Phase retrieval in propagation-based X-ray imaging beyond the limits of transport of intensity and contrast transfer function approaches.

We derive a phase retrieval formula for propagation-based phase contrast X-ray imaging that does not require weakly attenuating objects or short propagation distances. It is directly applicable to both single- and multiple-distance scenarios. We show the validity conditions and study the error of the underlying mutual intensity approximation, which uses the common assumptions of weak phase shift variations and phase-attenuation duality. The approximation generalizes those behind the transport of intensity (TIE) and contrast transfer function (CTF) models, and it approaches them when their respective additional assumptions are satisfied. When they are not, it clearly outperforms them, which we show both theoretically and practically on synthetic and measured data.

Disparity of turbinal bones in placental mammals.

Turbinals are key bony elements of the mammalian nasal cavity, involved in heat and moisture conservation as well as olfaction. While turbinals are well known in some groups, their diversity is poorly understood at the scale of placental mammals, which span 21 orders. Here, we investigated the turbinal bones and associated lamellae for one representative of each extant order of placental mammals. We segmented and isolated each independent turbinal and lamella and found an important diversity of variation in the number of turbinals, as well as their size, and shape. We found that the turbinal count varies widely, from zero in the La Plata dolphin, (Pontoporia blainvillei) to about 110 in the African bush elephant (Loxodonta africana). Multiple turbinal losses and additional gains took place along the phylogeny of placental mammals. Some changes are clearly attributed to ecological adaptation, while others are probably related to phylogenetic inertia. In addition, this work highlights the problem of turbinal nomenclature in some placental orders with numerous and highly complex turbinals, for which homologies are extremely difficult to resolve. Therefore, this work underscores the importance of developmental studies to better clarify turbinal homology and nomenclature and provides a standardized comparative framework for further research.

A multi-technique and multiscale comparative study on the efficiency of conservation methods for the stabilisation of waterlogged archaeological pine.

Archaeological wood can be preserved in waterlogged conditions. Due to their degradation in the ground, these archaeological remains are endangered after their discovery, since they decay irretrievably during drying. Conservation measures are used to preserve waterlogged archaeological objects, maintaining their shape and character as much as possible. However, different methods have been developed leading to varying results. This study compares their effectiveness in order to clarify their mode of action. The methods including alcohol-ether resin, lactitol/trehalose, melamine formaldehyde, polyethylene glycol impregnation prior to freeze-drying, saccharose and silicone oil were assessed by analysing mass changes and volume stability using structured-light 3D scanning. The state of the conserved wood samples including the spatial distribution of the conservation agent was examined using synchrotron micro-computed tomography. Raman spectroscopy was used to observe the agent´s spatial distribution within the cells. The findings demonstrated that melamine formaldehyde stabilises the degraded cell walls. The lumens are void, as in the case with alcohol-ether resin, while polyethylene glycol, silicone oil, saccharose and lactitol/trehalose also occupy the lumens. It is assumed that the drying method has an effect on the distribution of the solidifying agent. The knowledge gained affords insights into the mechanism of conservation methods, which in turn accounts for the varied outcomes. It also allows conclusions to be drawn about the condition and stability of conserved museum objects and serves as a starting point for the further development of conservation methods.

Biocatalytic Foams from Microdroplet-Formulated Self-Assembling Enzymes.

Industrial biocatalysis plays an important role in the development of a sustainable economy, as enzymes can be used to synthesize an enormous range of complex molecules under environmentally friendly conditions. To further develop the field, intensive research is being conducted on process technologies for continuous flow biocatalysis in order to immobilize large quantities of enzyme biocatalysts in microstructured flow reactors under conditions that are as gentle as possible in order to realize efficient material conversions. Here, monodisperse foams consisting almost entirely of enzymes covalently linked via SpyCatcher/SpyTag conjugation are reported. The biocatalytic foams are readily available from recombinant enzymes via microfluidic air-in-water droplet formation, can be directly integrated into microreactors, and can be used for biocatalytic conversions after drying. Reactors prepared by this method show surprisingly high stability and biocatalytic activity. The physicochemical characterization of the new materials is described and exemplary applications in biocatalysis are shown using two-enzyme cascades for the stereoselective synthesis of chiral alcohols and the rare sugar tagatose.

