Analytical registration of vertical image drifts in parallel beam tomographic data.

Reconstructing tomographic images of high resolution, as in x-ray microscopy or transmission electron microscopy, is often limited by the stability of the stages or sample drifts, which requires an image alignment prior to reconstruction. Feature-based image registration is routinely used to align images, but this technique relies on strong features in the sample or the application of gold tracer particles, for example. In this Letter, we present an analytic approach for achieving the vertical registration based on the inherent properties of the data acquired for tomographic reconstruction. It is computationally cheap to implement and can be easily integrated into existing reconstruction pipelines.

Determination of the packing fraction in photonic glass using synchrotron radiation nanotomography.

Photonic glass is a material class that can be used as photonic broadband reflectors, for example in the infrared regime as thermal barrier coating films. Photonic properties such as the reflectivity depend on the ordering and material packing fraction over the complete film thickness of up to 100 µm. Nanotomography allows acquiring these key parameters throughout the sample volume at the required resolution in a non-destructive way. By performing a nanotomography measurement at the PETRA III beamline P05 on a photonic glass film, the packing fraction throughout the complete sample thickness was analyzed. The results showed a packing fraction significantly smaller than the expected random close packing giving important information for improving the fabrication and processing methods of photonic glass material in the future.

Absorption and Phase Contrast X-Ray Imaging in Paleontology Using Laboratory and Synchrotron Sources.

X-ray micro-computed tomography (µCT) is commonly used for imaging of samples in biomedical or materials science research. Owing to the ability to visualize a sample in a nondestructive way, X-ray µCT is perfectly suited to inspect fossilized specimens, which are mostly unique or rare. In certain regions of the world where important sedimentation events occurred in the Precambrian geological time, several fossilized animals are studied to understand questions related to their origin, environment, and life evolution. This article demonstrates the advantages of applying absorption and phase-contrast CT on the enigmatic fossil Corumbella werneri, one of the oldest known animals capable of building hard parts, originally discovered in Corumbá (Brazil). Different tomographic setups were tested to visualize the fossilized inner structures: a commercial laboratory-based µCT device, two synchrotron-based imaging setups using conventional absorption and propagation-based phase contrast, and a commercial X-ray microscope with a lens-coupled detector system, dedicated for radiography and tomography. Based on our results we discuss the strengths and weaknesses of the different imaging setups for paleontological studies.

Intravenous iron-induced hypophosphatemia and kidney stone disease.

Patients with Crohn's disease are at increased risk for symptomatic nephrolithiasis. Stones in these patients are most commonly composed of calcium oxalate monohydrate or mixed calcium-oxalate and calcium-phosphate. Precipitation of both minerals depends on urinary pH, calcium, phosphate and oxalate excretion. The present manuscript reports on two patients with Crohn's disease and bowel resection, in whom the onset of symptomatic urolithiasis occurred after repeated infusions of ferric carboxymaltose - a drug, which is known to cause hyperphosphaturia. The present study shows that ferric carboxymaltose-induced hyperphosphaturia can be associated with kidney stone formation and symptomatic urolithiasis, especially in patients treated with calcitriol. Calcitriol has been shown to mitigate ferric carboxymaltose-induced secondary hyperparathyroidism and hyperphosphaturia, but is known to increase urinary calcium excretion. Chemical analysis of recovered stones revealed that they were mixed calcium oxalate and phosphate stones. Ring-like deposition of iron detected by spatially resolved elemental analysis using laser ablation-inductively coupled plasma mass spectrometry, showed that the stones also contained iron. Based on our findings, we propose that patients with inflammatory bowel disease requiring intravenous iron therapy should be carefully monitored for the development of hypophosphatemia and urolithiasis. If hypophosphatemia occurs in such patients, calcitriol should be used with caution.

Comparing x-ray phase-contrast imaging using a Talbot array illuminator to propagation-based imaging for non-homogeneous biomedical samples.

Phase-contrast computed tomography can visualize soft tissue samples with high contrast. At coherent sources, propagation-based imaging (PBI) techniques are among the most common, as they are easy to implement and produce high-resolution images. Their downside is a low degree of quantitative data due to simplifying assumptions of the sample properties in the reconstruction. These assumptions can be avoided, by using quantitative phase-contrast techniques as an alternative. However, these often compromise spatial resolution and require complicated setups. In order to overcome this limitation, we designed and constructed a new imaging setup using a 2D Talbot array illuminator as a wavefront marker and speckle-based imaging phase-retrieval techniques. We developed a post-processing chain that can compensate for wavefront marker drifts and that improves the overall sensitivity. By comparing two measurements of biomedical samples, we demonstrate that the spatial resolution of our setup is comparable to the one of PBI scans while being able to successfully image a sample that breaks the typical homogeneity assumption used in PBI.

