Explorative Imaging and Its Implementation at the FleX-ray Laboratory.

In tomographic imaging, the traditional process consists of an expert and an operator collecting data, the expert working on the reconstructed slices and drawing conclusions. The quality of reconstructions depends heavily on the quality of the collected data, except that, in the traditional process of imaging, the expert has very little influence over the acquisition parameters, experimental plan or the collected data. It is often the case that the expert has to draw limited conclusions from the reconstructions, or adapt a research question to data available. This method of imaging is static and sequential, and limits the potential of tomography as a research tool. In this paper, we propose a more dynamic process of imaging where experiments are tailored around a sample or the research question; intermediate reconstructions and analysis are available almost instantaneously, and expert has input at any stage of the process (including during acquisition) to improve acquisition or image reconstruction. Through various applications of 2D, 3D and dynamic 3D imaging at the FleX-ray Laboratory, we present the unexpected journey of exploration a research question undergoes, and the surprising benefits it yields.

Advanced X-ray CT scanning can boost tree ring research for earth system sciences.

BACKGROUND AND AIMS: Tree rings, as archives of the past and biosensors of the present, offer unique opportunities to study influences of the fluctuating environment over decades to centuries. As such, tree-ring-based wood traits are capital input for global vegetation models. To contribute to earth system sciences, however, sufficient spatial coverage is required of detailed individual-based measurements, necessitating large amounts of data. X-ray computed tomography (CT) scanning is one of the few techniques that can deliver such data sets. METHODS: Increment cores of four different temperate tree species were scanned with a state-of-the-art X-ray CT system at resolutions ranging from 60 µm down to 4.5 µm, with an additional scan at a resolution of 0.8 µm of a splinter-sized sample using a second X-ray CT system to highlight the potential of cell-level scanning. Calibration-free densitometry, based on full scanner simulation of a third X-ray CT system, is illustrated on increment cores of a tropical tree species. KEY RESULTS: We show how multiscale scanning offers unprecedented potential for mapping tree rings and wood traits without sample manipulation and with limited operator intervention. Custom-designed sample holders enable simultaneous scanning of multiple increment cores at resolutions sufficient for tree ring analysis and densitometry as well as single core scanning enabling quantitative wood anatomy, thereby approaching the conventional thin section approach. Standardized X-ray CT volumes are, furthermore, ideal input imagery for automated pipelines with neural-based learning for tree ring detection and measurements of wood traits. CONCLUSIONS: Advanced X-ray CT scanning for high-throughput processing of increment cores is within reach, generating pith-to-bark ring width series, density profiles and wood trait data. This would allow contribution to large-scale monitoring and modelling efforts with sufficient global coverage.

Art Forms in Nature: radiolaria from Haeckel and Blaschka to 3D nanotomography, quantitative image analysis, evolution, and contemporary art.

The illustrations of the late nineteenth-/twentieth-century scientist/artist Ernst Haeckel, as depicted in his book Art Forms in Nature (originally in German as Kunstformen der Natur, 1898-1904), have been at the intersection of art, biology, and mathematics for over a century. Haeckel's images of radiolaria (microscopic protozoans described as amoeba in glass houses) have influenced various artists for over a century (glass artists Leopold and Rudolph Blaschka; sculptor Henry Moore; architects Rene Binet, Zaha Hadid, Antoni Gaudi, Chris Bosse and Frank Gehry; and designers-filmmakers Charles and Ray Eames). We focus on this history and extend the artistic, biological, and mathematical contributions of this interdisciplinary legacy by going beyond the 3D visual, topological, and geometric analyses of radiolaria to include the nanoscale with graph theory, spatial statistics, and computational geometry. We analyze multiple visualizations of radiolaria generated through Haeckel's images, light microscopy, scanning electron microscopy, micro- and nanotomography, and three-dimensional computer rendering. Mathematical analyses are conducted using the image analysis package "Ka-me: A Voronoi Image Analyzer." Further analyses utilize three-dimensional printing, laser etched crystalline glass art, and sculpture. Open sharing of three-dimensional nanotomography of radiolaria and other protozoa through MorphoSource enables new possibilities for artists, architects, paleontologists, structural morphologists, taxonomists, museum curators, and mathematical biologists. Distinctively, newer models of radiolaria fit into a larger context of productive interdisciplinary collaboration that continues Haeckel's legacy that lay a foundation for new work in biomimetic design and additive manufacturing where artistic and scientific models mutually and robustly generate wonder, beauty, utility, curiosity, insight, environmentalism, theory, and questions.

