Three-Dimensional Chemical Mapping by EFTEM-TomoJ Including Improvement of SNR by PCA and ART Reconstruction of Volume by Noise Suppression

2013 ◽  
Vol 19 (6) ◽  
pp. 1669-1677 ◽  
Author(s):  
Cédric Messaoudi ◽  
Nicolas Aschman ◽  
Marcel Cunha ◽  
Tetsuo Oikawa ◽  
Carlos O. Sanchez Sorzano ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Noise Suppression ◽  
Chemical Elements ◽  
Electron Tomography ◽  
Signal To Noise Ratio ◽  
Three Dimensional ◽  
Reconstruction Technique ◽  
Chemical Mapping ◽  
Specialized Software ◽  
Alignment Algorithms

AbstractElectron tomography is becoming one of the most used methods for structural analysis at nanometric scale in biological and materials sciences. Combined with chemical mapping, it provides qualitative and semiquantitative information on the distribution of chemical elements on a given sample. Due to the current difficulties in obtaining three-dimensional (3D) maps by energy-filtered transmission electron microscopy (EFTEM), the use of 3D chemical mapping has not been widely adopted by the electron microscopy community. The lack of specialized software further complicates the issue, especially in the case of data with a low signal-to-noise ratio (SNR). Moreover, data interpretation is rendered difficult by the absence of efficient segmentation tools. Thus, specialized software for the computation of 3D maps by EFTEM needs to include optimized methods for image series alignment, algorithms to improve SNR, different background subtraction models, and methods to facilitate map segmentation. Here we present a software package (EFTEM-TomoJ, which can be downloaded from http://u759.curie.fr/fr/download/softwares/EFTEM-TomoJ), specifically dedicated to computation of EFTEM 3D chemical maps including noise filtering by image reconstitution based on multivariate statistical analysis. We also present an algorithm named BgART (for background removing algebraic reconstruction technique) allowing the discrimination between background and signal and improving the reconstructed volume in an iterative way.

scholarly journals Multimodal x-ray and electron microscopy of the Allende meteorite

2019 ◽  
Vol 5 (9) ◽  
pp. eaax3009 ◽  
Author(s):  
Yuan Hung Lo ◽  
Chen-Ting Liao ◽  
Jihan Zhou ◽  
Arjun Rana ◽  
Charles S. Bevis ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Spatial Resolution ◽  
Electron Tomography ◽  
Imaging Techniques ◽  
Three Dimensional ◽  
Functional Materials ◽  
Atomic Scale ◽  
Chemical Mapping ◽  
X Ray ◽  
Orientation Contrast

Multimodal microscopy that combines complementary nanoscale imaging techniques is critical for extracting comprehensive chemical, structural, and functional information, particularly for heterogeneous samples. X-ray microscopy can achieve high-resolution imaging of bulk materials with chemical, magnetic, electronic, and bond orientation contrast, while electron microscopy provides atomic-scale spatial resolution with quantitative elemental composition. Here, we combine x-ray ptychography and scanning transmission x-ray spectromicroscopy with three-dimensional energy-dispersive spectroscopy and electron tomography to perform structural and chemical mapping of an Allende meteorite particle with 15-nm spatial resolution. We use textural and quantitative elemental information to infer the mineral composition and discuss potential processes that occurred before or after accretion. We anticipate that correlative x-ray and electron microscopy overcome the limitations of individual imaging modalities and open up a route to future multiscale nondestructive microscopies of complex functional materials and biological systems.

scholarly journals Capturing Enveloped Viruses on Affinity Grids for Downstream Cryo-Electron Microscopy Applications

2013 ◽  
Vol 20 (1) ◽  
pp. 164-174 ◽  
Author(s):  
Gabriella Kiss ◽  
Xuemin Chen ◽  
Melinda A. Brindley ◽  
Patricia Campbell ◽  
Claudio L. Afonso ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Measles Virus ◽  
Influenza A ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Nitrilotriacetic Acid ◽  
Dimensional Structure ◽  
Enveloped Viruses ◽  
Cryo Electron Microscopy ◽  
Human Immunodeficiency Virus Virus

