1
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Kuttruff J, Holder J, Meng Y, Baum P. Real-time electron clustering in an event-driven hybrid pixel detector. Ultramicroscopy 2024; 255:113864. [PMID: 37839354 DOI: 10.1016/j.ultramic.2023.113864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/26/2023] [Accepted: 10/04/2023] [Indexed: 10/17/2023]
Abstract
Event-driven hybrid pixel detectors with nanosecond time resolution have opened up novel pathways in modern ultrafast electron microscopy, for example in hyperspectral electron-energy loss spectroscopy or free-electron quantum optics. However, the impinging electrons typically excite more than one pixel of the device, and an efficient algorithm is therefore needed to convert the measured pixel hits to real single-electron events. Here we present a robust clustering algorithm that is fast enough to find clusters in a continuous stream of raw data in real time. Each tuple of position and arrival time from the detector is continuously compared to a buffer of previous hits until the probability of a merger with an old event becomes irrelevant. In this way, the computation time becomes independent of the density of electron arrival and the algorithm does not break the operation chain. We showcase the performance of the algorithm with a 'timepix' camera in two regimes of electron microscopy, in continuous beam emission and laser-triggered femtosecond mode.
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Affiliation(s)
- J Kuttruff
- Universität Konstanz, Fachbereich Physik, 78464 Konstanz, Germany
| | - J Holder
- Universität Konstanz, Fachbereich Physik, 78464 Konstanz, Germany
| | - Y Meng
- Universität Konstanz, Fachbereich Physik, 78464 Konstanz, Germany
| | - P Baum
- Universität Konstanz, Fachbereich Physik, 78464 Konstanz, Germany.
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2
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Duncan CJR, Kaemingk M, Li WH, Andorf MB, Bartnik AC, Galdi A, Gordon M, Pennington CA, Bazarov IV, Zeng HJ, Liu F, Luo D, Sood A, Lindenberg AM, Tate MW, Muller DA, Thom-Levy J, Gruner SM, Maxson JM. Multi-scale time-resolved electron diffraction: A case study in moiré materials. Ultramicroscopy 2023; 253:113771. [PMID: 37301082 DOI: 10.1016/j.ultramic.2023.113771] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 05/09/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023]
Abstract
Ultrafast-optical-pump - structural-probe measurements, including ultrafast electron and x-ray scattering, provide direct experimental access to the fundamental timescales of atomic motion, and are thus foundational techniques for studying matter out of equilibrium. High-performance detectors are needed in scattering experiments to obtain maximum scientific value from every probe particle. We deploy a hybrid pixel array direct electron detector to perform ultrafast electron diffraction experiments on a WSe2/MoSe2 2D heterobilayer, resolving the weak features of diffuse scattering and moiré superlattice structure without saturating the zero order peak. Enabled by the detector's high frame rate, we show that a chopping technique provides diffraction difference images with signal-to-noise at the shot noise limit. Finally, we demonstrate that a fast detector frame rate coupled with a high repetition rate probe can provide continuous time resolution from femtoseconds to seconds, enabling us to perform a scanning ultrafast electron diffraction experiment that maps thermal transport in WSe2/MoSe2 and resolves distinct diffusion mechanisms in space and time.
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Affiliation(s)
- C J R Duncan
- Cornell Laboratory for Accelerator-Based Sciences and Education, Cornell University, Ithaca, NY 14850, USA.
