Three-dimensional analysis of plant structure using high-resolution X-ray computed tomography

High-resolution X-ray computed tomography (HRCT) is a non-invasive approach to 3D visualization and quantification of biological structure. The data, based on differential X-ray attenuation, are analogous to those otherwise obtainable only by serial sectioning. Requiring no fixing, sectioning or staining, HRCT produces a 3D digital map of the specimen that allows measurements and visualizations, including arbitrarily oriented sections. In spite of its application throughout the natural sciences, HRCT has yet to be applied in extant plant structural research.     

Three-dimensional visualization and morphometry of small airways from microfocal X-ray computed tomography

Physiological morphometry is a critical factor in the flow dynamics in small airways. In this study, we visualized and analyzed the three-dimensional structure of the small airways without dehydration and fixation. We developed a two-step method to visualize small airways in detail by staining the lung tissue with a radiopaque solution and then visualizing the tissue with a cone-beam microfocal X-ray computed tomographic (CT) system. To verify the applicability of this staining and CT imaging (SCT) method, we used the method to visualize small airways in excised rat lungs. By using the SCT method to obtain continuous CT images, three-dimensional branching and merging bronchi ranging from 500 to 150 microm (the airway generation=8-16) were successfully reconstructed. The morphometry of the small airways (diameter, length, branching angle and gravity angle between the gravity direction and airway vector) was analyzed using the three-dimensional thinning algorithm. The diameter and length exponentially decreased with the airway generation. The asymmetry of the bifurcation decreased with generation and one branching angle decided the other pair branching angle. The SCT method is the first reported method that yields faithful high-resolution images of soft tissue geometry without fixation and the three-dimensional morphometry of small airways is useful for studying the biomechanical dynamics in small airways.     

The naso-frontal joint in snakes as revealed by high-resolution X-ray computed tomography of intact and complete skulls

The naso-frontal joint of snakes is described on the basis of high-resolution X-ray computed tomography scans of single individuals of spirit-preserved snake specimens. The suspension of the snout unit from the braincase at the naso-frontal joint shows some broad evolutionary trends among snakes with potential phylogenetic implications, such as sutured or fused medial frontal flanges formed by the medial frontal pillars and the frontal subolfactory processes (in alethinophidians), the restriction of the usually extended dorsoventral contact of the medial nasal flange with the medial frontal flanges to a dorsal or ventral contact (in macrostomatans), and the transfer of the main element of snout suspension from the nasal to the septomaxilla (in colubroids). Some phylogenetic implications of the morphological characters identified in this study are outlined and discussed.     

Assessing the accuracy of high-resolution X-ray computed tomography of primate trabecular bone by comparisons with histological sections

Different lines of evidence suggest that trabecular bone architecture contains a functional signal related to an organism's locomotor behavior. An understanding of the interspecific and intraspecific variation in extant nonhuman primate trabecular structure is needed to evaluate its usefulness as a tool to reconstruct the locomotor habits of extinct primates. High-resolution X-ray computed tomography (HRXCT) is a new imaging approach with a resolution in the tens of microns that allows nondestructive access to the internal structure of bony elements. Previous studies indicate that such resolution is necessary to accurately quantify structural parameters of trabecular bone. The primary goal of this study was to test the accuracy of HRXCT by comparing stereological measurements from HRXCT images and histological thin sections of cancellous bone taken from the proximal femur and humerus of baboons. To this end, 11 bone samples were scanned on an HRXCT scanner and then thin-sectioned to reveal the scanned plane. HRXCT images were thresholded using a modified half-maximum height protocol. The stereological measurements included bone volume fraction (BV/TV), trabecular number (Tb.N), bone surface to volume ratio (BS/BV), trabecular thickness (Tb.Th), and trabecular spacing (Tb.Sp). The measurement errors on the HRXCT images were 10.90% for BV/TV, 6.06% for Tb.N, 14.19% for BS/BV, 14.33% for Tb.Th, and 7.09% for Tb.Sp, but none of these measurements were significantly different from the histological standards (alpha = 0.05). A second goal of this study was to examine the influence of thresholding, a necessary step in any morphometric study using computed tomography, on the accuracy of the quantitative morphometry. Threshold values derived from a modified half-maximum height protocol showed that parameters derived from the region of interest (area in which stereological measurements were later taken) produced better reconstructions of the actual bone structure than threshold values derived from more inclusive areas of bone. We conclude that HRXCT can accurately reconstruct the complex architecture of trabecular bone, and that thresholding is a nontrivial step in trabecular bone studies, with even slight changes in the protocol greatly affecting the morphometric data. HRXCT represents a valuable analytical tool that should be of interest to a great many researchers in physical anthropology because it allows nondestructive access to internal morphology, thereby preserving valuable and limited skeletal collections.     

