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Dickerson JL, McCubbin PTN, Brooks‐Bartlett JC, Garman EF. Doses for X-ray and electron diffraction: New features in RADDOSE-3D including intensity decay models. Protein Sci 2024; 33:e5005. [PMID: 38923423 PMCID: PMC11196903 DOI: 10.1002/pro.5005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/17/2024] [Accepted: 04/15/2024] [Indexed: 06/28/2024]
Abstract
New features in the dose estimation program RADDOSE-3D are summarised. They include the facility to enter a diffraction intensity decay model which modifies the "Diffraction Weighted Dose" output from a "Fluence Weighted Dose" to a "Diffraction-Decay Weighted Dose", a description of RADDOSE-ED for use in electron diffraction experiments, where dose is historically quoted in electrons/Å2 rather than in gray (Gy), and finally the development of a RADDOSE-3D GUI, enabling easy access to all the options available in the program.
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Affiliation(s)
- Joshua L. Dickerson
- Department of Biochemistry, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordUK
- MRC Laboratory of Molecular BiologyCambridge Biomedical CampusCambridgeUK
| | - Patrick T. N. McCubbin
- Department of Biochemistry, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordUK
- Division of Structural Biology, Nuffield Department of MedicineUniversity of OxfordOxfordUK
| | | | - Elspeth F. Garman
- Department of Biochemistry, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordUK
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2
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Dukes MD, Guo Y, Walden S, Krans N, Marusak K, Eldred T, Damiano J. Machine Vision Software Enables Normalization of Electron Dose Calibration Between Microscopes and Delivers Accurate Quantifiable Tracking of Electron Dose for In-Situ, Operando, and Dose Sensitive Experiments. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1849-1850. [PMID: 37613898 DOI: 10.1093/micmic/ozad067.955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
| | - Yaofeng Guo
- Protochips, Inc. Morrisville, NC, United States
| | | | - Nynke Krans
- Protochips, Inc. Morrisville, NC, United States
| | | | - Tim Eldred
- Protochips, Inc. Morrisville, NC, United States
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Krause FF, Schowalter M, Gerken B, Marquardt D, Grieb T, Mehrtens T, Mahr C, Rosenauer A. Dose efficient annular bright field contrast with the ISTEM method: A proof of principle demonstration. Ultramicroscopy 2023; 245:113661. [PMID: 36529039 DOI: 10.1016/j.ultramic.2022.113661] [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: 09/02/2022] [Revised: 11/21/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022]
Abstract
The ISTEM mode for TEM has been demonstrated to have several advantages in regard to resolution and precision. While previous works primarily focussed on the advantages due to the reduced spatial coherence, the actual image contrast, i.e. how bright or dark certain atom columns are imaged, has mostly been of secondary concern. The present work sets out to achieve the contrast of annular bright field STEM in ISTEM, producing the high contrast of light elements, for which this method is popular. It is shown from theoretical considerations that using an annular condenser aperture this aim can be realised. The optimal size of this aperture is found by simulative studies. It is then manufactured from platinum foil and installed in an image-aberration corrected microscope. ABF-like ISTEM images of strontium titanate in [100] projection are acquired. The pure oxygen columns are clearly resolved with significant contrast. The image pattern is indeed identical to what is achieved by ABF STEM. A close look at the image formation also shows that the dose needed for a given signal-to-noise ratio is at least a quarter smaller for ABF-like ISTEM compared to ABF STEM, assuming detectors of similar detective quantum efficiency.
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Affiliation(s)
- Florian F Krause
- Institut für Festkörperphysik, Universität Bremen, Otto-Hahn-Allee 1, 28359 Bremen, Germany.
| | - Marco Schowalter
- Institut für Festkörperphysik, Universität Bremen, Otto-Hahn-Allee 1, 28359 Bremen, Germany
| | - Beeke Gerken
- Institut für Festkörperphysik, Universität Bremen, Otto-Hahn-Allee 1, 28359 Bremen, Germany
| | - Dennis Marquardt
- Institut für Festkörperphysik, Universität Bremen, Otto-Hahn-Allee 1, 28359 Bremen, Germany
| | - Tim Grieb
- Institut für Festkörperphysik, Universität Bremen, Otto-Hahn-Allee 1, 28359 Bremen, Germany
| | - Thorsten Mehrtens
- Institut für Festkörperphysik, Universität Bremen, Otto-Hahn-Allee 1, 28359 Bremen, Germany
| | - Christoph Mahr
- Institut für Festkörperphysik, Universität Bremen, Otto-Hahn-Allee 1, 28359 Bremen, Germany
| | - Andreas Rosenauer
- Institut für Festkörperphysik, Universität Bremen, Otto-Hahn-Allee 1, 28359 Bremen, Germany
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Esser BD, Etheridge J. Complementary ADF-STEM: a Flexible Approach to Quantitative 4D-STEM. Ultramicroscopy 2023; 243:113627. [DOI: 10.1016/j.ultramic.2022.113627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/26/2022] [Accepted: 10/02/2022] [Indexed: 11/06/2022]
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An electron counting algorithm improves imaging of proteins with low-acceleration-voltage cryo-electron microscope. Commun Biol 2022; 5:321. [PMID: 35388174 PMCID: PMC8987035 DOI: 10.1038/s42003-022-03284-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 03/16/2022] [Indexed: 11/09/2022] Open
Abstract
Relative to the 300-kV accelerating field, electrons accelerated under lower voltages are potentially scattered more strongly. Lowering the accelerate voltage has been suggested to enhance the signal-to-noise ratio (SNR) of cryo-electron microscopy (cryo-EM) images of small-molecular-weight proteins (<100 kD). However, the detection efficient of current Direct Detection Devices (DDDs) and temporal coherence of cryo-EM decrease at lower voltage, leading to loss of SNR. Here, we present an electron counting algorithm to improve the detection of low-energy electrons. The counting algorithm increased the SNR of 120-kV and 200-kV cryo-EM image from a Falcon III camera by 8%, 20% at half the Nyquist frequency and 21%, 80% at Nyquist frequency, respectively, resulting in a considerable improvement in resolution of 3D reconstructions. Our results indicate that with further improved temporal coherence and a dedicated designed camera, a 120-kV cryo-electron microscope has potential to match the 300-kV microscope at imaging small proteins.
