scholarly journals Three-dimensional visualization of fossil flowers, fruits, seeds, and other plant remains using synchrotron radiation X-ray tomographic microscopy (SRXTM): new insights into Cretaceous plant diversity

2014 ◽  
Vol 88 (4) ◽  
pp. 684-701 ◽  
Author(s):  
Else Marie Friis ◽  
Federica Marone ◽  
Kaj Raunsgaard Pedersen ◽  
Peter R. Crane ◽  
Marco Stampanoni
Keyword(s):  
Synchrotron Radiation ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Fossil Plants ◽  
Post Processing ◽  
Thin Sections ◽  
X Ray ◽  
Rapid Acquisition ◽  
Fossil Material ◽  
Plant Fossil

The application of synchrotron radiation X-ray tomographic microscopy (SRXTM) to the study of mesofossils of Cretaceous age has created new possibilities for the three-dimensional visualization and analysis of the external and internal structure of critical plant fossil material. SRXTM provides cellular and subcellular resolution of comparable or higher quality to that obtained from permineralized material using thin sections or the peel technique. SRXTM also has the advantage of being non-destructive and results in the rapid acquisition of large quantities of data in digital form. SRXTM thus refocuses the effort of the investigator from physical preparation to the digital post-processing of X-ray tomographic data, which allows great flexibility in the reconstruction, visualization, and analysis of the internal and external structure of fossil material in multiple planes and in two or three dimensions. A review of recent applications in paleobotany demonstrates that SRXTM will dramatically expand the level of information available for diverse fossil plants. Future refinement of SRXTM approaches that further increases resolution and eases digital post-processing, will transform the study of mesofossils and create new possibilities for advancing paleobotanical knowledge. We illustrate these points using a variety of Cretaceous mesofossils, highlighting in particular those cases where SRXTM has been essential for resolving critical structural details that have enhanced systematic understanding and improved phylogenetic interpretations.

Dimensional Quantification of Embedded Voids or Objects in Three Dimensions Using X-Ray Tomography

2012 ◽  
Vol 18 (2) ◽  
pp. 390-398 ◽  
Author(s):  
Brian M. Patterson ◽  
Juan P. Escobedo-Diaz ◽  
Darcie Dennis-Koller ◽  
Ellen Cerreta
Keyword(s):  
Digital Imaging ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Post Processing ◽  
X Ray ◽  
Individual Object ◽  
Starting Point ◽  
X Ray Computed ◽  
The Individual ◽  
Processing Steps

AbstractScientific digital imaging in three dimensions such as when using X-ray computed tomography offers a variety of ways to obtain, filter, and quantify data that can produce vastly different results. These opportunities, performed during image acquisition or during the data processing, can include filtering, cropping, and setting thresholds. Quantifying features in these images can be greatly affected by how the above operations are performed. For example, during binarization, setting the threshold too low or too high can change the number of objects as well as their measured diameter. Here, two facets of three-dimensional quantification are explored. The first will focus on investigating the question of how many voxels are needed within an object to have accurate geometric statistics that are due to the properties of the object and not an artifact of too few voxels. These statistics include but are not limited to percent of total volume, volume of the individual object, Feret shape, and surface area. Using simple cylinders as a starting point, various techniques for smoothing, filtering, and other processing steps can be investigated to aid in determining if they are appropriate for a specific desired statistic for a real dataset. The second area of investigation is the influence of post-processing, particularly segmentation, on measuring the damage statistics in high purity Cu. The most important parts of the pathways of processing are highlighted.

3-D reconstruction of molecular shape from microcrystal thin sections

1983 ◽  
Vol 41 ◽  
pp. 748-749
Author(s):  
S. Cusack ◽  
J.-C. Jésior
Keyword(s):  
Three Dimensional ◽  
Molecular Shape ◽  
Biological Molecules ◽  
Fourier Space ◽  
Single Particles ◽  
Thin Sections ◽  
Standard Methods ◽  
X Ray ◽  
X Ray Crystallography ◽  
Dimensional Reconstruction

Three-dimensional reconstruction techniques using electron microscopy have been principally developed for application to 2-D arrays (i.e. monolayers) of biological molecules and symmetrical single particles (e.g. helical viruses). However many biological molecules that crystallise form multilayered microcrystals which are unsuitable for study by either the standard methods of 3-D reconstruction or, because of their size, by X-ray crystallography. The grid sectioning technique enables a number of different projections of such microcrystals to be obtained in well defined directions (e.g. parallel to crystal axes) and poses the problem of how best these projections can be used to reconstruct the packing and shape of the molecules forming the microcrystal.Given sufficient projections there may be enough information to do a crystallographic reconstruction in Fourier space. We however have considered the situation where only a limited number of projections are available, as for example in the case of catalase platelets where three orthogonal and two diagonal projections have been obtained (Fig. 1).

