scholarly journals Electron Tomography

2002 ◽  
Vol 10 (2) ◽  
pp. 3-5
Author(s):  
Stephen W. Carmichael
Keyword(s):  
Electron Tomography ◽  
Three Dimensional ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Specimen Preparation ◽  
Two Dimensional Image ◽  
Transmission Electron ◽  
Different Depths ◽  
Depth Dimension ◽  
Pass Through

The transmission electron microscope (TEM) was invented in the 1930's, and developments in specimen preparation in the 1950's led to its widespread use as a tool to study structure in biologic systems. Similar in principle to the light microscope, but utilizing a much shorter wavelength for better resolution, the TEM has the image-forming beam pass through the specimen. This results in a two-dimensional image which can be difficult to interpret because features from different depths of the three dimensional specimen are superimposed. Traditionally this was dealt with by cutting sections of plastic-embedded specimens so thin (in the 40 to SO nanometer range) that they effectively had only two dimensions. To allow biologists to examine structures in three dimensions, serial sections are stacked and structures reconstructed. Even though computers have made reconstruction easier, the reality is that resolution in the depth dimension is limited by the section thickness. The technique of electron tomography is emerging as a way to overcome this limitation.

Extending Energy-Filtered Transmission Electron Microscopy (EFTEM) into Three Dimensions Using Electron Tomography

2003 ◽  
Vol 9 (6) ◽  
pp. 542-555 ◽  
Author(s):  
Matthew Weyland ◽  
Paul A. Midgley
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Energy Loss ◽  
Electron Tomography ◽  
Three Dimensional ◽  
High Energy ◽  
Three Dimensions ◽  
Series Data ◽  
Elemental Distribution ◽  
Transmission Electron

The length scales on which materials microstructures are being formed, grown, and even designed are becoming increasingly small and increasingly three-dimensional. For such complex structures two-dimensional transmission electron microscopy (TEM) analysis is often inadequate and occasionally misleading. One approach to this problem is the modification of electron tomography techniques, developed for structural biology, for use in materials science. Energy-Filtered (EF) TEM elemental distribution images approximate to true projections of structure, and, as such, can be used to reconstruct the three-dimensional distribution of chemical species. A sample holder has been modified to allow the high tilt (±60°) required for tomography and a semiautomatic acquisition script designed to manage energy-loss acquisition. Tilt series data sets have been acquired from two widely different experimental systems, Cr carbides in 316 stainless steel and magnetite nanocrystals in magnetotactic bacteria, demonstrating single- and multiple-element tomography. It is shown that both elemental maps and jump-ratio images are suitable for reconstruction, despite the effects of diffraction contrast in the former and thickness changes in the latter. It is concluded that the image contrast, signal, and signal-to-noise ratio (SNR) are key to the achievable reconstruction quality and, as such, the technique may be of limited value for high energy loss/small inelastic cross section edges.

scholarly journals 3D Deconvolution Processing for STEM Cryo-Tomography

2020 ◽  
Author(s):  
Barnali Waugh ◽  
Sharon G. Wolf ◽  
Deborah Fass ◽  
Eric Branlund ◽  
Zvi Kam ◽  
...  
Keyword(s):  
Fluorescence Microscopy ◽  
Contrast Enhancement ◽  
Cross Talk ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Image Formation ◽  
Three Dimensions ◽  
Wide Field ◽  
Intact Cells ◽  
Transmission Electron

