Three-dimensional X-ray Micro-computed Tomography Research Articles

Uppermost Darriwilian radiolarians from the lower part of Wulalike Formation, Northwest Ordos Basin, North China

A well-preserved radiolarian assemblage is described from argillaceous limestone of the Wulalike Formation in the Northwest Ordos Basin, North China. A total of nine species of seven genera are described, including Inanigutta gansuensis, I. quadrispinosa, I. complanata, Inanibigutta pinglianensis, Oriundogutta bella, Triplococcus acanthicus, Haplentactinia juncta, Syntagentactinia pupila n. sp., and Kalimnasphaera maculosa. Three-dimensional X-ray micro-computed tomography is used to make a detailed examination of the new species. This is the first documentation of radiolarian fossils from the Wulalike Formation, which contributes to better understanding of the features of Ordovician radiolarian faunas and facilitate stratigraphic correlation and subdivision in the Ordos Basin.

Pore network modeling as a new tool for determining gas diffusivity in peat

Abstract. Peatlands are globally significant carbon stocks and may become major sources of the greenhouse gases (GHGs) carbon dioxide and methane in a changing climate and under anthropogenic management pressure. Diffusion is the dominant gas transport mechanism in peat; therefore, a proper knowledge of the soil gas diffusion coefficient is important for the estimation of GHG emissions from peatlands. Pore network modeling (PNM) is a potential tool for the determination of gas diffusivity in peat, as it explicitly connects the peat microstructure and the characteristics of the peat pore network to macroscopic gas transport properties. In the present work, we extracted macropore networks from three-dimensional X-ray micro-computed tomography (µCT) images of peat samples and simulated gas diffusion in these networks using PNM. These results were compared to the soil gas diffusion coefficients determined from the same samples in the laboratory using the diffusion chamber method. The measurements and simulations were conducted for peat samples from three depths. The soil gas diffusion coefficients were determined under varying water contents adjusted in a pressure plate apparatus. We also assessed the applicability of commonly used gas diffusivity models to peat. The laboratory measurements showed a decrease in gas diffusivity with depth due to a decrease in air-filled porosity and pore space connectivity. However, gas diffusivity was not extremely low close to saturation, which may indicate that the structure of the macropore network is such that it enables the presence of connected diffusion pathways through the peat matrix, even in wet conditions. The traditional gas diffusivity models were not very successful in predicting the soil gas diffusion coefficient. This may indicate that the microstructure of peat differs considerably from the structure of mineral soils and other kinds of porous materials for which these models have been constructed and calibrated. By contrast, the pore network simulations reproduced the laboratory-determined soil gas diffusion coefficients rather well. Thus, the combination of the µCT and PNM methods may offer a promising alternative to the traditional estimation of soil gas diffusivity through laboratory measurements.

Peat macropore networks – new insights into episodic and hotspot methane emission

