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Axelrod JJ, Zhang JT, Petrov PN, Glaeser RM, Müller H. Modern approaches to improving phase contrast electron microscopy. Curr Opin Struct Biol 2024; 86:102805. [PMID: 38531188 DOI: 10.1016/j.sbi.2024.102805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024]
Abstract
Although defocus can be used to generate partial phase contrast in transmission electron microscope images, cryo-electron microscopy (cryo-EM) can be further improved by the development of phase plates which increase contrast by applying a phase shift to the unscattered part of the electron beam. Many approaches have been investigated, including the ponderomotive interaction between light and electrons. We review the recent successes achieved with this method in high-resolution, single-particle cryo-EM. We also review the status of using pulsed or near-field enhanced laser light as alternatives, along with approaches that use scanning transmission electron microscopy (STEM) with a segmented detector rather than a phase plate.
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Affiliation(s)
- Jeremy J Axelrod
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA; Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Jessie T Zhang
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
| | - Petar N Petrov
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA; Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Robert M Glaeser
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Holger Müller
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA; Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA.
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Axelrod JJ, Petrov PN, Zhang JT, Remis J, Buijsse B, Glaeser RM, Mȕller H. Overcoming resolution loss due to thermal magnetic field fluctuations from phase plates in transmission electron microscopy. Ultramicroscopy 2023; 249:113730. [PMID: 37011498 PMCID: PMC11229668 DOI: 10.1016/j.ultramic.2023.113730] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023]
Abstract
We identify thermal magnetic field fluctuations, caused by thermal electron motion ("Johnson noise") in electrically conductive materials, as a potential resolution limit in transmission electron microscopy with a phase plate. Specifically, resolution loss can occur if the electron diffraction pattern is magnified to extend phase contrast to lower spatial frequencies, and if conductive materials are placed too close to the electron beam. While our initial implementation of a laser phase plate (LPP) was significantly affected by these factors, a redesign eliminated the problem and brought the performance close to the expected level. The resolution now appears to be limited by residual Johnson noise arising from the electron beam liner tube in the region of the LPP, together with the chromatic aberration of the relay optics. These two factors can be addressed during future development of the LPP.
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Affiliation(s)
- Jeremy J Axelrod
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA; Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA.
| | - Petar N Petrov
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA; Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Jessie T Zhang
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
| | - Jonathan Remis
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA; Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Bart Buijsse
- Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG, Eindhoven, the Netherlands
| | - Robert M Glaeser
- Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Holger Mȕller
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA; Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
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Axelrod JJ, Petrov PN, Zhang JT, Remis J, Buijsse B, Glaeser RM, Mȕller H. Overcoming resolution loss due to thermal magnetic field fluctuations from phase plates in transmission electron microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.12.528160. [PMID: 36824829 PMCID: PMC9949102 DOI: 10.1101/2023.02.12.528160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
We identify thermal magnetic field fluctuations, caused by thermal electron motion ("Johnson noise") in electrically conductive materials, as a potential resolution limit in transmission electron microscopy with a phase plate. Specifically, resolution loss can occur if the electron diffraction pattern is magnified to extend phase contrast to lower spatial frequencies, and if conductive materials are placed too close to the electron beam. While our initial implementation of a laser phase plate (LPP) was significantly affected by these factors, a redesign eliminated the problem and brought the performance close to the expected level. The resolution now appears to be limited by residual Johnson noise arising from the electron beam liner tube in the region of the LPP, together with the chromatic aberration of the relay optics. These two factors can be addressed during future development of the LPP.
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Affiliation(s)
- Jeremy J. Axelrod
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
- Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Petar N. Petrov
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
- Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Jessie T. Zhang
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
| | - Jonathan Remis
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
- Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Bart Buijsse
- Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG, Eindhoven, the Netherlands
| | - Robert M. Glaeser
- Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Holger Mȕller
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
- Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
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Zhang Y, Lu PH, Rotunno E, Troiani F, van Schayck JP, Tavabi AH, Dunin-Borkowski RE, Grillo V, Peters PJ, Ravelli RBG. Single-particle cryo-EM: alternative schemes to improve dose efficiency. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:1343-1356. [PMID: 34475283 PMCID: PMC8415325 DOI: 10.1107/s1600577521007931] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Imaging of biomolecules by ionizing radiation, such as electrons, causes radiation damage which introduces structural and compositional changes of the specimen. The total number of high-energy electrons per surface area that can be used for imaging in cryogenic electron microscopy (cryo-EM) is severely restricted due to radiation damage, resulting in low signal-to-noise ratios (SNR). High resolution details are dampened by the transfer function of the microscope and detector, and are the first to be lost as radiation damage alters the individual molecules which are presumed to be identical during averaging. As a consequence, radiation damage puts a limit on the particle size and sample heterogeneity with which electron microscopy (EM) can deal. Since a transmission EM (TEM) image is formed from the scattering process of the electron by the specimen interaction potential, radiation damage is inevitable. However, we can aim to maximize the information transfer for a given dose and increase the SNR by finding alternatives to the conventional phase-contrast cryo-EM techniques. Here some alternative transmission electron microscopy techniques are reviewed, including phase plate, multi-pass transmission electron microscopy, off-axis holography, ptychography and a quantum sorter. Their prospects for providing more or complementary structural information within the limited lifetime of the sample are discussed.
