Improved 3-D reconstruction using stereo computer graphics and multiple tilt EM images

1995 ◽  
Vol 53 ◽  
pp. 630-631
Author(s):  
Lee D. Peachey ◽  
Lou Fodor ◽  
John C. Haselgrove ◽  
Stanley M. Dunn ◽  
Junqing Huang
Keyword(s):  
Computer Graphics ◽  
High Performance ◽  
Transverse Section ◽  
Three Dimensional ◽  
Stereo Pair ◽  
3D Reconstructions ◽  
Video Cameras ◽  
Biological Objects ◽  
Microscope Images ◽  
High Performance Computer

Stereo pairs of electron microscope images provide valuable visual impressions of the three-dimensional nature of specimens, including biological objects. Beyond this one seeks quantitatively accurate models and measurements of the three dimensional positions and sizes of structures in the specimen. In our laboratory, we have sought to combine high resolution video cameras with high performance computer graphics systems to improve both the ease of building 3D reconstructions and the accuracy of 3D measurements, by using multiple tilt images of the same specimen tilted over a wider range of angles than can be viewed stereoscopically. Ultimately we also wish to automate the reconstruction and measurement process, and have initiated work in that direction.Figure 1 is a stereo pair of 400 kV images from a 1 micrometer thick transverse section of frog skeletal muscle stained with the Golgi stain. This stain selectively increases the density of the transverse tubular network in these muscle cells, and it is this network that we reconstruct in this example.

scholarly journals What do we need to trust in models?

2021 ◽  
Vol 1 ◽  
pp. 303-303
Author(s):  
Ingo Kock ◽  
Martin Navarro ◽  
Jens Eckel ◽  
Carsten Rücker ◽  
Stephan Hotzel
Keyword(s):  
High Performance ◽  
Numerical Models ◽  
Three Dimensional ◽  
Dimensional Representation ◽  
Model Calculations ◽  
The Public ◽  
Three Dimensional Representation ◽  
Persuasive Power ◽  
Weak Points ◽  
High Performance Computer

Abstract. Scientists working with numerical models may notice that their presentations of numerical results to non-specialists sometimes unfold substantial persuasive power. It seems obvious that someone has worked intensively on a topic, bundled information and solved complicated equations on a high-performance computer. The final result is a number, a curve or a three-dimensional representation. The computer has made no mistake, so the result can certainly be trusted. But can it? Those who do the modelling often know the weak points of their models and invest time in increasing the reliability of the model calculation. Trust in model calculations is usually based on rigorous quality assurance of data, programs, simulation calculations and result analyses. It requires appropriate handling of uncertainties. In view of the simplifications and idealizations of models it is also necessary to assess which model results are actually meaningful. Additionally, in most cases simplified or idealised models have been used and it is necessary to assess which model results are actually meaningful. We want to discuss what it takes to generate simulation results that can be considered reliable and how scientists can appropriately convey their confidence in their own models in discussions with the public. The framework of the discussion is provided by an introduction from Martin Navarro und Ingo Kock (BASE) and we are happy to have brief input from Thomas Nagel (TUBAF), Klaus-Jürgen Röhlig (TUC) and Wolfram Rühaak (BGE).

scholarly journals Scientists Simulate New Mechanism of Fluid Flow in Earth’s Crust

Eos ◽  
2017 ◽  
Author(s):  
Sarah Stanley
Keyword(s):  
Fluid Flow ◽  
Computer Modeling ◽  
Chemical Reactions ◽  
High Performance ◽  
Fluid Transport ◽  
Three Dimensional ◽  
Earth’S Crust ◽  
High Performance Computer ◽  
Earth's Crust

Three-dimensional high-performance computer modeling reveals the behavior of fluid transport waves generated by chemical reactions that take place during metamorphism.

High Resolution Microscopy of Multi-Layered Biological Crystals

1982 ◽  
Vol 40 ◽  
pp. 80-83
Author(s):  
H.A. Cohen ◽  
T.W. Jeng ◽  
W. Chiu
Keyword(s):  
High Resolution ◽  
Low Dose ◽  
Three Dimensional ◽  
Data Interpretation ◽  
Two Dimensional ◽  
Biological Objects ◽  
Density Maps ◽  
Density Map ◽  
Complex Crystal ◽  
High Resolution Microscopy

This tutorial will discuss the methodology of low dose electron diffraction and imaging of crystalline biological objects, the problems of data interpretation for two-dimensional projected density maps of glucose embedded protein crystals, the factors to be considered in combining tilt data from three-dimensional crystals, and finally, the prospects of achieving a high resolution three-dimensional density map of a biological crystal. This methodology will be illustrated using two proteins under investigation in our laboratory, the T4 DNA helix destabilizing protein gp32*I and the crotoxin complex crystal.

Simulation of three Dimensional Defect Images in Transmission Electron Microscopy

1976 ◽  
Vol 34 ◽  
pp. 470-471
Author(s):  
W. D. Cooper ◽  
C. S. Hartley ◽  
J. J. Hren
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Three Dimensional ◽  
Crystalline Lattice ◽  
Continuum Models ◽  
Thin Foils ◽  
Transmission Electron ◽  
Microscope Images ◽  
General Computer Program ◽  
General Computer

Interpretation of electron microscope images of crystalline lattice defects can be greatly aided by computer simulation of theoretical contrast from continuum models of such defects in thin foils. Several computer programs exist at the present time, but none are sufficiently general to permit their use as an aid in the identification of the range of defect types encountered in electron microscopy. This paper presents progress in the development of a more general computer program for this purpose which eliminates a number of restrictions contained in other programs. In particular, the program permits a variety of foil geometries and defect types to be simulated.The conventional approximation of non-interacting columns is employed for evaluation of the two-beam dynamical scattering equations by a piecewise solution of the Howie-Whelan equations.

Two-Dimensional Crystallization of Tetanus Toxin

1985 ◽  
Vol 43 ◽  
pp. 528-529
Author(s):  
Jeffry A. Reidler ◽  
John P. Robinson
Keyword(s):  
Electron Microscopy ◽  
Tetanus Toxin ◽  
Structural Information ◽  
Three Dimensional ◽  
Two Dimensional ◽  
Membrane Interface ◽  
3D Reconstructions ◽  
Cellular Receptors ◽  
Computer Reconstruction ◽  
2D Crystals

We have prepared two-dimensional (2D) crystals of tetanus toxin using procedures developed by Uzgiris and Kornberg for the directed production of 2D crystals of monoclonal antibodies at an antigen-phospholipid monolayer interface. The tetanus toxin crystals were formed using a small mole fraction of the natural receptor, GT1, incorporated into phosphatidyl choline monolayers. The crystals formed at low concentration overnight. Two dimensional crystals of this type are particularly useful for structure determination using electron microscopy and computer image refinement. Three dimensional (3D) structural information can be derived from these crystals by computer reconstruction of photographs of toxin crystals taken at different tilt angles. Such 3D reconstructions may help elucidate the mechanism of entry of the enzymatic subunit of toxins into cells, particularly since these crystals form directly on a membrane interface at similar concentrations of ganglioside GT1 to the natural cellular receptors.

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