1
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Koeck PJB. Alternative Forward Models for Imaging Thick Specimens in Transmission Electron Microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1071-1076. [PMID: 37749689 DOI: 10.1093/micmic/ozad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/10/2023] [Accepted: 03/09/2023] [Indexed: 09/27/2023]
Abstract
I have investigated two different forward models for image formation in transmission electron microscopy of thick specimens, the 3DCtf model, which introduces a defocus gradient in the linear approximation, and the multislice model. An important result is that the 3DCtf model does not seem to be compatible with the multislice image formation model. A second very useful finding is that the exit wave in the multislice model has an imaginary part, which, in first-order approximation, is a pure projection of the specimen and is not affected by the defocus gradient. The defocus gradient only comes into play in real valued and higher-order imaginary terms. If the multislice model is closer to reality than the 3DCtf-model, then the best way to retrieve the specimen projection for thicker specimens should be a procedure for retrieving the exit wave's imaginary term, for example using images recorded at different defocus values.
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Affiliation(s)
- Philip Johannes Barrett Koeck
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology, Hälsovägen 11 C, 14152 Huddinge, Sweden
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2
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Gureyev TE, Brown HG, Quiney HM, Allen LJ. Unified fast reconstruction algorithm for conventional, phase-contrast, and diffraction tomography. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2022; 39:C143-C155. [PMID: 36520754 DOI: 10.1364/josaa.468350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
A unified method for three-dimensional reconstruction of objects from transmission images collected at multiple illumination directions is described. The method may be applicable to experimental conditions relevant to absorption-based, phase-contrast, or diffraction imaging using x rays, electrons, and other forms of penetrating radiation or matter waves. Both the phase retrieval (also known as contrast transfer function correction) and the effect of Ewald sphere curvature (in the cases with a shallow depth of field and significant in-object diffraction) are incorporated in the proposed algorithm and can be taken into account. Multiple scattering is not treated explicitly but can be mitigated as a result of angular averaging that constitutes an essential feature of the method. The corresponding numerical algorithm is based on three-dimensional gridding which allows for fast computational implementation, including a straightforward parallelization. The algorithm can be used with any scanning geometry involving plane-wave illumination. A software code implementing the proposed algorithm has been developed, tested on simulated and experimental image data, and made publicly available.
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3
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Fan H, Sun F. Developing Graphene Grids for Cryoelectron Microscopy. Front Mol Biosci 2022; 9:937253. [PMID: 35911962 PMCID: PMC9326159 DOI: 10.3389/fmolb.2022.937253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Cryogenic electron microscopy (cryo-EM) single particle analysis has become one of the major techniques used to study high-resolution 3D structures of biological macromolecules. Specimens are generally prepared in a thin layer of vitrified ice using a holey carbon grid. However, the sample quality using this type of grid is not always ideal for high-resolution imaging even when the specimens in the test tube behave ideally. Various problems occur during a vitrification procedure, including poor/nonuniform distribution of particles, preferred orientation of particles, specimen denaturation/degradation, high background from thick ice, and beam-induced motion, which have become important bottlenecks in high-resolution structural studies using cryo-EM in many projects. In recent years, grids with support films made of graphene and its derivatives have been developed to efficiently solve these problems. Here, the various advantages of graphene grids over conventional holey carbon film grids, functionalization of graphene support films, production methods of graphene grids, and origins of pristine graphene contamination are reviewed and discussed.
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Affiliation(s)
- Hongcheng Fan
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fei Sun
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Bioland Laboratory, Guangzhou, China
- *Correspondence: Fei Sun,
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4
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Vilas JL, Carazo JM, Sorzano COS. Emerging Themes in CryoEM─Single Particle Analysis Image Processing. Chem Rev 2022; 122:13915-13951. [PMID: 35785962 PMCID: PMC9479088 DOI: 10.1021/acs.chemrev.1c00850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cryo-electron microscopy (CryoEM) has become a vital technique in structural biology. It is an interdisciplinary field that takes advantage of advances in biochemistry, physics, and image processing, among other disciplines. Innovations in these three basic pillars have contributed to the boosting of CryoEM in the past decade. This work reviews the main contributions in image processing to the current reconstruction workflow of single particle analysis (SPA) by CryoEM. Our review emphasizes the time evolution of the algorithms across the different steps of the workflow differentiating between two groups of approaches: analytical methods and deep learning algorithms. We present an analysis of the current state of the art. Finally, we discuss the emerging problems and challenges still to be addressed in the evolution of CryoEM image processing methods in SPA.