Abstract. Peatlands are important natural sources of atmospheric methane (CH4) emissions. The production and emission of CH4 are strongly influenced by the diffusion of oxygen into the soil and of CH4 from the soil to the atmosphere, respectively. This diffusion, in turn, is controlled by the structure of macropore networks. The characterization of peat pore structure and connectivity through complex network theory approaches can give conceptual insight into how the relationship between the microscale pore space properties and CH4 emissions on a macroscopic scale is shaped. The evolution of the pore space that is connected to the atmosphere can also be conceptualized through a pore network modeling approach. Pore regions isolated from the atmosphere may further develop into anaerobic pockets, which are local hotspots of CH4 production in unsaturated peat. In this study, we extracted interconnecting macropore networks from three-dimensional X-ray micro-computed tomography (µCT) images of peat samples and evaluated local and global connectivity metrics for the networks. We also simulated the water retention characteristics of the peat samples using a pore network modeling approach and compared the simulation results with measured water retention characteristics. The results showed large differences in peat macropore structure and pore network connectivity between vertical soil layers. The macropore space was more connected and the flow paths through the peat matrix were less tortuous near the soil surface than at deeper depths. In addition, macroporosity, structural anisotropy, and average pore throat diameter decreased with depth. Narrower and more winding air-filled diffusion channels may reduce the rate of gas transport as the distance from the peat layer to the soil–air interface increases. The network analysis also suggests that both local and global network connectivity metrics, such as the network average clustering coefficient and closeness centrality, might serve as proxies for assessing the efficiency of gas diffusion in air-filled pore networks. However, the applicability of the network metrics was restricted to the high-porosity near-surface layer. The spatial extent and continuity of the pore network and the spatial distribution of the pores may be reflected in different network metrics in contrasting ways. The hysteresis of peat water content between wetting and drying was found to affect the evolution of the volume of connected air-filled pore space in unsaturated peat. Thus, the formation of anaerobic pockets may occur in a smaller soil volume and methanogenesis may be slower when the peat is wetting compared to in drying conditions. This hysteretic behavior might explain the hotspots and episodic spikes of CH4 emissions, and therefore, it should be taken into account in biogeochemical models.

Morphological variability in the mucosal attachment site of Trichuris muris revealed by X-ray microcomputed tomography

Parasitic infections can be challenging to study because two dimensional light and electron microscopy are often limited in visualising complex and inaccessible attachment sites. Exemplifying this, Trichuris spp. inhabit a tunnel of epithelial cells within the host caecum and colon. A significant global burden of this infection persists, partly because available anthelminthics lack efficacy, although the mechanisms underlying this remain unknown. Consequently, there is a need to pioneer new approaches to better characterize the parasite niche within the host and investigate how variation in its morphology and integrity may contribute to resistance to therapeutic intervention. To address these aims, we exploited three-dimensional X-ray micro-computed tomography (microCT) to image the mouse whipworm, Trichuris muris, in caeca of wild-type C57BL/6 and SCID mice ex vivo. Using osmium tetroxide staining to effectively enhance the contrast of worms, we found that a subset exhibited preferential positioning towards the bases of the intestinal crypts. Moreover, in one rare event, we demonstrated whipworm traversal of the lamina propria. This morphological variability contradicts widely accepted conclusions from conventional microscopy of the parasite niche, showing Trichuris in close contact with the host proliferative and immune compartments that may facilitate immunomodulation. Furthermore, by using a skeletonization-based approach we demonstrate considerable variation in tunnel length and integrity. The qualitative and quantitative observations provide a new morphological point of reference for future in vitro study of host-Trichuris interactions, and highlight the potential of microCT to characterise enigmatic host-parasite interactions more accurately.

Middle Ordovician (middle Darriwilian) Archaeospicularia and Entactinaria (radiolarians) from the Table Cove Formation, Piccadilly Quarry, Newfoundland, Canada

AbstractNew, distinctive, well-preserved and previously undescribed constituents of a Middle Ordovician (middle Darriwilian, Dw2) radiolarian assemblage from the Table Cove Formation in Newfoundland are described. Three-dimensional X-ray micro-computed tomography (μ-CT) facilitates detailed examination of key specimens revealing hitherto unknown details of the internal morphologies of key lower Paleozoic taxonomic groups, among which a lack of knowledge has previously impeded resolution of higher taxonomic rankings.Twenty-seven archaeospiculid and entactinarian taxa are described and illustrated including six new species: Westernbrookia polygonata n. sp., Neopalaeospiculum piccadilliensis n. sp., Ramuspiculum laxum n. sp. Spongentactinia nazarovi n. sp., Aspiculum irregulare n. sp., and Nyfrieslandia ramosissima n. sp. The investigation extends the known ranges of the species: Pararcheoentactinia reedae Won and Iams, 2002; Sphaeroentactinia robusta Won and Iams, 2015; Varispiculum ectospiculatum Won and Iams, 2015; and Svalbardospiculum multifurcatum (Won, Iams, and Reed, 2005), together with the genus Echidnina to the mid-Darriwilian.UUID: http://zoobank.org/74826b7b-bb86-45d5-ad23-e6e65e0706df.