Data-fusion of high resolution X-ray CT, SEM and EDS for 3D and pseudo-3D chemical and structural characterization of sandstone.

When dealing with the characterization of the structure and composition of natural stones, problems of representativeness and choice of analysis technique almost always occur. Since feature-sizes are typically spread over the nanometer to centimeter range, there is never one single technique that allows a rapid and complete characterization. Over the last few decades, high resolution X-ray CT (µ-CT) has become an invaluable tool for the 3D characterization of many materials, including natural stones. This technique has many important advantages, but there are also some limitations, including a tradeoff between resolution and sample size and a lack of chemical information. For geologists, this chemical information is of importance for the determination of minerals inside samples. We suggest a workflow for the complete chemical and structural characterization of a representative volume of a heterogeneous geological material. This workflow consists of combining information derived from CT scans at different spatial resolutions with information from scanning electron microscopy and energy-dispersive X-ray spectroscopy.

High spectral and spatial resolution X-ray transmission radiography and tomography using a Color X-ray Camera.

High resolution X-ray radiography and computed tomography are excellent techniques for non-destructive characterization of an object under investigation at a spatial resolution in the micrometer range. However, as the image contrast depends on both chemical composition and material density, no chemical information is obtained from this data. Furthermore, lab-based measurements are affected by the polychromatic X-ray beam, which results in beam hardening effects. New types of X-ray detectors which provide spectral information on the measured X-ray beam can help to overcome these limitations. In this paper, an energy dispersive CCD detector with high spectral resolution is characterized for use in high resolution radiography and tomography, where a focus is put on the experimental conditions and requirements of both measurement techniques.

Heterogeneity of silica and glycan-epitope distribution in epidermal idioblast cell walls in Adiantum raddianum laminae.

Laminae of Adiantum raddianum Presl., a fern belonging to the family Pteridaceae, are characterised by the presence of epidermal fibre-like cells under the vascular bundles. These cells were thought to contain silica bodies, but their thickened walls leave no space for intracellular silica suggesting it may actually be deposited within their walls. Using advanced electron microscopy in conjunction with energy dispersive X-ray microanalysis we showed the presence of silica in the cell walls of the fibre-like idioblasts. However, it was specifically localised to the outer layers of the periclinal wall facing the leaf surface, with the thick secondary wall being devoid of silica. Immunocytochemical experiments were performed to ascertain the respective localisation of silica deposition and glycan polymers. Epitopes characteristic for pectic homogalacturonan and the hemicelluloses xyloglucan and mannan were detected in most epidermal walls, including the silica-rich cell wall layers. The monoclonal antibody, LM6, raised against pectic arabinan, labelled the silica-rich primary wall of the epidermal fibre-like cells and the guard cell walls, which were also shown to contain silica. We hypothesise that the silicified outer wall layers of the epidermal fibre-like cells support the lamina during cell expansion prior to secondary wall formation. This implies that silicification does not impede cell elongation. Although our results suggest that pectic arabinan may be implicated in silica deposition, further detailed analyses are needed to confirm this. The combinatorial approach presented here, which allows correlative screening and in situ localisation of silicon and cell wall polysaccharide distribution, shows great potential for future studies.

Effect of the degree of LAD stenosis on "competitive flow" and flow field characteristics in LIMA-to-LAD bypass surgery.

The long-term patency of the left internal mammary artery (LIMA) in left anterior descending (LAD) coronary stenosis bypass surgery is believed to be related to the degree of competitive flow between the LAD and LIMA. To investigate the effect of the LAD stenosis severity on this phenomenon and on haemodynamics in the LIMA and anastomosis region, a numerical LIMA-LAD model was developed based on 3D geometric (obtained from a cast) and hemodynamic data from an experimental pig study. Proximal LAD pressure was used as upstream boundary condition. The model counted 13 outlets (12 septal arteries and the distal LAD) where flow velocities were imposed in systole, while myocardial conductance was imposed in diastole via an implicit scheme. LAD stenoses of 100 (total occlusion), 90, 75 and 0 % area reduction were constructed. Low degree of LAD stenosis was associated with highly competitive flow and low wall shear stress (WSS) in the LIMA, an unfavourable hemodynamic regime which might contribute to WSS-related remodelling of the LIMA and suboptimal long-term LIMA bypass performance.