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Affiliation(s)
- Jose Luis Vilas
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - Jose Maria Carazo
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - Carlos Oscar S Sorzano
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
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5
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Gureyev TE, Paganin DM, Brown HG, Quiney HM, Allen LJ. A Method for High-Resolution Three-Dimensional Reconstruction with Ewald Sphere Curvature Correction from Transmission Electron Images. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-17. [PMID: 35485646 DOI: 10.1017/s1431927622000630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A method for three-dimensional reconstruction of objects from defocused images collected at multiple illumination directions in high-resolution transmission electron microscopy is presented. The method effectively corrects for the Ewald sphere curvature by taking into account the in-particle propagation of the electron beam. Numerical simulations demonstrate that the proposed method is capable of accurately reconstructing biological molecules or nanoparticles from high-resolution defocused images under conditions achievable in single-particle electron cryo-microscopy or electron tomography with realistic radiation doses, non-trivial aberrations, multiple scattering, and other experimentally relevant factors. The physics of the method is based on the well-known Diffraction Tomography formalism, but with the phase-retrieval step modified to include a conjugation of the phase (i.e., multiplication of the phase by a negative constant). At each illumination direction, numerically backpropagating the beam with the conjugated phase produces maximum contrast at the location of individual atoms in the molecule or nanoparticle. The resultant algorithm, Conjugated Holographic Reconstruction, can potentially be incorporated into established software tools for single-particle analysis, such as, for example, RELION or FREALIGN, in place of the conventional contrast transfer function correction procedure, in order to account for the Ewald sphere curvature and improve the spatial resolution of the three-dimensional reconstruction.
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Affiliation(s)
- Timur E Gureyev
- ARC Centre in Advanced Molecular Imaging, School of Physics, The University of Melbourne, Parkville, VIC3010, Australia
- School of Physics and Astronomy, Monash University, Clayton, VIC3800, Australia
| | - David M Paganin
- School of Physics and Astronomy, Monash University, Clayton, VIC3800, Australia
| | - Hamish G Brown
- ARC Centre in Advanced Molecular Imaging, School of Physics, The University of Melbourne, Parkville, VIC3010, Australia
| | - Harry M Quiney
- ARC Centre in Advanced Molecular Imaging, School of Physics, The University of Melbourne, Parkville, VIC3010, Australia
| | - Leslie J Allen
- ARC Centre in Advanced Molecular Imaging, School of Physics, The University of Melbourne, Parkville, VIC3010, Australia
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6
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Gureyev TE, Quiney HM, Kozlov A, Paganin DM, Schmalz G, Brown HG, Allen LJ. Relative roles of multiple scattering and Fresnel diffraction in the imaging of small molecules using electrons, Part II: Differential Holographic Tomography. Ultramicroscopy 2021; 230:113311. [PMID: 34011462 DOI: 10.1016/j.ultramic.2021.113311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 04/29/2021] [Accepted: 05/02/2021] [Indexed: 11/30/2022]
Abstract
It has been argued that in atomic-resolution transmission electron microscopy (TEM) of sparse weakly scattering structures, such as small biological molecules, multiple electron scattering usually has only a small effect, while the in-molecule Fresnel diffraction can be significant due to the intrinsically shallow depth of focus. These facts suggest that the three-dimensional reconstruction of such structures from defocus image series collected at multiple rotational orientations of a molecule can be effectively performed for each atom separately, using the incoherent first Born approximation. The corresponding reconstruction method, termed here Differential Holographic Tomography, is developed theoretically and demonstrated computationally on several numerical models of biological molecules. It is shown that the method is capable of accurate reconstruction of the locations of atoms in a molecule from TEM data collected at a small number of random orientations of the molecule, with one or more defocus images per orientation. Possible applications to cryogenic electron microscopy and other areas are briefly discussed.