Tofu: a fast, versatile and user-friendly image processing toolkit for computed tomography.

Tofu is a toolkit for processing large amounts of images and for tomographic reconstruction. Complex image processing tasks are organized as workflows of individual processing steps. The toolkit is able to reconstruct parallel and cone beam as well as tomographic and laminographic geometries. Many pre- and post-processing algorithms needed for high-quality 3D reconstruction are available, e.g. phase retrieval, ring removal and de-noising. Tofu is optimized for stand-alone GPU workstations on which it achieves reconstruction speed comparable with costly CPU clusters. It automatically utilizes all GPUs in the system and generates 3D reconstruction code with minimal number of instructions given the input geometry (parallel/cone beam, tomography/laminography), hence yielding optimal run-time performance. In order to improve accessibility for researchers with no previous knowledge of programming, tofu contains graphical user interfaces for both optimization of 3D reconstruction parameters and batch processing of data with pre-configured workflows for typical computed tomography reconstruction. The toolkit is open source and extensive documentation is available for both end-users and developers. Thanks to the mentioned features, tofu is suitable for both expert users with specialized image processing needs (e.g. when dealing with data from custom-built computed tomography scanners) and for application-specific end-users who just need to reconstruct their data on off-the-shelf hardware.

Inverted Hartmann mask made by deep X-ray lithography for single-shot multi-contrast X-ray imaging with laboratory setup.

This paper reports on the fabrication and characterization of an inverted Hartmann mask and its application for multi-contrast X-ray imaging of polymer composite material in a laboratory setup. Hartmann masks open new possibilities for high-speed X-ray imaging, obtaining orientation-independent information on internal structures without rotating the object. The mask was manufactured with deep X-ray lithography and gold electroplating on a low-absorbing polyimide substrate. Such an approach allows us to produce gratings with a small period and high aspect ratio, leading to a higher spatial resolution and extension towards higher X-ray energies. Tuning the manufacturing process, we achieved a homogeneous patterned area without supporting structures, thus avoiding losses on visibility. We tested mask performance in a laboratory setup with a conventional flat panel detector and assessed mask imaging capabilities using a tailored phantom sample of various sizes. We performed multi-modal X-ray imaging of epoxy matrix polymer composites reinforced with glass fibers and containing microcapsules filled with a healing agent. Hartmann masks made by X-ray lithography enabled fast-tracking of structural changes in low absorbing composite materials and of a self-healing mechanism triggered by mechanical stress.

Morphological determinants of bite force capacity in insects: a biomechanical analysis of polymorphic leaf-cutter ants.

The extraordinary success of social insects is partially based on division of labour, i.e. individuals exclusively or preferentially perform specific tasks. Task preference may correlate with morphological adaptations so implying task specialization, but the extent of such specialization can be difficult to determine. Here, we demonstrate how the physical foundation of some tasks can be leveraged to quantitatively link morphology and performance. We study the allometry of bite force capacity in Atta vollenweideri leaf-cutter ants, polymorphic insects in which the mechanical processing of plant material is a key aspect of the behavioural portfolio. Through a morphometric analysis of tomographic scans, we show that the bite force capacity of the heaviest colony workers is twice as large as predicted by isometry. This disproportionate 'boost' is predominantly achieved through increased investment in muscle volume; geometrical parameters such as mechanical advantage, fibre length or pennation angle are likely constrained by the need to maintain a constant mandibular opening range. We analyse this preference for an increase in size-specific muscle volume and the adaptations in internal and external head anatomy required to accommodate it with simple geometric and physical models, so providing a quantitative understanding of the functional anatomy of the musculoskeletal bite apparatus in insects.