A review of high-resolution X-ray computed tomography and other imaging modalities for small animal research

Dedicated high-resolution small animal systems have recently emerged as important new tools for laboratory animal research. These imaging systems permit researchers to noninvasively screen animal models for mutations or pathologies and to monitor disease progression and response to therapy. The authors survey various small animal imaging modalities, including MRI, PET, SPECT, and microCT, and discuss several representative microCT mouse imaging studies.     

Helical differential X-ray phase-contrast computed tomography

We report on the first experimental results of helical differential phase-contrast computed tomography (helical DPC-CT) with a laboratory X-ray tube source and a Talbot–Lau grating interferometer. The results experimentally verify the feasibility of helical data acquisition and reconstruction in phase-contrast imaging, in analogy to its use in clinical CT systems. This allows fast and continuous volumetric scans for long objects with lengths exceeding the dimension of the detector. Since helical CT revolutionized the field of medical CT several years ago, we anticipate that this method will bring the same significant impact on the future medical and industrial applications of X-ray DPC-CT.     

Three-dimensional cranial surface reconstructions using high-resolution computed tomography

Until recently, there has been no satisfactory way for anthropologists to visualize intracranial morphology in more than two dimensions without actually "invading" the skull in some manner. Images provided by conventional x-ray and computed tomography (CT) scans are often abstract, flat, two-dimensional representations that fail to reveal three-dimensional relationships. We describe new computer-imaging techniques that reconstruct three-dimensional images from sequential series of narrowly collimated (1-2 mm), high-resolution CT scans of the skull. These computed images represent three-dimensional surface data and can be viewed from any direction. Depth information is encoded in gray scale. In addition, selected portions of the anatomy can be "removed", i.e., made transparent, to allow visualization of previously hidden intracranial morphology. Since the geometric data obtained with the CT scanner are precise, parameters such as linear distances, angles, areas, and volumes can be accurately (and instantaneously) generated. The power and versatility of these computer-imaging techniques are demonstrated by examining living subjects with major craniofacial dysmorphology (Treacher-Collins syndrome and unilateral coronal synostosis); an anthropoid osteological specimen (Gorilla); and a fossil mammal skull.     

Microstructural insight into pedestrian pelvic fracture as assessed by high-resolution computed tomography

Pelvic and femoral neck bone surface strains were recorded in five full-body human cadaver vehicle-pedestrian impacts. Impacts were performed at 40 km/h using automotive front ends constructed to represent those used in previously reported finite element simulations. While experimental kinematics and bone strains closely matched model predictions, observed pelvic fractures did not consistently agree with the model, and could not be solely explained by vehicle geometry. In an attempt to reconcile injury outcome with factors apart from vehicle design, a proxy measure of subject skeletal health was assessed by high-resolution quantitative computed tomography (HRqCT) of the femoral neck. The incidence of hip/pelvis fracture was found to be consistent with low volumetric bone mineral density and low trabecular bone density. This finding lends quantitative support to the notion that healthy trabecular architecture is crucial in withstanding non-physiological impact loads. Furthermore, it is recommended that injury criteria used to assess vehicle safety with regard to pedestrians consider the increased susceptibility of elderly victims to pelvic fracture.     

