Virtual histology uncertainty in synchrotron x-ray micro-computed tomography evaluation.

A three-dimensional (3D) X-ray tomogram evaluation gives a full view of the bone distribution around an entire implant in contrast to the often-used two-dimensional (2D) histological methods. High-resolution X-ray absorption tomography was used to evaluate the 3D bone growth around dental implants in an experimental goat mandible reconstruction model. The tomograms allowed for the construction of virtual histological cross-sections that could be used to evaluate the statistical uncertainty of the histological methods, which was the purpose of this paper. The virtual 2D histological results showed a significantly higher uncertainty within the same sample than did the full 3D volume results.

Publisher Correction: Interactions of the Calcite {10.4} Surface with Organic Compounds: Structure and Behaviour at Mineral - Organic Interfaces.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

Interactions of the Calcite {10.4} Surface with Organic Compounds: Structure and Behaviour at Mineral - Organic Interfaces.

The structure and the strength of organic compound adsorption on mineral surfaces are of interest for a number of industrial and environmental applications, oil recovery, CO2 storage and contamination remediation. Biomineralised calcite plays an essential role in the function of many organisms that control crystal growth with organic macromolecules. Carbonate rocks, composed almost exclusively of calcite, host drinking water aquifers and oil reservoirs. In this study, we examined the ordering behaviour of several organic compounds and the thickness of the adsorbed layers formed on calcite {10.4} surfaces. We used X-ray reflectivity (XRR) to study calcite {10.4} surfaces that were prepared in three alcohols: methanol, isopropanol and pentanol and one carboxylic acid: octanoic acid. All molecules adsorbed in self-assembled layers, where thickness depended on the density and the length of the molecule. For methanol and isopropanol, molecular dynamic simulations (MD) provided complementary information, which allowed us to develop a surface model. Branching in isopropanol induced slightly less ordering because of the additional degree of freedom. Pentanol and octanoic acid adsorbed as single monolayers. The results of this work indicate that adhered organic compounds from the surrounding environment can affect the surface behaviour, depending on properties of the organic compound.

Visualization of subcutaneous insulin injections by x-ray computed tomography.

We report how the three-dimensional structure of subcutaneous injections of soluble insulin can be visualized by x-ray computed tomography using an iodine based contrast agent. The injections investigated are performed ex vivo in porcine adipose tissue. Full tomography scans carried out at a laboratory x-ray source with a total acquisition time of about 1 min yield CT-images with an effective pixel size of 109 × 109 µm². The depots are segmented using a modified Chan-Vese algorithm and we are able to observe differences in the shape of the injection depot and the position of the depot in the skin among equally performed injections. To overcome the beam hardening artefacts, which affect the quantitative prediction of the volume injected, we additionally present results concerning the visualization of two injections using synchrotron radiation. The spatial concentration distribution of iodine is calculated to show the dilution of the insulin drug inside the depot. Characterisation of the shape of the depot and the spatial concentration profile of the injected fluid is important knowledge when improving the clinical formulation of an insulin drug, the performance of injection devices and when predicting the effect of the drug through biomedical simulations.

X-ray tomography using the full complex index of refraction.

We report on x-ray tomography using the full complex index of refraction recorded with a grating-based x-ray phase-contrast setup. Combining simultaneous absorption and phase-contrast information, the distribution of the full complex index of refraction is determined and depicted in a bivariate graph. A simple multivariable threshold segmentation can be applied offering higher accuracy than with a single-variable threshold segmentation as well as new possibilities for the partial volume analysis and edge detection. It is particularly beneficial for low-contrast systems. In this paper, this concept is demonstrated by experimental results.

Atomic modifications by synchrotron radiation at the calcite-ethanol interface.

This article reports on studies of the chemical alterations induced by synchrotron radiation at the calcite-ethanol interface, a simple model system for interfaces between minerals and more complex organic molecules containing OH groups. A combination of X-ray reflectivity and X-ray photoelectron spectroscopy of natural calcite, cleaved in distilled ethanol to obtain new clean interfaces, indicated that, during a 5 h period, the two top atomic layers of calcite, CaCO(3), transform into calcium oxide, CaO, by releasing CO(2). Also, the occupation of the first ordered layer of ethanol attached to calcite by hydrogen bonds almost doubles. Comparison between radiated and non-radiated areas of the same samples demonstrate that these effects are induced only by radiation and not caused by aging. These observations contribute to establishing a time limit for synchrotron experiments involving fluid-mineral interfaces where the polar OH group, as present in ethanol, plays a key role in their molecular structure and bonding. Also, the chemical evolution observed in the interface provides new insight into the behavior of some complex organic molecules involved in biomineralization processes.

Structural and magnetic dynamics of a laser induced phase transition in FeRh.

We use time-resolved x-ray diffraction and magneto-optical Kerr effect to study the laser-induced antiferromagnetic to ferromagnetic phase transition in FeRh. The structural response is given by the nucleation of independent ferromagnetic domains (τ(1)~30 ps). This is significantly faster than the magnetic response (τ(2)~60 ps) given by the subsequent domain realignment. X-ray diffraction shows that the two phases coexist on short time scales and that the phase transition is limited by the speed of sound. A nucleation model describing both the structural and magnetic dynamics is presented.

Molecular ordering of ethanol at the calcite surface.