| | - M Kaemingk
- Cornell Laboratory for Accelerator-Based Sciences and Education, Cornell University, Ithaca, NY 14850, USA
| | - W H Li
- Cornell Laboratory for Accelerator-Based Sciences and Education, Cornell University, Ithaca, NY 14850, USA
| | - M B Andorf
- Cornell Laboratory for Accelerator-Based Sciences and Education, Cornell University, Ithaca, NY 14850, USA
| | - A C Bartnik
- Cornell Laboratory for Accelerator-Based Sciences and Education, Cornell University, Ithaca, NY 14850, USA
| | - A Galdi
- Cornell Laboratory for Accelerator-Based Sciences and Education, Cornell University, Ithaca, NY 14850, USA
| | - M Gordon
- Cornell Laboratory for Accelerator-Based Sciences and Education, Cornell University, Ithaca, NY 14850, USA
| | - C A Pennington
- Cornell Laboratory for Accelerator-Based Sciences and Education, Cornell University, Ithaca, NY 14850, USA
| | - I V Bazarov
- Cornell Laboratory for Accelerator-Based Sciences and Education, Cornell University, Ithaca, NY 14850, USA
| | - H J Zeng
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - F Liu
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - D Luo
- SLAC National Accelerator Laboratory, Menlo Park, CA 94205, USA
| | - A Sood
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08540, USA; Princeton Materials Institute, Princeton University, Princeton, NJ 08540, USA
| | - A M Lindenberg
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA
| | - M W Tate
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
| | - D A Muller
- Kavli Institute at Cornell for Nanoscale Science, Ithaca, NY 14853, USA; School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - J Thom-Levy
- Laboratory for Elementary-Particle Physics, Cornell University, Ithaca, NY 14853, USA
| | - S M Gruner
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA; Kavli Institute at Cornell for Nanoscale Science, Ithaca, NY 14853, USA
| | - J M Maxson
- Cornell Laboratory for Accelerator-Based Sciences and Education, Cornell University, Ithaca, NY 14850, USA.
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3
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Mücke D, Linck M, Guzzinati G, Müller H, Levin BDA, Bammes BE, Brouwer RG, Jelezko F, Qi H, Kaiser U. Effect of self and extrinsic encapsulation on electron resilience of porous 2D polymer nanosheets. Micron 2023; 174:103525. [PMID: 37595407 DOI: 10.1016/j.micron.2023.103525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/10/2023] [Accepted: 08/10/2023] [Indexed: 08/20/2023]
Abstract
Despite the exceptional resolution in aberration-corrected high-resolution transmission electron microscope (AC-HRTEM) images of inorganic two-dimensional (2D) materials, achieving high-resolution imaging of organic 2D materials remains a daunting challenge due to their low electron resilience. Optimizing the critical dose (the electron exposure, the material can accept before it is noticeably damaged) is vital to mitigate this challenge. An understanding of electron resilience in porous crystalline 2D polymers including the effect of sample thickness has not been derived thus far. It is assumed, that additional layers of the sample form a cage around inner layers, which are preventing fragments from escaping into the vacuum and enabling recombination. In the literature this so called caging effect has been reported for perylene and pythalocyanine. In this work we determine the critical dose of a porous, triazine-based 2D polymer as function of the sample thickness. The results show that the caging effect should not be generalized to more sophisticated polymer systems. We argue that pore channels in the framework structure serve as escape routes for free fragments preventing the caging effect and thus showing surprisingly a thickness-independent critical dose. Moreover, we demonstrate that graphene encapsulation prevents fragment escape and results in an increase in the critical electron dose and unit-cell image resolution.
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Affiliation(s)
- David Mücke
- Central Facility for Materials Science Electron Microscopy, Albert-Einstein-Allee 11, Universität Ulm, 89081 Ulm, Germany.
| | - Martin Linck
- Corrected Electron Optical Systems GmbH, Englerstr. 28, 69126 Heidelberg, Germany
| | - Giulio Guzzinati
- Corrected Electron Optical Systems GmbH, Englerstr. 28, 69126 Heidelberg, Germany
| | - Heiko Müller
- Corrected Electron Optical Systems GmbH, Englerstr. 28, 69126 Heidelberg, Germany
| | - Barnaby D A Levin
- Direct Electron LP, 13240 Evening Creek S Dr, Ste 311, San Diego, CA, USA
| | - Benjamin E Bammes
- Direct Electron LP, 13240 Evening Creek S Dr, Ste 311, San Diego, CA, USA
| | - Raúl González Brouwer
- Institute for Quantum Optics (IQO) and Center for Integrated Quantum Science and Technology (IQST), Ulm University, 89081 Ulm, Germany
| | - Fedor Jelezko
- Institute for Quantum Optics (IQO) and Center for Integrated Quantum Science and Technology (IQST), Ulm University, 89081 Ulm, Germany
| | - Haoyuan Qi
- Central Facility for Materials Science Electron Microscopy, Albert-Einstein-Allee 11, Universität Ulm, 89081 Ulm, Germany; Faculty of Chemistry and Food Chemistry, Mommsenstr. 4, Technische Universität Dresden, 01062 Dresden, Germany
| | - Ute Kaiser
- Central Facility for Materials Science Electron Microscopy, Albert-Einstein-Allee 11, Universität Ulm, 89081 Ulm, Germany.