Degradation behavior and osseointegration of Mg-Zn-Ca screws in different bone regions of growing sheep: a pilot study.

Magnesium (Mg)-based implants are highly attractive for the orthopedic field and may replace titanium (Ti) as support for fracture healing. To determine the implant-bone interaction in different bony regions, we implanted Mg-based alloy ZX00 (Mg < 0.5 Zn < 0.5 Ca, in wt%) and Ti-screws into the distal epiphysis and distal metaphysis of sheep tibiae. The implant degradation and osseointegration were assessed in vivo and ex vivo after 4, 6 and 12 weeks, using a combination of clinical computed tomography, medium-resolution micro computed tomography (µCT) and high-resolution synchrotron radiation µCT (SRµCT). Implant volume loss, gas formation and bone growth were evaluated for both implantation sites and each bone region independently. Additionally, histological analysis of bone growth was performed on embedded hard-tissue samples. We demonstrate that in all cases, the degradation rate of ZX00-implants ranges between 0.23 and 0.75 mm/year. The highest degradation rates were found in the epiphysis. Bone-to-implant contact varied between the time points and bone types for both materials. Mostly, bone-volume-to-total-volume was higher around Ti-implants. However, we found an increased cortical thickness around the ZX00-screws when compared with the Ti-screws. Our results showed the suitability of ZX00-screws for implantation into the distal meta- and epiphysis.

On the material dependency of peri-implant morphology and stability in healing bone.

The microstructural architecture of remodeled bone in the peri-implant region of screw implants plays a vital role in the distribution of strain energy and implant stability. We present a study in which screw implants made from titanium, polyetheretherketone and biodegradable magnesium-gadolinium alloys were implanted into rat tibia and subjected to a push-out test four, eight and twelve weeks after implantation. Screws were 4 mm in length and with an M2 thread. The loading experiment was accompanied by simultaneous three-dimensional imaging using synchrotron-radiation microcomputed tomography at 5 µm resolution. Bone deformation and strains were tracked by applying optical flow-based digital volume correlation to the recorded image sequences. Implant stabilities measured for screws of biodegradable alloys were comparable to pins whereas non-degradable biomaterials experienced additional mechanical stabilization. Peri-implant bone morphology and strain transfer from the loaded implant site depended heavily on the biomaterial utilized. Titanium implants stimulated rapid callus formation displaying a consistent monomodal strain profile whereas the bone volume fraction in the vicinity of magnesium-gadolinium alloys exhibited a minimum close to the interface of the implant and less ordered strain transfer. Correlations in our data suggest that implant stability benefits from disparate bone morphological properties depending on the biomaterial utilized. This leaves the choice of biomaterial as situational depending on local tissue properties.

MiniMelt: An instrument for real-time tracking of electron beam additive manufacturing using synchrotron x-ray techniques.

The development of a sample environment for in situ x-ray characterization during metal Electron Beam Powder Bed Fusion (PBF-EB), called MiniMelt, is presented. The design considerations, the features of the equipment, and its implementation at the synchrotron facility PETRA III at Deutsches Elektronen-Synchrotron, Hamburg, Germany, are described. The equipment is based on the commercially available Freemelt ONE PBF-EB system but has been customized with a unique process chamber to enable real-time synchrotron measurements during the additive manufacturing process. Furthermore, a new unconfined powder bed design to replicate the conditions of the full-scale PBF-EB process is introduced. The first radiography (15 kHz) and diffraction (1 kHz) measurements of PBF-EB with a hot-work tool steel and a Ni-base superalloy, as well as bulk metal melting with the CMSX-4 alloy, using the sample environment are presented. MiniMelt enables time-resolved investigations of the dynamic phenomena taking place during multi-layer PBF-EB, facilitating process understanding and development of advanced process strategies and materials for PBF-EB.

Is solid always best? Cranial performance in solid and fenestrated caecilian skulls.

