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Visheratina A, Visheratin A, Kumar P, Veksler M, Kotov NA. Chirality Analysis of Complex Microparticles using Deep Learning on Realistic Sets of Microscopy Images. ACS NANO 2023; 17:7431-7442. [PMID: 37058327 DOI: 10.1021/acsnano.2c12056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Nanoscale chirality is an actively growing research field spurred by the giant chiroptical activity, enantioselective biological activity, and asymmetric catalytic activity of chiral nanostructures. Compared to chiral molecules, the handedness of chiral nano- and microstructures can be directly established via electron microscopy, which can be utilized for the automatic analysis of chiral nanostructures and prediction of their properties. However, chirality in complex materials may have multiple geometric forms and scales. Computational identification of chirality from electron microscopy images rather than optical measurements is convenient but is fundamentally challenging, too, because (1) image features differentiating left- and right-handed particles can be ambiguous and (2) three-dimensional structure essential for chirality is 'flattened' into two-dimensional projections. Here, we show that deep learning algorithms can identify twisted bowtie-shaped microparticles with nearly 100% accuracy and classify them as left- and right-handed with as high as 99% accuracy. Importantly, such accuracy was achieved with as few as 30 original electron microscopy images of bowties. Furthermore, after training on bowtie particles with complex nanostructured features, the model can recognize other chiral shapes with different geometries without retraining for their specific chiral geometry with 93% accuracy, indicating the true learning abilities of the employed neural networks. These findings indicate that our algorithm trained on a practically feasible set of experimental data enables automated analysis of microscopy data for the accelerated discovery of chiral particles and their complex systems for multiple applications.
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Affiliation(s)
- Anastasia Visheratina
- Department of Chemical Engineering and Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Prashant Kumar
- Department of Chemical Engineering and Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Michael Veksler
- Department of Chemical Engineering and Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nicholas A Kotov
- Department of Chemical Engineering and Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Aeronautics, Faculty of Engineering, Imperial College London, South Kensington Campus London, SW7 2AZ, United Kingdom
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2
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Cheng A, Kim PT, Kuang H, Mendez JH, Chua EYD, Maruthi K, Wei H, Sawh A, Aragon MF, Serbynovskyi V, Neselu K, Eng ET, Potter CS, Carragher B, Bepler T, Noble AJ. Fully automated multi-grid cryoEM screening using Smart Leginon. IUCRJ 2023; 10:77-89. [PMID: 36598504 PMCID: PMC9812217 DOI: 10.1107/s2052252522010624] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
Single-particle cryo-electron microscopy (cryoEM) is a swiftly growing method for understanding protein structure. With increasing demand for high-throughput, high-resolution cryoEM services comes greater demand for rapid and automated cryoEM grid and sample screening. During screening, optimal grids and sample conditions are identified for subsequent high-resolution data collection. Screening is a major bottleneck for new cryoEM projects because grids must be optimized for several factors, including grid type, grid hole size, sample concentration, buffer conditions, ice thickness and particle behavior. Even for mature projects, multiple grids are commonly screened to select a subset for high-resolution data collection. Here, machine learning and novel purpose-built image-processing and microscope-handling algorithms are incorporated into the automated data-collection software Leginon, to provide an open-source solution for fully automated high-throughput grid screening. This new version, broadly called Smart Leginon, emulates the actions of an operator in identifying areas on the grid to explore as potentially useful for data collection. Smart Leginon Autoscreen sequentially loads and examines grids from an automated specimen-exchange system to provide completely unattended grid screening across a set of grids. Comparisons between a multi-grid autoscreen session and conventional manual screening by 5 expert microscope operators are presented. On average, Autoscreen reduces operator time from ∼6 h to <10 min and provides a percentage of suitable images for evaluation comparable to the best operator. The ability of Smart Leginon to target holes that are particularly difficult to identify is analyzed. Finally, the utility of Smart Leginon is illustrated with three real-world multi-grid user screening/collection sessions, demonstrating the efficiency and flexibility of the software package. The fully automated functionality of Smart Leginon significantly reduces the burden on operator screening time, improves the throughput of screening and recovers idle microscope time, thereby improving availability of cryoEM services.
