å resolution reconstructions of apoferritin and aldolase at 100 keV and detailed 2D averages of a 55 kDa sample using a side-entry cryo holder. Overall, we show that Gatan Alpine performs well with the standard 200 keV imaging systems and may potentially capture the benefits of lower accelerating voltages, bringing smaller sized particles within the scope of cryo-EM.
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Affiliation(s)
- Lieza M Chan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Brandon J Courteau
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Allison Maker
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Mengyu Wu
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States
| | - Benjamin Basanta
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States
| | - Hev Mehmood
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - David Bulkley
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, United States
| | | | | | | | | | | | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States.
| | - Kliment A Verba
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States.
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2
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Chan LM, Courteau BJ, Maker A, Wu M, Basanta B, Mehmood H, Bulkley D, Joyce D, Lee BC, Mick S, Gulati S, Lander GC, Verba KA. High-resolution single-particle imaging at 100-200 keV with the Gatan Alpine direct electron detector. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580363. [PMID: 38405886 PMCID: PMC10888765 DOI: 10.1101/2024.02.14.580363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Developments in direct electron detector technology have played a pivotal role in enabling high-resolution structural studies by cryo-EM at 200 and 300 keV. Yet, theory and recent experiments indicate advantages to imaging at 100 keV, energies for which the current detectors have not been optimized. In this study, we evaluated the Gatan Alpine detector, designed for operation at 100 and 200 keV. Compared to the Gatan K3, Alpine demonstrated a significant DQE improvement at these voltages, specifically a ~4-fold improvement at Nyquist at 100 keV. In single-particle cryo-EM experiments, Alpine datasets yielded better than 2 Å resolution reconstructions of apoferritin at 120 and 200 keV on a ThermoFisher Scientific (TFS) Glacios microscope. We also achieved a ~3.2 Å resolution reconstruction for a 115 kDa asymmetric protein complex, proving its effectiveness with complex biological samples. In-depth analysis revealed that Alpine reconstructions are comparable to K3 reconstructions at 200 keV, and remarkably, reconstruction from Alpine at 120 keV on a TFS Glacios surpassed all but the 300 keV data from a TFS Titan Krios with GIF/K3. Additionally, we show Alpine's capability for high-resolution data acquisition and screening on lower-end systems by obtaining ~3 Å resolution reconstructions of apoferritin and aldolase at 100 keV and detailed 2D averages of a 55 kDa sample using a side-entry cryo holder. Overall, we show that Gatan Alpine performs well with the standard 200 keV imaging systems and may potentially capture the benefits of lower accelerating voltages, possibly bringing smaller sized particles within the scope of cryo-EM.
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Affiliation(s)
- Lieza M Chan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Brandon J Courteau
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Allison Maker
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Mengyu Wu
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States
| | - Benjamin Basanta
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States
| | - Hevatib Mehmood
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - David Bulkley
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, United States
| | | | | | | | | | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States
| | - Kliment A Verba
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
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3
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Abstract
ConspectusQuantum materials refers to a class of materials with exotic properties that arise from the quantum mechanical nature of their constituent electrons, exhibiting, for example, high-temperature superconductivity, colossal magnetoresistivity, multiferroicity, and topological behavior. Quantum materials often have incompletely filled d- or f-electron shells with narrow energy bands, and the conduct of their electrons is strongly correlated. One distinct characteristic of the materials is that their electronic states are often spatially inhomogeneous and thus well suited for study using a spatially resolved electron beam with its great scattering power and sensitivity to atomic ionicity. Furthermore, most of these exotic properties only manifest at very low temperatures, posing a challenge to modern electron microscopy. It requires extraordinarily instrument stabilities at cryogenic temperatures with critical spatial, temporal, and energy resolutions in both static and dynamic manner to probe these materials. On the other hand, the ability to directly visualize the atomic, electronic and spin structures and inhomogeneities of quantum materials and correlate them to their functionalities creates enormous opportunities. At the most elementary levels of condensed matter physics, understanding the competing order of electron, spin, orbital, and lattice and their degrees of freedom, the impacts of defects and interfaces, and the site-specific quantum phenomena and phase transitions that give rise to the emergent behaviors allows us to discover and control novel materials for quantum information science and technologies.In this Account, several of our research examples are selected to highlight the use of cryogenic electron microscopy (cryo-EM) to study strongly correlated quantum materials. We focus on the critical roles of heterogeneity, interfaces, defects, and disorder in crystal structure, magnetic structure, and electronic structure to understand the physical properties of the materials that cryo-EM enables. We show how electron crystallography coupled with Bragg diffraction and diffuse scattering analysis empowers us to reveal the nature of structural modulations, lattice distortion, and phonons and how quantitative electron diffraction can be used to map the distributions of the valence electrons that bond atoms together. We exploit transformative advances in imaging capabilities including the use of femtosecond laser and ultrafast electron diffraction to probe electron-lattice interactions and photoinduced transitions beyond equilibrium of matter. We review our Lorentz phase microscopy studies to illustrate the intriguing transformations among various topological chiral spin states under applied magnetic field at various cryogenic temperatures. Finally, we show that atomically resolved imaging and electron energy-loss spectroscopy at 10 K can be used to understand interface-enhanced superconductivity. The wide range of research and progress on quantum materials at low temperature reported here may inspire and attract more researchers in this ever-expanding field of cryo-EM.
