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Gradov OV, Gradova MA. Methods of electron microscopy of biological and abiogenic structures in artificial gas atmospheres. SURFACE ENGINEERING AND APPLIED ELECTROCHEMISTRY 2016. [DOI: 10.3103/s1068375516010063] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Afanasyev P, Ravelli RBG, Matadeen R, De Carlo S, van Duinen G, Alewijnse B, Peters PJ, Abrahams JP, Portugal RV, Schatz M, van Heel M. A posteriori correction of camera characteristics from large image data sets. Sci Rep 2015; 5:10317. [PMID: 26068909 PMCID: PMC4464200 DOI: 10.1038/srep10317] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/31/2015] [Indexed: 11/18/2022] Open
Abstract
Large datasets are emerging in many fields of image processing including: electron microscopy, light microscopy, medical X-ray imaging, astronomy, etc. Novel computer-controlled instrumentation facilitates the collection of very large datasets containing thousands of individual digital images. In single-particle cryogenic electron microscopy (“cryo-EM”), for example, large datasets are required for achieving quasi-atomic resolution structures of biological complexes. Based on the collected data alone, large datasets allow us to precisely determine the statistical properties of the imaging sensor on a pixel-by-pixel basis, independent of any “a priori” normalization routinely applied to the raw image data during collection (“flat field correction”). Our straightforward “a posteriori” correction yields clean linear images as can be verified by Fourier Ring Correlation (FRC), illustrating the statistical independence of the corrected images over all spatial frequencies. The image sensor characteristics can also be measured continuously and used for correcting upcoming images.
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Affiliation(s)
- Pavel Afanasyev
- 1] Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands [2] The Institute of Nanoscopy, Maastricht University, 6211 LK Maastricht, The Netherlands
| | - Raimond B G Ravelli
- The Institute of Nanoscopy, Maastricht University, 6211 LK Maastricht, The Netherlands
| | - Rishi Matadeen
- Netherlands Centre for Electron Nanoscopy (NeCEN), 2333 CC Leiden, The Netherlands
| | - Sacha De Carlo
- 1] Netherlands Centre for Electron Nanoscopy (NeCEN), 2333 CC Leiden, The Netherlands [2] FEI Company, 5651 GG Eindhoven, The Netherlands
| | | | - Bart Alewijnse
- 1] Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands [2] The Institute of Nanoscopy, Maastricht University, 6211 LK Maastricht, The Netherlands
| | - Peter J Peters
- The Institute of Nanoscopy, Maastricht University, 6211 LK Maastricht, The Netherlands
| | - Jan-Pieter Abrahams
- Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands
| | - Rodrigo V Portugal
- Brazilian Nanotechnology National Laboratory - LNNano, CNPEM, C.P. 6192, 13083-970 Campinas SP, Brasil
| | - Michael Schatz
- Image Science Software GmbH, Gillweg 3, D-14193 Berlin, Germany
| | - Marin van Heel
- 1] Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands [2] Brazilian Nanotechnology National Laboratory - LNNano, CNPEM, C.P. 6192, 13083-970 Campinas SP, Brasil [3] Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
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van de Put MWP, Patterson JP, Bomans PHH, Wilson NR, Friedrich H, van Benthem RATM, de With G, O'Reilly RK, Sommerdijk NAJM. Graphene oxide single sheets as substrates for high resolution cryoTEM. SOFT MATTER 2015; 11:1265-70. [PMID: 25516333 DOI: 10.1039/c4sm02587c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
CryoTEM is an important tool in the analysis of soft matter, where generally defocus conditions are used to enhance the contrast in the images, but this is at the expense of the maximum resolution that can be obtained. Here, we demonstrate the use of graphene oxide single sheets as support for the formation of 10 nm thin films for high resolution cryoTEM imaging, using DNA as an example. With this procedure, the overlap of objects in the vitrified film is avoided. Moreover, in these thin films less background scattering occurs and as a direct result, an increased contrast can be observed in the images. Hence, imaging closer to focus as compared with conventional cryoTEM procedures is achieved, without losing contrast. In addition, we demonstrate an ~1.8 fold increase in resolution, which is crucial for accurate size analysis of nanostructures.
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Affiliation(s)
- Marcel W P van de Put
- Laboratory of Materials and Interface Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.
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Karimi Nejadasl F, Karuppasamy M, Newman ER, McGeehan JE, Ravelli RBG. Non-rigid image registration to reduce beam-induced blurring of cryo-electron microscopy images. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:58-66. [PMID: 23254656 PMCID: PMC3526921 DOI: 10.1107/s0909049512044408] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 10/25/2012] [Indexed: 06/01/2023]
Abstract
The typical dose used to record cryo-electron microscopy images from vitrified biological specimens is so high that radiation-induced structural alterations are bound to occur during data acquisition. Integration of all scattered electrons into one image can lead to significant blurring, particularly if the data are collected from an unsupported thin layer of ice suspended over the holes of a support film. Here, the dose has been fractioned and exposure series have been acquired in order to study beam-induced specimen movements under low dose conditions, prior to bubbling. Gold particles were added to the protein sample as fiducial markers. These were automatically localized and tracked throughout the exposure series and showed correlated motions within small patches, with larger amplitudes of motion vectors at the start of a series compared with the end of each series. A non-rigid scheme was used to register all images within each exposure series, using natural neighbor interpolation with the gold particles as anchor points. The procedure increases the contrast and resolution of the examined macromolecules.
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Affiliation(s)
- Fatemeh Karimi Nejadasl
- Department of Molecular Cell Biology, Leiden University Medical Center, PO Box 9600, 2300RC Leiden, The Netherlands
| | - Manikandan Karuppasamy
- Department of Molecular Cell Biology, Leiden University Medical Center, PO Box 9600, 2300RC Leiden, The Netherlands
| | - Emily R. Newman
- Biophysics Laboratories, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - John E. McGeehan
- Biophysics Laboratories, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Raimond B. G. Ravelli
- Department of Molecular Cell Biology, Leiden University Medical Center, PO Box 9600, 2300RC Leiden, The Netherlands
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Garman EF, Weik M. Radiation damage to biological macromolecules: some answers and more questions. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:1-6. [PMID: 23254650 DOI: 10.1107/s0909049512050418] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 12/11/2012] [Indexed: 06/01/2023]
Abstract
Research into radiation damage in macromolecular crystallography has matured over the last few years, resulting in a better understanding of both the processes and timescales involved. In turn this is now allowing practical recommendations for the optimization of crystal dose lifetime to be suggested. Some long-standing questions have been answered by recent investigations, and from these answers new challenges arise and areas of investigation can be proposed. Six papers published in this volume give an indication of some of the current directions of this field and also that of single-particle cryo-microscopy, and the brief summary below places them into the overall framework of ongoing research into macromolecular crystallography radiation damage.
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Affiliation(s)
- Elspeth F Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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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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