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4
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Denisov N, Jannis D, Orekhov A, Müller-Caspary K, Verbeeck J. Characterization of a Timepix detector for use in SEM acceleration voltage range. Ultramicroscopy 2023; 253:113777. [PMID: 37336162 DOI: 10.1016/j.ultramic.2023.113777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
Hybrid pixel direct electron detectors are gaining popularity in electron microscopy due to their excellent properties. Some commercial cameras based on this technology are relatively affordable which makes them attractive tools for experimentation especially in combination with an SEM setup. To support this, a detector characterization (Modulation Transfer Function, Detective Quantum Efficiency) of an Advacam Minipix and Advacam Advapix detector in the 15-30 keV range was made. In the current work we present images of Point Spread Function, plots of MTF/DQE curves and values of DQE(0) for these detectors. At low beam currents, the silicon detector layer behaviour should be dominant, which could make these findings transferable to any other available detector based on either Medipix2, Timepix or Timepix3 provided the same detector layer is used.
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Affiliation(s)
- Nikita Denisov
- EMAT, University of Antwerp, Groenenborgerlaan 171, Antwerp, 2020, Belgium.
| | - Daen Jannis
- EMAT, University of Antwerp, Groenenborgerlaan 171, Antwerp, 2020, Belgium
| | - Andrey Orekhov
- EMAT, University of Antwerp, Groenenborgerlaan 171, Antwerp, 2020, Belgium
| | - Knut Müller-Caspary
- Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, Munich, 81377, Germany
| | - Johan Verbeeck
- EMAT, University of Antwerp, Groenenborgerlaan 171, Antwerp, 2020, Belgium.
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5
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Basha A, Levi G, Houben L, Amrani T, Goldfarb I, Kohn A. Evaluating direct detection detectors for short-range order characterization of amorphous materials by electron scattering. Ultramicroscopy 2023; 249:113737. [PMID: 37037087 DOI: 10.1016/j.ultramic.2023.113737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 04/12/2023]
Abstract
The introduction of direct electron detectors (DEDs) to transmission electron microscopy has set off the 'resolution revolution', especially for cryoTEM low-dose imaging of soft matter. In comparison to traditional indirect electron detectors such as Charged-Coupled Devices (CCD), DEDs show an improved modulation transfer function (MTF) and detective quantum efficiency (DQE) across all spatial frequencies, as well as faster frame rates which enable single electron counting. The benefits of such characteristics for imaging, spectroscopy and electron holography have been demonstrated previously. However, studies are lacking on the application of DEDs for localized characterization of short- to medium- range-order (SRO, MRO) in amorphous materials using electron scattering. Therefore, we evaluate the performance of a Monolithic Active Pixel Sensor DED for the characterization of SRO and MRO in nanoscale volumes of amorphous materials, using SiO2 and Ta2O5 thin films as test cases. The performance of the detector is compared systematically to electron scattering measurements recorded on an indirect detector (CCD) using 200 keV electrons and electron doses starting at approximately 500e-Å2 . In addition, the effects of sample cooling and energy-filtering on the measured SRO of the oxides were investigated. We demonstrate that the performance of the DED resulted in improved SRO characterization in comparison to that obtained from the CCD measurements. The DED enabled to achieve a larger measured maximal scattering vector, ∼16.51Å compared to ∼151Å, for the CCD. Furthermore, an improved signal-to-noise ratio of approximately two-fold was observed across all spatial frequencies for both 200 keV and 80 keV electrons. These improvements are shown to result from the superior DQE of the DED. Consequently, the DED measurements enabled to determine the coordination numbers of atomic bonds more accurately. We expect that further benefits of the DED for S/MRO characterization will be highlighted for ultra- sensitive materials that cannot withstand electron doses above several e-Å2 .