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Affiliation(s)
- Yimei Zhu
- Department of Condensed Matter Physics and Materials Science, Brookhaven National Laboratory Upton, New York 11973, United States
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4
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Paton KA, Veale MC, Mu X, Allen CS, Maneuski D, Kübel C, O'Shea V, Kirkland AI, McGrouther D. Quantifying the performance of a hybrid pixel detector with GaAs:Cr sensor for transmission electron microscopy. Ultramicroscopy 2021; 227:113298. [PMID: 34051540 DOI: 10.1016/j.ultramic.2021.113298] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 02/01/2021] [Accepted: 04/24/2021] [Indexed: 10/21/2022]
Abstract
Hybrid pixel detectors (HPDs) have been shown to be highly effective for diffraction-based and time-resolved studies in transmission electron microscopy, but their performance is limited by the fact that high-energy electrons scatter over long distances in their thick Si sensors. An advantage of HPDs compared to monolithic active pixel sensors is that their sensors do not need to be fabricated from Si. We have compared the performance of the Medipix3 HPD with a Si sensor and a GaAs:Cr sensor using primary electrons in the energy range of 60-300 keV. We describe the measurement and calculation of the detectors' modulation transfer function (MTF) and detective quantum efficiency (DQE), which show that the performance of the GaAs:Cr device is markedly superior to that of the Si device for high-energy electrons.
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Affiliation(s)
- Kirsty A Paton
- Scottish Universities Physics Alliance, School of Physics and Astronomy, University of Glasgow, G12 8QQ, UK.
| | - Matthew C Veale
- UKRI Science & Technology Facilities Council, Rutherford Appleton Laboratory, Didcot, OX11 0QX, UK
| | - Xiaoke Mu
- Karlsruhe Nano Micro Facility, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Christopher S Allen
- Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH, UK; electron Physical Sciences Imaging Centre (ePSIC), Diamond Lightsource Ltd., Didcot, OX11 0DE, UK
| | - Dzmitry Maneuski
- Scottish Universities Physics Alliance, School of Physics and Astronomy, University of Glasgow, G12 8QQ, UK
| | - Christian Kübel
- Karlsruhe Nano Micro Facility, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany; Department of Materials and Earth Science, Technische Universität Darmstadt and Karlsruhe Institute of Technology, Otto-Berndt-Str. 3, 64287 Darmstadt, Germany
| | - Val O'Shea
- Scottish Universities Physics Alliance, School of Physics and Astronomy, University of Glasgow, G12 8QQ, UK
| | - Angus I Kirkland
- Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH, UK; electron Physical Sciences Imaging Centre (ePSIC), Diamond Lightsource Ltd., Didcot, OX11 0DE, UK
| | - Damien McGrouther
- Scottish Universities Physics Alliance, School of Physics and Astronomy, University of Glasgow, G12 8QQ, UK
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Liebschner D, Afonine PV, Moriarty NW, Poon BK, Chen VB, Adams PD. CERES: a cryo-EM re-refinement system for continuous improvement of deposited models. Acta Crystallogr D Struct Biol 2021; 77:48-61. [PMID: 33404525 PMCID: PMC7787109 DOI: 10.1107/s2059798320015879] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/03/2020] [Indexed: 11/10/2022] Open
Abstract
The field of electron cryomicroscopy (cryo-EM) has advanced quickly in recent years as the result of numerous technological and methodological developments. This has led to an increase in the number of atomic structures determined using this method. Recently, several tools for the analysis of cryo-EM data and models have been developed within the Phenix software package, such as phenix.real_space_refine for the refinement of atomic models against real-space maps. Also, new validation metrics have been developed for low-resolution cryo-EM models. To understand the quality of deposited cryo-EM structures and how they might be improved, models deposited in the Protein Data Bank that have map resolutions of better than 5 Å were automatically re-refined using current versions of Phenix tools. The results are available on a publicly accessible web page (https://cci.lbl.gov/ceres). The implementation of a Cryo-EM Re-refinement System (CERES) for the improvement of models deposited in the wwPDB, and the results of the re-refinements, are described. Based on these results, contents are proposed for a `cryo-EM Table 1', which summarizes experimental details and validation metrics in a similar way to `Table 1' in crystallography. The consistent use of robust metrics for the evaluation of cryo-EM models and data should accompany every structure deposition and be reported in scientific publications.