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Affiliation(s)
- T E Gureyev
- ARC Centre in Advanced Molecular Imaging, School of Physics, The University of Melbourne, Parkville 3010, Australia; School of Physics and Astronomy, Monash University, Clayton 3800, Australia; School of Science and Technology, University of New England, Armidale 2351, Australia; Faculty of Health Science, The University of Sydney, Sydney 2006, Australia.
| | - H M Quiney
- ARC Centre in Advanced Molecular Imaging, School of Physics, The University of Melbourne, Parkville 3010, Australia
| | - A Kozlov
- ARC Centre in Advanced Molecular Imaging, School of Physics, The University of Melbourne, Parkville 3010, Australia
| | - D M Paganin
- School of Physics and Astronomy, Monash University, Clayton 3800, Australia
| | - G Schmalz
- School of Science and Technology, University of New England, Armidale 2351, Australia
| | - H G Brown
- ARC Centre in Advanced Molecular Imaging, School of Physics, The University of Melbourne, Parkville 3010, Australia
| | - L J Allen
- ARC Centre in Advanced Molecular Imaging, School of Physics, The University of Melbourne, Parkville 3010, Australia
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7
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Relative roles of multiple scattering and Fresnel diffraction in the imaging of small molecules using electrons. Ultramicroscopy 2020; 218:113094. [DOI: 10.1016/j.ultramic.2020.113094] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 07/06/2020] [Accepted: 08/09/2020] [Indexed: 11/18/2022]
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8
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Tegunov D, Cramer P. Real-time cryo-electron microscopy data preprocessing with Warp. Nat Methods 2019; 16:1146-1152. [PMID: 31591575 PMCID: PMC6858868 DOI: 10.1038/s41592-019-0580-y] [Citation(s) in RCA: 642] [Impact Index Per Article: 128.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 08/21/2019] [Indexed: 12/22/2022]
Abstract
The acquisition of cryo-electron microscopy (cryo-EM) data from biological specimens must be tightly coupled to data preprocessing to ensure the best data quality and microscope usage. Here we describe Warp, a software that automates all preprocessing steps of cryo-EM data acquisition and enables real-time evaluation. Warp corrects micrographs for global and local motion, estimates the local defocus and monitors key parameters for each recorded micrograph or tomographic tilt series in real time. The software further includes deep-learning-based models for accurate particle picking and image denoising. The output from Warp can be fed into established programs for particle classification and 3D-map refinement. Our benchmarks show improvement in the nominal resolution, which went from 3.9 Å to 3.2 Å, of a published cryo-EM data set for influenza virus hemagglutinin. Warp is easy to install from http://github.com/cramerlab/warp and computationally inexpensive, and has an intuitive, streamlined user interface.
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Affiliation(s)
- Dimitry Tegunov
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany.
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany.
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9
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Obr M, Schur FKM. Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. Adv Virus Res 2019; 105:117-159. [PMID: 31522703 DOI: 10.1016/bs.aivir.2019.07.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Describing the protein interactions that form pleomorphic and asymmetric viruses represents a considerable challenge to most structural biology techniques, including X-ray crystallography and single particle cryo-electron microscopy. Obtaining a detailed understanding of these interactions is nevertheless important, considering the number of relevant human pathogens that do not follow strict icosahedral or helical symmetry. Cryo-electron tomography and subtomogram averaging methods provide structural insights into complex biological environments and are well suited to go beyond structures of perfectly symmetric viruses. This chapter discusses recent developments showing that cryo-ET and subtomogram averaging can provide high-resolution insights into hitherto unknown structural features of pleomorphic and asymmetric virus particles. It also describes how these methods have significantly added to our understanding of retrovirus capsid assemblies in immature and mature viruses. Additional examples of irregular viruses and their associated proteins, whose structures have been studied via cryo-ET and subtomogram averaging, further support the versatility of these methods.
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Affiliation(s)
- Martin Obr
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Florian K M Schur
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria.