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Affiliation(s)
- Adham Basha
- Department of Materials Science and Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Ramat Aviv, Tel Aviv 6997801, Israel
| | - George Levi
- Department of Materials Science and Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Ramat Aviv, Tel Aviv 6997801, Israel
| | - Lothar Houben
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tamir Amrani
- Department of Materials Science and Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Ramat Aviv, Tel Aviv 6997801, Israel
| | - Ilan Goldfarb
- Department of Materials Science and Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Ramat Aviv, Tel Aviv 6997801, Israel
| | - Amit Kohn
- Department of Materials Science and Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Ramat Aviv, Tel Aviv 6997801, Israel.
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6
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Peng R, Fu X, Mendez JH, Randolph PS, Bammes BE, Stagg SM. Characterizing the resolution and throughput of the Apollo direct electron detector. J Struct Biol X 2022; 7:100080. [PMID: 36578473 PMCID: PMC9791170 DOI: 10.1016/j.yjsbx.2022.100080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Advances in electron detection have been essential to the success of high-resolution cryo-EM structure determination. A new generation of direct electron detector called the Apollo, has been developed by Direct Electron. The Apollo uses a novel event-based MAPS detector custom designed for ultra-fast electron counting. We have evaluated this new camera, finding that it delivers high detective quantum efficiency (DQE) and low coincidence loss, enabling high-quality electron counting data acquisition at up to nearly 80 input electrons per pixel per second. We further characterized the performance of Apollo for single particle cryo-EM on real biological samples. Using mouse apoferritin, Apollo yielded better than 1.9 Å resolution reconstructions at all three tested dose rates from a half-day data collection session each. With longer collection time and improved specimen preparation, mouse apoferritin was reconstructed to 1.66 Å resolution. Applied to a more challenging small protein aldolase, we obtained a 2.24 Å resolution reconstruction. The high quality of the map indicates that the Apollo has sufficiently high DQE to reconstruct smaller proteins and complexes with high-fidelity. Our results demonstrate that the Apollo camera performs well across a broad range of dose rates and is capable of capturing high quality data that produce high-resolution reconstructions for large and small single particle samples.
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Affiliation(s)
- Ruizhi Peng
- Institute of Molecular Biophysics, 91 Chieftain Way, Florida State University, Tallahassee, FL 32306, United States
| | - Xiaofeng Fu
- Department of Biological Sciences, 319 Stadium Drive, Tallahassee, FL 32306, United States
| | - Joshua H. Mendez
- Simons Electron Microscopy Center, 89 Convent Avenue, New York, NY 10027, United States
| | - Peter S. Randolph
- Institute of Molecular Biophysics, 91 Chieftain Way, Florida State University, Tallahassee, FL 32306, United States
| | - Benjamin E. Bammes
- Direct Electron LP, 13240 Evening Creek Drive South, Suite 311, San Diego, CA 92128, United States
| | - Scott M. Stagg
- Institute of Molecular Biophysics, 91 Chieftain Way, Florida State University, Tallahassee, FL 32306, United States,Department of Biological Sciences, 319 Stadium Drive, Tallahassee, FL 32306, United States,Corresponding author at: Institute of Molecular Biophysics, 91 Chieftain Way, Florida State University, Tallahassee, FL 32306, United States
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7
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Clabbers MTB, Martynowycz MW, Hattne J, Nannenga BL, Gonen T. Electron-counting MicroED data with the K2 and K3 direct electron detectors. J Struct Biol 2022; 214:107886. [PMID: 36044956 PMCID: PMC9999727 DOI: 10.1016/j.jsb.2022.107886] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/19/2022] [Accepted: 08/24/2022] [Indexed: 12/30/2022]
Abstract
Microcrystal electron diffraction (MicroED) uses electron cryo-microscopy (cryo-EM) to collect diffraction data from small crystals during continuous rotation of the sample. As a result of advances in hardware as well as methods development, the data quality has continuously improved over the past decade, to the point where even macromolecular structures can be determined ab initio. Detectors suitable for electron diffraction should ideally have fast readout to record data in movie mode, and high sensitivity at low exposure rates to accurately report the intensities. Direct electron detectors are commonly used in cryo-EM imaging for their sensitivity and speed, but despite their availability are generally not used in diffraction. Primary concerns with diffraction experiments are the dynamic range and coincidence loss, which will corrupt the measurement if the flux exceeds the count rate of the detector. Here, we describe instrument setup and low-exposure MicroED data collection in electron-counting mode using K2 and K3 direct electron detectors and show that the integrated intensities can be effectively used to solve structures of two macromolecules between 1.2 Å and 2.8 Å resolution. Even though a beam stop was not used with the K3 studies we did not observe damage to the camera. As these cameras are already available in many cryo-EM facilities, this provides opportunities for users who do not have access to dedicated facilities for MicroED.