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Affiliation(s)
- Dorothee Liebschner
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Pavel V. Afonine
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Nigel W. Moriarty
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Billy K. Poon
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Vincent B. Chen
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Paul D. Adams
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720, USA
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6
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Pham TN, Marchand P, Finck C, Boisson F, Brasse D, Laquerriere P. 18F autoradiography With the Mimosa-28: Characterization and Application. IEEE TRANSACTIONS ON RADIATION AND PLASMA MEDICAL SCIENCES 2020. [DOI: 10.1109/trpms.2020.2996912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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7
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Chen L, Baker B, Santos E, Sheep M, Daftarian D. A Visualization Tool for Cryo-EM Protein Validation with an Unsupervised Machine Learning Model in Chimera Platform. MEDICINES (BASEL, SWITZERLAND) 2019; 6:E86. [PMID: 31390767 PMCID: PMC6789601 DOI: 10.3390/medicines6030086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 11/22/2022]
Abstract
Background: Cryo-electron microscopy (cryo-EM) has become a major technique for protein structure determination. However, due to the low quality of cryo-EM density maps, many protein structures derived from cryo-EM contain outliers introduced during the modeling process. The current protein model validation system lacks identification features for cryo-EM proteins making it not enough to identify outliers in cryo-EM proteins. Methods: This study introduces an efficient unsupervised outlier detection model for validating protein models built from cryo-EM technique. The current model uses a high-resolution X-ray dataset (<1.5 Å) as the reference dataset. The distal block distance, side-chain length, phi, psi, and first chi angle of the residues in the reference dataset are collected and saved as a database of the histogram-based outlier score (HBOS). The HBOS value of the residues in target cryo-EM proteins can be read from this HBOS database. Results: Protein residues with a HBOS value greater than ten are labeled as outliers by default. Four datasets containing proteins derived from cryo-EM density maps were tested with this probabilistic anomaly detection model. Conclusions: According to the proposed model, a visualization assistant tool was designed for Chimera, a protein visualization platform.
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Affiliation(s)
- Lin Chen
- Department of Computer Science, Valdosta State University, Valdosta, GA 31693, USA.
| | - Brandon Baker
- Department of Natural Science, Elizabeth City State University, Elizabeth City, NC 27909, USA
| | - Eduardo Santos
- Department of Natural Science, Elizabeth City State University, Elizabeth City, NC 27909, USA
| | - Michell Sheep
- Department of Mathematics & Computer Science, Elizabeth City State University, Elizabeth City, NC 27909, USA
| | - Darius Daftarian
- Department of Mathematics & Computer Science, Elizabeth City State University, Elizabeth City, NC 27909, USA
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8
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9
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Mitra AK. Visualization of biological macromolecules at near-atomic resolution: cryo-electron microscopy comes of age. Acta Crystallogr F Struct Biol Commun 2019; 75:3-11. [PMID: 30605120 PMCID: PMC6317457 DOI: 10.1107/s2053230x18015133] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/26/2018] [Indexed: 11/11/2022] Open
Abstract
Structural biology is going through a revolution as a result of transformational advances in the field of cryo-electron microscopy (cryo-EM) driven by the development of direct electron detectors and ultrastable electron microscopes. High-resolution cryo-EM images of isolated biomolecules (single particles) suspended in a thin layer of vitrified buffer are subjected to powerful image-processing algorithms, enabling near-atomic resolution structures to be determined in unprecedented numbers. Prior to these advances, electron crystallography of two-dimensional crystals and helical assemblies of proteins had established the feasibility of atomic resolution structure determination using cryo-EM. Atomic resolution single-particle analysis, without the need for crystals, now promises to resolve problems in structural biology that were intractable just a few years ago.