The effect of loading direction on the fracture behaviors of cortical bone at a dynamic loading rate

In this study, the dynamic cracking processes in porcine cortical bone were visualized in real-time using the high-speed synchrotron X-ray phase-contrast imaging (PCI) technique in three osteon orientations: in-plane transverse, out-of-plane transverse and in-plane longitudinal. The dynamic flexural loading applied on the pre-notched bone specimens was introduced by a modified Kolsky compression bar. High-speed X-ray images of the entire loading events were documented with a high-speed camera. Three-dimensional X-ray micro-computed tomography was conducted to examine the intact microstructures and obtain the basic material properties of the bone material used for mechanical characterizations. The onset location, where crack initiated, and the subsequent direction, along which the incipient crack propagated, were measured quantitatively using the high-speed X-ray images and the latter was found dependent on the osteon direction significantly. The crack propagation velocities were dependent on crack extension over the entire crack path significantly for all the three directions while the initial velocity for in-plane longitudinal direction was lower than the other two directions. Straight-through crack paths were observed for in-plane longitudinal specimens while the cracks were deflected and twisted in the in-plane transverse direction. For out-of-plane transverse direction, the cracks follow paths with tortuosity fall in between the other two directions, showing a mixed mode of fractures of the former two extreme cases. The toughening mechanisms, visualized by the high-speed X-ray images, and the corresponding fracture toughness, evaluated in terms of fracture initiation toughness and crack growth resistance curve (R-curve), were also found significantly different among the three osteon directions, suggesting an overall transition from brittle to ductile-like fracture behaviors at the dynamic displacement rate (5.4 m/s) as the osteon orientation varies from in-plane longitudinal to out-of-plane transverse, and to in-plane transverse eventually.

Micro-CT study of Middle Ordovician Spumellaria (radiolarians) from western Newfoundland, Canada

AbstractA new, previously undescribed Middle Ordovician (middle Darriwilian: Dw2) radiolarian assemblage has been recovered from the Table Cove Formation at Piccadilly Quarry, western Newfoundland. Constituents of the fauna described herein are both distinctive and exceptionally well preserved. Three-dimensional X-ray micro-computed tomography (μ-CT) is used to make a detailed examination of four key spumellarian specimens. This technology enables visualization of hitherto ambiguous details of the internal morphologies of key lower Paleozoic taxonomic groups, among which a lack of knowledge has impeded resolution of higher taxonomic rankings.

Morphological Analysis of Spherical Adsorptive Carbon Granules Using Three-Dimensional X-Ray Micro-computed Tomography.

The purpose of this study was to clarify applicability of three-dimensional X-ray micro-computed tomography (3D X-ray micro-CT) to elucidate interior morphology of spherical adsorptive carbon fine granules. Scanning of small single spherical granule hold on the rotating sample stage provided the structural information without particular preparation (e.g., slicing) that can affect the definite morphology. The three model formulations with similar appearance showed different internal structure in the 3D images, including large hollow in one of them. Other formulations showed some small empty or higher density area in the filled granules, suggesting uneven distribution of carbon. The results indicated relevance of the X-ray micro-CT analysis on the physical characterization of the spherical adsorptive carbon granule formulations.