Airway narrowing in excised canine lungs measured by high-resolution computed tomography.

The exact site of airway narrowing in asthma and chronic obstructive pulmonary disease is unknown. High-resolution computed tomography (HRCT) is a sensitive noninvasive imaging technique that can be used to measure airway dimensions. After determining the optimal computed tomographic parameters using a phantom, we measured lobe volume and airway dimensions of isolated canine lung lobes at a transpulmonary pressure of 25 cmH2O. These measurements were repeated after deflation and administration of aerosolized saline and carbachol (256 mg/ml). Lobe volume decreased with all treatments. The maximal lobar volume change was 26% at 6 cmH2O after carbachol. Average airway lumen area decreased with all treatments. After carbachol, at transpulmonary pressures of 25, 15, 10, 8, and 6 cmH2O, lumen area decreased by 7.3 +/- 4.1, 62.0 +/- 4.9, 77.5 +/- 3.0, 31.9 +/- 9.0, and 95.2 +/- 1.0% (SE), respectively. When the airways were divided into four categories on the basis of initial lumen diameter (less than 2, 2-4, 4-6, and greater than 6 mm), the greatest decreases in luminal area after carbachol were seen in intermediate-sized airways (2-4 mm, 56 +/- 4%; 4-6 mm, 59 +/- 3%). HRCT can be used to make accurate measurements of airway dimensions and airway narrowing in excised lungs. HRCT may allow measurement of airway wall thickness and determination of the site of airway narrowing in asthma.     

The skull of the rare Malaysian snake Anomochilus leonardi Smith, based on high-resolution X-ray computed tomography

The skull of the rare Malaysian snake Anomochilus leonardi is described in detail on the basis of a high-resolution X-ray computed tomographic scan of a mature specimen. Its skull anatomy is compared with that of Anomochilus weberi , as well as with that of scolecophidians and basal alethinophidians such as Anilius , Cylindrophis , uropeltines and selected Booidea. Anomochilus leonardi is found to be more paedomorphic than Anomochilus weberi . The genus Anomochilus most closely resembles uropeltines in skull anatomy. Both Anomochilus and uropeltines develop a 'central rod design' of skull morphology, which requires the presence of medial frontal pillars, in adaptation to burrowing habits. These pillars are an alethinophidian characteristic, absent in the skull of scolecophidians, which develop an 'outer shell design' in adaptation to burrowing. These results are discussed in the light of the hypothesis that scolecophidians and basal (i.e. non-macrostomatan) alethinophidians are 'regressed macrostomatans'.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 149 , 671–685.     

Crystal structure determination of thymoquinone by high-resolution X-ray powder diffraction

The crystal structure of 2-isopropyl-5-methyl-1,4-benzoquinone (thymoquinone) and its thermal behavior--as necessary physical and chemical properties--were determined in order to enhance the current understanding of thymoquinone chemical action by using high resolution x-ray powder diffraction, Fourier transform infrared spectroscopy (FTIR), and 3 thermo-analytical techniques thermogravimetric analysis (TGA), differential thermal analysis (DTA), and differential scanning calorimetry (DSC). The findings obtained with high-resolution x-ray powder diffraction and molecular location methods based on a simulated annealing algorithm after Rietveld refinement showed that the triclinic unit cell was a = 6.73728(8) A, b = 6.91560(8) A, c = 10.4988(2) A, alpha = 88.864(2) degrees, beta = 82.449(1) degrees, gamma = 77.0299(9) degrees; cell volume = 472.52(1) A3, Z = 2, and space group P1. In addition, FTIR spectrum revealed absorption bands corresponding to the carbonyl and C-H stretching of aliphatic and vinylic groups characteristically observed in such p-benzoquinones. Also, a chemical decomposition process starting at 65 degrees C and ending at 213 degrees C was noted when TGA was used. DSC allowed for the determination of onset at 43.55 degrees C and a melting enthalpy value of DeltaH(m) = 110.6 J/g. The low value obtained for the fusion point displayed a van der Waals pattern for molecular binding, and the thermograms performed evidence that thymoquinone can only be found in crystalline triclinic form, as determined by DRX methods.     