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Affiliation(s)
- Max T B Clabbers
- Department of Biological Chemistry, University of California, Los Angeles CA 90095, United States; Howard Hughes Medical Institute, University of California, Los Angeles CA 90095, United States
| | - Michael W Martynowycz
- Department of Biological Chemistry, University of California, Los Angeles CA 90095, United States; Howard Hughes Medical Institute, University of California, Los Angeles CA 90095, United States
| | - Johan Hattne
- Department of Biological Chemistry, University of California, Los Angeles CA 90095, United States; Howard Hughes Medical Institute, University of California, Los Angeles CA 90095, United States
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Arizona State University, Tempe, AZ, United States; Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Tamir Gonen
- Department of Biological Chemistry, University of California, Los Angeles CA 90095, United States; Howard Hughes Medical Institute, University of California, Los Angeles CA 90095, United States; Department of Physiology, University of California, Los Angeles CA 90095, United States.
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8
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Heymann JB. The progressive spectral signal-to-noise ratio of cryo-electron micrograph movies as a tool to assess quality and radiation damage. Comput Methods Programs Biomed 2022; 220:106799. [PMID: 35405434 PMCID: PMC9149132 DOI: 10.1016/j.cmpb.2022.106799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/15/2022] [Accepted: 03/31/2022] [Indexed: 06/03/2023]
Abstract
BACKGROUND AND OBJECTIVE The quality of a cryoEM reconstruction is fundamentally a function of the signal-to-noise ratio (SNR) of the original micrographs. The SNR embodies multiple aspects of image formation, including microscope details and alignment, specimen composition and thickness, how it is recorded, and how the specimen degrades during imaging. With the advent of direct electron detectors and the recording of a series of images for each micrograph (a movie), we have an opportunity to count every electron and derive fully quantitative results. After alignment of the movie frames of a micrograph, we can calculate the SNR, or its spatial frequency equivalent, the spectral SNR (SSNR). This SSNR reflects residual movement between frames and the progressive effect of radiation damage. The goal is to develop a quantitative analysis of the SSNR and radiation damage to assess and improve the quality of micrographs. METHODS Several test cases were selected from the EMPIAR database and ten micrograph movies downloaded for each case. The movie frames were aligned as rigid bodies to compensate for stage and support movement. The SSNR for subsets of frames was then calculated to assess the effect of residual movement. The progressive SSNR (PSSNR) was subsequently calculated to determine the decrease in signal accumulation as a result of radiation damage. RESULTS In all cases the alignment of the movie frames compensated for global movement to the extent that the effect on the SSNR is negligible. The subset SSNR can be used as a tool to further confirm the extent of residual movement. The progressive SSNR indicates an increase in value up to an asymptote, consistent with the theory for radiation damage. Fitting these curves gives the inherent SNR before exposure, and the critical dose, which decreases with spatial frequency with an exponential parameter roughly between one and two. CONCLUSIONS The implementation of the PSSNR for movie frames provides a tool for assessing micrograph quality and progression of radiation damage. The estimation of the critical dose further quantifies radiation damage and may shed some light on the mechanisms of damage. These are likely both a function of the specimen composition and the imaging parameters used.