scholarly journals Synchrotron radiation X-ray tomographic microscopy (SRXTM) of brachiopod shell interiors for taxonomy: Preliminary report

2010 ◽  
pp. 109-117 ◽  
Author(s):  
Neda Motchurova-Dekova ◽  
David Harper
Keyword(s):  
Synchrotron Radiation ◽  
Three Dimensional ◽  
X Rays ◽  
X Ray ◽  
Fine Grained ◽  
Internal Structures ◽  
Efficient Alternative ◽  
Micro Tomography ◽  
Light Beams ◽  
Non Destructive

Synchrotron radiation X-ray tomographic microscopy (SRXTM) is a non-destructive technique for the investigation and visualization of the internal features of solid opaque objects, which allows reconstruction of a complete three-dimensional image of internal structures by recording of the differences in the effects on the passage of waves of energy reacting with those structures. Contrary to X-rays, produced in a conventional X-ray tube, the intense synchrotron light beams are sharply focused like a laser beam. We report encouraging results from the use of SRXTM for purely taxonomic purposes in brachiopods: an attempt to find a non-destructive and more efficient alternative to serial sectioning and several other methods of dissection together with the non-destructive method of X-ray computerised micro-tomography. Two brachiopod samples were investigated using SRXTM. In ?Rhynchonella? flustracea it was possible to visualise the 3D shape of the crura and dental plates. In Terebratulina imbricata it was possible to reveal the form of the brachidium. It is encouraging that we have obtained such promising results using SRXTM with our very first two fortuitous samples, which had respectively fine-grained limestone and marl as infilling sediment, in contrast to the discouraging results communicated to us by some colleagues who have tested specimens with such infillings using X-ray micro-tomography. In future the holotypes, rare museum specimens or delicate Recent material may be preferentially subjected to this mode of analysis.

scholarly journals Three-dimensional propagation in near-field tomographic X-ray phase retrieval

2016 ◽  
Vol 72 (2) ◽  
pp. 215-221 ◽  
Author(s):  
Aike Ruhlandt ◽  
Tim Salditt
Keyword(s):  
Phase Retrieval ◽  
Near Field ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Current Phase ◽  
Computationally Efficient ◽  
X Ray ◽  
Reconstruction Quality ◽  
Consistency Constraints

This paper presents an extension of phase retrieval algorithms for near-field X-ray (propagation) imaging to three dimensions, enhancing the quality of the reconstruction by exploiting previously unused three-dimensional consistency constraints. The approach is based on a novel three-dimensional propagator and is derived for the case of optically weak objects. It can be easily implemented in current phase retrieval architectures, is computationally efficient and reduces the need for restrictive prior assumptions, resulting in superior reconstruction quality.

Three-dimensional X-ray diffraction imaging of process-induced dislocation loops in silicon

2011 ◽  
Vol 44 (3) ◽  
pp. 526-531 ◽  
Author(s):  
David Allen ◽  
Jochen Wittge ◽  
Jennifer Stopford ◽  
Andreas Danilewsky ◽  
Patrick McNally
Keyword(s):  
Semiconductor Industry ◽  
Three Dimensional ◽  
Crystal Defects ◽  
Three Dimensions ◽  
Dimensional Structure ◽  
Dislocation Loops ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Imaging ◽  
Relationship Of

In the semiconductor industry, wafer handling introduces micro-cracks at the wafer edge and the causal relationship of these cracks to wafer breakage is a difficult task. By way of understanding the wafer breakage process, a series of nano-indents were introduced both into 20 × 20 mm (100) wafer pieces and into whole wafers as a means of introducing controlled strain. Visualization of the three-dimensional structure of crystal defects has been demonstrated. The silicon samples were then treated by various thermal anneal processes to initiate the formation of dislocation loops around the indents. This article reports the three-dimensional X-ray diffraction imaging and visualization of the structure of these dislocations. A series of X-ray section topographs of both the indents and the dislocation loops were taken at the ANKA Synchrotron, Karlsruhe, Germany. The topographs were recorded on a CCD system combined with a high-resolution scintillator crystal and were measured by repeated cycles of exposure and sample translation along a direction perpendicular to the beam. The resulting images were then rendered into three dimensions utilizing open-source three-dimensional medical tomography algorithms that show the dislocation loops formed. Furthermore this technique allows for the production of a video (avi) file showing the rotation of the rendered topographs around any defined axis. The software also has the capability of splitting the image along a segmentation line and viewing the internal structure of the strain fields.

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.

