Loes Brabant

Three-dimensional analysis of high-resolution X-ray computed tomography data with Morpho+

Three-dimensional (3D) analysis is an essential tool to obtain quantitative results from 3D datasets. Considerable progress has been made in 3D imaging techniques, resulting in a growing need for more flexible, complete analysis packages containing advanced algorithms. At the Centre for X-ray Tomography of the Ghent University (UGCT), research is being done on the improvement of both hardware and software for high-resolution X-ray computed tomography (CT). UGCT collaborates with research groups from different disciplines, each having specific needs. To meet these requirements the analysis software package, Morpho+, was developed in-house. Morpho+ contains an extensive set of high-performance 3D operations to obtain object segmentation, separation, and parameterization (orientation, maximum opening, equivalent diameter, sphericity, connectivity, etc.), or to extract a 3D geometrical representation (surface mesh or skeleton) for further modeling. These algorithms have a relatively short processing time when analyzing large datasets. Additionally, Morpho+ is equipped with an interactive and intuitive user interface in which the results are visualized. The package allows scientists from various fields to obtain the necessary quantitative results when applying high-resolution X-ray CT as a research tool to the nondestructive investigation of the microstructure of materials.

An exploratory study of contrast agents for soft tissue visualization by means of high resolution X-ray computed tomography imaging.

High resolution X‐ray computed tomography (CT), or microCT, is a promising and already widely used technique in various scientific fields. Also for histological purposes it has great potential. Although microCT has proven to be a valuable technique for the imaging of bone structures, the visualization of soft tissue structures is still an important challenge due to their low inherent X‐ray contrast. One way to achieve contrast enhancement is to make use of contrast agents. However, contrary to light and electron microscopy, knowledge about contrast agents and staining procedures is limited for X‐ray CT. The purpose of this paper is to identify useful X‐ray contrast agents for soft tissue visualization, which can be applied in a simple way and are also suited for samples larger than (1 cm)3. And 28 chemical substances have been investigated. All chemicals were applied in the form of concentrated aqueous solutions in which the samples were immersed. First, strips of green Bacon were stained to evaluate contrast enhancement between muscle and adipose tissue. Furthermore it was also tested whether the contrast agents remained fixed in the tissue after staining by re‐immersing them in water. Based on the results, 12 contrast agents were selected for further testing on postmortem mice hind legs, containing a variety of different tissues, including muscle, fat, bone, cartilage and tendons. It was evaluated whether the contrast agents allowed a clearer distinction between the different soft tissue structures present. Finally also penetration depth was measured. And 26 chemicals resulted in contrast enhancement between muscle and adipose tissue in the Bacon strips. Mercury(II)chloride (HgCl2), phosphotungstic acid (PTA), phosphomolybdic acid (PMA) and ammonium orthomolybdate ((NH4)2MoO4) remained fixed after re‐immersion in water. The penetration tests showed that potassium iodide (KI) and sodium tungstate can be most efficiently used for large samples of the order of several tens of cm3. PMA, PTA, HgCl2 and also to a lesser extent Na2WO4 and (NH4)2MoO4 allowed a clearer distinction between the different soft tissue structures present.

HECTOR : a 240kV micro-CT setup optimized for research

X-ray micro-CT has become a very powerful and common tool for non-destructive three-dimensional (3D) visualization and analysis of objects. Many systems are commercially available, but they are typically limited in terms of operational freedom both from a mechanical point of view as well as for acquisition routines. HECTOR is the latest system developed by the Ghent University Centre for X-ray Tomography (http://www.ugct.ugent.be) in collaboration with X-Ray Engineering (XRE bvba, Ghent, Belgium). It consists of a mechanical setup with nine motorized axes and a modular acquisition software package and combines a microfocus directional target X-ray source up to 240 kV with a large flat-panel detector. Provisions are made to install a line-detector for a maximal operational range. The system can accommodate samples up to 80 kg, 1 m long and 80 cm in diameter while it is also suited for high resolution (down to 4 μm) tomography. The bi-directional detector tiling is suited for large samples while the variable source-detector distance optimizes the signal to noise ratio (SNR) for every type of sample, even with peripheral equipment such as compression stages or climate chambers. The large vertical travel of 1 m can be used for helical scanning and a vertical detector rotation axis allows laminography experiments. The setup is installed in a large concrete bunker to allow accommodation of peripheral equipment such as pumps, chillers, etc., which can be integrated in the modular acquisition software to obtain a maximal correlation between the environmental control and the CT data taken. The acquisition software does not only allow good coupling with the peripheral equipment but its scripting feature is also particularly interesting for testing new and exotic acquisition routines.