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Affiliation(s)
- Anchi Cheng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Paul T. Kim
- Simons Machine Learning Center, New York Structural Biology Center, New York, NY, USA
| | - Huihui Kuang
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Joshua H. Mendez
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Eugene Y. D. Chua
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Kashyap Maruthi
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Hui Wei
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Anjelique Sawh
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Mahira F. Aragon
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | | | - Kasahun Neselu
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Edward T. Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Clinton S. Potter
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Bridget Carragher
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Tristan Bepler
- Simons Machine Learning Center, New York Structural Biology Center, New York, NY, USA
| | - Alex J. Noble
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Simons Machine Learning Center, New York Structural Biology Center, New York, NY, USA
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3
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Kim PT, Noble AJ, Cheng A, Bepler T. Learning to automate cryo-electron microscopy data collection with Ptolemy. IUCRJ 2023; 10:90-102. [PMID: 36598505 PMCID: PMC9812219 DOI: 10.1107/s2052252522010612] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
Over the past decade, cryo-electron microscopy (cryoEM) has emerged as an important method for determining near-native, near-atomic resolution 3D structures of biological macromolecules. To meet the increasing demand for cryoEM, automated methods that improve throughput and efficiency of microscope operation are needed. Currently, the targeting algorithms provided by most data-collection software require time-consuming manual tuning of parameters for each grid, and, in some cases, operators must select targets completely manually. However, the development of fully automated targeting algorithms is non-trivial, because images often have low signal-to-noise ratios and optimal targeting strategies depend on a range of experimental parameters and macromolecule behaviors that vary between projects and collection sessions. To address this, Ptolemy provides a pipeline to automate low- and medium-magnification targeting using a suite of purpose-built computer vision and machine-learning algorithms, including mixture models, convolutional neural networks and U-Nets. Learned models in this pipeline are trained on a large set of images from real-world cryoEM data-collection sessions, labeled with locations selected by human operators. These models accurately detect and classify regions of interest in low- and medium-magnification images, and generalize to unseen sessions, as well as to images collected on different microscopes at another facility. This open-source, modular pipeline can be integrated with existing microscope control software to enable automation of cryoEM data collection and can serve as a foundation for future cryoEM automation software.
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Affiliation(s)
- Paul T. Kim
- Simons Machine Learning Center, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
| | - Alex J. Noble
- Simons Machine Learning Center, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
| | - Anchi Cheng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
| | - Tristan Bepler
- Simons Machine Learning Center, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
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4
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Hohle MM, Lammens K, Gut F, Wang B, Kahler S, Kugler K, Till M, Beckmann R, Hopfner KP, Jung C. Ice thickness monitoring for cryo-EM grids by interferometry imaging. Sci Rep 2022; 12:15330. [PMID: 36097274 PMCID: PMC9468024 DOI: 10.1038/s41598-022-16978-7] [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: 02/18/2022] [Accepted: 07/19/2022] [Indexed: 11/16/2022] Open
Abstract
While recent technological developments contributed to breakthrough advances in single particle cryo-electron microscopy (cryo-EM), sample preparation remains a significant bottleneck for the structure determination of macromolecular complexes. A critical time factor is sample optimization that requires the use of an electron microscope to screen grids prepared under different conditions to achieve the ideal vitreous ice thickness containing the particles. Evaluating sample quality requires access to cryo-electron microscopes and a strong expertise in EM. To facilitate and accelerate the selection procedure of probes suitable for high-resolution cryo-EM, we devised a method to assess the vitreous ice layer thickness of sample coated grids. The experimental setup comprises an optical interferometric microscope equipped with a cryogenic stage and image analysis software based on artificial neural networks (ANN) for an unbiased sample selection. We present and validate this approach for different protein complexes and grid types, and demonstrate its performance for the assessment of ice quality. This technique is moderate in cost and can be easily performed on a laboratory bench. We expect that its throughput and its versatility will contribute to facilitate the sample optimization process for structural biologists.
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Affiliation(s)
- Markus Matthias Hohle
- Gene Center and Department of Biochemistry, (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377, München, Germany
| | - Katja Lammens
- Gene Center and Department of Biochemistry, (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377, München, Germany
| | - Fabian Gut
- Gene Center and Department of Biochemistry, (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377, München, Germany
| | - Bingzhi Wang
- Gene Center and Department of Biochemistry, (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377, München, Germany
| | - Sophia Kahler
- Gene Center and Department of Biochemistry, (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377, München, Germany
| | | | - Michael Till
- Gene Center and Department of Biochemistry, (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377, München, Germany
| | - Roland Beckmann
- Gene Center and Department of Biochemistry, (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377, München, Germany
| | - Karl-Peter Hopfner
- Gene Center and Department of Biochemistry, (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377, München, Germany
| | - Christophe Jung
- Gene Center and Department of Biochemistry, (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377, München, Germany.