Caecilians (Lissamphibia: Gymnophiona) are characterized by a fossorial lifestyle that appears to play a role in the many anatomical specializations in the group. The skull, in particular, has been the focus of previous studies because it is driven into the substrate for burrowing. There are two different types of skulls in caecilians: (1) stegokrotaphic, where the squamosal completely covers the temporal region and the jaw closing muscles, and (2) zygokrotaphic, with incomplete coverage of the temporal region by the squamosal. We used 3-D imaging and modeling techniques to explore the functional consequences of these skull types in an evolutionary context. We digitally converted stegokrotaphic skulls into zygokrotaphic skulls and vice versa. We also generated a third, akinetic skull type that was presumably present in extinct caecilian ancestors. We explored the benefits and costs of the different skull types under frontal loading at different head angles with finite element analysis (FEA). Surprisingly, the differences in stress distributions and bending between the three tested skull types were minimal and not significant. This suggests that the open temporal region in zygokrotaphic skulls does not lead to poorer performance during burrowing. However, the results of the FEA suggest a strong relationship between the head angle and skull performance, implying there is an optimal head angle during burrowing.

Revival of Palaeoptera-head characters support a monophyletic origin of Odonata and Ephemeroptera (Insecta).

The earliest branching event in winged insects, one of the core problems regarding early insect evolution, was addressed using characters of the head. The head is arguably one of the most complex body regions in insects and the phylogenetic information content of its features has been demonstrated. In contrast, the wings and other body parts related to the flight apparatus and sperm transmission are not useful in the context of this problem, as the outgroups (silverfish and bristletails) are wingless and transmit spermatophores externally. Therefore, they show profound differences in the organization of the postcephalic body, and assessment of homology and subsequent phylogenetic analysis of features of these body regions is extremely difficult. The core of this study is the investigation of head structures of representatives of the major clades of dragonflies. A detailed description of the head of Lestes virens is presented and was used as a starting point for the compilation of a character set and a character state matrix for the entire Dicondylia (winged insects + silverfish), with a main focus on the placement of dragonflies and consequently the basal branching event within winged insects. Our results indicate a sister-group relationship between a clade Palaeoptera (dragonflies + mayflies) and the megadiverse monophyletic lineage Neoptera. We show that despite considerable structural similarity between the odonate and neopteran mandible, the muscle equipment in dragonflies is more plesiomorphic with respect to Dicondylia than previously known. Odonata and Ephemeroptera also share presumably derived features of the antenna, maxilla, and labial musculature. Parsimony analyses of the head data unambiguously support a clade Palaeoptera. © The Willi Hennig Society 2012.

Synchrotron radiation-based phase-contrast microtomography of human dental calculus allows nondestructive analysis of inclusions: implications for archeological samples.

Purpose: Dental calculus forms on teeth during the life of an individual and its investigation can yield information about diet, health status, and environmental pollution. Currently, the analytical techniques used to visualize the internal structure of human dental calculus and entrapped inclusions are limited and require destructive sampling, which cannot always be justified. Approach: We used propagation phase-contrast synchrotron radiation micro-computed tomography (PPC-SR- µ CT ) to non-destructively examine the internal organization of dental calculus, including its microstructure and entrapped inclusions, on both modern and archeological samples. Results: The virtual histological exploration of the samples shows that PPC-SR- µ CT is a powerful approach to visualize the internal organization of dental calculus. We identified several important features, including previously undetected negative imprints of enamel and dentine growth markers (perikymata and periradicular bands, respectively), the non-contiguous structure of calculus layers with multiple voids, and entrapped plant remains. Conclusions: PPC-SR- µ CT is an effective technique to explore dental calculus structural organization, and is especially powerful for enabling the identification of inclusions. The non-destructive nature of synchrotron tomography helps protect samples for future research. However, the irregular layers and frequent voids reveal a high heterogeneity and variability within calculus, with implications for research focusing on inclusions.

The contractile sponge epithelium sensu lato--body contraction of the demosponge Tethya wilhelma is mediated by the pinacoderm.

Sponges constitute one of the two metazoan phyla that are able to contract their bodies despite a complete lack of muscle cells. Two competing hypotheses on the mechanisms behind this have been postulated to date: (1) mesohyl-mediated contraction originating from fusiform smooth muscle-like actinocytes ('myocytes') and (2) epidermal contraction originating in pinacocytes. No direct support exists for either hypothesis. The question of agonist-antagonist interaction in sponge contraction seems to have been completely neglected so far. In the present study we addressed this by studying sponge contraction kinetics. We also tested both hypotheses by carrying out volumetric studies of 3D synchrotron radiation-based x-ray microtomography data obtained from contracted and expanded specimens of Tethya wilhelma. Our results support the pinacoderm contraction hypothesis. Should mesohyl contraction be present, it is likely to be part of the antagonist system. We conclude that epithelial contraction plays a major role in sponges. Contractile epithelia sensu lato may be regarded as part of the ground pattern of the Metazoa.

Morphological and molecular evidence converge upon a robust phylogeny of the megadiverse Holometabola.

