scholarly journals Fast and Robust Orientation of Cryo-Electron Microscopy Images

2015 ◽  
Vol 3 (1) ◽  
Author(s):  
Guoliang Xu ◽  
Xia Wang ◽  
Ming Li ◽  
Zhucui Jing
Keyword(s):  
Sparse Matrix ◽  
Three Dimensional ◽  
Image Plane ◽  
Real Space ◽  
Computation Method ◽  
Common Line ◽  
The Matrix ◽  
Common Lines ◽  
The Common ◽  
Dimensional Object

AbstractWe present an efficient and reliable algorithm for determining the orientations of noisy images obtained fromprojections of a three-dimensional object. Based on the linear relationship among the common line vectors in one image plane, we construct a sparse matrix, and show that the coordinates of the common line vectors are the eigenvectors of the matrix with respect to the eigenvalue 1. The projection directions and in-plane rotation angles can be determined fromthese coordinates. A robust computation method of common lines in the real space using aweighted cross-correlation function is proposed to increase the robustness of the algorithm against the noise. A small number of good leading images, which have the maximal dissimilarity, are used to increase the reliability of orientations and improve the efficiency for determining the orientations of all the images. Numerical experiments show that the proposed algorithm is effective and efficient.

scholarly journals 6D electron microscopy: combining real-space and reciprocal-space tomography

2014 ◽  
Vol 70 (a1) ◽  
pp. C368-C368 ◽  
Author(s):  
Alexander Eggeman ◽  
Robert Krakow ◽  
Paul Midgley
Keyword(s):  
Reciprocal Lattice ◽  
Three Dimensional ◽  
Real Space ◽  
Dark Field ◽  
Reciprocal Space ◽  
Data Set ◽  
Wide Range ◽  
The Matrix ◽  
Precession Electron Diffraction ◽  
Tilt Series

STEM and TEM-based tomography has been used widely to study the 3D morphology of a wide range of materials. Similarly reciprocal space tomography in which a tilt-series of diffraction patterns are acquired offers a powerful method for the analysis of the atomic structure of crystalline materials. The natural progression is to combine these techniques into a complete three dimensional morphology and crystallography data set, allowing both features to be studied simultaneously. Using a tilt series of scanning precession electron diffraction measurements from a commercially available Ni-base superalloy as an example, the complete reciprocal lattice orientation for a number of components embedded within the matrix could be determined. It was straightforward to identify reciprocal lattice vectors that allowed dark-field images representing each phase to be produced post-acquisition. In turn these were combined using geometric tomography methods to yield a 3-D tomogram of the superalloy. Imaging these phases using conventional ADF STEM tomography would potentially be challenging given the compositional similarity between the different phases. From the combined dataset the spatial distribution of the component phases could be easily recovered but more importantly the orientational relationships between these different components could be unambiguously determined. In this way the thermo-mechanical history of the sample could be inferred from the arrangement of coherent and semi-coherent interfaces and a previously unreported crystallographic registry between metal carbide (MC) and the matrix f.c.c. phases could been identified. The possibilities for development and applications of this technique will be discussed further.

Xe Precipitates in Aluminum

2003 ◽  
Vol 792 ◽  
Author(s):  
Robert C. Birtcher ◽  
Stephen E. Donnelly ◽  
Ian Morrison ◽  
Charles W. Allen ◽  
Kazuo Furuya ◽  
...  
Keyword(s):  
Surface Energy ◽  
Room Temperature ◽  
Weak Interactions ◽  
Three Dimensional ◽  
Real Space ◽  
Cubic Phase ◽  
Equilibrium Pressure ◽  
Yield Information ◽  
The Matrix ◽  
Dynamics Simulations

ABSTRACTReal space, high-resolution transmission electron microscopy observations of Xe confined in nanometer size faceted cavities in Al yield information on both the inert gas and the matrix in which it is confined. At room temperature, Xe in such cavities can be liquid or an fcc solid. In larger cavities, Xe within can undergo melting and recrystallization. The Al surface energy can be deduced from the largest Xe nanocrystal at 300 K by setting the corresponding calculated Laplace pressure equal to the equilibrium pressure for melting of Xe, obtained from empirical bulk compression data. These surface energy values are 1.05 J m-2 for {111} facets and 1.10 Jm-2 for {200} facets. Because of the weak interactions, these values correspond to the surface tensions for Al at 300 K.At room temperature, fluid Xe confined in small faceted cavities in aluminum has up to three ordered layers of Xe atoms at the Al interface. Conceptually in a three-dimensionally confined system of sufficiently small size, complete three-dimensional ordering of the fluid may occur. Molecular dynamics simulations have revealed that such ordering would result in fluid Xe confined to a small tetragonal volume solidifying as a body-centered cubic phase on compression.