4D imaging and quantification of pore structure modifications inside natural building stones by means of high resolution X-ray CT.

Weathering processes have been studied in detail for many natural building stones. The most commonly used analytical techniques in these studies are thin-section petrography, SEM, XRD and XRF. Most of these techniques are valuable for chemical and mineralogical analysis of the weathering patterns. However, to obtain crucial quantitative information on structural evolutions like porosity changes and growth of weathering crusts in function of time, non-destructive techniques become necessary. In this study, a Belgian historical calcareous sandstone, the Lede stone, was exposed to gaseous SO(2) under wet surface conditions according to the European Standard NBN EN 13919 (2003). Before, during and after the strong acid test, high resolution X-ray tomography has been performed to visualize gypsum crust formation to yield a better insight into the effects of gaseous SO(2) on the pore modification in 3D. The tomographic scans were taken at the Centre for X-ray Tomography at Ghent University (UGCT). With the aid of image analysis, partial porosity changes were calculated in different stadia of the process. Increasing porosity has been observed visually and quantitatively below the new superficial formed layer of gypsum crystals. In some cases micro-cracks and dissolution zones were detected on the grain boundaries of quartz. By using Morpho+, an in-house developed image analysis program, radial porosity, partial porosity, ratio of open and closed porosity and equivalent diameter of individual pore structures have been calculated. The results obtained in this study are promising for a better understanding of gypsum weathering mechanisms, porosity changes and patterns on natural building stones in four dimensions.

High-Resolution X-Ray CT for 3D Petrography of Ferruginous Sandstone for an Investigation of Building Stone Decay

Diestian ferruginous sandstone has been used as the dominant building stone for monuments in the Hageland, a natural landscape in east‐central Belgium. Like all rocks, this stone type is sensitive to weathering. Case hardening was observed in combination with blackening of the exterior parts of the dressed stones. To determine the 3D petrography and to identify the structural differences between the exterior and interior parts, X‐ray computed tomography was used in combination with more traditional research techniques like optical microscopy and scanning electron microscopy. The 3D characterization of the ferruginous sandstone was performed with a high‐resolution X‐ray CT scanner (www.ugct.ugent.be) in combination with the flexible 3D analysis software Morpho+, which provides the necessary petrophysical parameters of the scanned samples in 3D. Besides providing the required 3D parameters like porosity, pore‐size distribution, grain size, grain orientation, and surface analysis, the results of the 3D analysis can also be visualized, which enables to understand and interpret the analysis results in a straightforward way. The complementarities between high‐quality X‐ray CT images and flexible 3D software and its relation with the more traditional microscopical research techniques are opening up new gateways in the study of weathering processes of natural building stones. Microsc. Res. Tech., 2011.

Sustained release from hot-melt extruded matrices based on ethylene vinyl acetate and polyethylene oxide.

The aim of the present study was to evaluate the importance of matrix flexibility of hot-melt extruded (HME) ethylene vinyl acetate (EVA) matrices (with vinyl acetate (VA) contents of 9%, 15%, 28% and 40%), through the addition of hydrophilic polymers with distinct swelling capacity. Polyethylene oxide (PEO 100K, 1M and 7M) was used as swelling agent and metoprolol tartrate (MPT) as model drug. The processability via HME and drug release profiles of EVA/MPT/PEO formulations were assessed. Solid state characteristics, porosity and polymer miscibility of EVA/PEO matrices were evaluated by means of DSC, X-ray tomography and Raman spectroscopy. The processability via HME varied according to the VA content: EVA 40 and 28 were extruded at 90°C, whereas higher viscosity EVA grades (EVA 15 and 9) required a minimum extrusion temperature of 110°C to obtain high-quality extrudates. Drug release from EVA matrices depended on the VA content, PEO molecular weight and PEO content, matrix porosity as well as pore size distribution. Interestingly, the interplay of PEO leaching, matrix swelling, water influx and changes in matrix porosity influenced drug release: EVA 40- and 28-based matrices extruded with PEO of higher MW accelerated drug release, whereas for EVA 15- and 9-based matrices, drug release slowed down. These differences were related to the distinct polymer flexibility imposed by the VA content (lower VA content presents higher crystallinity and less free movement of the amorphous segments resulting in a higher rigidity). In all cases, diffusional mass transport seems to play a major role, as demonstrated by mathematical modeling using an analytical solution of Ficks second law. The bioavailability of EVA 40 and 28 matrices in dogs was not significantly different, independent of PEO 7M concentration.