To produce biominerals, such as shells, bones, and teeth, living beings create organic compounds that control the growth of the solid phase. Investigating the atomic scale behavior of individual functional groups at the mineral-fluid interface provides fundamental information that is useful for constructing accurate predictive models for natural systems. Previous investigations of the activity of coccolith-associated polysaccharides (CAP) on calcite, using atomic force microscopy (AFM) [Henriksen, K., Young, J. R., Bown, P. R., and Stipp, S. L. S. Palentology 2004, 43 (Part 3), 725-743] and molecular dynamics (MD) modeling [Yang, M., Stipp, S. L. S., and Harding, J. H. Cryst. Growth Des. 2008, 8 (11), 4066-4074], have suggested that OH functional groups control polysaccharide attachment. The purpose of this work was to characterize, using X-ray reflectivity (XR) combined with molecular dynamics (MD) simulations, the structuring on calcite of a layer of the simplest carbon chain molecule that contains an OH group, ethanol (CH(3)-CH(2)-OH). We found evidence that EtOH forms a highly ordered structure at the calcite surface, where the first layer molecules bond with calcite. The ethanol molecules stand up perpendicularly at the interface or nearly so. As a consequence, the fatty, CH(3) ends form a new surface, about 6 Å from the termination of the bulk calcite, and beyond that, there is a thin gap where ethanol density is low. Following is a more disordered layer that is two to three ethanol molecules thick, about 14 Å, where density more resembles that of bulk liquid ethanol. The good agreement between theory and experiment gives confidence that a theoretical approach can offer information about behavior in more complex systems.

Molecular X-ray computed tomography of myelin in a rat brain.

In this work we demonstrate the feasibility of applying small-angle X-ray scattering computed tomography (SAXS-CT) for non-invasive molecular imaging of myelin sheaths in a rat brain. Our results show that the approach yields information on several quantities, including the relative myelin concentration, its periodicity, the total thickness of the myelin sheaths, and the relative concentration of cytoskeletal neurofilaments. For example the periodicity of the myelin sheaths varied in the range from 17.0 to 18.2 nm around an average of 17.6 (±0.3) nm. We believe that imaging, i.e., spatially resolved measuring these quantities could provide general means for understanding the relation to a number of neurodegenerative diseases.

Quantitative x-ray dark-field computed tomography.

The basic principles of x-ray image formation in radiology have remained essentially unchanged since Röntgen first discovered x-rays over a hundred years ago. The conventional approach relies on x-ray attenuation as the sole source of contrast and draws exclusively on ray or geometrical optics to describe and interpret image formation. Phase-contrast or coherent scatter imaging techniques, which can be understood using wave optics rather than ray optics, offer ways to augment or complement the conventional approach by incorporating the wave-optical interaction of x-rays with the specimen. With a recently developed approach based on x-ray optical gratings, advanced phase-contrast and dark-field scatter imaging modalities are now in reach for routine medical imaging and non-destructive testing applications. To quantitatively assess the new potential of particularly the grating-based dark-field imaging modality, we here introduce a mathematical formalism together with a material-dependent parameter, the so-called linear diffusion coefficient and show that this description can yield quantitative dark-field computed tomography (QDFCT) images of experimental test phantoms.

Subsurface dimerization in III-V semiconductor (001) surfaces.

We present the atomic structure of the c(8 x 2) reconstructions of InSb-, InAs-, and GaAs-(001) surfaces as determined by surface x-ray diffraction using direct methods. Contrary to common belief, group III dimers are not prominent on the surface, instead subsurface dimerization of group III atoms takes place in the second bilayer, accompanied by a major rearrangement of the surface atoms above the dimers to form linear arrays. By varying the occupancies of four surface sites the (001)-c(8 x 2) reconstructions of III-V semiconductors can be described in a unified model.

Low-temperature structure of indium quantum chains on silicon

The array of quasi-one-dimensional indium chains in the Si(111)- (4x1)-In surface reconstruction exhibits a phase transition to a low-temperature (8x2) phase. It has been suggested that this phase transition is related to a charge density wave (CDW) formation. The x-ray diffraction results presented here demonstrate that at 20 K the CDW has not yet condensed into a superstructure even though good transverse coupling was established. This indicates that CDW formation cannot be the driving force for the phase transition. Furthermore we elucidate the subtle highly anisotropic interchain correlations and reveal the detailed atomic structure of the low-temperature (8x2) phase.

Applications of high-energy synchrotron radiation for structural studies of polycrystalline materials.

The large penetration power of high-energy X-rays (>60 keV) raises interesting prospects for new types of structural characterizations of polycrystalline materials. It becomes possible in a non-destructive manner to perform local studies, within the bulk of the material, of the fundamental materials physics properties: grain orientations, strain, dislocation densities etc. In favourable cases these properties may be mapped in three dimensions with a spatial resolution that matches the dimensions of the individual grains. Imbedded volumes and interfaces become accessible. Moreover, the high energies allow better in-situ studies of samples in complicated environments (industrial process optimization). General techniques for research in this energy range have been developed using broad-band angle-dispersive methods, on-line two-dimensional detectors and conical slits. Characterizations have been made at the level of the individual grains and grain boundaries as well as on ensembles of grains. The spatial resolution is presently of the order of 10-100 micom. Four examples of applications are presented along with an outlook.