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Affiliation(s)
- Yue Zhang
- Maastricht Multimodal Molecular Imaging Institute, Division of Nanoscopy, Maastricht University, Universiteitssingel 50, Maastricht 6229 ER, The Netherlands
| | - Peng-Han Lu
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, Jülich 52425, Germany
| | - Enzo Rotunno
- CNR-Istituto Nanoscienze, Centro S3, Via G Campi 213/A, I-41125 Modena, Italy
| | - Filippo Troiani
- CNR-Istituto Nanoscienze, Centro S3, Via G Campi 213/A, I-41125 Modena, Italy
| | - J. Paul van Schayck
- Maastricht Multimodal Molecular Imaging Institute, Division of Nanoscopy, Maastricht University, Universiteitssingel 50, Maastricht 6229 ER, The Netherlands
| | - Amir H. Tavabi
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, Jülich 52425, Germany
| | - Rafal E. Dunin-Borkowski
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, Jülich 52425, Germany
| | - Vincenzo Grillo
- CNR-Istituto Nanoscienze, Centro S3, Via G Campi 213/A, I-41125 Modena, Italy
| | - Peter J. Peters
- Maastricht Multimodal Molecular Imaging Institute, Division of Nanoscopy, Maastricht University, Universiteitssingel 50, Maastricht 6229 ER, The Netherlands
| | - Raimond B. G. Ravelli
- Maastricht Multimodal Molecular Imaging Institute, Division of Nanoscopy, Maastricht University, Universiteitssingel 50, Maastricht 6229 ER, The Netherlands
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Artusio-Glimpse AB, Rogers KA, Williams PA, Lehman JH. High amplification laser-pressure optic enables ultra-low uncertainty measurements of the optical laser power at kilowatt levels. METROLOGIA 2021; 58:10.1088/1681-7575/ac1e34. [PMID: 36733973 PMCID: PMC9890404 DOI: 10.1088/1681-7575/ac1e34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
We present the first measurements of kilowatt laser power with an uncertainty less than 1 %. These represent progress toward the most accurate measurements of laser power above 1 kW at 1070 nm wavelength and establish a more precise link between force metrology and laser power metrology. Radiation pressure, or photon momentum, is a relatively new method of non-destructively measuring laser power. We demonstrate how a multiple reflection optical system amplifies the pressure of a kilowatt class laser incoherently to improve the signal to noise ratio in a radiation pressure-based measurement. With 14 incoherent reflections of the laser, we measure a total uncertainty of 0.26 % for an input power of 10 kW and 0.46 % for an input power of 1 kW at the 95 % confidence level. These measurements of absolute power are traceable to the SI kilogram and mark a state-of-the-art improvement in measurement precision by a factor of four.
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Affiliation(s)
| | - Kyle A Rogers
- National Institute of Standards and Technology, Boulder, CO, United States of America
| | - Paul A Williams
- National Institute of Standards and Technology, Boulder, CO, United States of America
| | - John H Lehman
- National Institute of Standards and Technology, Boulder, CO, United States of America
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Axelrod JJ, Campbell SL, Schwartz O, Turnbaugh C, Glaeser RM, Müller H. Observation of the Relativistic Reversal of the Ponderomotive Potential. PHYSICAL REVIEW LETTERS 2020; 124:174801. [PMID: 32412292 PMCID: PMC7357394 DOI: 10.1103/physrevlett.124.174801] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 04/07/2020] [Indexed: 05/29/2023]
Abstract
The secular dynamics of a nonrelativistic charged particle in an electromagnetic wave can be described by the ponderomotive potential. Although ponderomotive electron-laser interactions at relativistic velocities are important for emerging technologies from laser-based particle accelerators to laser-enhanced electron microscopy, the effects of special relativity on the interaction have only been studied theoretically. Here, we use a transmission electron microscope to measure the position-dependent phase shift imparted to a relativistic electron wave function when it traverses a standing laser wave. The kinetic energy of the electrons is varied between 80 and 300 keV, and the laser standing wave has a continuous-wave intensity of 175 GW/cm^{2}. In contrast to the nonrelativistic case, we demonstrate that the phase shift depends on both the electron velocity and the wave polarization, confirming the predictions of a quasiclassical theory of the interaction. Remarkably, if the electron's speed is greater than 1/sqrt[2] of the speed of light, the phase shift at the electric field nodes of the wave can exceed that at the antinodes. In this case there exists a polarization such that the phase shifts at the nodes and antinodes are equal, and the electron does not experience Kapitza-Dirac diffraction. Our results thus provide new capabilities for coherent electron beam manipulation.