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MESH Headings
- Algorithms
- Bibliometrics
- Cryoelectron Microscopy/history
- Cryoelectron Microscopy/instrumentation
- Cryoelectron Microscopy/methods
- Crystallography, X-Ray/history
- Crystallography, X-Ray/instrumentation
- Crystallography, X-Ray/methods
- Equipment Design/history
- History, 20th Century
- History, 21st Century
- Humans
- Image Processing, Computer-Assisted/statistics & numerical data
- Imaging, Three-Dimensional/instrumentation
- Imaging, Three-Dimensional/methods
- Macromolecular Substances/chemistry
- Macromolecular Substances/ultrastructure
- Microscopy, Electron, Transmission/history
- Microscopy, Electron, Transmission/instrumentation
- Microscopy, Electron, Transmission/methods
- Specimen Handling/instrumentation
- Specimen Handling/methods
- Vitrification
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Affiliation(s)
- Alok K. Mitra
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
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10
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Afonine PV, Klaholz BP, Moriarty NW, Poon BK, Sobolev OV, Terwilliger TC, Adams PD, Urzhumtsev A. New tools for the analysis and validation of cryo-EM maps and atomic models. Acta Crystallogr D Struct Biol 2018; 74:814-840. [PMID: 30198894 PMCID: PMC6130467 DOI: 10.1107/s2059798318009324] [Citation(s) in RCA: 455] [Impact Index Per Article: 75.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 06/27/2018] [Indexed: 11/25/2022] Open
Abstract
Recent advances in the field of electron cryomicroscopy (cryo-EM) have resulted in a rapidly increasing number of atomic models of biomacromolecules that have been solved using this technique and deposited in the Protein Data Bank and the Electron Microscopy Data Bank. Similar to macromolecular crystallography, validation tools for these models and maps are required. While some of these validation tools may be borrowed from crystallography, new methods specifically designed for cryo-EM validation are required. Here, new computational methods and tools implemented in PHENIX are discussed, including d99 to estimate resolution, phenix.auto_sharpen to improve maps and phenix.mtriage to analyze cryo-EM maps. It is suggested that cryo-EM half-maps and masks should be deposited to facilitate the evaluation and validation of cryo-EM-derived atomic models and maps. The application of these tools to deposited cryo-EM atomic models and maps is also presented.
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Affiliation(s)
- Pavel V. Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Physics and International Centre for Quantum and Molecular Structures, Shanghai University, Shanghai, 200444, People’s Republic of China
| | - Bruno P. Klaholz
- Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS–INSERM–UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch, France
| | - Nigel W. Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Billy K. Poon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Oleg V. Sobolev
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Thomas C. Terwilliger
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- New Mexico Consortium, Los Alamos, NM 87544, USA
| | - Paul D. Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720, USA
| | - Alexandre Urzhumtsev
- Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS–INSERM–UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch, France
- Faculté des Sciences et Technologies, Université de Lorraine, BP 239, 54506 Vandoeuvre-lès-Nancy, France
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11
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Direct Detection Electron Energy-Loss Spectroscopy: A Method to Push the Limits of Resolution and Sensitivity. Sci Rep 2017; 7:8243. [PMID: 28811485 PMCID: PMC5557959 DOI: 10.1038/s41598-017-07709-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 07/03/2017] [Indexed: 12/17/2022] Open
Abstract
In many cases, electron counting with direct detection sensors offers improved resolution, lower noise, and higher pixel density compared to conventional, indirect detection sensors for electron microscopy applications. Direct detection technology has previously been utilized, with great success, for imaging and diffraction, but potential advantages for spectroscopy remain unexplored. Here we compare the performance of a direct detection sensor operated in counting mode and an indirect detection sensor (scintillator/fiber-optic/CCD) for electron energy-loss spectroscopy. Clear improvements in measured detective quantum efficiency and combined energy resolution/energy field-of-view are offered by counting mode direct detection, showing promise for efficient spectrum imaging, low-dose mapping of beam-sensitive specimens, trace element analysis, and time-resolved spectroscopy. Despite the limited counting rate imposed by the readout electronics, we show that both core-loss and low-loss spectral acquisition are practical. These developments will benefit biologists, chemists, physicists, and materials scientists alike.