Comparison of two single-image phase-retrieval algorithms for in-line x-ray phase-contrast imaging

The attenuation of x-rays in a material forms the basis of x-ray radiography and tomography. By measuring the transmission of the x-rays over a large amount of raypaths, the three-dimensional (3D) distribution of the x-ray linear attenuation coefficient can be reconstructed in a 3D volume. In x-ray microtomography (μCT), however, the x-ray refraction yields a significant signal in the transmission image and the 3D distribution of the refractive index can be reconstructed in a 3D volume. To do so, several methods exist, on both a hardware and software level. In this paper, we compare two similar software methods, the modified Bronnikov algorithm and the simultaneous phase-and-amplitude retrieval. The first method assumes a pure phase object, whereas the latter assumes a homogeneous object. Although these assumptions seem very restrictive, both methods have proven to yield good results on experimental data.

Holistic approach of pre-existing flaws on the decay of two limestones

This study aims to understand the influence of the microfacies and the determination of pre-existing flaws on the weathering behavior of two types of limestones. Therefore, both Lede and Noyant limestones were independently weathered by strong acid tests and freeze-thaw cycles. In order to characterize the weathering patterns inside the stones, a combination of high resolution X-ray CT, SEM-EDS and thin section microscopy was used. The advantage of high resolution X-ray CT is its non-destructive character and the obtained 3D structural information. By using this technique, a time-lapse sequence of the weathering patterns was obtained for both gypsum crust formation as well as crack formation due to freezing and thawing. This way, a clear link could be made with the initial non-weathered state. Thin section microscopy and SEM-EDS provided additional chemical information. The focus of this study lies in the processes that occur in the bioclast fragments in the stone and the influence of the surrounding cement or matrix. The results show that weathering patterns vary for both limestones although the causes of weathering were similar. In case of the Noyant stone, the weathering by crystallizing gypsum was mainly restricted to the microporous matrix of the stone, while in case of the Lede stone, several foraminifera and shell fragments were preferentially recrystallized. In general, the underlying microstructure determines the weathering pattern of the stone.

Structural tissue organization in the beak of Java and Darwin's finches.

Birds are well known for occupying diverse feeding niches, and for having evolved diverse beak morphologies associated with dietary specialization. Birds that feed on hard seeds typically possess beaks that are both deep and wide, presumably because of selection for fracture avoidance, as suggested by prior studies. It follows then that birds that eat seeds of different size and hardness should vary in one or more aspects of beak morphology, including the histological organization of the rhamphotheca, the cellular interface that binds the rhamphotheca to the bone, and the organization of trabeculae in the beak. To explore this expectation we here investigate tissue organization in the rhamphotheca of the Java finch, a large granivorous bird, and describe interspecific differences in the trabecular organization of the beak across 11 species of Darwins finches. We identify specializations in multiple layers of the horny beak, with the dermis anchored to the bone by Sharpeys fibers in those regions that are subjected to high stresses during biting. Moreover, the rhamphotheca is characterized by a tight dermo‐epidermal junction through interdigitations of these two tissues. Herbst corpuscles are observed in high density in the dermis of the lateral aspect of the beak as observed in other birds. Finally, the trabecular organization of the beak in Darwins finches appears most variable in regions involved most in food manipulation, with the density of trabeculae in the beak generally mirroring loading regimes imposed by different feeding habits and beak use in this clade.

Carbon mineralisation and pore size classes in undisturbed soil cores

Soil pore network effects on organic matter turnover have, until now, been studied indirectly because of lack of data on the 3D structure of the pore network. Application of X-ray computed tomography (X-ray CT) to quantify the distribution of pore neck size and related pore sizes from undisturbed soil cores, with simultaneous assessment of carbon (C) mineralisation, could establish a relationship between soil organic matter (SOM) decomposition and soil pore volumes. Eighteen miniature soil cores (diameter 1.2 cm, height 1.2 cm) covering a range of bulk densities were incubated at 20°C for 35 days. Respiration was modelled with a parallel first- and zero-order kinetic model. The cores were scanned at 9.44 µm resolution using an X-ray CT scanner developed in-house. Correlation analysis between the slow pool C mineralisation rate, ks, and pore volume per pore neck class yielded significant (P  350 µm pore neck classes, respectively. Because larger pores are most probably mainly air-filled, a positive relation with ks was ascribed to enhanced aeration of smaller pores surrounding large pores. The weak and insignificant relationship between the smallest pore neck class (<9.44 µm) and ks could be explained by obstructed microbial activity and mobility or diffusion of exo-enzymes and hydrolysis products as a result of limited oxygen availability. This study supports the hypothesis that the impact of soil structure on microbial processes occurs primarily via its determination of soil water distribution, which is possibly the main driver for the location of C mineralisation in the soil matrix.