SEEMORE: Combining Color, Shape, and Texture Histogramming in a Neurally Inspired Approach to Visual Object Recognition

1997 ◽  
Vol 9 (4) ◽  
pp. 777-804 ◽  
Author(s):  
Bartlett W. Mel
Keyword(s):  
Object Recognition ◽  
Visual System ◽  
Three Dimensional ◽  
Feature Space ◽  
Image Plane ◽  
Classification Performance ◽  
Visual Object ◽  
Visual Object Recognition ◽  
Real Objects ◽  
Dimensional Object

Severe architectural and timing constraints within the primate visual system support the conjecture that the early phase of object recognition in the brain is based on a feedforward feature-extraction hierarchy. To assess the plausibility of this conjecture in an engineering context, a difficult three-dimensional object recognition domain was developed to challenge a pure feedforward, receptive-field based recognition model called SEEMORE. SEEMORE is based on 102 viewpoint-invariant nonlinear filters that as a group are sensitive to contour, texture, and color cues. The visual domain consists of 100 real objects of many different types, including rigid (shovel), nonrigid (telephone cord), and statistical (maple leaf cluster) objects and photographs of complex scenes. Objects were in dividually presented in color video images under normal room lighting conditions. Based on 12 to 36 training views, SEEMORE was required to recognize unnormalized test views of objects that could vary in position, orientation in the image plane and in depth, and scale (factor of 2); for non rigid objects, recognition was also tested under gross shape deformations. Correct classification performance on a test set consisting of 600 novel object views was 97 percent (chance was 1 percent) and was comparable for the subset of 15 nonrigid objects. Performance was also measured under a variety of image degradation conditions, including partial occlusion, limited clutter, color shift, and additive noise. Generalization behavior and classification errors illustrate the emergence of several striking natural shape categories that are not explicitly encoded in the dimensions of the feature space. It is concluded that in the light of the vast hardware resources available in the ventral stream of the primate visual system relative to those exercised here, the appealingly simple feature-space conjecture remains worthy of serious consideration as a neurobiological model.

Radon transforms, alignment, and 3d-reconstruction from random projections

1996 ◽  
Vol 54 ◽  
pp. 588-589
Author(s):  
Michael Radermacher
Keyword(s):  
Radon Transform ◽  
Fourier Transforms ◽  
Three Dimensional ◽  
Radon Transforms ◽  
One Dimensional ◽  
Dimensional Reconstruction ◽  
Section Theorem ◽  
Common Lines ◽  
The Common ◽  
Polar Grid

Since their inception three-dimensional reconstruction techniques have been based on the theory of Radon transforms. Only much later have Radon transforms been recognized as powerful tools for image processing and pattern recognition. Techniques like the “common lines ” technique for finding the orientation of projections of highly symmetrical particles, which had been developed using Fourier transforms, can easily be translated into a technique that uses Radon transforms. In contrast to Fourier transforms Radon transforms have the advantage of being real valued which simplifies many interpolation steps. The central section theorem known for Fourier transforms also applies to Radon transforms. The two- or three-dimensional Fourier transform on a polar grid can be obtained from the two- or three-dimensional Radon transform by a one-dimensional (radial) Fourier transforms and vice versa. Fourier transforms obtained by a one-dimensional transformation of the Radon transform will be referred to a Fourier/Radon transforms.

Reconstruction of Objects from their Projections Using Orthogonal Functions

1973 ◽  
Vol 31 ◽  
pp. 268-269
Author(s):  
Elrnar Zeitler
Keyword(s):  
Unit Area ◽  
Three Dimensional ◽  
One Dimension ◽  
Spatial Density ◽  
Dimensional Representation ◽  
Orthogonal Functions ◽  
Object A ◽  
Plane Normal ◽  
Dimensional Object ◽  
Spatial Density Distribution

Considering any finite three-dimensional object, a “projection” is here defined as a two-dimensional representation of the object's mass per unit area on a plane normal to a given projection axis, here taken as they-axis. Since the object can be seen as being built from parallel, thin slices, the relation between object structure and its projection can be reduced by one dimension. It is assumed that an electron microscope equipped with a tilting stage records the projectionWhere the object has a spatial density distribution p(r,ϕ) within a limiting radius taken to be unity, and the stage is tilted by an angle 9 with respect to the x-axis of the recording plane.