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Affiliation(s)
- J Bernard Heymann
- Laboratory for Structural Biology Research, NIAMS, NIH, Bethesda, MD 20892, USA; National Cryo-EM Program, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA.
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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Paterson GW, Lamb RJ, Ballabriga R, Maneuski D, O'Shea V, McGrouther D. Sub-100 nanosecond temporally resolved imaging with the Medipix3 direct electron detector. Ultramicroscopy 2019; 210:112917. [PMID: 31841837 DOI: 10.1016/j.ultramic.2019.112917] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/13/2019] [Accepted: 12/03/2019] [Indexed: 11/17/2022]
Abstract
Detector developments are currently enabling new capabilities in the field of transmission electron microscopy (TEM). We have investigated the limits of a hybrid pixel detector, Medipix3, to record dynamic, time varying, electron signals. Operating with an energy of 60 keV, we have utilised electrostatic deflection to oscillate electron beam position on the detector. Adopting a pump-probe imaging strategy, we have demonstrated that temporal resolutions three orders of magnitude smaller than are available for typically used TEM imaging detectors are possible. Our experiments have shown that energy deposition of the primary electrons in the hybrid pixel detector limits the overall temporal resolution. Through adjustment of user specifiable thresholds or the use of charge summing mode, we have obtained images composed from summing 10,000s frames containing single electron events to achieve temporal resolution less than 100 ns. We propose that this capability can be directly applied to studying repeatable material dynamic processes but also to implement low-dose imaging schemes in scanning transmission electron microscopy.
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Affiliation(s)
- Gary W Paterson
- SUPA, School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom.
| | - Raymond J Lamb
- SUPA, School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom.
| | | | - Dima Maneuski
- SUPA, School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Val O'Shea
- SUPA, School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Damien McGrouther
- SUPA, School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom.
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11
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Leijten ZJWA, Wirix MJM, Strauss M, Plitzko JM, de With G, Friedrich H. Low-dose (S)TEM elemental analysis of water and oxygen uptake in beam sensitive materials. Ultramicroscopy 2020; 208:112855. [PMID: 31634656 DOI: 10.1016/j.ultramic.2019.112855] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 07/18/2019] [Accepted: 10/07/2019] [Indexed: 11/23/2022]
Abstract
The performance stability of organic photovoltaics (OPVs) is largely determined by their nanoscale morphology and composition and is highly dependent on the interaction with oxygen and water from air. Low-dose cryo-(S)TEM techniques, in combination with OPV donor-acceptor model systems, can be used to assess oxygen- and water-uptake in the donor, acceptor and their interface. By determining a materials dependent critical electron dose from the decay of the oxygen K-edge intensity in Electron Energy Loss Spectra, we reliably measured oxygen- and water-uptake minimizing and correcting electron beam effects. With measurements below the dose limit the capability of STEM-EDX, EFTEM and STEM-EELS techniques are compared to qualitatively and quantitatively measure oxygen and water uptake in these OPV model systems. Here we demonstrate that oxygen and water is mainly taken up in acceptor-rich regions, and that specific oxygen uptake at the donor-acceptor interphase does not occur. STEM-EELS is shown to be the best suitable technique, enabling quantification of the local oxygen concentration in OPV model systems.