AbstractThe complex environment of biological cells and tissues has motivated development of three dimensional imaging in both light and electron microscopies. To this end, one of the primary tools in fluorescence microscopy is that of computational deconvolution. Wide-field fluorescence images are often corrupted by haze due to out-of-focus light, i.e., to cross-talk between different object planes as represented in the 3D image. Using prior understanding of the image formation mechanism, it is possible to suppress the cross-talk and reassign the unfocused light to its proper source post facto. Electron tomography based on tilted projections also exhibits a cross-talk between distant planes due to the discrete angular sampling and limited tilt range. By use of a suitably synthesized 3D point spread function, we show here that deconvolution leads to similar improvements in volume data reconstructed from cryo-scanning transmission electron tomography (CSTET), namely a dramatic in-plane noise reduction and improved representation of features in the axial dimension. Contrast enhancement is demonstrated first with colloidal gold particles, and then in representative cryo-tomograms of intact cells. Deconvolution of CSTET data collected from the periphery of an intact nucleus revealed partially condensed, extended structures in interphase chromatin.Significance statementElectron tomography is used to reveal the structure of cells in three dimensions. The combination with cryogenic fixation provides a snapshot in time of the living state. However, cryo-tomography normally requires very thin specimens due to image formation by conventional phase contrast transmission electron microscopy (TEM). The thickness constraint can be relaxed considerably by scanning TEM (STEM), yet three-dimensional (3D) reconstruction is still subject to artifacts inherent in the collection of data by tilted projections. We show here that deconvolution algorithms developed for fluorescence microscopy can suppress these artifacts, resulting in significant contrast enhancement. The method is demonstrated by cellular tomography of complex membrane structures, and by segmentation of chromatin into distinct, contiguous domains of heterochromatin and euchromatin at high and low density, respectively.

convergent-beam diffraction from surfaces

1987 ◽  
Vol 45 ◽  
pp. 30-33
Author(s):  
J. A. Eades ◽  
A. E. Smith ◽  
D. F. Lynch
Keyword(s):  
Reciprocal Lattice ◽  
Three Dimensional ◽  
Grazing Incidence ◽  
Three Dimensions ◽  
Plane Figure ◽  
Transmission Electron ◽  
Convergent Beam ◽  
Beam Patterns ◽  
Beam Diffraction

It is quite simple (in the transmission electron microscope) to obtain convergent-beam patterns from the surface of a bulk crystal. The beam is focussed onto the surface at near grazing incidence (figure 1) and if the surface is flat the appropriate pattern is obtained in the diffraction plane (figure 2). Such patterns are potentially valuable for the characterization of surfaces just as normal convergent-beam patterns are valuable for the characterization of crystals.There are, however, several important ways in which reflection diffraction from surfaces differs from the more familiar electron diffraction in transmission.GeometryIn reflection diffraction, because of the surface, it is not possible to describe the specimen as periodic in three dimensions, nor is it possible to associate diffraction with a conventional three-dimensional reciprocal lattice.

scholarly journals Free partition functions and an averaged holographic duality

2021 ◽  
Vol 2021 (1) ◽  
Author(s):  
Nima Afkhami-Jeddi ◽  
Henry Cohn ◽  
Thomas Hartman ◽  
Amirhossein Tajdini
Keyword(s):  
Partition Function ◽  
Spectral Gap ◽  
Central Charge ◽  
Three Dimensional ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Partition Functions ◽  
General Constraints ◽  
Dimensional Gravity ◽  
Holographic Duality

Abstract We study the torus partition functions of free bosonic CFTs in two dimensions. Integrating over Narain moduli defines an ensemble-averaged free CFT. We calculate the averaged partition function and show that it can be reinterpreted as a sum over topologies in three dimensions. This result leads us to conjecture that an averaged free CFT in two dimensions is holographically dual to an exotic theory of three-dimensional gravity with U(1)c×U(1)c symmetry and a composite boundary graviton. Additionally, for small central charge c, we obtain general constraints on the spectral gap of free CFTs using the spinning modular bootstrap, construct examples of Narain compactifications with a large gap, and find an analytic bootstrap functional corresponding to a single self-dual boson.