Modeling the impact of partial hepatectomy on the hepatic hemodynamics using a rat model.

Due to the growing shortage of donor livers, more patients are waiting for transplantation. Living donor liver transplantation may help expanding the donor pool, but is often confronted with the small-for-size syndrome. Since the hemodynamic effects of partial hepatectomy are not fully understood, we developed an electrical rat liver model to compare normal with resected liver hemodynamics. Detailed geometrical data and 3-D reconstructions of the liver vasculature of two rats were gathered by combining vascular corrosion casting, micro-CT scanning, and image processing. Data extrapolations allowed obtaining a total liver pressure- and flow-driven electrical analog. Subsequently, virtual resections led to 70%, 80%, or 90% partial hepatectomy models. Results demonstrated hyperperfusion effects such as portal hypertension and elevated lobe-specific portal venous flows (11, 12, and 24 mmHg, and 1.0-3.0, 1.8-3.5, and 7.4 ml/min for 70%, 80%, and 90% hepatectomy, respectively). Comparison of two 90% resection techniques demonstrated different total arterial flows (0.28 ml/min versus 0.61 ml/min), portal (24 mmHg versus 21 mmHg), and sinusoidal pressures (14 mmHg versus 9.5-12 mmHg), probably leading to better survival for lower portal and sinusoidal pressures. Toward the future, the models may be extrapolated to human livers and help us to optimize hepatectomy planning.

Perfusion characteristics of the human hepatic microcirculation based on three-dimensional reconstructions and computational fluid dynamic analysis.

The perfusion of the liver microcirculation is often analyzed in terms of idealized functional units (hexagonal liver lobules) based on a porous medium approach. More elaborate research is essential to assess the validity of this approach and to provide a more adequate and quantitative characterization of the liver microcirculation. To this end, we modeled the perfusion of the liver microcirculation using an image-based three-dimensional (3D) reconstruction of human liver sinusoids and computational fluid dynamics techniques. After vascular corrosion casting, a microvascular sample (±0.134 mm(3)) representing three liver lobules, was dissected from a human liver vascular replica and scanned using a high resolution (2.6 µm) micro-CT scanner. Following image processing, a cube (0.15 × 0.15 × 0.15 mm(3)) representing a sample of intertwined and interconnected sinusoids, was isolated from the 3D reconstructed dataset to define the fluid domain. Three models were studied to simulate flow along three orthogonal directions (i.e., parallel to the central vein and in the radial and circumferential directions of the lobule). Inflow and outflow guidances were added to facilitate solution convergence, and good quality volume meshes were obtained using approximately 9 × 10(6) tetrahedral cells. Subsequently, three computational fluid dynamics models were generated and solved assuming Newtonian liquid properties (viscosity 3.5 mPa s). Post-processing allowed to visualize and quantify the microvascular flow characteristics, to calculate the permeability tensor and corresponding principal permeability axes, as well as the 3D porosity. The computational fluid dynamics simulations provided data on pressure differences, preferential flow pathways and wall shear stresses. Notably, the pressure difference resulting from the flow simulation parallel to the central vein (0-100 Pa) was clearly smaller than the difference from the radial (0-170 Pa) and circumferential (0-180 Pa) flow directions. This resulted in a higher permeability along the central vein direction (k(d,33) = 3.64 × 10(-14) m(2)) in comparison with the radial (k(d,11) = 1.56 × 10(-14) m(2)) and circumferential (k(d,22) = 1.75 × 10(-14) m(2)) permeabilities which were approximately equal. The mean 3D porosity was 14.3. Our data indicate that the human hepatic microcirculation is characterized by a higher permeability along the central vein direction, and an about two times lower permeability along the radial and circumferential directions of a lobule. Since the permeability coefficients depend on the flow direction, (porous medium) liver microcirculation models should take into account sinusoidal anisotropy.