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Biyani N, Scherer S, Righetto RD, Kowal J, Chami M, Stahlberg H. Image processing techniques for high-resolution structure determination from badly ordered 2D crystals. J Struct Biol 2018; 203:120-134. [PMID: 29689299 DOI: 10.1016/j.jsb.2018.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 03/29/2018] [Accepted: 03/30/2018] [Indexed: 11/19/2022]
Abstract
2D electron crystallography can be used to study small membrane proteins in their native environment. Obtaining highly ordered 2D crystals is difficult and time-consuming. However, 2D crystals diffracting to only 10-12 Å can be prepared relatively conveniently in most cases. We have developed image-processing algorithms allowing to generate a high resolution 3D structure from cryo-electron crystallography images of badly ordered crystals. These include movie-mode unbending, refinement over sub-tiles of the images in order to locally refine the sample tilt geometry, implementation of different CTF correction schemes, and an iterative method to apply known constraints in the real and reciprocal space to approximate amplitudes and phases in the so-called missing cone regions. These algorithms applied to a dataset of the potassium channel MloK1 show significant resolution improvements to better than 5 Å.
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Affiliation(s)
- Nikhil Biyani
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, CH-4058 Basel, Switzerland
| | - Sebastian Scherer
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, CH-4058 Basel, Switzerland
| | - Ricardo D Righetto
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, CH-4058 Basel, Switzerland
| | - Julia Kowal
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, CH-4058 Basel, Switzerland
| | - Mohamed Chami
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, CH-4058 Basel, Switzerland; BioEM Lab, C-CINA, Biozentrum, University of Basel, CH-4058 Basel, Switzerland
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, CH-4058 Basel, Switzerland.
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Spear JM, Noble AJ, Xie Q, Sousa DR, Chapman MS, Stagg SM. The influence of frame alignment with dose compensation on the quality of single particle reconstructions. J Struct Biol 2015; 192:196-203. [PMID: 26391007 DOI: 10.1016/j.jsb.2015.09.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 09/15/2015] [Accepted: 09/16/2015] [Indexed: 12/21/2022]
Abstract
As direct electron detection devices in cryo-electron microscopy become ubiquitous, the field is now ripe for new developments in image analysis techniques that take advantage of their increased SNR coupled with their high-throughput frame collection abilities. In approaching atomic resolution of native-like biomolecules, the accurate extraction of structural locations and orientations of side-chains from frames depends not only on the electron dose that a sample receives but also on the ability to accurately estimate the CTF. Here we use a new 2.8Å resolution structure of a recombinant gene therapy virus, AAV-DJ with Arixtra, imaged on an FEI Titan Krios with a DE-20 direct electron detector to probe new metrics including relative side-chain density and ResLog analysis for optimizing the compensation of electron beam damage and to characterize the factors that are limiting the resolution of the reconstruction. The influence of dose compensation on the accuracy of CTF estimation and particle classifiability are also presented. We show that rigorous dose compensation allows for better particle classifiability and greater recovery of structural information from negatively charged, electron-sensitive side-chains, resulting in a more accurate macromolecular model.
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Affiliation(s)
- John M Spear
- Institute of Molecular Biophysics, 91 Chieftan Way, Florida State University, Tallahassee, FL 32306-4380, United States
| | - Alex J Noble
- Department of Physics, 77 Chieftan Way, Florida State University, Tallahassee, FL 32306-4350, United States
| | - Qing Xie
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239-3098, United States
| | - Duncan R Sousa
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, United States
| | - Michael S Chapman
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239-3098, United States
| | - Scott M Stagg
- Institute of Molecular Biophysics, 91 Chieftan Way, Florida State University, Tallahassee, FL 32306-4380, United States; Departments of Chemistry and Biochemistry, 95 Chieftain Way, Florida State University, Tallahassee, FL 32306-4390, United States.