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10
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Schur FK. Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. Curr Opin Struct Biol 2019; 58:1-9. [PMID: 31005754 DOI: 10.1016/j.sbi.2019.03.018] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 01/03/2023]
Abstract
Cryo-electron tomography (cryo-ET) provides unprecedented insights into the molecular constituents of biological environments. In combination with an image processing method called subtomogram averaging (STA), detailed 3D structures of biological molecules can be obtained in large, irregular macromolecular assemblies or in situ, without the need for purification. The contextual meta-information these methods also provide, such as a protein's location within its native environment, can then be combined with functional data. This allows the derivation of a detailed view on the physiological or pathological roles of proteins from the molecular to cellular level. Despite their tremendous potential in in situ structural biology, cryo-ET and STA have been restricted by methodological limitations, such as the low obtainable resolution. Exciting progress now allows one to reach unprecedented resolutions in situ, ranging in optimal cases beyond the nanometer barrier. Here, I review current frontiers and future challenges in routinely determining high-resolution structures in in situ environments using cryo-ET and STA.
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Affiliation(s)
- Florian Km Schur
- Institute of Science and Technology Austria, Am Campus 1, A-3400 Klosterneuburg, Austria.
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11
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12
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Su M. goCTF: Geometrically optimized CTF determination for single-particle cryo-EM. J Struct Biol 2019; 205:22-29. [PMID: 30496818 PMCID: PMC6692911 DOI: 10.1016/j.jsb.2018.11.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 11/20/2018] [Accepted: 11/26/2018] [Indexed: 10/27/2022]
Abstract
Preferred particle orientation represents a recurring problem in single-particle cryogenic electron microcopy (cryo-EM). A specimen-independent approach through tilting has been attempted to increase particle orientation coverage, thus minimizing anisotropic three-dimensional (3D) reconstruction. However, focus gradient is a critical issue hindering tilt applications from being a general practice in single-particle cryo-EM. The present study describes a newly developed geometrically optimized approach, goCTF, to reliably determine the global focus gradient. A novel strategy of determining contrast transfer function (CTF) parameters from a sector of the signal preserved power spectrum is applied to increase reliability. Subsequently, per-particle based local focus refinement is conducted in an iterative manner to further improve the defocus accuracy. Novel diagnosis methods using a standard deviation defocus plot and goodness of fit heatmap have also been proposed to evaluate CTF fitting quality prior to 3D refinement. In a benchmark study, goCTF processed a published single-particle cryo-EM dataset for influenza hemagglutinin trimer collected at a 40-degree specimen tilt. The resulting 3D reconstruction map was improved from 4.1 Å to 3.7 Å resolution. The goCTF program is built on the open-source code of CTFFIND4, which adopts a consistent user interface for ease of use.
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Affiliation(s)
- Min Su
- University of Michigan Life Sciences Institute, Ann Arbor 48109, USA.
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13
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Ekman A, Weinhardt V, Chen JH, McDermott G, Le Gros MA, Larabell C. PSF correction in soft X-ray tomography. J Struct Biol 2018; 204:9-18. [PMID: 29908247 DOI: 10.1016/j.jsb.2018.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/05/2018] [Accepted: 06/07/2018] [Indexed: 11/29/2022]
Abstract
In this article, we introduce a linear approximation of the forward model of soft X-ray tomography, such that the reconstruction is solvable by standard iterative schemes. This linear model takes into account the three-dimensional point spread function (PSF) of the optical system, which consequently enhances the reconstruction of data. The feasibility of the model is demonstrated on both simulated and experimental data, based on theoretically estimated and experimentally measured PSFs.
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Affiliation(s)
- Axel Ekman
- Department of Anatomy, University of California, San Francisco, CA 94143, USA
| | - Venera Weinhardt
- Department of Anatomy, University of California, San Francisco, CA 94143, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jian-Hua Chen
- Department of Anatomy, University of California, San Francisco, CA 94143, USA
| | - Gerry McDermott
- Department of Anatomy, University of California, San Francisco, CA 94143, USA
| | - Mark A Le Gros
- Department of Anatomy, University of California, San Francisco, CA 94143, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Carolyn Larabell
- Department of Anatomy, University of California, San Francisco, CA 94143, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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14
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Galaz-Montoya JG, Ludtke SJ. The advent of structural biology in situ by single particle cryo-electron tomography. BIOPHYSICS REPORTS 2017; 3:17-35. [PMID: 28781998 PMCID: PMC5516000 DOI: 10.1007/s41048-017-0040-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 03/30/2017] [Indexed: 01/06/2023] Open
Abstract
Single particle tomography (SPT), also known as subtomogram averaging, is a powerful technique uniquely poised to address questions in structural biology that are not amenable to more traditional approaches like X-ray crystallography, nuclear magnetic resonance, and conventional cryoEM single particle analysis. Owing to its potential for in situ structural biology at subnanometer resolution, SPT has been gaining enormous momentum in the last five years and is becoming a prominent, widely used technique. This method can be applied to unambiguously determine the structures of macromolecular complexes that exhibit compositional and conformational heterogeneity, both in vitro and in situ. Here we review the development of SPT, highlighting its applications and identifying areas of ongoing development.