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5
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Bouvette J, Huang Q, Riccio AA, Copeland WC, Bartesaghi A, Borgnia MJ. Automated systematic evaluation of cryo-EM specimens with SmartScope. eLife 2022; 11:80047. [PMID: 35997703 PMCID: PMC9398423 DOI: 10.7554/elife.80047] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/21/2022] [Indexed: 12/22/2022] Open
Abstract
Finding the conditions to stabilize a macromolecular target for imaging remains the most critical barrier to determining its structure by cryo-electron microscopy (cryo-EM). While automation has significantly increased the speed of data collection, specimens are still screened manually, a laborious and subjective task that often determines the success of a project. Here, we present SmartScope, the first framework to streamline, standardize, and automate specimen evaluation in cryo-EM. SmartScope employs deep-learning-based object detection to identify and classify features suitable for imaging, allowing it to perform thorough specimen screening in a fully automated manner. A web interface provides remote control over the automated operation of the microscope in real time and access to images and annotation tools. Manual annotations can be used to re-train the feature recognition models, leading to improvements in performance. Our automated tool for systematic evaluation of specimens streamlines structure determination and lowers the barrier of adoption for cryo-EM.
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Affiliation(s)
- Jonathan Bouvette
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, United States
| | - Qinwen Huang
- Department of Computer Science, Duke University, Durham, United States
| | - Amanda A Riccio
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, United States
| | - William C Copeland
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, United States
| | - Alberto Bartesaghi
- Department of Computer Science, Duke University, Durham, United States.,Department of Electrical and Computer Engineering, Duke University, Durham, United States.,Department of Biochemistry, Duke University School of Medicine, Durham, United States
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, United States
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6
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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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7
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Chua EYD, Mendez JH, Rapp M, Ilca SL, Tan YZ, Maruthi K, Kuang H, Zimanyi CM, Cheng A, Eng ET, Noble AJ, Potter CS, Carragher B. Better, Faster, Cheaper: Recent Advances in Cryo-Electron Microscopy. Annu Rev Biochem 2022; 91:1-32. [PMID: 35320683 PMCID: PMC10393189 DOI: 10.1146/annurev-biochem-032620-110705] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cryo-electron microscopy (cryo-EM) continues its remarkable growth as a method for visualizing biological objects, which has been driven by advances across the entire pipeline. Developments in both single-particle analysis and in situ tomography have enabled more structures to be imaged and determined to better resolutions, at faster speeds, and with more scientists having improved access. This review highlights recent advances at each stageof the cryo-EM pipeline and provides examples of how these techniques have been used to investigate real-world problems, including antibody development against the SARS-CoV-2 spike during the recent COVID-19 pandemic.
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Affiliation(s)
- Eugene Y D Chua
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Joshua H Mendez
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Micah Rapp
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
| | - Serban L Ilca
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
| | - Yong Zi Tan
- Department of Biological Sciences, National University of Singapore, Singapore;
- Disease Intervention Technology Laboratory, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Kashyap Maruthi
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Huihui Kuang
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Christina M Zimanyi
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Anchi Cheng
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Edward T Eng
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Alex J Noble
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
- National Center for In-Situ Tomographic Ultramicroscopy, New York, NY, USA
- Simons Machine Learning Center, New York, NY, USA
| | - Clinton S Potter
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
- National Center for In-Situ Tomographic Ultramicroscopy, New York, NY, USA
- Simons Machine Learning Center, New York, NY, USA
| | - Bridget Carragher
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
- National Center for In-Situ Tomographic Ultramicroscopy, New York, NY, USA
- Simons Machine Learning Center, New York, NY, USA
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8
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Olek M, Cowtan K, Webb D, Chaban Y, Zhang P. IceBreaker: Software for high-resolution single-particle cryo-EM with non-uniform ice. Structure 2022; 30:522-531.e4. [PMID: 35150604 PMCID: PMC9033277 DOI: 10.1016/j.str.2022.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 12/01/2021] [Accepted: 01/18/2022] [Indexed: 12/23/2022]
Abstract
Despite the abundance of available software tools, optimal particle selection is still a vital issue in single-particle cryoelectron microscopy (cryo-EM). Regardless of the method used, most pickers struggle when ice thickness varies on a micrograph. IceBreaker allows users to estimate the relative ice gradient and flatten it by equalizing the local contrast. It allows the differentiation of particles from the background and improves overall particle picking performance. Furthermore, we introduce an additional parameter corresponding to local ice thickness for each particle. Particles with a defined ice thickness can be grouped and filtered based on this parameter during processing. These functionalities are especially valuable for on-the-fly processing to automatically pick as many particles as possible from each micrograph and to select optimal regions for data collection. Finally, estimated ice gradient distributions can be stored separately and used to inspect the quality of prepared samples.