Influence of pore structure on the effectiveness of a biogenic carbonate surface treatment for limestone conservation.

A ureolytic biodeposition treatment was applied to five types of limestone in order to investigate the effect of pore structure on the protective performance of a biogenic carbonate surface treatment. Protective performance was assessed by means of transport and degradation processes, and the penetration depth of the treatment was visualized by microtomography. Pore size governs bacterial adsorption and hence the location and amount of carbonate precipitated. This study indicated that in macroporous stone, biogenic carbonate formation occurred to a larger extent and at greater depths than in microporous stone. As a consequence, the biodeposition treatment exhibited the greatest protective performance on macroporous stone. While precipitation was limited to the outer surface of microporous stone, biogenic carbonate formation occurred at depths of greater than 2 mm for Savonnières and Euville. For Savonnières, the presence of biogenic carbonate resulted in a 20-fold decreased rate of water absorption, which resulted in increased resistance to sodium sulfate attack and to freezing and thawing. While untreated samples were completely degraded after 15 cycles of salt attack, no damage was observed in biodeposition-treated Savonnières. From this study, it is clear that biodeposition is very effective and more feasible for macroporous stones than for microporous stones.

Impact of carotid stent cell design on vessel scaffolding: a case study comparing experimental investigation and numerical simulations.

PURPOSE: To quantitatively evaluate the impact of carotid stent cell design on vessel scaffolding by using patient-specific finite element analysis of carotid artery stenting (CAS). METHODS: The study was organized in 2 parts: (1) validation of a patient-specific finite element analysis of CAS and (2) evaluation of vessel scaffolding. Micro-computed tomography (CT) images of an open-cell stent deployed in a patient-specific silicone mock artery were compared with the corresponding finite element analysis results. This simulation was repeated for the closed-cell counterpart. In the second part, the stent strut distribution, as reflected by the inter-strut angles, was evaluated for both cell types in different vessel cross sections as a measure of scaffolding. RESULTS: The results of the patient-specific finite element analysis of CAS matched well with experimental stent deployment both qualitatively and quantitatively, demonstrating the reliability of the numerical approach. The measured inter-strut angles suggested that the closed-cell design provided superior vessel scaffolding compared to the open-cell counterpart. However, the full strut interconnection of the closed-cell design reduced the stent's ability to accommodate to the irregular eccentric profile of the vessel cross section, leading to a gap between the stent surface and the vessel wall. CONCLUSION: Even though this study was limited to a single stent design and one vascular anatomy, the study confirmed the capability of dedicated computer simulations to predict differences in scaffolding by open- and closed-cell carotid artery stents. These simulations have the potential to be used in the design of novel carotid stents or for procedure planning.

From vascular corrosion cast to electrical analog model for the study of human liver hemodynamics and perfusion.

Hypothermic machine perfusion (HMP) is experiencing a revival in organ preservation due to the limitations of static cold storage and the need for better preservation of expanded criteria donor organs. For livers, perfusion protocols are still poorly defined, and damage of sinusoidal endothelial cells and heterogeneous perfusion are concerns. In this study, an electrical model of the human liver blood circulation is developed to enlighten internal pressure and flow distributions during HMP. Detailed vascular data on two human livers, obtained by combining vascular corrosion casting, micro-CT-imaging and image processing, were used to set up the electrical model. Anatomical data could be measured up to 5--6 vessel generations in each tree and showed exponential trend lines, used to predict data for higher generations. Simulated flow and pressure were in accordance with literature data. The model was able to simulate effects of pressure-driven HMP on liver hemodynamics and reproduced observations such as flow competition between the hepatic artery and portal vein. Our simulations further indicate that, from a pure biomechanical (shear stress) standpoint, HMP with low pressures should not result in organ damage, and that fluid viscosity has no effect on the shear stress experienced by the liver microcirculation in pressure-driven HMP.

High-resolution imaging of kidney vascular corrosion casts with Nano-CT.