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Affiliation(s)
- Jesús G Galaz-Montoya
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030 USA
| | - Steven J Ludtke
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030 USA
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15
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Three-dimensional CTF correction improves the resolution of electron tomograms. J Struct Biol 2016; 197:114-122. [PMID: 27343995 DOI: 10.1016/j.jsb.2016.06.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 11/22/2022]
Abstract
Correction of the contrast transfer function (CTF) of the microscope is a necessary step, in order to achieve high resolution from averaged electron microscopic images. Thereby, the CTF is first estimated and subsequently the electron micrograph is corrected, so that the negative oscillations of the CTF are equalized. Typically, the CTF correction is performed in 2D and the tilt-induced focus gradient is taken into account. Most often, the sample-thickness-induced focus gradient is ignored. Theoretical considerations, as well as implementation suggestions, for a 3D CTF correction that considers both gradients have been proposed before, although an implementation achieving a resolution improvement has been lacking, primarily due to computational reasons. Here, we present a comprehensive solution for a 3D CTF correction based on the Jensen-Kornberg scheme, which performs a slice-by-slice correction of the CTF within the tomographic reconstruction. We show that the computational requirements are comparable to those of 2D CTF correction. Using the examples of mitochondrial ribosomes and tobacco mosaic virus we demonstrate the improvement of the reconstruction quality with the 3D CTF correction, and the resolution gain on sub-tomogram averaging. More interestingly, for tomographic applications, the quality of the individual sub-tomograms before averaging increases significantly. We find that 3D CTF correction always produces equal or better results than 2D CTF correction.
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16
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Abstract
Cryo-electron tomography (cryo-ET) allows 3D volumes to be reconstructed from a set of 2D projection images of a tilted biological sample. It allows densities to be resolved in 3D that would otherwise overlap in 2D projection images. Cryo-ET can be applied to resolve structural features in complex native environments, such as within the cell. Analogous to single-particle reconstruction in cryo-electron microscopy, structures present in multiple copies within tomograms can be extracted, aligned, and averaged, thus increasing the signal-to-noise ratio and resolution. This reconstruction approach, termed subtomogram averaging, can be used to determine protein structures in situ. It can also be applied to facilitate more conventional 2D image analysis approaches. In this chapter, we provide an introduction to cryo-ET and subtomogram averaging. We describe the overall workflow, including tomographic data collection, preprocessing, tomogram reconstruction, subtomogram alignment and averaging, classification, and postprocessing. We consider theoretical issues and practical considerations for each step in the workflow, along with descriptions of recent methodological advances and remaining limitations.
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Affiliation(s)
- W Wan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - J A G Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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17
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Galaz-Montoya JG, Hecksel CW, Baldwin PR, Wang E, Weaver SC, Schmid MF, Ludtke SJ, Chiu W. Alignment algorithms and per-particle CTF correction for single particle cryo-electron tomography. J Struct Biol 2016; 194:383-94. [PMID: 27016284 DOI: 10.1016/j.jsb.2016.03.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 03/11/2016] [Accepted: 03/21/2016] [Indexed: 10/22/2022]
Abstract
Single particle cryo-electron tomography (cryoSPT) extracts features from cryo-electron tomograms, followed by 3D classification, alignment and averaging to generate improved 3D density maps of such features. Robust methods to correct for the contrast transfer function (CTF) of the electron microscope are necessary for cryoSPT to reach its resolution potential. Many factors can make CTF correction for cryoSPT challenging, such as lack of eucentricity of the specimen stage, inherent low dose per image, specimen charging, beam-induced specimen motions, and defocus gradients resulting both from specimen tilting and from unpredictable ice thickness variations. Current CTF correction methods for cryoET make at least one of the following assumptions: that the defocus at the center of the image is the same across the images of a tiltseries, that the particles all lie at the same Z-height in the embedding ice, and/or that the specimen, the cryo-electron microscopy (cryoEM) grid and/or the carbon support are flat. These experimental conditions are not always met. We have developed a CTF correction algorithm for cryoSPT without making any of the aforementioned assumptions. We also introduce speed and accuracy improvements and a higher degree of automation to the subtomogram averaging algorithms available in EMAN2. Using motion-corrected images of isolated virus particles as a benchmark specimen, recorded with a DE20 direct detection camera, we show that our CTF correction and subtomogram alignment routines can yield subtomogram averages close to 4/5 Nyquist frequency of the detector under our experimental conditions.
