A new Electron Microscopy tomography: Least squares pseudoimage reconstruction technique

1991 ◽  
Vol 49 ◽  
pp. 538-539
Author(s):  
Nengyu Zhang
Keyword(s):  
Electron Microscopy ◽  
Electron Micrographs ◽  
Three Dimensional ◽  
Matrix Inversion ◽  
Least Square ◽  
Reconstruction Technique ◽  
Reconstruction Problem ◽  
Tilt Axis ◽  
3D Object ◽  
The Matrix

The least square pseudoimage (LSP) Reconstruction technique is based on matrix inversion. Due to the absence of information in electron microscopy, usually in an angle range from 60° to 90°, the matrix is degraded. The degraded matrix is used to compute two-dimensional (2D) projections of the three-dimensional (3D) object along the Z-axis (direction of the electron beam) and tilted around the Y-axis (tilt axis). Applying the pseudoinverse of the degraded matrix to electron micrographs, which are 2D projections of the 3D object, gives the pseudoimage.Since all of the slices which are perpendicular to the Y axis are related to the same degraded matrix, the 3D reconstruction problem can be simplified as series 2D reconstruction problems. All of the 2D pseudoimages are formed by the same pseudoinverse of a degraded matrix. In this case, however, the degraded matrix projects a 2D object onto an ID projection along the Z axis. Each slice is computed from a single line in all of the electron micrographs.

Three-Dimensional Algebraic Reconstruction From Three Mutually Orthogonal Projections

1985 ◽  
Vol 43 ◽  
pp. 306-307
Author(s):  
Ximen Jiye ◽  
Shao Zhifeng
Keyword(s):  
Electron Microscopy ◽  
Approximate Solution ◽  
Three Dimensional ◽  
Reconstruction Technique ◽  
Algebraic Reconstruction Technique ◽  
Reconstruction Problem ◽  
Orthogonal Projections ◽  
3 Dimensional ◽  
Dimensional Reconstruction ◽  
Algebraic Reconstruction

The classic reconstruction problem is that of reconstructing a 3D object from its 2D projections /1-5/. It is also well known that the principal difficulty in solving this problem in electron microscopy is that a very large number of independent projections are normally required. Recently it has been shown /3,4/ that if we restrict our attention to binary or Boolean objects, far fewer projections are needed in order to obtain an approximate solution. 2-dimensional solutions of ID projections were demonstrated using only four views and 3-dimensional reconstruction of 2D projections were obtained by dividing the projections into identifiable slices.In the present paper, an algebraic reconstruction technique (ART) has been studied which uses three mutually orthogonal projections.

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.

Electromagnetic modeling of 3-D structures by the method of system iteration using integral equations

Geophysics ◽  
1992 ◽  
Vol 57 (12) ◽  
pp. 1556-1561 ◽  
Author(s):  
Zonghou Xiong
Keyword(s):  
Integral Equations ◽  
Three Dimensional ◽  
Computation Time ◽  
Iterative Solution ◽  
Matrix Inversion ◽  
Electromagnetic Modeling ◽  
Direct Inversion ◽  
Conductivity Structure ◽  
The Matrix ◽  
Earth Conductivity

A new approach for electromagnetic modeling of three‐dimensional (3-D) earth conductivity structures using integral equations is introduced. A conductivity structure is divided into many substructures and the integral equation governing the scattering currents within a substructure is solved by a direct matrix inversion. The influence of all other substructures are treated as external excitations and the solution for the whole structure is then found iteratively. This is mathematically equivalent to partitioning the scattering matrix into many block submatrices and solving the whole system by a block iterative method. This method reduces computer memory requirements since only one submatrix at a time needs to be stored. The diagonal submatrices that require direct inversion are defined by local scatterers only and thus are generally better conditioned than the matrix for the whole structure. The block iterative solution requires much less computation time than direct matrix inversion or conventional point iterative methods as the convergence depends on the number of the submatrices, not on the total number of unknowns in the solution. As the submatrices are independent of each other, this method is suitable for parallel processing.

scholarly journals Three-dimensional structure of myosin subfragment-1 from electron microscopy of sectioned crystals.