We present the largest morphological character set ever compiled for Holometabola. This was made possible through an optimized acquisition of data. Based on our analyses and recently published hypotheses based on molecular data, we discuss higher-level phylogeny and evolutionary changes. We comment on the information content of different character systems and discuss the role of morphology in the age of phylogenomics. Microcomputer tomography in combination with other techniques proved highly efficient for acquiring and documenting morphological data. Detailed anatomical information (356 characters) is now available for 30 representatives of all holometabolan orders. A combination of traditional and novel techniques complemented each other and rapidly provided reliable data. In addition, our approach facilitates documenting the anatomy of model organisms. Our results show little congruence with studies based on rRNA, but confirm most clades retrieved in a recent study based on nuclear genes: Holometabola excluding Hymenoptera, Coleopterida (= Strepsiptera + Coleoptera), Neuropterida excl. Neuroptera, and Mecoptera. Mecopterida (= Antliophora + Amphiesmenoptera) was retrieved only in Bayesian analyses. All orders except Megaloptera are monophyletic. Problems in the analyses are caused by taxa with numerous autapomorphies and/or inapplicable character states due to the loss of major structures (such as wings). Different factors have contributed to the evolutionary success of various holometabolan lineages. It is likely that good flying performance, the ability to occupy different habitats as larvae and adults, parasitism, liquid feeding, and co-evolution with flowering plants have played important roles. We argue that even in the "age of phylogenomics", comparative morphology will still play a vital role. In addition, morphology is essential for reconstructing major evolutionary transformations at the phenotypic level, for testing evolutionary scenarios, and for placing fossil taxa. © The Willi Hennig Society 2010.

Electrochemical Surface Structuring for Strong SMA Wire-Polymer Interface Adhesion.

Active hybrid composites represent a novel class of smart materials used to design morphing surfaces, opening up new applications in the aircraft and automotive industries. The bending of the active hybrid composite is induced by the contraction of electrically activated shape memory alloy (SMA) wires, which are placed with an offset to the neutral axis of the composite. Therefore, the adhesion strength between the SMA wire and the surrounding polymer matrix is crucial to the load transfer and the functionality of the composite. Thus, the interface adhesion strength is of great importance for the performance and the actuation potential of active hybrid composites. In this work, the surface of a commercially available one-way effect NiTi SMA wire with a diameter of 1 mm was structured by selective electrochemical etching that preferably starts at defect sites, leaving the most thermodynamically stable surfaces of the wire intact. The created etch pits lead to an increase in the surface area of the wire and a mechanical interlocking with the polymer, resulting in a combination of adhesive and cohesive failure modes after a pull-out test. Consequently, the force of the first failure determined by an optical stress measurement was increased by more than 3 times when compared to the as-delivered SMA wire. The actuation characterization test showed that approximately the same work capacity could be retrieved from structured SMA wires. Moreover, structured SMA wires exhibited the same shape of the stress-strain curve as the as-delivered SMA wire, and the mechanical performance was not influenced by the structuring process. The austenite start As and austenite finish Af transformation temperatures were also not found to be affected by the structuring process. The formation of etching pits with different geometries and densities was discussed with regard to the kinetics of oxide formation and dissolution.

High-resolution and sensitivity bi-directional x-ray phase contrast imaging using 2D Talbot array illuminators.

Two-dimensional (2D) Talbot array illuminators (TAIs) were designed, fabricated, and evaluated for high-resolution high-contrast x-ray phase imaging of soft tissue at 10-20 keV. The TAIs create intensity modulations with a high compression ratio on the micrometer scale at short propagation distances. Their performance was compared with various other wavefront markers in terms of period, visibility, flux efficiency, and flexibility to be adapted for limited beam coherence and detector resolution. Differential x-ray phase contrast and dark-field imaging were demonstrated with a one-dimensional, linear phase stepping approach yielding 2D phase sensitivity using unified modulated pattern analysis (UMPA) for phase retrieval. The method was employed for x-ray phase computed tomography reaching a resolution of 3 µm on an unstained murine artery. It opens new possibilities for three-dimensional, non-destructive, and quantitative imaging of soft matter such as virtual histology. The phase modulators can also be used for various other x-ray applications such as dynamic phase imaging, super-resolution structured illumination microscopy, or wavefront sensing.

Histology and synchrotron radiation-based microtomography of the inner ear in a molecularly confirmed case of CHARGE syndrome.