A vascular corrosion cast of an entire mouse kidney was scanned with a modular multiresolution X-ray nanotomography system. Using an isotropic voxel pitch of 0.5 µm, capillary systems such as the vasa recta, peritubular capillaries and glomeruli were clearly resolved. This represents a considerable improvement over corrosion casts scanned with microcomputed tomography systems. The resolving power of this system was clearly demonstrated by the unique observation of a dense, subcapsular mat of capillaries enveloping the entire outer surface of the cortical region. Resolution of glomerular capillaries was comparable to similar models derived from laser scanning confocal microscopy. The high-resolution, large field of view and the three-dimensional nature of the resulting data opens new possibilities for the use of corrosion casting in research.

High-resolution proxies for wood density variations in Terminalia superba.

BACKGROUND AND AIMS: Density is a crucial variable in forest and wood science and is evaluated by a multitude of methods. Direct gravimetric methods are mostly destructive and time-consuming. Therefore, faster and semi- to non-destructive indirect methods have been developed. METHODS: Profiles of wood density variations with a resolution of approx. 50 µm were derived from one-dimensional resistance drillings, two-dimensional neutron scans, and three-dimensional neutron and X-ray scans. All methods were applied on Terminalia superba Engl. & Diels, an African pioneer species which sometimes exhibits a brown heart (limba noir). KEY RESULTS: The use of X-ray tomography combined with a reference material permitted direct estimates of wood density. These X-ray-derived densities overestimated gravimetrically determined densities non-significantly and showed high correlation (linear regression, R(2) = 0·995). When comparing X-ray densities with the attenuation coefficients of neutron scans and the amplitude of drilling resistance, a significant linear relation was found with the neutron attenuation coefficient (R(2) = 0·986) yet a weak relation with drilling resistance (R(2) = 0·243). When density patterns are compared, all three methods are capable of revealing the same trends. Differences are mainly due to the orientation of tree rings and the different characteristics of the indirect methods. CONCLUSIONS: High-resolution X-ray computed tomography is a promising technique for research on wood cores and will be explored further on other temperate and tropical species. Further study on limba noir is necessary to reveal the causes of density variations and to determine how resistance drillings can be further refined.

Topography of the rabbit paranasal sinuses as a prerequisite to model human sinusitis.

BACKGROUND: Anatomical studies of the rabbit paranasal cavities are impelled by the increasing interest in the rabbit model to investigate human sinusitis. Although several such studies have already been performed, the topography of the rabbit dorsal conchal and maxillary sinuses is described ambiguously and the existence of the ethmoidal, frontal and sphenoidal sinuses is controversial. METHODOLOGY: The paranasal cavities were investigated using corrosion casting, gross and histological cross-sectioning, and micro-CT scanning of rabbit noses followed by computerized three-dimensional reconstruction. RESULTS: Micro-CT scanning was most useful to illustrate the dorsal conchal sinus, the large maxillary sinus consisting of a dorsal and a ventral recess, and the sphenoidal sinus. All these sinuses are paired and symmetrical. A large connection is present between the dorsal conchal sinus and the maxillary sinus resulting in one large conchomaxillary cavity. The sphenoidal sinus lies most caudal and is surrounded by the presphenoid bone. The openings from the nasal cavity into the conchomaxillary cavity and the sphenoidal sinus are very small. CONCLUSIONS: The absence of frontal and ethmoidal sinuses in any of the rabbits examined is a major difference between the rabbit and human sinuses. The rabbit maxillary sinus seems most appropriate for experimental work.

Vascular corrosion casting: analyzing wall shear stress in the portal vein and vascular abnormalities in portal hypertensive and cirrhotic rodents.

Vascular corrosion casting is an established method of anatomical preparation that has recently been revived and has proven to be an excellent tool for detailed three-dimensional (3D) morphological examination of normal and pathological microcirculation. In addition, the geometry provided by vascular casts can be further used to calculate wall shear stress (WSS) in a vascular bed using computational techniques. In the first part of this study, the microvascular morphological changes associated with portal hypertension (PHT) and cirrhosis in vascular casts are described. The second part of this study consists of a quantitative analysis of the WSS in the portal vein in casts of different animal models of PHT and cirrhosis using computational fluid dynamics (CFD). Microvascular changes in the splanchnic, hepatic and pulmonary territory of portal hypertensive and cirrhotic mice are described in detail with stereomicroscopic examination and scanning electron microscopy. To our knowledge, our results are the first to report the vascular changes in the common bile duct ligation cirrhotic model. Calculating WSS using CFD methods is a feasible technique in PHT and cirrhosis, enabling the differentiation between different animal models. First, a dimensional analysis was performed, followed by a CFD calculation describing the spatial and temporal WSS distributions in the portal vein. WSS was significantly different between sham/cirrhotic/pure PHT animals with the highest values in the latter. Up till now, no techniques have been developed to quantify WSS in the portal vein in laboratory animals. This study showed for the first time that vascular casting has an important role not only in the morphological evaluation of animal models of PHT and cirrhosis, but also in defining the biological response of the portal vein wall to hemodynamic changes. CFD in 3D geometries can be used to describe the spatial and temporal variations in WSS in the portal vein and to better understand the forces affecting mechanotransduction in the endothelium.