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Rubinstein JL, Brubaker MA. Alignment of cryo-EM movies of individual particles by optimization of image translations. J Struct Biol 2015; 192:188-95. [PMID: 26296328 DOI: 10.1016/j.jsb.2015.08.007] [Citation(s) in RCA: 186] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 08/11/2015] [Accepted: 08/12/2015] [Indexed: 11/21/2022]
Abstract
Direct detector device (DDD) cameras have revolutionized single particle electron cryomicroscopy (cryo-EM). In addition to an improved camera detective quantum efficiency, acquisition of DDD movies allows for correction of movement of the specimen, due to both instabilities in the microscope specimen stage and electron beam-induced movement. Unlike specimen stage drift, beam-induced movement is not always homogeneous within an image. Local correlation in the trajectories of nearby particles suggests that beam-induced motion is due to deformation of the ice layer. Algorithms have already been described that can correct movement for large regions of frames and for >1 MDa protein particles. Another algorithm allows individual <1 MDa protein particle trajectories to be estimated, but requires rolling averages to be calculated from frames and fits linear trajectories for particles. Here we describe an algorithm that allows for individual <1 MDa particle images to be aligned without frame averaging or linear trajectories. The algorithm maximizes the overall correlation of the shifted frames with the sum of the shifted frames. The optimum in this single objective function is found efficiently by making use of analytically calculated derivatives of the function. To smooth estimates of particle trajectories, rapid changes in particle positions between frames are penalized in the objective function and weighted averaging of nearby trajectories ensures local correlation in trajectories. This individual particle motion correction, in combination with weighting of Fourier components to account for increasing radiation damage in later frames, can be used to improve 3-D maps from single particle cryo-EM.
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Zhao J, Brubaker MA, Benlekbir S, Rubinstein JL. Description and comparison of algorithms for correcting anisotropic magnification in cryo-EM images. J Struct Biol 2015; 192:209-15. [PMID: 26087140 DOI: 10.1016/j.jsb.2015.06.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 06/11/2015] [Accepted: 06/14/2015] [Indexed: 11/23/2022]
Abstract
Single particle electron cryomicroscopy (cryo-EM) allows for structures of proteins and protein complexes to be determined from images of non-crystalline specimens. Cryo-EM data analysis requires electron microscope images of randomly oriented ice-embedded protein particles to be rotated and translated to allow for coherent averaging when calculating three-dimensional (3D) structures. Rotation of 2D images is usually done with the assumption that the magnification of the electron microscope is the same in all directions. However, due to electron optical aberrations, this condition is not met with some electron microscopes when used with the settings necessary for cryo-EM with a direct detector device (DDD) camera. Correction of images by linear interpolation in real space has allowed high-resolution structures to be calculated from cryo-EM images for symmetric particles. Here we describe and compare a simple real space method, a simple Fourier space method, and a somewhat more sophisticated Fourier space method to correct images for a measured anisotropy in magnification. Further, anisotropic magnification causes contrast transfer function (CTF) parameters estimated from image power spectra to have an apparent systematic astigmatism. To address this problem we develop an approach to adjust CTF parameters measured from distorted images so that they can be used with corrected images. The effect of anisotropic magnification on CTF parameters provides a simple way of detecting magnification anisotropy in cryo-EM datasets.
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Ruskin RS, Yu Z, Grigorieff N. Quantitative characterization of electron detectors for transmission electron microscopy. J Struct Biol 2013; 184:385-93. [PMID: 24189638 PMCID: PMC3876735 DOI: 10.1016/j.jsb.2013.10.016] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 10/24/2013] [Accepted: 10/28/2013] [Indexed: 12/01/2022]
Abstract
A new generation of direct electron detectors for transmission electron microscopy (TEM) promises significant improvement over previous detectors in terms of their modulation transfer function (MTF) and detective quantum efficiency (DQE). However, the performance of these new detectors needs to be carefully monitored in order to optimize imaging conditions and check for degradation over time. We have developed an easy-to-use software tool, FindDQE, to measure MTF and DQE of electron detectors using images of a microscope's built-in beam stop. Using this software, we have determined the DQE curves of four direct electron detectors currently available: the Gatan K2 Summit, the FEI Falcon I and II, and the Direct Electron DE-12, under a variety of total dose and dose rate conditions. We have additionally measured the curves for the Gatan US4000 and TVIPS TemCam-F416 scintillator-based cameras. We compare the results from our new method with published curves.
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Affiliation(s)
- Rachel S. Ruskin
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, MS029, 415 South Street, Waltham, MA 02454, USA
| | - Zhiheng Yu
- Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn VA 20147 USA
| | - Nikolaus Grigorieff
- Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn VA 20147 USA
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