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Affiliation(s)
- Mateusz Olek
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Department of Chemistry, University of York, York, UK
| | - Kevin Cowtan
- Department of Chemistry, University of York, York, UK
| | - Donovan Webb
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Yuriy Chaban
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
| | - Peijun Zhang
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford OX3 7BN, UK.
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9
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Treder KP, Huang C, Kim JS, Kirkland AI. Applications of deep learning in electron microscopy. Microscopy (Oxf) 2022; 71:i100-i115. [DOI: 10.1093/jmicro/dfab043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/30/2021] [Accepted: 11/08/2021] [Indexed: 12/25/2022] Open
Abstract
Abstract
We review the growing use of machine learning in electron microscopy (EM) driven in part by the availability of fast detectors operating at kiloHertz frame rates leading to large data sets that cannot be processed using manually implemented algorithms. We summarize the various network architectures and error metrics that have been applied to a range of EM-related problems including denoising and inpainting. We then provide a review of the application of these in both physical and life sciences, highlighting how conventional networks and training data have been specifically modified for EM.
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Affiliation(s)
- Kevin P Treder
- Department of Materials, University of Oxford, Oxford, Oxfordshire OX1 3PH, UK
| | - Chen Huang
- Rosalind Franklin Institute, Harwell Research Campus, Didcot, Oxfordshire OX11 0FA, UK
| | - Judy S Kim
- Department of Materials, University of Oxford, Oxford, Oxfordshire OX1 3PH, UK
- Rosalind Franklin Institute, Harwell Research Campus, Didcot, Oxfordshire OX11 0FA, UK
| | - Angus I Kirkland
- Department of Materials, University of Oxford, Oxford, Oxfordshire OX1 3PH, UK
- Rosalind Franklin Institute, Harwell Research Campus, Didcot, Oxfordshire OX11 0FA, UK
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10
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Wu JG, Yan Y, Zhang DX, Liu BW, Zheng QB, Xie XL, Liu SQ, Ge SX, Hou ZG, Xia NS. Machine Learning for Structure Determination in Single-Particle Cryo-Electron Microscopy: A Systematic Review. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2022; 33:452-472. [PMID: 34932487 DOI: 10.1109/tnnls.2021.3131325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Recently, single-particle cryo-electron microscopy (cryo-EM) has become an indispensable method for determining macromolecular structures at high resolution to deeply explore the relevant molecular mechanism. Its recent breakthrough is mainly because of the rapid advances in hardware and image processing algorithms, especially machine learning. As an essential support of single-particle cryo-EM, machine learning has powered many aspects of structure determination and greatly promoted its development. In this article, we provide a systematic review of the applications of machine learning in this field. Our review begins with a brief introduction of single-particle cryo-EM, followed by the specific tasks and challenges of its image processing. Then, focusing on the workflow of structure determination, we describe relevant machine learning algorithms and applications at different steps, including particle picking, 2-D clustering, 3-D reconstruction, and other steps. As different tasks exhibit distinct characteristics, we introduce the evaluation metrics for each task and summarize their dynamics of technology development. Finally, we discuss the open issues and potential trends in this promising field.
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11
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Barrantes FJ. Fluorescence sensors for imaging membrane lipid domains and cholesterol. CURRENT TOPICS IN MEMBRANES 2021; 88:257-314. [PMID: 34862029 DOI: 10.1016/bs.ctm.2021.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Lipid membrane domains are supramolecular lateral heterogeneities of biological membranes. Of nanoscopic dimensions, they constitute specialized hubs used by the cell as transient signaling platforms for a great variety of biologically important mechanisms. Their property to form and dissolve in the bulk lipid bilayer endow them with the ability to engage in highly dynamic processes, and temporarily recruit subpopulations of membrane proteins in reduced nanometric compartments that can coalesce to form larger mesoscale assemblies. Cholesterol is an essential component of these lipid domains; its unique molecular structure is suitable for interacting intricately with crevices and cavities of transmembrane protein surfaces through its rough β face while "talking" to fatty acid acyl chains of glycerophospholipids and sphingolipids via its smooth α face. Progress in the field of membrane domains has been closely associated with innovative improvements in fluorescence microscopy and new fluorescence sensors. These advances enabled the exploration of the biophysical properties of lipids and their supramolecular platforms. Here I review the rationale behind the use of biosensors over the last few decades and their contributions towards elucidation of the in-plane and transbilayer topography of cholesterol-enriched lipid domains and their molecular constituents. The challenges introduced by super-resolution optical microscopy are discussed, as well as possible scenarios for future developments in the field, including virtual ("no staining") staining.