Fluid mechanics and rheology of the jumping spider body fluid.

Spiders use their inner body fluid ("blood" or hemolymph) to drive hydraulic extension of their legs. In hydraulic systems, performance is highly dependent on the working fluid, which needs to be chosen according to the required operating speed and pressure. Here, we provide new insights into the fluid mechanics of spider locomotion. We present the three-dimensional structure of one of the crucial joints in spider hydraulic actuation, elucidate the fluid flow inside the spider leg, and quantify the rheological properties of hemolymph under physiological conditions. We observe that hemolymph behaves as a shear-thinning non-Newtonian fluid with a fluid behavior index n = 0.5, unlike water (n = 1.0).

Introducing Biomedisa as an open-source online platform for biomedical image segmentation.

We present Biomedisa, a free and easy-to-use open-source online platform developed for semi-automatic segmentation of large volumetric images. The segmentation is based on a smart interpolation of sparsely pre-segmented slices taking into account the complete underlying image data. Biomedisa is particularly valuable when little a priori knowledge is available, e.g. for the dense annotation of the training data for a deep neural network. The platform is accessible through a web browser and requires no complex and tedious configuration of software and model parameters, thus addressing the needs of scientists without substantial computational expertise. We demonstrate that Biomedisa can drastically reduce both the time and human effort required to segment large images. It achieves a significant improvement over the conventional approach of densely pre-segmented slices with subsequent morphological interpolation as well as compared to segmentation tools that also consider the underlying image data. Biomedisa can be used for different 3D imaging modalities and various biomedical applications.

Drought-Induced Xylem Embolism Limits the Recovery of Leaf Gas Exchange in Scots Pine.

Climate change increases the occurrence of prolonged drought periods with large implications for forest functioning. Scots pine (Pinus sylvestris) is one of the most abundant conifers worldwide, and evidence is rising that its resilience to severe drought is limited. However, we know little about its ability to recover from drought-induced embolism. To analyze postdrought hydraulic recovery, we investigated stress and recovery dynamics of leaf gas exchange, nonstructural carbohydrates, and hydraulic properties in 2.5-year-old Scots pine seedlings. We quantified the degree of xylem embolism by combining in vivo x-ray microtomography with intrusive techniques including measurements of hydraulic conductivity and dye staining during drought progression and short-term (2 d) and long-term (4 weeks) recovery. Seedlings were grown under controlled conditions, and irrigation was withheld until stomata closed and xylem water potential declined to -3.2 MPa on average, causing a 46% loss of stem hydraulic conductivity. Following drought release, we found a gradual recovery of leaf gas exchange to 50% to 60% of control values. This partial recovery indicates hydraulic limitations due to drought-induced damage. Whereas xylem water potential recovered close to control values within 2 d, both x-ray microtomography and intrusive measurements revealed no recovery of stem hydraulic conductivity. Moreover, we did not find indications for nonstructural carbohydrate reserves limiting hydraulic recovery. Our findings demonstrate that Scots pine is able to survive severe drought and to partially recover, although we assume that xylem development during the next growing season might compensate for some of the hydraulic impairment. Such drought-induced legacy effects are important when considering vegetation responses to extreme events.

In situ speciation and spatial mapping of Zn products during pulsed laser ablation in liquids (PLAL) by combined synchrotron methods.