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Affiliation(s)
- Jesús G Galaz-Montoya
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Corey W Hecksel
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Philip R Baldwin
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Eryu Wang
- Institute for Human Infections and Immunity and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Scott C Weaver
- Institute for Human Infections and Immunity and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Michael F Schmid
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Steven J Ludtke
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Wah Chiu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
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Trampert P, Bogachev S, Marniok N, Dahmen T, Slusallek P. Marker Detection in Electron Tomography: A Comparative Study. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2015; 21:1591-1601. [PMID: 26601573 DOI: 10.1017/s1431927615015433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We conducted a comparative study of three widely used algorithms for the detection of fiducial markers in electron microscopy images. The algorithms were applied to four datasets from different sources. For the purpose of obtaining comparable results, we introduced figures of merit and implemented all three algorithms in a unified code base to exclude software-specific differences. The application of the algorithms revealed that none of the three algorithms is superior to the others in all cases. This leads to the conclusion that the choice of a marker detection algorithm highly depends on the properties of the dataset to be analyzed, even within the narrowed domain of electron tomography.
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Affiliation(s)
- Patrick Trampert
- 1German Research Center for Artificial Intelligence GmbH (DFKI),66123 Saarbrücken,Germany
| | | | - Nico Marniok
- 1German Research Center for Artificial Intelligence GmbH (DFKI),66123 Saarbrücken,Germany
| | - Tim Dahmen
- 1German Research Center for Artificial Intelligence GmbH (DFKI),66123 Saarbrücken,Germany
| | - Philipp Slusallek
- 1German Research Center for Artificial Intelligence GmbH (DFKI),66123 Saarbrücken,Germany
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Zhang K. Gctf: Real-time CTF determination and correction. J Struct Biol 2015; 193:1-12. [PMID: 26592709 PMCID: PMC4711343 DOI: 10.1016/j.jsb.2015.11.003] [Citation(s) in RCA: 2515] [Impact Index Per Article: 279.4] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/08/2015] [Accepted: 11/11/2015] [Indexed: 11/26/2022]
Abstract
Accurate estimation of the contrast transfer function (CTF) is critical for a near-atomic resolution cryo electron microscopy (cryoEM) reconstruction. Here, a GPU-accelerated computer program, Gctf, for accurate and robust, real-time CTF determination is presented. The main target of Gctf is to maximize the cross-correlation of a simulated CTF with the logarithmic amplitude spectra (LAS) of observed micrographs after background subtraction. Novel approaches in Gctf improve both speed and accuracy. In addition to GPU acceleration (e.g. 10–50×), a fast ‘1-dimensional search plus 2-dimensional refinement (1S2R)’ procedure further speeds up Gctf. Based on the global CTF determination, the local defocus for each particle and for single frames of movies is accurately refined, which improves CTF parameters of all particles for subsequent image processing. Novel diagnosis method using equiphase averaging (EPA) and self-consistency verification procedures have also been implemented in the program for practical use, especially for aims of near-atomic reconstruction. Gctf is an independent program and the outputs can be easily imported into other cryoEM software such as Relion (Scheres, 2012) and Frealign (Grigorieff, 2007). The results from several representative datasets are shown and discussed in this paper.