Ovarian tissue cryopreservation by stepped vitrification and monitored by X-ray computed tomography

Ovarian tissue cryopreservation is, in most cases, the only fertility preservation option available for female patients soon to undergo gonadotoxic treatment. To date, cryopreservation of ovarian tissue has been carried out by both traditional slow freezing method and vitrification, but even with the best techniques, there is still a considerable loss of follicle viability. In this report, we investigated a stepped cryopreservation procedure which combines features of slow cooling and vitrification (hereafter called stepped vitrification). Bovine ovarian tissue was used as a tissue model. Stepwise increments of the Me₂SO concentration coupled with stepwise drops-in temperature in a device specifically designed for this purpose and X-ray computed tomography were combined to investigate loading times at each step, by monitoring the attenuation of the radiation proportional to Me₂SO permeation. Viability analysis was performed in warmed tissues by immunohistochemistry. Although further viability tests should be conducted after transplantation, preliminary results are very promising. Four protocols were explored. Two of them showed a poor permeation of the vitrification solution (P1 and P2). The other two (P3 and P4), with higher permeation, were studied in deeper detail. Out of these two protocols, P4, with a longer permeation time at −40 °C, showed the same histological integrity after warming as fresh controls.     

A minute fossil phoretic mite recovered by phase-contrast X-ray computed tomography

High-resolution phase-contrast X-ray computed tomography (CT) reveals the phoretic deutonymph of a fossil astigmatid mite (Acariformes: Astigmata) attached to a spider's carapace (Araneae: Dysderidae) in Eocene (44-49 Myr ago) Baltic amber. Details of appendages and a sucker plate were resolved, and the resulting three-dimensional model demonstrates the potential of tomography to recover morphological characters of systematic significance from even the tiniest amber inclusions without the need for a synchrotron. Astigmatids have an extremely sparse palaeontological record. We confirm one of the few convincing fossils, potentially the oldest record of Histiostomatidae. At 176 μm long, we believe this to be the smallest arthropod in amber to be CT-scanned as a complete body fossil, extending the boundaries for what can be recovered using this technique. We also demonstrate a minimum age for the evolution of phoretic behaviour among their deutonymphs, an ecological trait used by extant species to disperse into favourable environments. The occurrence of the fossil on a spider is noteworthy, as modern histiostomatids tend to favour other arthropods as carriers.     

The skull of the Round Island boa, Casarea dussumieri Schlegel, based on high-resolution X-ray computed tomography

The skull of the rare bolyeriid snake Casarea dussumieri is described in detail based on high-resolution X-ray CT data. Bolyeriids are unique in their possession of a separate suborbital ossification and a maxilla subdivided into two movably jointed parts, which may be the result of paedomorphic truncation of the development of the maxilla from multiple ossification centers. Comparison of the skull of C. dussumieri to that of larger booids suggests additional paedomorphic features including reduction of the dorsal lamina of the nasal and prefrontal and reduction of their contacts with the frontal, limited posterior extent of the posterior free process of the supratemporal, and reduction of the coronoid and splenial. The observations herein do not resolve competing phylogenetic hypotheses based on morphology, which either place tropidophiids as the sister-taxon of bolyeriids, Acrochordus and colubroids, or place bolyeriids as the sister-taxon of the other three. But these observations provide no support whatsoever for the heterodox placement of tropidophiids at the base of alethinophidian snakes, as obtained recently with molecular data.     