1991 ◽  
Vol 114 (4) ◽  
pp. 701-713 ◽  
Author(s):  
D A Winkelmann ◽  
T S Baker ◽  
I Rayment
Keyword(s):  
Electron Microscopy ◽  
Electron Micrographs ◽  
Myosin Head ◽  
Three Dimensional ◽  
Unit Cell ◽  
Molecular Organization ◽  
Myosin Subfragment ◽  
Myosin S1 ◽  
Myosin Subfragment 1 ◽  
Molecular Envelope

Image analysis of electron micrographs of thin-sectioned myosin subfragment-1 (S1) crystals has been used to determine the structure of the myosin head at approximately 25-A resolution. Previous work established that the unit cell of type I crystals of myosin S1 contains eight molecules arranged with orthorhombic space group symmetry P212121 and provided preliminary information on the size and shape of the myosin head (Winkelmann, D. A., H. Mekeel, and I. Rayment. 1985. J. Mol. Biol. 181:487-501). We have applied a systematic method of data collection by electron microscopy to reconstruct the three-dimensional (3D) structure of the S1 crystal lattice. Electron micrographs of thin sections were recorded at angles of up to 50 degrees by tilting the sections about the two orthogonal unit cell axes in sections cut perpendicular to the three major crystallographic axes. The data from six separate tilt series were merged to form a complete data set for 3D reconstruction. This approach has yielded an electron density map of the unit cell of the S1 crystals of sufficient detail. to delineate the molecular envelope of the myosin head. Myosin S1 has a tadpole-shaped molecular envelope that is very similar in appearance to the pear-shaped myosin heads observed by electron microscopy of rotary-shadowed and negatively stained myosin. The molecule is divided into essentially three morphological domains: a large domain on one end of the molecule corresponding to approximately 60% of the total molecular volume, a smaller central domain of approximately 30% of the volume that is separated from the larger domain by a cleft on one side of the molecule, and the smallest domain corresponding to a thin tail-like region containing approximately 10% of the volume. This molecular organization supports models of force generation by myosin which invoke conformational mobility at interdomain junctions within the head.

scholarly journals Correlation of organelle dynamics between light microscopic live imaging and electron microscopic 3D architecture using FIB-SEM

Microscopy ◽  
2020 ◽  
Author(s):  
Keisuke Ohta ◽  
Shingo Hirashima ◽  
Yoshihiro Miyazono ◽  
Akinobu Togo ◽  
Kei-ichiro Nakamura
Keyword(s):  
Electron Microscopy ◽  
Cell Biology ◽  
Focused Ion Beam ◽  
Ion Beam ◽  
Light And Electron Microscopy ◽  
Three Dimensional ◽  
Optical Microscope ◽  
Live Imaging ◽  
Reconstruction Technique ◽  
Electron Microscopic

Abstract Correlative light and electron microscopy (CLEM) methods combined with live imaging can be applied to understand the dynamics of organelles. Although recent advances in cell biology and light microscopy have helped in visualizing the details of organelle activities, observing their ultrastructure or organization of surrounding microenvironments is a challenging task. Therefore, CLEM, which allows us to observe the same area as an optical microscope with an electron microscope, has become a key technique in cell biology. Unfortunately, most CLEM methods have technical drawbacks, and many researchers face difficulties in applying CLEM methods. Here, we propose a live three-dimensional CLEM method, combined with a three-dimensional reconstruction technique using focused ion beam scanning electron microscopy tomography, as a solution to such technical barriers. We review our method, the associated technical limitations and the options considered to perform live CLEM.

scholarly journals Involvement of the Endoplasmic Reticulum in Peroxisome Formation

2003 ◽  
Vol 14 (7) ◽  
pp. 2900-2907 ◽  
Author(s):  
Hans J. Geuze ◽  
Jean Luc Murk ◽  
An K. Stroobants ◽  
Janice M. Griffith ◽  
Monique J. Kleijmeer ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Endoplasmic Reticulum ◽  
Dendritic Cells ◽  
Three Dimensional ◽  
Matrix Proteins ◽  
Peroxisomal Membrane ◽  
Present Evidence ◽  
Transporter Protein ◽  
Atp Binding Cassette Transporter ◽  
The Matrix

The traditional view holds that peroxisomes are autonomous organelles multiplying by growth and division. More recently, new observations have challenged this concept. Herein, we present evidence supporting the involvement of the endoplasmic reticulum (ER) in peroxisome formation by electron microscopy, immunocytochemistry and three-dimensional image reconstruction of peroxisomes and associated compartments in mouse dendritic cells. We found the peroxisomal membrane protein Pex13p and the ATP-binding cassette transporter protein PMP70 present in specialized subdomains of the ER that were continuous with a peroxisomal reticulum from which mature peroxisomes arose. The matrix proteins catalase and thiolase were only detectable in the reticula and peroxisomes. Our results suggest the existence of a maturation pathway from the ER to peroxisomes and implicate the ER as a major source from which the peroxisomal membrane is derived.