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12
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Clough R, Kirkland A. Direct Digital Electron Detectors. ADVANCES IN IMAGING AND ELECTRON PHYSICS 2016. [DOI: 10.1016/bs.aiep.2016.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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13
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Kuijper M, van Hoften G, Janssen B, Geurink R, De Carlo S, Vos M, van Duinen G, van Haeringen B, Storms M. FEI’s direct electron detector developments: Embarking on a revolution in cryo-TEM. J Struct Biol 2015; 192:179-87. [DOI: 10.1016/j.jsb.2015.09.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/23/2015] [Accepted: 09/25/2015] [Indexed: 10/23/2022]
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14
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Han HL, Melaet G, Alayoglu S, Somorjai GA. In Situ Microscopy and Spectroscopy Applied to Surfaces at Work. ChemCatChem 2015. [DOI: 10.1002/cctc.201500642] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Hui-Ling Han
- Materials Sciences Division; Lawrence Berkeley National Laboratory; 1 Cyclotron Road Berkeley CA 94720 USA
| | - Gérôme Melaet
- Materials Sciences Division; Lawrence Berkeley National Laboratory; 1 Cyclotron Road Berkeley CA 94720 USA
| | - Selim Alayoglu
- Chemical Sciences Division; Lawrence Berkeley National Laboratory; 1 Cyclotron Road Berkeley CA 94720-8176 USA
| | - Gabor A. Somorjai
- Chemical Sciences Division; Lawrence Berkeley National Laboratory; 1 Cyclotron Road Berkeley CA 94720-8176 USA
- College of Chemistry; University of California at Berkeley; 420 Latimer Hall Berkeley CA 94720-1460 USA
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15
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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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Faruqi A, Henderson R, McMullan G. Progress and Development of Direct Detectors for Electron Cryomicroscopy. ADVANCES IN IMAGING AND ELECTRON PHYSICS 2015. [DOI: 10.1016/bs.aiep.2015.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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17
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Gabrielli A. Fast readout architectures for large arrays of digital pixels: examples and applications. ScientificWorldJournal 2014; 2014:523429. [PMID: 24778588 PMCID: PMC3977470 DOI: 10.1155/2014/523429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 12/29/2013] [Indexed: 01/26/2023] Open
Abstract
Modern pixel detectors, particularly those designed and constructed for applications and experiments for high-energy physics, are commonly built implementing general readout architectures, not specifically optimized in terms of speed. High-energy physics experiments use bidimensional matrices of sensitive elements located on a silicon die. Sensors are read out via other integrated circuits bump bonded over the sensor dies. The speed of the readout electronics can significantly increase the overall performance of the system, and so here novel forms of readout architectures are studied and described. These circuits have been investigated in terms of speed and are particularly suited for large monolithic, low-pitch pixel detectors. The idea is to have a small simple structure that may be expanded to fit large matrices without affecting the layout complexity of the chip, while maintaining a reasonably high readout speed. The solutions might be applied to devices for applications not only in physics but also to general-purpose pixel detectors whenever online fast data sparsification is required. The paper presents also simulations on the efficiencies of the systems as proof of concept for the proposed ideas.
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Affiliation(s)
- A. Gabrielli
- Physics and Astronomy Department and INFN, University of Bologna, Viale Berti Pichat 6/2, I 40127 Bologna, Italy
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18
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Gontard LC, Moldovan G, Carmona-Galán R, Lin C, Kirkland AI. Detecting single-electron events in TEM using low-cost electronics and a silicon strip sensor. Microscopy (Oxf) 2014; 63:119-30. [PMID: 24401331 DOI: 10.1093/jmicro/dft051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
There is great interest in developing novel position-sensitive direct detectors for transmission electron microscopy (TEM) that do not rely in the conversion of electrons into photons. Direct imaging improves contrast and efficiency and allows the operation of the microscope at lower energies and at lower doses without loss in resolution, which is especially important for studying soft materials and biological samples. We investigate the feasibility of employing a silicon strip detector as an imaging detector for TEM. This device, routinely used in high-energy particle physics, can detect small variations in electric current associated with the impact of a single charged particle. The main advantages of using this type of sensor for direct imaging in TEM are its intrinsic radiation hardness and large detection area. Here, we detail design, simulation, fabrication and tests in a TEM of the front-end electronics developed using low-cost discrete components and discuss the limitations and applications of this technology for TEM.
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Affiliation(s)
- Lionel C Gontard
- Department of Materials, University of Oxford, 16 Parks Road, Oxford OX1 3PH, UK
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19
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The Young-Feynman two-slits experiment with single electrons: Build-up of the interference pattern and arrival-time distribution using a fast-readout pixel detector. Ultramicroscopy 2012. [DOI: 10.1016/j.ultramic.2012.03.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Wisedchaisri G, Reichow SL, Gonen T. Advances in structural and functional analysis of membrane proteins by electron crystallography. Structure 2012; 19:1381-93. [PMID: 22000511 DOI: 10.1016/j.str.2011.09.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 09/01/2011] [Accepted: 09/06/2011] [Indexed: 12/27/2022]
Abstract
Electron crystallography is a powerful technique for the study of membrane protein structure and function in the lipid environment. When well-ordered two-dimensional crystals are obtained the structure of both protein and lipid can be determined and lipid-protein interactions analyzed. Protons and ionic charges can be visualized by electron crystallography and the protein of interest can be captured for structural analysis in a variety of physiologically distinct states. This review highlights the strengths of electron crystallography and the momentum that is building up in automation and the development of high throughput tools and methods for structural and functional analysis of membrane proteins by electron crystallography.