Pulsed laser ablation in liquids is a hierarchical multi-step process to produce pure inorganic nanoparticle colloids. Controlling this process is hampered by the partial understanding of individual steps and structure formation. In situ X-ray methods are employed to resolve macroscopic dynamics of nanosecond PLAL as well to analyse the distribution and speciation of ablated species with a microsecond time resolution. High time resolution can be achieved by synchrotron-based methods that are capable of 'single-shot' acquisition. X-ray multicontrast imaging by a Shack-Hartmann setup (XHI) and small angle X-ray scattering (SAXS) resolve evolving nanoparticles inside the transient cavitation bubble, while X-ray absorption spectroscopy in dispersive mode opens access to the total material yield and the chemical state of the ejecta. It is confirmed that during ablation nanoparticles are produced directly as well as reactive material is detected, which is identified in the early stage as Zn atoms. Nanoparticles within the cavitation bubble show a metal signature, which prevails for milliseconds, before gradual oxidation sets in. Ablation is described by a phase explosion of the target coexisting with full evaporation. Oxidation occurs only as a later step to already formed nanoparticles.

Cranial shape evolution of extant and fossil crocodile newts and its relation to reproduction and ecology.

The diversity of the vertebrate cranial shape of phylogenetically related taxa allows conclusions on ecology and life history. As pleurodeline newts (the genera Echinotriton, Pleurodeles and Tylototriton) have polymorphic reproductive modes, they are highly suitable for following cranial shape evolution in relation to reproduction and environment. We investigated interspecific differences externally and differences in the cranial shape of pleurodeline newts via two-dimensional geometric morphometrics. Our analyses also included the closely related but extinct genus Chelotriton to better follow the evolutionary history of cranial shape. Pleurodeles was morphologically distinct in relation to other phylogenetically basal salamanders. The subgenera within Tylototriton (Tylototriton and Yaotriton) were well separated in morphospace, whereas Echinotriton resembled the subgenus Yaotriton more than Tylototriton. Oviposition site choice correlated with phylogeny and morphology. Only the mating mode, with a random distribution along the phylogenetic tree, separated crocodile newts into two morphologically distinct groups. Extinct Chelotriton likely represented several species and were morphologically and ecologically more similar to Echinotriton and Yaotriton than to Tylototriton subgenera. Our data also provide the first comprehensive morphological support for the molecular phylogeny of pleurodeline newts.

Flexible Inkjet-Printed Triple Cation Perovskite X-ray Detectors.

Flexible direct conversion X-ray detectors enable a variety of novel applications in medicine, industry, and science. Hybrid organic-inorganic perovskite semiconductors containing elements of high atomic number combine an efficient X-ray absorption with excellent charge transport properties. Due to their additional cost-effective and low-temperature processability, perovskite semiconductors represent promising candidates to be used as active materials in flexible X-ray detectors. Inspired by the promising results recently reported on X-ray detectors that are based on either triple cation perovskites or inkjet-printed perovskite quantum dots, we here investigate flexible inkjet-printed triple cation perovskite X-ray detectors. The performance of the detectors is evaluated by the X-ray sensitivity, the dark current, and the X-ray stability. Exposed to 70 kVp X-ray radiation, reproducible and highly competitive X-ray sensitivities of up to 59.9 µC/(Gyaircm2) at low operating voltages of 0.1 V are achieved. Furthermore, a significant dark current reduction is demonstrated in our detectors by replacing spin-coated poly(3,4-ethylenedioxythiophene)/poly(styrenesulfonate) (PEDOT:PSS) with sputtered NiOx hole transport layers. Finally, stable operation of a flexible X-ray detector for a cumulative X-ray exposure of 4 Gyair is presented, and the applicability of our devices as X-ray imaging detectors is shown. The results of this study represent a proof of concept toward flexible direct conversion X-ray detectors realized by cost-effective and high-throughput digital inkjet printing.

Novel multicomponent organic-inorganic WPI/gelatin/CaP hydrogel composites for bone tissue engineering.