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.

Structural organization of escherichia coli ribosomes as determined by immuno electron microscopy

1978 ◽  
Vol 36 (2) ◽  
pp. 166-167 ◽  
Author(s):  
G. Stöffler ◽  
R.W. Bald ◽  
J. Dieckhoff ◽  
H. Eckhard ◽  
R. Lührmann ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Escherichia Coli ◽  
Ribosomal Proteins ◽  
Structural Organization ◽  
Three Dimensional ◽  
Ribosomal Subunit ◽  
Spatial Arrangement ◽  
Small Subunit ◽  
Antibody Binding ◽  
Immuno Electron Microscopy

A central step towards an understanding of the structure and function of the Escherichia coli ribosome, a large multicomponent assembly, is the elucidation of the spatial arrangement of its 54 proteins and its three rRNA molecules. The structural organization of ribosomal components has been investigated by a number of experimental approaches. Specific antibodies directed against each of the 54 ribosomal proteins of Escherichia coli have been performed to examine antibody-subunit complexes by electron microscopy. The position of the bound antibody, specific for a particular protein, can be determined; it indicates the location of the corresponding protein on the ribosomal surface.The three-dimensional distribution of each of the 21 small subunit proteins on the ribosomal surface has been determined by immuno electron microscopy: the 21 proteins have been found exposed with altogether 43 antibody binding sites. Each one of 12 proteins showed antibody binding at remote positions on the subunit surface, indicating highly extended conformations of the proteins concerned within the 30S ribosomal subunit; the remaining proteins are, however, not necessarily globular in shape (Fig. 1).

Three-Dimensional Visualization of the T-System of Frog Muscle Using High Voltage Electron Microscopy and a Lanthanum Stain

1977 ◽  
Vol 35 ◽  
pp. 570-571 ◽  
Author(s):  
Lee D. Peachey ◽  
Clara Franzini-Armstrong
Keyword(s):  
Electron Microscopy ◽  
High Voltage ◽  
Three Dimensional ◽  
Biological Tissues ◽  
High Voltage Electron Microscopy ◽  
Transverse Tubular System ◽  
Peroxidase Reaction ◽  
Voltage Electron ◽  
High Voltage Electron ◽  
T System

The effective study of biological tissues in thick slices of embedded material by high voltage electron microscopy (HVEM) requires highly selective staining of those structures to be visualized so that they are not hidden or obscured by other structures in the image. A tilt pair of micrographs with subsequent stereoscopic viewing can be an important aid in three-dimensional visualization of these images, once an appropriate stain has been found. The peroxidase reaction has been used for this purpose in visualizing the T-system (transverse tubular system) of frog skeletal muscle by HVEM (1). We have found infiltration with lanthanum hydroxide to be particularly useful for three-dimensional visualization of certain aspects of the structure of the T- system in skeletal muscles of the frog. Specifically, lanthanum more completely fills the lumen of the tubules and is denser than the peroxidase reaction product.

Electron microscopy and diffraction studies of polyimides

1983 ◽  
Vol 41 ◽  
pp. 28-29
Author(s):  
O.C. de Hodgins ◽  
K. R. Lawless ◽  
R. Anderson
Keyword(s):  
Electron Microscopy ◽  
Electron Microscope ◽  
Structural Features ◽  
Inert Atmosphere ◽  
Polyimide Films ◽  
Resolution Electron ◽  
The Matrix ◽  
High Resolution Electron Microscope ◽  
Diffraction Patterns ◽  
Polymeric Samples

Commercial polyimide films have shown to be homogeneous on a scale of 5 to 200 nm. The observation of Skybond (SKB) 705 and PI5878 was carried out by using a Philips 400, 120 KeV STEM. The objective was to elucidate the structural features of the polymeric samples. The specimens were spun and cured at stepped temperatures in an inert atmosphere and cooled slowly for eight hours. TEM micrographs showed heterogeneities (or nodular structures) generally on a scale of 100 nm for PI5878 and approximately 40 nm for SKB 705, present in large volume fractions of both specimens. See Figures 1 and 2. It is possible that the nodulus observed may be associated with surface effects and the structure of the polymers be regarded as random amorphous arrays. Diffraction patterns of the matrix and the nodular areas showed different amorphous ring patterns in both materials. The specimens were viewed in both bright and dark fields using a high resolution electron microscope which provided magnifications of 100,000X or more on the photographic plates if desired.

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