AbstractElectron microscopy (EM), cryo-electron microscopy (cryo-EM), and cryo-electron tomography (cryo-ET) are essential techniques used for characterizing basic virus morphology and determining the three-dimensional structure of viruses. Enveloped viruses, which contain an outer lipoprotein coat, constitute the largest group of pathogenic viruses to humans. The purification of enveloped viruses from cell culture presents certain challenges. Specifically, the inclusion of host-membrane-derived vesicles, the complete destruction of the viruses, and the disruption of the internal architecture of individual virus particles. Here, we present a strategy for capturing enveloped viruses on affinity grids (AG) for use in both conventional EM and cryo-EM/ET applications. We examined the utility of AG for the selective capture of human immunodeficiency virus virus-like particles, influenza A, and measles virus. We applied nickel-nitrilotriacetic acid lipid layers in combination with molecular adaptors to selectively adhere the viruses to the AG surface. This further development of the AG method may prove essential for the gentle and selective purification of enveloped viruses directly onto EM grids for ultrastructural analyses.

scholarly journals A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy

2017 ◽  
Vol 2017 ◽  
pp. 1-17 ◽  
Author(s):  
C. O. S. Sorzano ◽  
J. Vargas ◽  
J. Otón ◽  
J. M. de la Rosa-Trevín ◽  
J. L. Vilas ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Electron Tomography ◽  
Tomographic Reconstruction ◽  
Three Dimensional ◽  
Iterative Algorithms ◽  
Projection Methods ◽  
Particle Analysis ◽  
Reconstruction Algorithms ◽  
Large Families ◽  
Key Steps

One of the key steps in Electron Microscopy is the tomographic reconstruction of a three-dimensional (3D) map of the specimen being studied from a set of two-dimensional (2D) projections acquired at the microscope. This tomographic reconstruction may be performed with different reconstruction algorithms that can be grouped into several large families: direct Fourier inversion methods, back-projection methods, Radon methods, or iterative algorithms. In this review, we focus on the latter family of algorithms, explaining the mathematical rationale behind the different algorithms in this family as they have been introduced in the field of Electron Microscopy. We cover their use in Single Particle Analysis (SPA) as well as in Electron Tomography (ET).

scholarly journals Novel nonlinear reconstruction method with grey-level quantisation units for electron tomography

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Norio Baba ◽  
Kenji Kaneko ◽  
Misuzu Baba
Keyword(s):  
Cross Section ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Reconstruction Technique ◽  
Reconstruction Method ◽  
Back Projection ◽  
Grey Level ◽  
Discrete Processing ◽  
Structural Image ◽  
Tomography Reconstruction

AbstractWe report a new computed tomography reconstruction method, named quantisation units reconstruction technique (QURT), applicable to electron and other fields of tomography. Conventional electron tomography methods such as filtered back projection, weighted back projection, simultaneous iterative reconstructed technique, etc. suffer from the ‘missing wedge’ problem due to the limited tilt-angle range. QURT demonstrates improvements to solve this problem by recovering a structural image blurred due to the missing wedge and substantially reconstructs the structure even if the number of projection images is small. QURT reconstructs a cross-section image by arranging grey-level quantisation units (QU pieces) in three-dimensional image space via unique discrete processing. Its viability is confirmed by model simulations and experimental results. An important difference from recently developed methods such as discrete algebraic reconstruction technique (DART), total variation regularisation—DART, and compressed sensing is that prior knowledge of the conditions regarding the specimen or the expected cross-section image is not necessary.

scholarly journals The Resolution in X-ray Crystallography and Single-Particle Cryogenic Electron Microscopy

Crystals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 580
Author(s):  
Victor R.A. Dubach ◽  
Albert Guskov
Keyword(s):  
Electron Microscopy ◽  
Single Particle ◽  
Signal To Noise Ratio ◽  
Three Dimensional ◽  
Particle Analysis ◽  
Biological Macromolecules ◽  
Single Particle Analysis ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Fourier Transform