The present work focuses on the development of novel multicomponent organic-inorganic hydrogel composites for bone tissue engineering. For the first time, combination of the organic components commonly used in food industry, namely whey protein isolate (WPI) and gelatin from bovine skin, as well as inorganic material commonly used as a major component of hydraulic bone cements, namely α-TCP in various concentrations (0-70 wt%) was proposed. The results showed that α-TCP underwent incomplete transformation to calcium-deficient hydroxyapatite (CDHA) during preparation process of the hydrogels. Microcomputer tomography showed inhomogeneous distribution of the calcium phosphate (CaP) phase in the resulting composites. Nevertheless, hydrogels containing 30-70 wt% α-TCP showed significantly improved mechanical properties. The values of Young's modulus and the stresses corresponding to compression of a sample by 50% increased almost linearly with increasing concentration of ceramic phase. Incomplete transformation of α-TCP to CDHA during preparation process of composites provides them high reactivity in simulated body fluid during 14-day incubation. Preliminary in vitro studies revealed that the WPI/gelatin/CaP composite hydrogels support the adhesion, spreading, and proliferation of human osteoblast-like MG-63 cells. The WPI/gelatin/CaP composite hydrogels obtained in this work showed great potential for the use in bone tissue engineering and regenerative medicine applications.

A new megaspilid wasp from Eocene Baltic amber (Hymenoptera: Ceraphronoidea), with notes on two non-ceraphronoid families: Radiophronidae and Stigmaphronidae.

Ceraphronoids are some of the most commonly collected hymenopterans, yet they remain rare in the fossil record. Conostigmus talamasi Mikó and Trietsch, sp. nov. from Baltic amber represents an intermediate form between the type genus, Megaspilus, and one of the most species-rich megaspilid genera, Conostigmus. We describe the new species using 3D data collected with synchrotron-based micro-CT equipment. This non-invasive technique allows for quick data collection in unusually high resolution, revealing morphological traits that are otherwise obscured by the amber. In describing this new species, we revise the diagnostic characters for Ceraphronoidea and discuss possible reasons why minute wasps with a pterostigma are often misidentified as ceraphronoids. Based on the lack of ceraphronoid characteristics, we remove Dendrocerus dubitatus Brues, 1937, Stigmaphronidae, and Radiophronidae from Ceraphronoidea and consider them as incertae sedis. We also provide some guidance for their future classification.

Augmented laminography, a correlative 3D imaging method for revealing the inner structure of compressed fossils.

Non-destructive imaging techniques can be extremely useful tools for the investigation and the assessment of palaeontological objects, as mechanical preparation of rare and valuable fossils is precluded in most cases. However, palaeontologists are often faced with the problem of choosing a method among a wide range of available techniques. In this case study, we employ x-ray computed tomography (CT) and computed laminography (CL) to study the first fossil xiphosuran from the Muschelkalk (Middle Triassic) of the Netherlands. The fossil is embedded in micritic limestone, with the taxonomically important dorsal shield invisible, and only the outline of its ventral part traceable. We demonstrate the complementarity of CT and CL which offers an excellent option to visualize characteristic diagnostic features. We introduce augmented laminography to correlate complementary information of the two methods in Fourier space, allowing to combine their advantages and finally providing increased anatomical information about the fossil. This method of augmented laminography enabled us to identify the xiphosuran as a representative of the genus Limulitella.

On the origin and nature of the grating interferometric dark-field contrast obtained with low-brilliance x-ray sources.

The x-ray dark-field contrast accessible via grating interferometry is sensitive to features at length scales well below what is resolvable by a detector system. It is commonly explained as arising from small-angle x-ray scattering (SAXS), and can be implemented both at synchrotron beamlines and with low-brilliance sources such as x-ray tubes. Here, we demonstrate that for tube based setups the underlying process of image formation can be fundamentally different. For focal spots or detector pixels that comprise multiple grating periods, we show that dark-field images contain a strong artificial and system-specific component not arising from SAXS. Based on experiments carried out with a nanofocus x-ray tube and the example of an excised rat lung, we demonstrate that the dark-field contrast observed for porous media transforms into a differential phase contrast for large geometric magnifications. Using a photon counting detector with an adjustable point spread function, we confirm that a dark-field image can indeed be formed by an intra-pixel differential phase contrast that cannot be resolved as such due to a dephasing between the periodicities of the absorption grating and the Talbot carpet. Our findings are further corroborated by a link between the strength of this pseudo-dark-field contrast and our x-ray tube's focal spot size in a three-grating setup. These results must not be ignored when measurements are intended to be reproducible across systems.