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Affiliation(s)
- Jeremy J. Axelrod
- Dept. of Physics, University of California, Berkeley, USA
- Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Sara L. Campbell
- Dept. of Physics, University of California, Berkeley, USA
- Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Osip Schwartz
- Dept. of Physics, University of California, Berkeley, USA
- Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Carter Turnbaugh
- Dept. of Physics, University of California, Berkeley, USA
- Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Robert M. Glaeser
- Lawrence Berkeley National Laboratory, Berkeley, USA
- Dept. of Molecular and Cell Biology, Univeristy of California, Berkeley, USA
| | - Holger Müller
- Dept. of Physics, University of California, Berkeley, USA
- Lawrence Berkeley National Laboratory, Berkeley, USA
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Affiliation(s)
- Radostin Danev
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
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Schwartz O, Axelrod JJ, Campbell SL, Turnbaugh C, Glaeser RM, Müller H. Laser phase plate for transmission electron microscopy. Nat Methods 2019; 16:1016-1020. [PMID: 31562475 PMCID: PMC6768090 DOI: 10.1038/s41592-019-0552-2] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 08/06/2019] [Indexed: 12/21/2022]
Abstract
Transmission electron microscopy (TEM) of rapidly frozen biological specimens, or cryo-EM, would benefit from the development of a phase plate for in-focus phase contrast imaging. Several types of phase plates have been investigated, but rapid electrostatic charging of all such devices has hindered these efforts. Here, we demonstrate electron phase manipulation with a high-intensity continuous-wave laser beam, and utilize it as a phase plate for TEM. We demonstrate the laser phase plate by imaging an amorphous carbon film. The laser phase plate provides a stable and tunable phase shift without charging or unwanted electron scattering. These results suggest the possibility for dose-efficient imaging of unstained biological macromolecules and cells.
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Affiliation(s)
- Osip Schwartz
- Department of Physics, University of California-Berkeley, Berkeley, CA, USA.,Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeremy J Axelrod
- Department of Physics, University of California-Berkeley, Berkeley, CA, USA.,Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sara L Campbell
- Department of Physics, University of California-Berkeley, Berkeley, CA, USA.,Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Carter Turnbaugh
- Department of Physics, University of California-Berkeley, Berkeley, CA, USA.,Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Robert M Glaeser
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Holger Müller
- Department of Physics, University of California-Berkeley, Berkeley, CA, USA. .,Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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Wang HW, Fan X. Challenges and opportunities in cryo-EM with phase plate. Curr Opin Struct Biol 2019; 58:175-182. [PMID: 31374473 DOI: 10.1016/j.sbi.2019.06.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 12/15/2022]
Abstract
Not long after the invention of transmission electron microscope (TEM), phase plate was proposed as a novel electron-optical apparatus at the back-focal plane of the objective lens to modulate the magnified specimen images with enhanced contrast, especially in cryo-electron microscopy (cryo-EM) application of biological specimens. In the past two decades, novel phase plates of different kinds were designed and fabricated for cryo-EM application. Some of them such as the Volta phase plate have already been proved very useful in single particle cryo-EM and cryo-electron tomography (cryo-ET) analysis. In this review, we discuss the current progress, challenges and opportunities of cryo-EM with phase plate.
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Affiliation(s)
- Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Xiao Fan
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
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Abstract
Cryogenic electron microscopy (cryo-EM) enables structure determination of macromolecular objects and their assemblies. Although the techniques have been developing for nearly four decades, they have gained widespread attention in recent years due to technical advances on numerous fronts, enabling traditional microscopists to break into the world of molecular structural biology. Many samples can now be routinely analyzed at near-atomic resolution using standard imaging and image analysis techniques. However, numerous challenges to conventional workflows remain, and continued technical advances open entirely novel opportunities for discovery and exploration. Here, I will review some of the main methods surrounding cryo-EM with an emphasis specifically on single-particle analysis, and I will highlight challenges, open questions, and opportunities for methodology development.
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Affiliation(s)
- Dmitry Lyumkis
- From the Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, La Jolla, California 92037
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