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Affiliation(s)
- Kai Zhang
- Medical Research Council Laboratory of Molecular Biology, Division of Structural Studies, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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20
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Ercius P, Alaidi O, Rames MJ, Ren G. Electron Tomography: A Three-Dimensional Analytic Tool for Hard and Soft Materials Research. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2015; 27:5638-63. [PMID: 26087941 PMCID: PMC4710474 DOI: 10.1002/adma.201501015] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 04/22/2015] [Indexed: 05/23/2023]
Abstract
Three-dimensional (3D) structural analysis is essential to understand the relationship between the structure and function of an object. Many analytical techniques, such as X-ray diffraction, neutron spectroscopy, and electron microscopy imaging, are used to provide structural information. Transmission electron microscopy (TEM), one of the most popular analytic tools, has been widely used for structural analysis in both physical and biological sciences for many decades, in which 3D objects are projected into two-dimensional (2D) images. In many cases, 2D-projection images are insufficient to understand the relationship between the 3D structure and the function of nanoscale objects. Electron tomography (ET) is a technique that retrieves 3D structural information from a tilt series of 2D projections, and is gradually becoming a mature technology with sub-nanometer resolution. Distinct methods to overcome sample-based limitations have been separately developed in both physical and biological science, although they share some basic concepts of ET. This review discusses the common basis for 3D characterization, and specifies difficulties and solutions regarding both hard and soft materials research. It is hoped that novel solutions based on current state-of-the-art techniques for advanced applications in hybrid matter systems can be motivated.
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Affiliation(s)
- Peter Ercius
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Osama Alaidi
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Matthew J. Rames
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Gang Ren
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
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21
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Visualization and quality assessment of the contrast transfer function estimation. J Struct Biol 2015; 192:222-34. [PMID: 26080023 DOI: 10.1016/j.jsb.2015.06.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/20/2015] [Accepted: 06/11/2015] [Indexed: 11/20/2022]
Abstract
The contrast transfer function (CTF) describes an undesirable distortion of image data from a transmission electron microscope. Many users of full-featured processing packages are often new to electron microscopy and are unfamiliar with the CTF concept. Here we present a common graphical output to clearly demonstrate the CTF fit quality independent of estimation software. Separately, many software programs exist to estimate the four CTF parameters, but their results are difficult to compare across multiple runs and it is all but impossible to select the best parameters to use for further processing. A new measurement is presented based on the correlation falloff of the calculated CTF oscillations against the normalized oscillating signal of the data, called the CTF resolution. It was devised to provide a robust numerical quality metric of every CTF estimation for high-throughput screening of micrographs and to select the best parameters for each micrograph. These new CTF visualizations and quantitative measures will help users better assess the quality of their CTF parameters and provide a mechanism to choose the best CTF tool for their data.
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22
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Quantifying resolution limiting factors in subtomogram averaged cryo-electron tomography using simulations. J Struct Biol 2014; 187:103-111. [PMID: 24998892 DOI: 10.1016/j.jsb.2014.06.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 06/22/2014] [Accepted: 06/23/2014] [Indexed: 11/21/2022]
Abstract
Cryo-electron tomography (CET) is the only available technique capable of characterizing the structure of biological macromolecules in conditions close to the native state. With the advent of subtomogram averaging, as a post-processing step to CET, resolutions in the (sub-) nanometer range have become within reach. In addition to advances in instrumentation and experiments, the reconstruction scheme has improved by inclusion of more accurate contrast transfer function (CTF) correction methods, better defocus estimation, and better alignments of the tilt-series and subtomograms. To quantify the importance of each contribution, we have split the full process from data collection to reconstruction into different steps. For the purpose of evaluation we have acquired tilt-series of ribosomes in such a way that we could precisely determine the defocus of each macromolecule. Then, we simulated tilt-series using the InSilicoTEM package and applied tomogram reconstruction and subtomogram averaging. Through large scale simulations under different conditions and parameter settings we find that tilt-series alignment is the resolution limiting factor for our experimental data. Using simulations, we find that when this alignment inaccuracy is alleviated, tilted CTF correction improves the final resolution, or equivalently, the same resolution can be achieved using less particles. Furthermore, we predict from which resolution onwards better CTF correction and defocus estimation methods are required. We obtain a final average using 3198 ribosomes with a resolution of 2.2nm on the experimental data. Our simulations suggest that with the same number of particles a resolution of 1.2nm could be achieved by improving the tilt-series alignment.