Turbulent three-dimensional dielectric electrohydrodynamic convection between two plates

2012 ◽  
Vol 696 ◽  
pp. 228-262 ◽  
Author(s):  
A. Kourmatzis ◽  
J. S. Shrimpton
Keyword(s):  
Spatial Data ◽  
Three Dimensional ◽  
Reynolds Numbers ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Energy Budgets ◽  
Turbulent Regime ◽  
Scalar Flux ◽  
Wide Range ◽  
Scalar Variance

AbstractThe fundamental mechanisms responsible for the creation of electrohydrodynamically driven roll structures in free electroconvection between two plates are analysed with reference to traditional Rayleigh–Bénard convection (RBC). Previously available knowledge limited to two dimensions is extended to three-dimensions, and a wide range of electric Reynolds numbers is analysed, extending into a fully inherently three-dimensional turbulent regime. Results reveal that structures appearing in three-dimensional electrohydrodynamics (EHD) are similar to those observed for RBC, and while two-dimensional EHD results bear some similarities with the three-dimensional results there are distinct differences. Analysis of two-point correlations and integral length scales show that full three-dimensional electroconvection is more chaotic than in two dimensions and this is also noted by qualitatively observing the roll structures that arise for both low (${\mathit{Re}}_{E} = 1$) and high electric Reynolds numbers (up to ${\mathit{Re}}_{E} = 120$). Furthermore, calculations of mean profiles and second-order moments along with energy budgets and spectra have examined the validity of neglecting the fluctuating electric field ${ E}_{i}^{\ensuremath{\prime} } $ in the Reynolds-averaged EHD equations and provide insight into the generation and transport mechanisms of turbulent EHD. Spectral and spatial data clearly indicate how fluctuating energy is transferred from electrical to hydrodynamic forms, on moving through the domain away from the charging electrode. It is shown that ${ E}_{i}^{\ensuremath{\prime} } $ is not negligible close to the walls and terms acting as sources and sinks in the turbulent kinetic energy, turbulent scalar flux and turbulent scalar variance equations are examined. Profiles of hydrodynamic terms in the budgets resemble those in the literature for RBC; however there are terms specific to EHD that are significant, indicating that the transfer of energy in EHD is also attributed to further electrodynamic terms and a strong coupling exists between the charge flux and variance, due to the ionic drift term.

scholarly journals On the forces that cable webs under tension can support and how to design cable webs to channel stresses

2019 ◽  
Vol 475 (2223) ◽  
pp. 20180781 ◽  
Author(s):  
Guy Bouchitté ◽  
Ornella Mattei ◽  
Graeme W. Milton ◽  
Pierre Seppecher
Keyword(s):  
Linear Programming ◽  
Convex Hull ◽  
Structural Engineering ◽  
Three Dimensional ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Sufficient Condition ◽  
Necessary And Sufficient Condition ◽  
Finite Dimensional ◽  
Necessary And Sufficient

In many applications of structural engineering, the following question arises: given a set of forces f 1 ,  f 2 , …,  f N applied at prescribed points x 1 ,  x 2 , …,  x N , under what constraints on the forces does there exist a truss structure (or wire web) with all elements under tension that supports these forces? Here we provide answer to such a question for any configuration of the terminal points x 1 ,  x 2 , …,  x N in the two- and three-dimensional cases. Specifically, the existence of a web is guaranteed by a necessary and sufficient condition on the loading which corresponds to a finite dimensional linear programming problem. In two dimensions, we show that any such web can be replaced by one in which there are at most P elementary loops, where elementary means that the loop cannot be subdivided into subloops, and where P is the number of forces f 1 ,  f 2 , …,  f N applied at points strictly within the convex hull of x 1 ,  x 2 , …,  x N . In three dimensions, we show that, by slightly perturbing f 1 ,  f 2 , …,  f N , there exists a uniloadable web supporting this loading. Uniloadable means it supports this loading and all positive multiples of it, but not any other loading. Uniloadable webs provide a mechanism for channelling stress in desired ways.

The Brain Stem Saccadic Burst Generator Encodes Gaze in Three-Dimensional Space

2008 ◽  
Vol 99 (5) ◽  
pp. 2602-2616 ◽  
Author(s):  
Marion R. Van Horn ◽  
Pierre A. Sylvestre ◽  
Kathleen E. Cullen
Keyword(s):  
Eye Movements ◽  
Brain Stem ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Saccadic Eye Movements ◽  
Three Dimensions ◽  
Related Information ◽  
Computer Based ◽  
Different Depths ◽  
The Brain