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Affiliation(s)
- Goragot Wisedchaisri
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
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21
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Bammes BE, Rochat RH, Jakana J, Chen DH, Chiu W. Direct electron detection yields cryo-EM reconstructions at resolutions beyond 3/4 Nyquist frequency. J Struct Biol 2012; 177:589-601. [PMID: 22285189 DOI: 10.1016/j.jsb.2012.01.008] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 12/21/2011] [Accepted: 01/11/2012] [Indexed: 11/28/2022]
Abstract
One limitation in electron cryo-microscopy (cryo-EM) is the inability to recover high-resolution signal from the image-recording media at the full-resolution limit of the transmission electron microscope. Direct electron detection using CMOS-based sensors for digitally recording images has the potential to alleviate this shortcoming. Here, we report a practical performance evaluation of a Direct Detection Device (DDD®) for biological cryo-EM at two different microscope voltages: 200 and 300 kV. Our DDD images of amorphous and graphitized carbon show strong per-pixel contrast with image resolution near the theoretical sampling limit of the data. Single-particle reconstructions of two frozen-hydrated bacteriophages, P22 and ε15, establish that the DDD is capable of recording usable signal for 3D reconstructions at about 4/5 of the Nyquist frequency, which is a vast improvement over the performance of conventional imaging media. We anticipate the unparalleled performance of this digital recording device will dramatically benefit cryo-EM for routine tomographic and single-particle structural determination of biological specimens.
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Affiliation(s)
- Benjamin E Bammes
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
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22
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Reconstructing virus structures from nanometer to near-atomic resolutions with cryo-electron microscopy and tomography. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 726:49-90. [PMID: 22297510 DOI: 10.1007/978-1-4614-0980-9_4] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The past few decades have seen tremendous advances in single-particle electron -cryo-microscopy (cryo-EM). The field has matured to the point that near-atomic resolution density maps can be generated for icosahedral viruses without the need for crystallization. In parallel, substantial progress has been made in determining the structures of nonicosahedrally arranged proteins in viruses by employing either single-particle cryo-EM or cryo-electron tomography (cryo-ET). Implicit in this course have been the availability of a new generation of electron cryo-microscopes and the development of the computational tools that are essential for generating these maps and models. This methodology has enabled structural biologists to analyze structures in increasing detail for virus particles that are in different morphogenetic states. Furthermore, electron imaging of frozen, hydrated cells, in the process of being infected by viruses, has also opened up a new avenue for studying virus structures "in situ". Here we present the common techniques used to acquire and process cryo-EM and cryo-ET data and discuss their implications for structural virology both now and in the future.
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Abstract
The electron microscope has contributed deep insights into biological structure since its invention nearly 80 years ago. Advances in instrumentation and methodology in recent decades have now enabled electron tomography to become the highest resolution three-dimensional (3D) imaging technique available for unique objects such as cells. Cells can be imaged either plastic-embedded or frozen-hydrated. Then the series of projection images are aligned and back-projected to generate a 3D reconstruction or 'tomogram'. Here, we review how electron tomography has begun to reveal the molecular organization of cells and how the existing and upcoming technologies promise even greater insights into structural cell biology.
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25
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Milazzo AC, Cheng A, Moeller A, Lyumkis D, Jacovetty E, Polukas J, Ellisman MH, Xuong NH, Carragher B, Potter CS. Initial evaluation of a direct detection device detector for single particle cryo-electron microscopy. J Struct Biol 2011; 176:404-8. [PMID: 21933715 DOI: 10.1016/j.jsb.2011.09.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Revised: 09/04/2011] [Accepted: 09/07/2011] [Indexed: 11/18/2022]
Abstract
We report on initial results of using a new direct detection device (DDD) for single particle reconstruction of vitreous ice embedded specimens. Images were acquired on a Tecnai F20 at 200keV and a nominal magnification of 29,000×. This camera has a significantly improved signal to noise ratio and modulation transfer function (MTF) at 200keV compared to a standard CCD camera installed on the same microscope. Control of the DDD has been integrated into Leginon, an automated data collection system. Using GroEL as a test specimen, we obtained images of ∼30K particles with the CCD and the DDD from the same specimen sample using essentially identical imaging conditions. Comparison of the maps reconstructed from the CCD images and the DDD images demonstrates the improved performance of the DDD. We also obtained a 3D reconstruction from ∼70K GroEL particles acquired using the DDD; the quality of the density map demonstrates the potential of this new recording device for cryoEM data acquisition.