Bacterial behavior on coated porous titanium substrates for biomedical applications

In this work, bacterial behavior on dense and porous titanium substrates is discussed. Porous titanium was fabricated by a space holder technique (using 50 vol%, NH4HCO3 with particle sizes between 250 and 355 μm). These substrates were coated by sulfonated PEEK (termed SPEEK). Characterization of the porous substrate was carried out using the Archimedes Method, Image Analysis, and three-dimensional X-ray Micro-Computed Tomography (including total and interconnected porosity, equivalent diameter, and pore shape factor), as well as mechanical characterization (specifically stiffness and yield strength). A detailed study was performed here to investigate the influence of substrate porosity on the adhesion and proliferation of E. coli, MRSA, and P. aeruginosa (common causes of orthopedic device-associated infections). Bacterial colonization was examined in terms of the initial bacterial concentration, as well as bacterial adherence to and growth on the surface and inside the pores. Results suggest that fully dense titanium supported the least bacterial colonization, while the porous titanium promoted bacterial growth in the medium and inside the cavities. Furthermore, the SPEEK coating deposited onto the samples inhibited bacteria growth inside the porous materials. In this manner, this study showed for the first time that SPEEK could have potential antibacterial properties to offset the increase in bacteria growth commonly observed in porous materials.

Non-destructive, high-resolution X-ray micro-CT of a Hairy Stalagmite: investigating the structural details of a biogenic speleothem

Three-dimensional X-ray micro-computed tomography permits to investigate the internal structure of objects at a high resolution without altering its original form. It also facilitates the rendering and visualization of a virtual replica, which can be subjected to rigorous and complex analyses. In the present study, micro-computed tomography was used to investigate a unique and fragile speleothem (cave formation) named a “Hairy Stalagmite”. Non-destructive analyses have revealed the calcareous internal structure of this speleothem, which consists of hollow, interconnected tubes. Rendered two-dimensional cross-sections also clearly revealed the outline of a once dense root nest that formed part of the speleothem’s biogenic origin. The internal structure was further visualized using an image sequence of two-dimensional cross-sections to create a video that “brings the speleothem to life”, also illustrating its complexity and variability. Statistical analyses revealed structural variability in void fraction, which is likely related to changing environmental conditions. In addition, the micro-computed tomography data were used as input for additive manufacturing (three-dimensional printing) in order to produce an enlarged replica of the Hairy Stalagmite sample, which made physical inspection possible. This combined approach represents the first of its kind and provides much benefit for future studies.

CFD modeling of convective scalar transport in a macroporous material for drying applications

Convective drying is one of the most important forms of moisture removal in macroporous materials exposed to environmental loads. In this study, the influence of airflow on the convective removal of water vapor (passive scalar) from porous asphalt (PA), a macroporous material, is investigated for different wind speeds and levels of liquid water height within the material, using computational fluid dynamics (CFD). The PA domain for the CFD simulations is reconstructed from three-dimensional X-ray micro-computed tomography images. Steady Reynolds-averaged Navier-Stokes (RANS) k-ε model with low Reynolds number modeling for the near-wall region is used for the turbulence modeling. Simulations are carried out for three wind speeds, 0.1, 1.5 and 10 m/s, and three depths of the scalar (vapor) source, 0.13, 15 and 29 mm, within the specimen. Only the highest wind speed has a clear influence on the total vapor flux measured at the interface. Additionally, at the highest wind speed, air entrainment in pores near the air-material interface plays an important role in vapor removal. At lower wind speeds, diffusion within the material is the dominant vapor transport mechanism. At a wind speed of 10 m/s, strong vortices are observed which inhibit vapor removal in cavity-type pores by recirculating vapor within the pore. However, at the same wind speed, vapor transport in a non-cavity-type pore system is found to be very strong due to strong air convection.

An investigation of single sand particle fracture using X-ray micro-tomography

Particle breakage is of fundamental importance for understanding the mechanical behaviour of sands and is relevant to many geotechnical engineering problems. In order to gain new insights into the mechanism of breakage of individual sand particles under single-particle compression, this study combines mechanical tests with three-dimensional X-ray micro-computed tomography (μCT) performed ‘in situ’, that is, during loading. A novel mini-loading apparatus was developed to perform in-situ compression tests within a laboratory nanofocus X-ray CT. The tests were performed on eight particles, four Leighton Buzzard sand (LBS) particles and four highly decomposed granite (HDG) particles, to study their different fracture mechanisms. A series of image processing and analysing techniques was utilised to obtain both qualitative and quantitative results. The most important factors in determining the fracture patterns of the LBS and HDG particles were found to be particle morphology and initial microstructure, respectively. Versatile fracture patterns deviating from simple vertical splitting were observed, particularly in HDG particles. The change of morphology parameters during loading was found to depend on the fracture mechanisms and material properties, independently of their initial values. The fragments of both the LBS and HDG particles satisfy the fractal distribution, which indicates that the fragmentation is scale invariant. Different energy dissipation mechanisms were found. The energy dissipation by friction gradually prevails against the energy dissipated in generating new surfaces.