X-ray crystallography and single-particle analysis cryogenic electron microscopy are essential techniques for uncovering the three-dimensional structures of biological macromolecules. Both techniques rely on the Fourier transform to calculate experimental maps. However, one of the crucial parameters, resolution, is rather broadly defined. Here, the methods to determine the resolution in X-ray crystallography and single-particle analysis are summarized. In X-ray crystallography, it is becoming increasingly more common to include reflections discarded previously by traditionally used standards, allowing for the inclusion of incomplete and anisotropic reflections into the refinement process. In general, the resolution is the smallest lattice spacing given by Bragg’s law for a particular set of X-ray diffraction intensities; however, typically the resolution is truncated by the user during the data processing based on certain parameters and later it is used during refinement. However, at which resolution to perform such a truncation is not always clear and this makes it very confusing for the novices entering the structural biology field. Furthermore, it is argued that the effective resolution should be also reported as it is a more descriptive measure accounting for anisotropy and incompleteness of the data. In single particle cryo-EM, the situation is not much better, as multiple ways exist to determine the resolution, such as Fourier shell correlation, spectral signal-to-noise ratio and the Fourier neighbor correlation. The most widely accepted is the Fourier shell correlation using a threshold of 0.143 to define the resolution (so-called “gold-standard”), although it is still debated whether this is the correct threshold. Besides, the resolution obtained from the Fourier shell correlation is an estimate of varying resolution across the density map. In reality, the interpretability of the map is more important than the numerical value of the resolution.

Three-Dimensional Imaging of Shear Band Produced by ECAP Process in Al-Ag Alloy

2006 ◽  
Vol 503-504 ◽  
pp. 603-608
Author(s):  
Koji Inoke ◽  
Kenji Kaneko ◽  
Z. Horita
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Electron Tomography ◽  
Shear Bands ◽  
Three Dimensional ◽  
Angular Pressing ◽  
Ecap Process ◽  
Transmission Electron ◽  
Scanning Transmission ◽  
The Matrix

A significant change in microstructure occurs during the application of severe plastic deformation (SPD) such as by equal-channel angular pressing (ECAP). In this study, intense plastic strain was imposed on an Al-10.8wt%Ag alloy by the ECAP process. The amount of strain was controlled by the numbers of passes. After 1 pass of ECAP, shear bands became visible within the matrix. With increasing numbers of ECAP passes, the fraction of shear bands was increased. In this study, the change in microstructures was examined by three-dimensional electron tomography (3D-ET) in transmission electron microscopy (TEM) or scanning transmission electron microscopy (STEM). With this 3D-ET method, it was possible to conduct a precise analysis of the sizes, widths and distributions of the shear bands produced by the ECAP process. It is demonstrated that the 3D-ET method is promising to understand mechanisms of microstructural refinement using the ECAP process.

Three-Dimensional Chemistry of Multiphase Nanomaterials by Energy-Filtered Transmission Electron Microscopy Tomography

2012 ◽  
Vol 18 (5) ◽  
pp. 1118-1128 ◽  
Author(s):  
Lucian Roiban ◽  
Loïc Sorbier ◽  
Christophe Pichon ◽  
Pascale Bayle-Guillemaud ◽  
Jacques Werckmann ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Point Of View ◽  
Analysis Tool ◽  
Shell Nanoparticles ◽  
3D Nanostructures ◽  
Transmission Electron ◽  
Silica Alumina

AbstractA three-dimensional (3D) study of multiphase nanostructures by chemically selective electron tomography combining tomographic approach and energy-filtered imaging is reported. The implementation of this technique at the nanometer scale requires careful procedures for data acquisition, computing, and analysis. Based on the performances of modern transmission electron microscopy equipment and on developments in data processing, electron tomography in the energy-filtered imaging mode is shown to be a very appropriate analysis tool to provide 3D chemical maps at the nanoscale. Two examples highlight the usefulness of analytical electron tomography to investigate inhomogeneous 3D nanostructures, such as multiphase specimens or core-shell nanoparticles. The capability of discerning in a silica-alumina porous particle the two different components is illustrated. A quantitative analysis in the whole specimen and toward the pore surface is reported. This tool is shown to open new perspectives in catalysis by providing a way to characterize precisely 3D nanostructures from a chemical point of view.

scholarly journals Current data processing strategies for cryo-electron tomography and subtomogram averaging

2021 ◽  
Vol 478 (10) ◽  
pp. 1827-1845
Author(s):  
Euan Pyle ◽  
Giulia Zanetti
Keyword(s):  
Data Processing ◽  
Electron Tomography ◽  
Signal To Noise Ratio ◽  
Three Dimensional ◽  
Current Data ◽  
Processing Strategies ◽  
Cryo Electron Tomography ◽  
Subtomogram Averaging ◽  
The Individual