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Affiliation(s)
- Anna-Clare Milazzo
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
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Abstract
Electron microscopy (EM) is an important tool for high-resolution structure determination in applications ranging from condensed matter to biology. Electronic detectors are now used in most applications in EM as they offer convenience and immediate feedback that is not possible with film or image plates. The earliest forms of electronic detector used routinely in transmission electron microscopy (TEM) were charge coupled devices (CCDs) and for many applications these remain perfectly adequate. There are however applications, such as the study of radiation-sensitive biological samples, where film is still used and improved detectors would be of great value. The emphasis in this review is therefore on detectors for use in such applications. Two of the most promising candidates for improved detection are: monolithic active pixel sensors (MAPS) and hybrid pixel detectors (of which Medipix2 was chosen for this study). From the studies described in this review, a back-thinned MAPS detector appears well suited to replace film in for the study of radiation-sensitive samples at 300 keV, while Medipix2 is suited to use at lower energies and especially in situations with very low count rates. The performance of a detector depends on the energy of electrons to be recorded, which in turn is dependent on the application it is being used for; results are described for a wide range of electron energies ranging from 40 to 300 keV. The basic properties of detectors are discussed in terms of their modulation transfer function (MTF) and detective quantum efficiency (DQE) as a function of spatial frequency.
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Milazzo AC, Moldovan G, Lanman J, Jin L, Bouwer JC, Klienfelder S, Peltier ST, Ellisman MH, Kirkland AI, Xuong NH. Characterization of a direct detection device imaging camera for transmission electron microscopy. Ultramicroscopy 2010; 110:744-7. [PMID: 20382479 DOI: 10.1016/j.ultramic.2010.03.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Revised: 09/23/2009] [Accepted: 03/17/2010] [Indexed: 10/19/2022]
Abstract
The complete characterization of a novel direct detection device (DDD) camera for transmission electron microscopy is reported, for the first time at primary electron energies of 120 and 200 keV. Unlike a standard charge coupled device (CCD) camera, this device does not require a scintillator. The DDD transfers signal up to 65 lines/mm providing the basis for a high-performance platform for a new generation of wide field-of-view high-resolution cameras. An image of a thin section of virus particles is presented to illustrate the substantially improved performance of this sensor over current indirectly coupled CCD cameras.
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Affiliation(s)
- Anna-Clare Milazzo
- University of California at San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA.
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28
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Faruqi AR. Principles and prospects of direct high resolution electron image acquisition with CMOS detectors at low energies. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:314004. [PMID: 21828565 DOI: 10.1088/0953-8984/21/31/314004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Two types of direct electron detectors, potentially useful in low energy electron microscopy and photoemission electron microscopy (LEEM/PEEM) experiments, are reviewed in this paper. Hybrid pixel detectors, using a silicon sensor and based on Medipix2 offer a high detective quantum efficiency, due to an essentially noiseless readout, but are technically challenging. Backthinned monolithic active pixel sensors (MAPS) are not noise-free but have other advantages as discussed in this review.
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Affiliation(s)
- A R Faruqi
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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29
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McMullan G, Faruqi A, Henderson R, Guerrini N, Turchetta R, Jacobs A, van Hoften G. Experimental observation of the improvement in MTF from backthinning a CMOS direct electron detector. Ultramicroscopy 2009; 109:1144-7. [PMID: 19541421 PMCID: PMC2937214 DOI: 10.1016/j.ultramic.2009.05.005] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Revised: 04/03/2009] [Accepted: 05/01/2009] [Indexed: 11/23/2022]
Abstract
The advantages of backthinning monolithic active pixel sensors (MAPS) based on complementary metal oxide semiconductor (CMOS) direct electron detectors for electron microscopy have been discussed previously; they include better spatial resolution (modulation transfer function or MTF) and efficiency at all spatial frequencies (detective quantum efficiency or DQE). It was suggested that a 'thin' CMOS detector would have the most outstanding properties [1-3] because of a reduction in the proportion of backscattered electrons. In this paper we show, theoretically (using Monte Carlo simulations of electron trajectories) and experimentally that this is indeed the case. The modulation transfer functions of prototype backthinned CMOS direct electron detectors have been measured at 300keV. At zero spatial frequency, in non-backthinned 700-mum-thick detectors, the backscattered component makes up over 40% of the total signal but, by backthinning to 100, 50 or 35mum, this can be reduced to 25%, 15% and 10%, respectively. For the 35mum backthinned detector, this reduction in backscatter increases the MTF by 40% for spatial frequencies between 0.1 and 1.0 Nyquist. As discussed in the main text, reducing backscattering in backthinned detectors should also improve DQE.
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Affiliation(s)
- G. McMullan
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - A.R. Faruqi
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - R. Henderson
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - N. Guerrini
- STFC Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, UK
| | - R. Turchetta
- STFC Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, UK
| | - A. Jacobs
- Technical University of Eindhoven, 5600 MB Eindhoven, Netherlands
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McMullan G, Clark AT, Turchetta R, Faruqi AR. Enhanced imaging in low dose electron microscopy using electron counting. Ultramicroscopy 2009; 109:1411-6. [PMID: 19647366 PMCID: PMC2868354 DOI: 10.1016/j.ultramic.2009.07.004] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Revised: 06/24/2009] [Accepted: 07/07/2009] [Indexed: 10/26/2022]
Abstract
We compare the direct electron imaging performance at 120keV of a monolithic active pixel sensor (MAPS) operated in a conventional integrating mode with the performance obtained when operated in a single event counting mode. For the combination of sensor and incident electron energy used here, we propose a heuristic approach with which to process the single event images in which each event is renormalised to have an integrated weight of unity. Using this approach we find enhancements in the Nyquist frequency modulation transfer function (MTF) and detective quantum efficiency (DQE) over the corresponding integrating mode values by factors of 8 and 3, respectively.