Imaging properties of high aspect ratio absorption gratings for use in preclinical x-ray grating interferometry.

X-ray grating interferometry is one among various methods that allow extracting the so-called phase and visibility contrasts in addition to the well-known transmission images. Crucial to achieving a high image quality are the absorption gratings employed. Here, we present an in-depth analysis of how the grating type and lamella heights influence the final images. Benchmarking gratings of two different designs, we show that a frequently used proxy for image quality, a grating's so-called visibility, is insufficient to predict contrast-to-noise ratios (CNRs). Presenting scans from an excised rat lung, we demonstrate that the CNRs obtained for transmission and visibility images anti-correlate. This is explained by the stronger attenuation implied by gratings that are engineered to provide high visibilities by means of an increased lamella height. We show that even the visibility contrast can suffer from this effect when the associated reduced photon flux on the detector is not outweighed by a corresponding gain in visibility. Resulting in an inevitable trade-off between the quality of the two contrasts, the question of how an optimal grating should be designed can hence only be answered in terms of Pareto optimality.

Performance of a Medipix3RX spectroscopic pixel detector with a high resistivity gallium arsenide sensor.

High resistivity gallium arsenide is considered a suitable sensor material for spectroscopic X-ray imaging detectors. These sensors typically have thicknesses between a few hundred µm and 1 mm to ensure a high photon detection efficiency. However, for small pixel sizes down to several tens of µm, an effect called charge sharing reduces a detector's spectroscopic performance. The recently developed Medipix3RX readout chip overcomes this limitation by implementing a charge summing circuit, which allows the reconstruction of the full energy information of a photon interaction in a single pixel. In this work, we present the characterization of the first Medipix3RX detector assembly with a 500 µm thick high resistivity, chromium compensated gallium arsenide sensor. We analyze its properties and demonstrate the functionality of the charge summing mode by means of energy response functions recorded at a synchrotron. Furthermore, the imaging properties of the detector, in terms of its modulation transfer functions and signal-to-noise ratios, are investigated. After more than one decade of attempts to establish gallium arsenide as a sensor material for photon counting detectors, our results represent a breakthrough in obtaining detector-grade material. The sensor we introduce is therefore suitable for high resolution X-ray imaging applications.

How spectroscopic x-ray imaging benefits from inter-pixel communication.

Spectroscopic x-ray imaging based on pixellated semiconductor detectors can be sensitive to charge sharing and K-fluorescence, depending on the sensor material used, its thickness and the pixel pitch employed. As a consequence, spectroscopic resolution is partially lost. In this paper, we study a new detector ASIC, the Medipix3RX, that offers a novel feature called charge summing, which is established by making adjacent pixels communicate with each other. Consequently, single photon interactions resulting in multiple hits are almost completely avoided. We investigate this charge summing mode with respect to those of its imaging properties that are of interest in medical physics and benchmark them against the case without charge summing. In particular, we review its influence on spectroscopic resolution and find that the low energy bias normally present when recording energy spectra is dramatically reduced. Furthermore, we show that charge summing provides a modulation transfer function which is almost independent of the energy threshold setting, which is in contrast to approaches common so far. We demonstrate that this property is directly linked to the detective quantum efficiency, which is found to increase by a factor of three or more when the energy threshold approaches the photon energy and when using charge summing. As a consequence, the contrast-to-noise ratio is found to double at elevated threshold levels and the dynamic range increases for a given counter depth. All these effects are shown to lead to an improved ability to perform material discrimination in spectroscopic CT, using iodine and gadolinium contrast agents. Hence, when compared to conventional photon counting detectors, these benefits carry the potential of substantially reducing the imaging dose a patient is exposed to during diagnostic CT examinations.