Mechanical strength of tibial trabecular bone evaluated by X-ray computed tomography

The prospects for the use of quantitative computed tomography (QCT) for evaluation of mechanical properties of tibial trabecular bone were investigated. Computed tomography (CT) data from the proximal tibial epi- and metaphysis of six human cadaver knees were correlated with mechanical data obtained from compression tests and penetration strength measurements. In addition CT and intraoperative penetration data were compared in 20 patients. If spatial agreement between CT and mechanical measurement sites is optimized, close correlations are found between the relative linear attenuation coefficient determined by CT and the ultimate strength (r = 0.84), the yield strength (r = 0.85), the elastic modulus (r = 0.78), the ultimate energy absorption (r = 0.83), the yield energy absorption (r = 0.81), and the penetration strength (r = 0.82). It is concluded that these correlations are sufficient to make QCT a valuable tool for non-invasive evaluation of the spatial distribution of bone properties in several clinical applications.     

Procedure for visualization of carbonic materials in maxillofacial surgery by spiral computed tomography

The paper considers whether carbonic materials whose contrasting is achieved when they contain 8-12% of metallic boron power may be applied to restore bone defects of the facial skull. Implants of this composition were employed to operate on 4 patients with different defects of the facial skull. A three-projection of SCT image obtained in the "SOFT" mode was used as a way of registration. The results of the studies have indicated that the materials under study have X-ray contrast, a complete biological compatibility, and non-toxicity when they are used in clinical practice.     

Automated analysis of three-dimensional xylem networks using high-resolution computed tomography

Connections between xylem vessels represent important links in the vascular network, but the complexity of three-dimensional (3D) organization has been difficult to access. This study describes the development of a custom software package called TANAX (Tomography-derived Automated Network Analysis of Xylem) that automatically extracts vessel dimensions and the distribution of intervessel connections from high-resolution computed tomography scans of grapevine (Vitis vinifera) stems, although the method could be applied to other species. Manual and automated analyses of vessel networks yielded similar results, with the automated method generating orders of magnitude more data in a fraction of the time. In 4.5-mm-long internode sections, all vessels and all intervessel connections among 115 vessels were located, and the connections were analyzed for their radial distribution, orientation, and predicted shared wall area. Intervessel connections were more frequent in lateral than in dorsal/ventral zones. The TANAX-reconstructed network, in combination with commercial software, was used to visualize vessel networks in 3D. The 3D volume renderings of vessel networks were freely rotated for observation from any angle, and the 4.5?μm virtual serial sections were capable of being viewed in any plane, revealing aspects of vessel organization not possible with traditional serial sections.     

Atherosclerotic plaque imaging using phase-contrast X-ray computed tomography

Reliable, noninvasive imaging modalities to characterize plaque components are clinically desirable for detecting unstable coronary plaques, which cause acute coronary syndrome. Although recent clinical developments in computed tomography (CT) have enabled the visualization of luminal narrowing and calcified plaques in coronary arteries, the identification of noncalcified plaque components remains difficult. Phase-contrast X-ray CT imaging has great potentials to reveal the structures inside biological soft tissues, because its sensitivity to light elements is almost 1,000 times greater than that of absorption-contrast X-ray imaging. Moreover, a specific mass density of tissue can be estimated using phase-contrast X-ray CT. Ex vivo phase-contrast X-ray CT was performed using a synchrotron radiation source (SPring-8, Japan) to investigate atherosclerotic plaque components of apolipoprotein E-deficient mice. Samples were also histologically analyzed. Phase-contrast X-ray CT at a spatial resolution of 10-20 mum revealed atherosclerotic plaque components easily, and thin fibrous caps were detected. The specific mass densities of these plaque components were quantitatively estimated. The mass density of lipid area was significantly lower (1.011 +/- 0.001766 g/ml) than that of smooth muscle area or collagen area (1.057 +/- 0.001407 and 1.080 +/- 0.001794 g/ml, respectively). Moreover, the three-dimensional assessment of plaques could provide their anatomical information. Phase-contrast X-ray CT can estimate the tissue mass density of atherosclerotic plaques and detect lipid-rich areas. It can be a promising noninvasive technique for the investigation of plaque components and detection of unstable coronary plaques.