When we look between objects located at different depths the horizontal movement of each eye is different from that of the other, yet temporally synchronized. Traditionally, a vergence-specific neuronal subsystem, independent from other oculomotor subsystems, has been thought to generate all eye movements in depth. However, recent studies have challenged this view by unmasking interactions between vergence and saccadic eye movements during disconjugate saccades. Here, we combined experimental and modeling approaches to address whether the premotor command to generate disconjugate saccades originates exclusively in “vergence centers.” We found that the brain stem burst generator, which is commonly assumed to drive only the conjugate component of eye movements, carries substantial vergence-related information during disconjugate saccades. Notably, facilitated vergence velocities during disconjugate saccades were synchronized with the burst onset of excitatory and inhibitory brain stem saccadic burst neurons (SBNs). Furthermore, the time-varying discharge properties of the majority of SBNs (>70%) preferentially encoded the dynamics of an individual eye during disconjugate saccades. When these experimental results were implemented into a computer-based simulation, to further evaluate the contribution of the saccadic burst generator in generating disconjugate saccades, we found that it carries all the vergence drive that is necessary to shape the activity of the abducens motoneurons to which it projects. Taken together, our results provide evidence that the premotor commands from the brain stem saccadic circuitry, to the target motoneurons, are sufficient to ensure the accurate control shifts of gaze in three dimensions.

scholarly journals The House of Marie Shannon

2021 ◽  
Author(s):  
◽  
Sally Margaret Apthorp
Keyword(s):  
Three Dimensional ◽  
Two Dimensions ◽  
Domestic Architecture ◽  
Three Dimensions ◽  
Camera Obscura ◽  
Architectural Space ◽  
Domestic Lives ◽  
Architectural Tradition ◽  
Light And Shadow ◽  
Insight Into

<p>This thesis creatively explores the architectural implications present in the photographs by New Zealand photographer Marie Shannon. The result of this exploration is a house for Shannon. The focus is seven of Shannon's interior panoramas from 1985-1987 in which architectural space is presented as a domestic stage. In these photograph's furniture and objects are the props and Shannon is an actress. This performance, with Shannon both behind and in front of her camera, creates a double insight into her world; architecture as a stage to domestic life, and a photographers view of domestic architecture. Shannon's view on the world enables a greater understanding to our ordinary, domestic lives. Photography is a revealing process that teaches us to see more richly in terms of detail, shading, texture, light and shadow. Through an engagement with photographs and understanding architectural space through a photographer's eye, the hidden, secret or unnoticed aspects to Shannon's reality will be revealed. This insight into another's reality may in turn enable a deeper understanding of our own. The methodology was a revealing process that involved experimenting with Shannon's panoramic photographs. Models and drawing, through photographic techniques, lead to insights both formally in three dimensions and at surface level in two dimensions. These techniques and insights were applied to the site through the framework of a camera obscura. Shannon's new home is created by looking at her photographs with an architect's 'eye'. Externally the home acts as a closed vessel, a camera obscura. But internally rich and intriguing forms, surfaces, textures and shadings are created. Just as the camera obscura projects an exterior scene onto the interior, so does the home. Shannon will inhabit this projection of the shadows which oppose 30 O'Neill Street, Ponsonby, Auckland; her past home and site of her photographs. Photographers, and in particular Shannon, look at the architectural world with fresh eyes, free from an architectural tradition. Photography and the camera enable an improved power of sight. More is revealed to the camera. Beauty is seen in the ordinary, with detail, tone, texture, light and dark fully revealed. As a suspended moment, a deeper understanding and opportunity is created to observe and appreciate this beauty. Through designing with a photographer's eye greater insight is gained into Shannon's 'reality'. This 'revealing' process acts as a means of teaching us how to see pictorial beauty that is inherent in our ordinary lives. This is the beauty that is often hidden in secret, due to our unseeing eyes. This project converts the photographs beauty back into three dimensional architecture.</p>

Diffraction by crystals

2002 ◽  
Author(s):  
David Blow
Keyword(s):  
Fourier Transform ◽  
Three Dimensional ◽  
Incident Beam ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Dimensional Structure ◽  
Angle Of Incidence ◽  
X Ray ◽  
Max Von Laue ◽  
The Fourier Transform