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Affiliation(s)
- G McMullan
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.
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31
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McMullan G, Chen S, Henderson R, Faruqi AR. Detective quantum efficiency of electron area detectors in electron microscopy. Ultramicroscopy 2009; 109:1126-43. [PMID: 19497671 PMCID: PMC2864625 DOI: 10.1016/j.ultramic.2009.04.002] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Revised: 04/03/2009] [Accepted: 04/21/2009] [Indexed: 11/17/2022]
Abstract
Recent progress in detector design has created the need for a careful side-by-side comparison of the modulation transfer function (MTF) and resolution-dependent detective quantum efficiency (DQE) of existing electron detectors with those of detectors based on new technology. We present MTF and DQE measurements for four types of detector: Kodak SO-163 film, TVIPS 224 charge coupled device (CCD) detector, the Medipix2 hybrid pixel detector, and an experimental direct electron monolithic active pixel sensor (MAPS) detector. Film and CCD performance was measured at 120 and 300 keV, while results are presented for the Medipix2 at 120 keV and for the MAPS detector at 300 keV. In the case of film, the effects of electron backscattering from both the holder and the plastic support have been investigated. We also show that part of the response of the emulsion in film comes from light generated in the plastic support. Computer simulations of film and the MAPS detector have been carried out and show good agreement with experiment. The agreement enables us to conclude that the DQE of a backthinned direct electron MAPS detector is likely to be equal to, or better than, that of film at 300 keV.
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Affiliation(s)
- G McMullan
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB20QH, UK.
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Fernández-Oliveras A, Pozo A, Rubiño M. Analysis of the Modulation Transfer Function Spectral Variation in Different Detector Arrays by Means of Speckle Patterns. J Imaging Sci Technol 2009. [DOI: 10.2352/j.imagingsci.technol.2009.53.3.031101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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Hoenger A, McIntosh JR. Probing the macromolecular organization of cells by electron tomography. Curr Opin Cell Biol 2009; 21:89-96. [PMID: 19185480 DOI: 10.1016/j.ceb.2008.12.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Revised: 12/18/2008] [Accepted: 12/19/2008] [Indexed: 11/24/2022]
Abstract
A major goal in cell biology is to understand the functional organization of macromolecular complexes in vivo. Electron microscopy is helping cell biologists to achieve this goal, thanks to its ability to resolve structural details in the nanometer range. While issues related to specimen preparation, imaging, and image interpretation make this approach to cell architecture difficult, recent improvements in methods, equipment, and software have facilitated the study of both important macromolecular complexes and comparatively large volumes from cellular specimens. Here, we describe recent progress in electron microscopy of cells and the ways in which the relevant methodologies are helping to elucidate cell architecture.
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Affiliation(s)
- Andreas Hoenger
- Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells and Molecules, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309-0347, USA
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Jin L, Milazzo AC, Kleinfelder S, Li S, Leblanc P, Duttweiler F, Bouwer JC, Peltier ST, Ellisman MH, Xuong NH. Applications of direct detection device in transmission electron microscopy. J Struct Biol 2007; 161:352-8. [PMID: 18054249 DOI: 10.1016/j.jsb.2007.10.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Revised: 10/18/2007] [Accepted: 10/19/2007] [Indexed: 10/22/2022]
Abstract
A prototype direct detection device (DDD) camera system has shown great promise in improving both the spatial resolution and the signal to noise ratio for electron microscopy at 120-400 keV beam energies (Xuong et al., 2007. Methods in Cell Biology, 79, 721-739). Without the need for a resolution-limiting scintillation screen as in the charge coupled device (CCD), the DDD camera can outperform CCD based systems in terms of spatial resolution, due to its small pixel size (5 microm). In this paper, the modulation transfer function (MTF) of the DDD prototype is measured and compared with the specifications of commercial scientific CCD camera systems. Combining the fast speed of the DDD with image mosaic techniques, fast wide-area imaging is now possible. In this paper, the first large area mosaic image and the first tomography dataset from the DDD camera are presented, along with an image processing algorithm to correct the specimen drift utilizing the fast readout of the DDD system.
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Affiliation(s)
- Liang Jin
- University of California at San Diego, La Jolla, CA 92093, USA.
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