An Image Reconstruction System Applied to High Voltage Microscopy

1975 ◽  
Vol 33 ◽  
pp. 292-293
Author(s):  
D. E. Johnson
Keyword(s):  
High Voltage ◽  
Prior Information ◽  
Block Diagram ◽  
Three Dimensional ◽  
Real Space ◽  
Two Dimensional ◽  
Efficient Manner ◽  
Fourier Methods ◽  
Tilt Series ◽  
Methods Of Reconstruction

Increased specimen penetration; the principle advantage of high voltage microscopy, is accompanied by an increased need to utilize information on three dimensional specimen structure available in the form of two dimensional projections (i.e. micrographs). We are engaged in a program to develop methods which allow the maximum use of information contained in a through tilt series of micrographs to determine three dimensional speciman structure.In general, we are dealing with structures lacking in symmetry and with projections available from only a limited span of angles (±60°). For these reasons, we must make maximum use of any prior information available about the specimen. To do this in the most efficient manner, we have concentrated on iterative, real space methods rather than Fourier methods of reconstruction. The particular iterative algorithm we have developed is given in detail in ref. 3. A block diagram of the complete reconstruction system is shown in fig. 1.

Measurements in 3D images

1991 ◽  
Vol 49 ◽  
pp. 408-409
Author(s):  
John C. Russ
Keyword(s):  
Three Dimensional ◽  
Image Plane ◽  
X Rays ◽  
Traditional Use ◽  
3D Images ◽  
Confocal Scanning Laser Microscope ◽  
Hard Materials ◽  
Depth Direction ◽  
Confocal Scanning ◽  
Confocal Scanning Laser

Three-dimensional (3D) images consisting of arrays of voxels can now be routinely obtained from several different types of microscopes. These include both the transmission and emission modes of the confocal scanning laser microscope (but not its most common reflection mode), the secondary ion mass spectrometer, and computed tomography using electrons, X-rays or other signals. Compared to the traditional use of serial sectioning (which includes sequential polishing of hard materials), these newer techniques eliminate difficulties of alignment of slices, and maintain uniform resolution in the depth direction. However, the resolution in the z-direction may be different from that within each image plane, which makes the voxels non-cubic and creates some difficulties for subsequent analysis.

Designing TIMP (tissue inhibitor of metalloproteinases) variants that are selective metalloproteinase inhibitors

2003 ◽  
Vol 70 ◽  
pp. 201-212 ◽  
Author(s):  
Hideaki Nagase ◽  
Keith Brew
Keyword(s):  
Three Dimensional ◽  
Therapeutic Interventions ◽  
Tissue Inhibitors Of Metalloproteinases ◽  
Structural Basis ◽  
Structural Elements ◽  
Ridge Structure ◽  
Extracellular Matrix Components ◽  
Metalloproteinase Inhibitors ◽  
The Matrix ◽  
A Disintegrin And Metalloproteinase

The tissue inhibitors of metalloproteinases (TIMPs) are endogenous inhibitors of the matrix metalloproteinases (MMPs), enzymes that play central roles in the degradation of extracellular matrix components. The balance between MMPs and TIMPs is important in the maintenance of tissues, and its disruption affects tissue homoeostasis. Four related TIMPs (TIMP-1 to TIMP-4) can each form a complex with MMPs in a 1:1 stoichiometry with high affinity, but their inhibitory activities towards different MMPs are not particularly selective. The three-dimensional structures of TIMP-MMP complexes reveal that TIMPs have an extended ridge structure that slots into the active site of MMPs. Mutation of three separate residues in the ridge, at positions 2, 4 and 68 in the amino acid sequence of the N-terminal inhibitory domain of TIMP-1 (N-TIMP-1), separately and in combination has produced N-TIMP-1 variants with higher binding affinity and specificity for individual MMPs. TIMP-3 is unique in that it inhibits not only MMPs, but also several ADAM (a disintegrin and metalloproteinase) and ADAMTS (ADAM with thrombospondin motifs) metalloproteinases. Inhibition of the latter groups of metalloproteinases, as exemplified with ADAMTS-4 (aggrecanase 1), requires additional structural elements in TIMP-3 that have not yet been identified. Knowledge of the structural basis of the inhibitory action of TIMPs will facilitate the design of selective TIMP variants for investigating the biological roles of specific MMPs and for developing therapeutic interventions for MMP-associated diseases.

Sign in / Sign up

Export Citation Format

Share Document