In Chapter 4 many two-dimensional examples were shown, in which a diffraction pattern represents the Fourier transform of the scattering object. When a diffracting object is three-dimensional, a new effect arises. In diffraction by a repetitive object, rays are scattered in many directions. Each unit of the lattice scatters, but a diffracted beam arises only if the scattered rays from each unit are all in phase. Otherwise the scattering from one unit is cancelled out by another. In two dimensions, there is always a direction where the scattered rays are in phase for any order of diffraction (just as shown for a one-dimensional scatterer in Fig. 4.1). In three dimensions, it is only possible for all the points of a lattice to scatter in phase if the crystal is correctly oriented in the incident beam. The amplitudes and phases of all the scattered beams from a three-dimensional crystal still provide the Fourier transform of the three-dimensional structure. But when a crystal is at a particular angular orientation to the X-ray beam, the scattering of a monochromatic beam provides only a tiny sample of the total Fourier transform of its structure. In the next section, we are going to find what is needed to allow a diffracted beam to be generated. We shall follow a treatment invented by Lawrence Bragg in 1913. Max von Laue, who discovered X-ray diffraction in 1912, used a different scheme of analysis; and Paul Ewald introduced a new way of looking at it in 1921. These three methods are referred to as the Laue equations, Bragg’s law and the Ewald construction, and they give identical results. All three are described in many crystallographic text books. Bragg’s method is straightforward, understandable, and suffices for present needs. I had heard J.J. Thomson lecture about…X-rays as very short pulses of radiation. I worked out that such pulses…should be reflected at any angle of incidence by the sheets of atoms in the crystal as if these sheets were mirrors.…It remained to explain why certain of the atomic mirrors in the zinc blende [ZnS] crystal reflected more powerfully than others.

Radiolaria: validating the Turing theory

2017 ◽  
Author(s):  
Bernard Richards
Keyword(s):  
Diffusion Mechanism ◽  
Three Dimensional ◽  
Reaction Diffusion ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Black And White ◽  
Alan Turing ◽  
School Sports ◽  
The University ◽  
University Of Manchester

In his 1952 paper ‘The chemical basis of morphogenesis’ Turing postulated his now famous Morphogenesis Equation. He claimed that his theory would explain why plants and animals took the shapes they did. When I joined him, Turing suggested that I might solve his equation in three dimensions, a new problem. After many manipulations using rather sophisticated mathematics and one of the first factory-produced computers in the UK, I derived a series of solutions to Turing’s equation. I showed that these solutions explained the shapes of specimens of the marine creatures known as Radiolaria, and that they corresponded very closely to the actual spiny shapes of real radiolarians. My work provided further evidence for Turing’s theory of morphogenesis, and in particular for his belief that the external shapes exhibited by Radiolaria can be explained by his reaction–diffusion mechanism. While working in the Computing Machine Laboratory at the University of Manchester in the early 1950s, Alan Turing reignited the interests he had had in both botany and biology from his early youth. During his school-days he was more interested in the structure of the flowers on the school sports field than in the games played there (see Fig. 1.3). It is known that during the Second World War he discussed the problem of phyllotaxis (the arrangement of leaves and florets in plants), and then at Manchester he had some conversations with Claude Wardlaw, the Professor of Botany in the University. Turing was keen to take forward the work that D’Arcy Thompson had published in On Growth and Form in 1917. In his now-famous paper of 1952 Turing solved his own ‘Equation of Morphogenesis’ in two dimensions, and demonstrated a solution that could explain the ‘dappling’—the black-and-white patterns—on cows. The next step was for me to solve Turing’s equation in three dimensions. The two-dimensional case concerns only surface features of organisms, such as dappling, spots, and stripes, whereas the three-dimensional version concerns the overall shape of an organism. In 1953 I joined Turing as a research student in the University of Manchester, and he set me the task of solving his equation in three dimensions. A remarkable journey of collaboration began. Turing chatted to me in a very friendly fashion.

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