CHARGE (Coloboma of the iris or retina, heart defects, atresia of the choanae, retardation of growth and/or development, genital anomalies, ear anomalies) syndrome (OMIM #214800) affects about 1 in 10,000 children and is most often caused by chromodomain helicase DNA-binding protein-7 (CHD7) mutations. Inner ear defects and vestibular abnormalities are particularly common. Specifically, semicircular canal (SCC) hypoplasia/aplasia and the presence of a Mondini malformation can be considered pathognomonic in the context of congenital malformations of the CHARGE syndrome. We obtained a temporal bone (TB) of a patient with CHARGE syndrome who died from bacteremia at 3 months of age. The clinical diagnosis was confirmed in the patient by direct DNA sequencing and the detection of a de novo, truncating CHD7 mutation, c.6169dup (p.R2057fs). We assessed changes of the TB and the degree of neural preservation, which may influence the potential benefit of cochlear implantation. The TB was analyzed using synchrotron radiation-based micro computed tomography, and by light microscopy. The vestibular partition consisted of a rudimentary vestibule with agenesis of the SCCs. The cochlea was hypoplastic with poor or deficient interscaling and shortened (Mondini dysplasia). The organ of Corti had near normal structure and innervation. Modiolus and Rosenthal's canal were hypoplastic with perikarya displaced along the axon bundles into the internal acoustic meatus, which may be explained by the arrest or limited migration and translocation of the cell nuclei into the cochlear tube during development.

Reconstructing the anatomy of the 42-million-year-old fossil Mengea tertiaria (Insecta, Strepsiptera).

Fossilization in amber is unique in preserving specimens with microscopic fidelity; however, arthropod inclusions are rarely examined beyond the exoskeleton as this requires destructive sampling when traditional techniques are used. We report the first complete, digital 3D, non-destructive reconstruction of the anatomy of an insect fossil, a specimen of Mengea tertiaria embedded in a 42-Ma Baltic amber. This was made possible using Synchrotron micro-CT. The species belongs to the stem group of the phylogenetically enigmatic and extremely specialized Strepsiptera. Most internal structures of the fossil are preserved, but small parts of the lumen had decayed due to incomplete infiltration of the resin. Data on internal organs provided additional information for resolving phylogenetic relationships. A sister group relationship between Mengea and all extant lineages of the group was confirmed with characters previously not accessible. The newly gained information also yielded some insights in the biology of Mengea and the early evolutionary history of Strepsiptera. The technique has a tremendous potential for a more accurate interpretation of diverse fossil arthropods preserved in ambers from 130 Ma to the present.

Quantitative phase-contrast tomography of a liquid phantom using a conventional x-ray tube source.

Over the last few years, differential phase-contrast x-ray computed tomography (PC-CT) using a hard x-ray grating interferometer and polychromatic x-ray tube sources has been developed. The method allows for simultaneous determination of the attenuation coefficient and the refractive index decrement distribution inside an object in three dimensions. Here we report experimental results of our investigation on the quantitativeness and accuracy of this method. For this study, a phantom consisting of several tubes filled with chemically well-defined liquids was built and measured in PC-CT. We find, that the measured attenuation coefficients and refractive index decrements closely match calculated, theoretical values. Moreover, the study demonstrates, how substances with similar attenuation coefficient or refractive index decrement, can be uniquely distinguished by the simultaneous, quantitative measurement of both quantities.

Sponge budding is a spatiotemporal morphological patterning process: Insights from synchrotron radiation-based x-ray microtomography into the asexual reproduction of Tethya wilhelma.

BACKGROUND: Primary agametic-asexual reproduction mechanisms such as budding and fission are present in all non-bilaterian and many bilaterian animal taxa and are likely to be metazoan ground pattern characters. Cnidarians display highly organized and regulated budding processes. In contrast, budding in poriferans was thought to be less specific and related to the general ability of this group to reorganize their tissues. Here we test the hypothesis of morphological pattern formation during sponge budding. RESULTS: We investigated the budding process in Tethya wilhelma (Demospongiae) by applying 3D morphometrics to high resolution synchrotron radiation-based x-ray microtomography (SR-muCT) image data. We followed the morphogenesis of characteristic body structures and identified distinct morphological states which indeed reveal characteristic spatiotemporal morphological patterns in sponge bud development. We discovered the distribution of skeletal elements, canal system and sponge tissue to be based on a sequential series of distinct morphological states. Based on morphometric data we defined four typical bud stages. Once they have reached the final stage buds are released as fully functional juvenile sponges which are morphologically and functionally equivalent to adult specimens. CONCLUSION: Our results demonstrate that budding in demosponges is considerably more highly organized and regulated than previously assumed. Morphological pattern formation in asexual reproduction with underlying genetic regulation seems to have evolved early in metazoans and was likely part of the developmental program of the last common ancestor of all Metazoa (LCAM).