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Kryshtal A, Mielczarek M, Pawlak J. Effect of electron beam irradiation on the temperature of single AuGe nanoparticles in a TEM. Ultramicroscopy 2022; 233:113459. [PMID: 34942542 DOI: 10.1016/j.ultramic.2021.113459] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 10/21/2021] [Accepted: 12/05/2021] [Indexed: 11/28/2022]
Abstract
Knowledge of the actual temperature of nanoparticles under electron beam irradiation is of growing demand for in situ TEM studies. In this work, we addressed the problem with an experimental study of the temperature increment of single AuGe nanoparticles in a TEM and a STEM. The two-phase hemispherical AuGe nanoparticles were formed by the dewetting of an Au/Ge film on a SiNx substrate. The nanoparticles were thermally cycled in an electron microscope in the 293-653 K temperature range, under a wide range of electron beam currents. The jump-like change of the morphology of the AuGe nanoparticles at melting was used as a temperature label. The melting-crystallization process in binary alloy nanoparticles is fully reversible, with a large temperature hysteresis. It could be repeated on the same nanoparticle, providing a simple and robust way to measure the local temperature increment induced by the electron beam. It was shown that the temperature of the AuGe nanoparticles rose linearly with the e-beam current density J, and the temperature increment reached 25 K at J ∼ 1.8 × 106 A/m2 in the TEM. Given a fully known specimen geometry, the temperature increment was calculated when using theoretical approaches and compared with the experimental observations. As a result, recommendations for the assessment of real temperature in similar configurations were provided. In the STEM mode, no change in the temperature of the nanoparticles was registered at conventional parameters of the electron beam and the raster scans, which makes this mode preferable for in situ studies of metal and alloy nanoparticles.
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Affiliation(s)
- Aleksandr Kryshtal
- Faculty of Metals Engineering and Industrial Computer Science, AGH University of Science and Technology, al. Mickiewicza 30, Krakow 30-059, Poland.
| | - Mikolaj Mielczarek
- Faculty of Metals Engineering and Industrial Computer Science, AGH University of Science and Technology, al. Mickiewicza 30, Krakow 30-059, Poland
| | - Jakub Pawlak
- Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, al. Mickiewicza 30, Krakow 30-059, Poland; Academic Center for Materials and Nanotechnology, AGH University of Science and Technology, al. Mickiewicza 30, Krakow 30-059, Poland
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Jannis D, Hofer C, Gao C, Xie X, Béché A, Pennycook TJ, Verbeeck J. Event driven 4D STEM acquisition with a Timepix3 detector: Microsecond dwell time and faster scans for high precision and low dose applications. Ultramicroscopy 2022; 233:113423. [PMID: 34837737 DOI: 10.1016/j.ultramic.2021.113423] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/11/2021] [Accepted: 10/31/2021] [Indexed: 10/19/2022]
Abstract
Four dimensional scanning transmission electron microscopy (4D STEM) records the scattering of electrons in a material in great detail. The benefits offered by 4D STEM are substantial, with the wealth of data it provides facilitating for instance high precision, high electron dose efficiency phase imaging via centre of mass or ptychography based analysis. However the requirement for a 2D image of the scattering to be recorded at each probe position has long placed a severe bottleneck on the speed at which 4D STEM can be performed. Recent advances in camera technology have greatly reduced this bottleneck, with the detection efficiency of direct electron detectors being especially well suited to the technique. However even the fastest frame driven pixelated detectors still significantly limit the scan speed which can be used in 4D STEM, making the resulting data susceptible to drift and hampering its use for low dose beam sensitive applications. Here we report the development of the use of an event driven Timepix3 direct electron camera that allows us to overcome this bottleneck and achieve 4D STEM dwell times down to 100 ns; orders of magnitude faster than what has been possible with frame based readout. We characterize the detector for different acceleration voltages and show that the method is especially well suited for low dose imaging and promises rich datasets without compromising dwell time when compared to conventional STEM imaging.
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Affiliation(s)
- D Jannis
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - C Hofer
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - C Gao
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - X Xie
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - A Béché
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - T J Pennycook
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - J Verbeeck
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium.
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Dose measurement in the TEM and STEM. Ultramicroscopy 2021; 229:113363. [PMID: 34343770 DOI: 10.1016/j.ultramic.2021.113363] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 10/20/2022]
Abstract
Practical aspects of dosimetry are considered, including the measurement of electron-beam current and current density. Complications that arise in the case of a focused probe or a STEM image are discussed and solutions proposed. Advantages of expressing the radiation dose in Grays are listed and a simple formula given for converting electron fluence to Gray units, based on a near constancy of the stopping power per atomic electron. Comparisons with stopping-power calculations and EELS measurements suggest that this formula is accurate to within 5%. Based on the stopping power formula, a new way of measuring the local mass-thickness of light-element specimens is proposed. The average energy loss per inelastic collision is shown to be higher than previous expectations.
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