Three-dimensional X-ray micro-computed tomography of cracks in a furnace cycled air plasma sprayed thermal barrier coating

Using X-ray micro-computed tomography, a total of 3 × 3 mm2 area of an air plasma sprayed (APS) thermal barrier coating (TBC) was imaged with a resolution of 0.76 μm at 60% cyclic furnace life. Over 10,000 X-ray micrographs were used to extract the 3-D geometry of the cracks in the top coat. The true shape, center and location of the cracks with respect to bond coat peak–valley roughness features were obtained, which revealed the real nature of cracking characteristics of APS TBCs.

Canola and hydrogenated soybean oils accelerate ectopic bone formation induced by implantation of bone morphogenetic protein in mice

Canola oil (Can) and hydrogenated soybean oil (H2-Soy) are commonly used edible oils. However, in contrast to soybean oil (Soy), they shorten the survival of stroke-prone spontaneously hypertensive (SHRSP) rats. It has been proposed that the adverse effects of these oils on the kidney and testis are caused at least in part by dihydro-vitamin K (VK) 1 in H2-Soy and unidentified component(s) in Can. Increased intake of dihydro-VK1 is associated with decreased tissue VK2 levels and bone mineral density in rats and humans, respectively. The aim of the present study was to determine the effects of these oils on bone morphogenetic protein (BMP)-induced ectopic bone formation, which is promoted by VK2 deficiency, in relation to the role of VK in the γ-carboxylation of osteocalcin and matrix Gla protein. A crude extract of BMPs was implanted into a gap in the fascia of the femoral muscle in 5-week-old mice maintained on a Soy, Can, or H2-Soy diet. Newly formed bone volume, assessed by three-dimensional X-ray micro-computed tomography and three-dimensional reconstruction imaging for bone, was 4-fold greater in the Can and H2-Soy groups than in the Soy group. The plasma carboxylated osteocalcin (Gla-OC) and total OC (Gla-OC plus undercarboxylated osteocalcin [Glu-OC]) levels were significantly lower in the Can group than in the Soy group (p < 0.05). However, these levels did not significantly differ between the H2-Soy and Soy groups. The plasma Gla-OC/Glu-OC ratio in the Can and H2-Soy groups was significantly lower (in Can; p = 0.044) or was almost significantly lower (in H2-Soy; p = 0.053) than that in the Soy group. In conclusion, Can and H2-Soy accelerated BMP-induced bone formation in mice to a greater extent than Soy. Further research is required to evaluate whether the difference in accelerated ectopic bone formation is associated with altered levels of VK2 and VK-dependent protein(s) among the three dietary groups.

Three-dimensional X-ray micro-computed tomography analysis of polymerization shrinkage vectors in flowable composite.

The polymerization shrinkage of flowable resin composites was evaluated using air bubbles as traceable markers. Three different surface treatments i.e. an adhesive silane coupling agent, a separating silane coupling agent, and a combination of both, were applied to standard cavities. Before and after polymerization, X-ray micro-computed tomography images were recorded. Their superimposition and comparison allowed position changes of the markers to be visualized as vectors. The movement of the markers in the resin composite was, therefore, quantitatively evaluated from the tomographic images. Adhesion was found to significantly influence shrinkage patterns. The method used here could be employed to visualize shrinkage vectors and shrinkage volume.