Expression and localization of angiogenic growth factors in developing porcine mesonephric glomeruli.

The development and growth of renal glomeruli is regulated by specific angiogenic growth factors, including vascular endothelial growth factor (VEGF) and the angiopoietins (ANGPT1 and ANGPT2). The expression of these factors has already been studied during metanephric glomerulogenesis, but it remains to be elucidated during the development of the embryonic mesonephros, which can function as an interesting model for glomerular development and senescence. In this study, the presence of the angiogenic growth factors was studied in developing porcine mesonephroi, using IHC and real-time RT-qPCR on laser capture microdissected glomeruli. In addition, mesonephric glomerular growth was measured by using stereological methods. ANGPT2 remained upregulated during maturation of glomeruli, which may be explained by the continuous growth of the glomeruli, as observed by stereological examination. The mRNA for VEGFA was expressed in early developing and in maturing glomeruli. The VEGF receptor VEGFR1 was stably expressed during the whole lifespan of mesonephric glomeruli, whereas VEGFR2 mRNA was only upregulated in early glomerulogenesis, suggesting that VEGFR2 is important for the vascular growth but that VEGFR1 is important for the maintenance of endothelial fenestrations.

Impact of competitive flow on wall shear stress in coronary surgery: computational fluid dynamics of a LIMA-LAD model.

AIMS: Competitive flow from native coronary vessels is considered a major factor in the failure of coronary bypass grafts. However, the pathophysiological effects are not fully understood. Low and oscillatory wall shear stress (WSS) is known to induce endothelial dysfunction and vascular disease, like atherosclerosis and intimal hyperplasia. The aim was to investigate the impact of competitive flow on WSS in mammary artery bypass grafts. METHODS AND RESULTS: Using computational fluid dynamics, WSS was calculated in a left internal mammary artery (LIMA) graft to the left anterior descending artery in a three-dimensional in vivo porcine coronary artery bypass graft model. The following conditions were investigated: high competitive flow (non-significant coronary lesion), partial competitive flow (significant coronary lesion), and no competitive flow (totally occluded coronary vessel). Time-averaged WSS of LIMA at high, partial, and no competitive flow were 0.3-0.6, 0.6-3.0, and 0.9-3.0 Pa, respectively. Further, oscillatory WSS quantified as the oscillatory shear index (OSI) ranged from (maximum OSI = 0.5 equals zero net WSS) 0.15 to 0.35, <0.05, and <0.05, respectively. Thus, high competitive flow resulted in substantial oscillatory and low WSS. Moderate competitive flow resulted in WSS and OSI similar to the no competitive flow condition. CONCLUSION: Graft flow is highly dependent on the degree of competitive flow. High competitive flow was found to produce unfavourable WSS consistent with endothelial dysfunction and subsequent graft narrowing and failure. Partial competitive flow, however, may be better tolerated as it was found to be similar to the ideal condition of no competitive flow.

Plant structure visualization by high-resolution X-ray computed tomography.

New developments in high-resolution X-ray computed tomography (HRXCT) are promising for the broader application of this non-destructive imaging method in plant sciences. Here, we demonstrate how detailed three-dimensional morphological traits can be extracted rapidly from in vivoArabidopsis thaliana seedlings without sample manipulation. Furthermore, ex vivo scanning at sub-micron resolution allows the quantification and visualization of the cellular organization of plant tissue samples, making HRXCT a desired tool in developmental plant biology.