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Affiliation(s)
- Francisco J Barrantes
- Biomedical Research Institute (BIOMED), Catholic University of Argentina (UCA)-National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina.
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Wu K, Wu D, Zhu L, Wu Y. Application of Monolayer Graphene and Its Derivative in Cryo-EM Sample Preparation. Int J Mol Sci 2021; 22:8940. [PMID: 34445650 PMCID: PMC8396334 DOI: 10.3390/ijms22168940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/17/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022] Open
Abstract
Cryo-electron microscopy (Cryo-EM) has become a routine technology for resolving the structure of biological macromolecules due to the resolution revolution in recent years. The specimens are typically prepared in a very thin layer of vitrified ice suspending in the holes of the perforated amorphous carbon film. However, the samples prepared by directly applying to the conventional support membranes may suffer from partial or complete denaturation caused by sticking to the air-water interface (AWI). With the application in materials, graphene has also been used recently to improve frozen sample preparation instead of a suspended conventional amorphous thin carbon. It has been proven that graphene or graphene oxide and various chemical modifications on its surface can effectively prevent particles from adsorbing to the AWI, which improves the dispersion, adsorbed number, and orientation preference of frozen particles in the ice layer. Their excellent properties and thinner thickness can significantly reduce the background noise, allowing high-resolution three-dimensional reconstructions using a minimum data set.
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Affiliation(s)
- Ke Wu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; (K.W.); (D.W.)
| | - Di Wu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; (K.W.); (D.W.)
| | - Li Zhu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; (K.W.); (D.W.)
- Electron Microscopy Centre of Lanzhou University, Lanzhou 730000, China
| | - Yi Wu
- MOE Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an 710049, China
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Abstract
Abstract
Deep learning is transforming most areas of science and technology, including electron microscopy. This review paper offers a practical perspective aimed at developers with limited familiarity. For context, we review popular applications of deep learning in electron microscopy. Following, we discuss hardware and software needed to get started with deep learning and interface with electron microscopes. We then review neural network components, popular architectures, and their optimization. Finally, we discuss future directions of deep learning in electron microscopy.
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Abstract
After first describing the issue contents (Biophysical Reviews-Volume 12 Issue 6), this Editorial goes on to provide a short round-up of the activities of the journal in 2020. Directly following this Editorial are two obituaries marking the recent deaths of Prof. Fumio Oosawa (Japan) and Dr. Herbert Tabor (USA)-two major figures in Biophysical/Biochemical science from the last 100 years.
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Affiliation(s)
- Damien Hall
- Department of Life Sciences and Applied Chemistry, Nagoya Institute of Technology, Gokiso Showa, Nagoya, 466-8555 Japan
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Hall D. Biophysical Reviews' national biophysical society partnership program. Biophys Rev 2020; 12:187-192. [PMID: 32350823 PMCID: PMC7242517 DOI: 10.1007/s12551-020-00693-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 03/06/2020] [Indexed: 02/07/2023] Open
Abstract
This Special Issue is focused on the Biophysical Society of Japan. It represents the first in a series tasked with introducing an individual national biophysical society to the wider biophysical community. In this Editorial for Volume 12 Issue 2, I first outline the nature and goals of this program before going on to describe the contents of the Special Issue that relate to the activities organized by the Biophysical Society of Japan and the scope of the research performed by its members.
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Affiliation(s)
- Damien Hall
- Laboratory of Biochemistry and Genetics, NIDDK, NIH, Bld. 8, Bethesda, MD, 20892-0830, USA.
- Institute for Protein Research, Osaka University, 3-1-Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan.
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Shirai T, Terada T. Overview of the big data bioinformatics symposium (2SCA) at BSJ2019. Biophys Rev 2020; 12:277-278. [PMID: 32060733 PMCID: PMC7242527 DOI: 10.1007/s12551-020-00639-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 02/06/2020] [Indexed: 12/21/2022] Open
Affiliation(s)
- Tsuyoshi Shirai
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga, 526-0829, Japan.
| | - Tohru Terada
- Interfaculty Initiative in Information Studies, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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