Diffraction

2002 ◽  
Author(s):  
David Blow
Keyword(s):  
Red Light ◽  
Three Dimensional ◽  
Three Dimensions ◽  
X Rays ◽  
X Ray ◽  
Original Direction ◽  
Computational Procedures ◽  
Scattering Material ◽  
Opaque Object ◽  
Diffraction Effects

Diffraction refers to the effects observed when light is scattered into directions other than the original direction of the light, without change of wavelength. An X-ray photon may interact with an electron and set the electron oscillating with the X-ray frequency. The oscillating electron may radiate an X-ray photon of the same wavelength, in a random direction, when it returns to its unexcited state. Other processes may also occur, akin to fluorescence, which emit X-rays of longer wavelengths, but these processes do not give diffraction effects. Just as we see a red card because red light is scattered off the card into our eyes, objects are observed with X-rays because an illuminating X-ray beam is scattered into the X-ray detector. Our eye can analyse details of the card because its lens forms an image on the retina. Since no X-ray lens is available, the scattered X-ray beam cannot be converted directly into an image. Indirect computational procedures have to be used instead. X-rays are penetrating radiation, and can be scattered from electrons throughout the whole scattering object, while light only shows the external shape of an opaque object like a red card. This allows X-rays to provide a truly three-dimensional image. When X-rays pass near an atom, only a tiny fraction of them is scattered: most of the X-rays pass further into the object, and usually most of them come straight out the other side of the whole object. In forming an image, these ‘straight through’ X-rays tell us nothing about the structure, and they are usually captured by a beam stop and ignored. This chapter begins by explaining that the diffraction of light or X-rays can provide a precise physical realization of Fourier’s method of analysing a regularly repeating function. This method may be used to study regularly repeating distributions of scattering material. Beginning in one dimension, examples will be used to bring out some fundamental features of diffraction analysis. Graphic examples of two-dimensional diffraction provide further demonstrations. Although the analysis in three dimensions depends on exactly the same principles, diffraction by a three-dimensional crystal raises additional complications.

scholarly journals Gold Exploration in Two and Three Dimensions: Improved and Correlative Insights from Microscopy and X-Ray Computed Tomography

Minerals ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 476
Author(s):  
Joshua Chisambi ◽  
Bjorn von der Heyden ◽  
Muofhe Tshibalanganda ◽  
Stephan Le Roux
Keyword(s):  
Computed Tomography ◽  
Spatial Distribution ◽  
Gold Mineralization ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Low Grade ◽  
X Ray ◽  
3D Space ◽  
X Ray Computed ◽  
2D And 3D

In this contribution, we highlight a correlative approach in which three-dimensional structural/positional data are combined with two dimensional chemical and mineralogical data to understand a complex orogenic gold mineralization system; we use the Kirk Range (southern Malawi) as a case study. Three dimensional structures and semi-quantitative mineral distributions were evaluated using X-ray Computed Tomography (XCT) and this was augmented with textural, mineralogical and chemical imaging using Scanning Electron Microscopy (SEM) and optical microscopy as well as fire assay. Our results detail the utility of the correlative approach both for quantifying gold concentrations in core samples (which is often nuggety and may thus be misrepresented by quarter- or half-core assays), and for understanding the spatial distribution of gold and associated structures and microstructures in 3D space. This approach overlays complementary datasets from 2D and 3D analytical protocols, thereby allowing a better and more comprehensive understanding on the distribution and structures controlling gold mineralization. Combining 3D XCT analyses with conventional 2D microscopies derive the full value out of a given exploration drilling program and it provides an excellent tool for understanding gold mineralization. Understanding the spatial distribution of gold and associated structures and microstructures in 3D space holds vast potential for exploration practitioners, especially if the correlative approach can be automated and if the resultant spatially-constrained microstructural information can be fed directly into commercially available geological modelling software. The extra layers of information provided by using correlative 2D and 3D microscopies offer an exciting new tool to enhance and optimize mineral exploration workflows, given that modern exploration efforts are targeting increasingly complex and low-grade ore deposits.

scholarly journals Development of an X-ray real-time stereo imaging technique using synchrotron radiation

2011 ◽  
Vol 18 (4) ◽  
pp. 569-574 ◽  
Author(s):  
Masato Hoshino ◽  
Kentaro Uesugi ◽  
James Pearson ◽  
Takashi Sonobe ◽  
Mikiyasu Shirai ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Real Time ◽  
Imaging System ◽  
Silicon Crystal ◽  
Three Dimensional ◽  
Stereo Image ◽  
Large Field ◽  
Depth Information ◽  
Stereo Imaging ◽  
X Ray

An X-ray stereo imaging system with synchrotron radiation was developed at BL20B2, SPring-8. A portion of a wide X-ray beam was Bragg-reflected by a silicon crystal to produce an X-ray beam which intersects with the direct X-ray beam. Samples were placed at the intersection point of the two beam paths. X-ray stereo images were recorded simultaneously by a detector with a large field of view placed close to the sample. A three-dimensional wire-frame model of a sample was created from the depth information that was obtained from the lateral positions in the stereo image. X-ray stereo angiography of a mouse femoral region was performed as a demonstration of real-time stereo imaging. Three-dimensional arrangements of the femur and blood vessels were obtained.

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