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23
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When to use the projection assumption and the weak-phase object approximation in phase contrast cryo-EM. Ultramicroscopy 2014; 136:61-6. [DOI: 10.1016/j.ultramic.2013.08.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 07/31/2013] [Accepted: 08/08/2013] [Indexed: 11/22/2022]
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Vulović M, Ravelli RBG, van Vliet LJ, Koster AJ, Lazić I, Lücken U, Rullgård H, Öktem O, Rieger B. Image formation modeling in cryo-electron microscopy. J Struct Biol 2013; 183:19-32. [PMID: 23711417 DOI: 10.1016/j.jsb.2013.05.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 05/07/2013] [Accepted: 05/14/2013] [Indexed: 11/16/2022]
Abstract
Accurate modeling of image formation in cryo-electron microscopy is an important requirement for quantitative image interpretation and optimization of the data acquisition strategy. Here we present a forward model that accounts for the specimen's scattering properties, microscope optics, and detector response. The specimen interaction potential is calculated with the isolated atom superposition approximation (IASA) and extended with the influences of solvent's dielectric and ionic properties as well as the molecular electrostatic distribution. We account for an effective charge redistribution via the Poisson-Boltzmann approach and find that the IASA-based potential forms the dominant part of the interaction potential, as the contribution of the redistribution is less than 10%. The electron wave is propagated through the specimen by a multislice approach and the influence of the optics is included via the contrast transfer function. We incorporate the detective quantum efficiency of the camera due to the difference between signal and noise transfer characteristics, instead of using only the modulation transfer function. The full model was validated against experimental images of 20S proteasome, hemoglobin, and GroEL. The simulations adequately predict the effects of phase contrast, changes due to the integrated electron flux, thickness, inelastic scattering, detective quantum efficiency and acceleration voltage. We suggest that beam-induced specimen movements are relevant in the experiments whereas the influence of the solvent amorphousness can be neglected. All simulation parameters are based on physical principles and, when necessary, experimentally determined.
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Affiliation(s)
- Miloš Vulović
- Quantitative Imaging Group, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
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25
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Fernandez JJ. Computational methods for electron tomography. Micron 2012; 43:1010-30. [DOI: 10.1016/j.micron.2012.05.003] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 05/08/2012] [Accepted: 05/08/2012] [Indexed: 01/13/2023]
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26
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Eibauer M, Hoffmann C, Plitzko JM, Baumeister W, Nickell S, Engelhardt H. Unraveling the structure of membrane proteins in situ by transfer function corrected cryo-electron tomography. J Struct Biol 2012; 180:488-96. [PMID: 23000705 DOI: 10.1016/j.jsb.2012.09.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 08/30/2012] [Accepted: 09/03/2012] [Indexed: 01/05/2023]
Abstract
Cryo-electron tomography in combination with subtomogram averaging allows to investigate the structure of protein assemblies in their natural environment in a close to live state. To make full use of the structural information contained in tomograms it is necessary to analyze the contrast transfer function (CTF) of projections and to restore the phases of higher spatial frequencies. CTF correction is however hampered by the difficulty of determining the actual defocus values from tilt series data, which is due to the low signal-to-noise ratio of electron micrographs. In this study, an extended acquisition scheme is introduced that enables an independent CTF determination. Two high-dose images are recorded along the tilt axis on both sides of each projection, which allow an accurate determination of the defocus values of these images. These values are used to calculate the CTF for each image of the tilt series. We applied this scheme to the mycobacterial outer membrane protein MspA reconstituted in lipid vesicles and tested several variants of CTF estimation in combination with subtomogram averaging and correction of the modulation transfer function (MTF). The 3D electron density map of MspA was compared with a structure previously determined by X-ray crystallography. We were able to demonstrate that structural information up to a resolution of 16.8Å can be recovered using our CTF correction approach, whereas the uncorrected 3D map had a resolution of only 26.2Å.
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Voortman LM, Franken EM, van Vliet LJ, Rieger B. Fast, spatially varying CTF correction in TEM. Ultramicroscopy 2012; 118:26-34. [DOI: 10.1016/j.ultramic.2012.05.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 05/02/2012] [Accepted: 05/04/2012] [Indexed: 10/28/2022]
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28
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Vulović M, Franken E, Ravelli RB, van Vliet LJ, Rieger B. Precise and unbiased estimation of astigmatism and defocus in transmission electron microscopy. Ultramicroscopy 2012. [DOI: 10.1016/j.ultramic.2012.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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