Cryo-electron tomography (cryo-ET) can be used to reconstruct three-dimensional (3D) volumes, or tomograms, from a series of tilted two-dimensional images of biological objects in their near-native states in situ or in vitro. 3D subvolumes, or subtomograms, containing particles of interest can be extracted from tomograms, aligned, and averaged in a process called subtomogram averaging (STA). STA overcomes the low signal to noise ratio within the individual subtomograms to generate structures of the particle(s) of interest. In recent years, cryo-ET with STA has increasingly been capable of reaching subnanometer resolution due to improvements in microscope hardware and data processing strategies. There has also been an increase in the number and quality of software packages available to process cryo-ET data with STA. In this review, we describe and assess the data processing strategies available for cryo-ET data and highlight the recent software developments which have enabled the extraction of high-resolution information from cryo-ET datasets.

scholarly journals In situ structure of virus capsids within cell nuclei by correlative light and cryo-electron tomography

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Swetha Vijayakrishnan ◽  
Marion McElwee ◽  
Colin Loney ◽  
Frazer Rixon ◽  
David Bhella
Keyword(s):  
Electron Microscopy ◽  
Structure Determination ◽  
Electron Tomography ◽  
3D Structure ◽  
Three Dimensional ◽  
Cell Nuclei ◽  
Nuclear Egress ◽  
Virus Capsids ◽  
Cryo Electron Tomography

Abstract Cryo electron microscopy (cryo-EM), a key method for structure determination involves imaging purified material embedded in vitreous ice. Images are then computationally processed to obtain three-dimensional structures approaching atomic resolution. There is increasing interest in extending structural studies by cryo-EM into the cell, where biological structures and processes may be imaged in context. The limited penetrating power of electrons prevents imaging of thick specimens (> 500 nm) however. Cryo-sectioning methods employed to overcome this are technically challenging, subject to artefacts or involve specialised and costly equipment. Here we describe the first structure of herpesvirus capsids determined by sub-tomogram averaging from nuclei of eukaryotic cells, achieved by cryo-electron tomography (cryo-ET) of re-vitrified cell sections prepared using the Tokuyasu method. Our reconstructions confirm that the capsid associated tegument complex is present on capsids prior to nuclear egress. We demonstrate that this method is suited to both 3D structure determination and correlative light/electron microscopy, thus expanding the scope of cryogenic cellular imaging.

scholarly journals Quantifying Morphology and Diffusion Properties of Mesoporous Carbon From High-Fidelity 3D Reconstructions

2019 ◽  
Vol 25 (4) ◽  
pp. 891-902 ◽  
Author(s):  
Wu Wang ◽  
Artur Svidrytski ◽  
Di Wang ◽  
Alberto Villa ◽  
Horst Hahn ◽  
...  
Keyword(s):  
Mesoporous Carbon ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Morphological Description ◽  
Reconstruction Technique ◽  
Reconstruction Algorithms ◽  
Scanning Transmission ◽  
Dimensional Reconstruction ◽  
Iterative Reconstruction Technique ◽  
Diffusion Properties

AbstractA reliable quantitative analysis in electron tomography, which depends on the segmentation of the three-dimensional reconstruction, is challenging because of constraints during tilt-series acquisition (missing wedge) and reconstruction artifacts introduced by reconstruction algorithms such as the Simultaneous Iterative Reconstruction Technique (SIRT) and Discrete Algebraic Reconstruction Technique (DART). We have carefully evaluated the fidelity of segmented reconstructions analyzing a disordered mesoporous carbon used as support in catalysis. Using experimental scanning transmission electron microscopy (STEM) tomography data as well as realistic phantoms, we have quantitatively analyzed the effect on the morphological description as well as on diffusion properties (based on a random-walk particle-tracking simulation) to understand the role of porosity in catalysis. The morphological description of the pore structure can be obtained reliably both using SIRT and DART reconstructions even in the presence of a limited missing wedge. However, the measured pore volume is sensitive to the threshold settings, which are difficult to define globally for SIRT reconstructions. This leads to noticeable variations of the diffusion coefficients in the case of SIRT reconstructions, whereas DART reconstructions resulted in more reliable data. In addition, the anisotropy of the determined diffusion properties was evaluated, which was significant in the presence of a limited missing wedge for SIRT and strongly reduced for DART.

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