darfix - data analysis for dark-field X-ray microscopy.

A Python package for the analysis of dark-field X-ray microscopy (DFXM) and rocking curve imaging (RCI) data is presented. DFXM is a non-destructive diffraction imaging technique that provides three-dimensional maps of lattice strain and orientation. The darfix package enables fast processing and visualization of these data, providing the user with the essential tools to extract information from the acquired images in a fast and intuitive manner. These data processing and visualization tools can be either imported as library components or accessed through a graphical user interface as an Orange add-on. In the latter case, the different analysis modules can be easily chained to define computational workflows. Operations on larger-than-memory image sets are supported through the implementation of online versions of the data processing algorithms, effectively trading performance for feasibility when the computing resources are limited. The software can automatically extract the relevant instrument angle settings from the input files' metadata. The currently available input file format is EDF and in future releases HDF5 will be incorporated.

Fourier ptychographic dark field x-ray microscopy.

Dark-field x-ray microscopy (DFXM) is an x-ray imaging technique for mapping three-dimensional (3D) lattice strain and rotation in bulk crystalline materials. At present, these maps of local structural distortions are derived from the raw intensity images using an incoherent analysis framework. In this work, we describe a coherent, Fourier ptychographic approach that requires little change in terms of instrumentation and acquisition strategy, and may be implemented on existing DFXM instruments. We demonstrate the method experimentally and are able to achieve quantitative phase reconstructions of thin film samples and maps of the aberrations in the objective lens. The method holds particular promise for the characterization of crystalline materials containing weak structural contrast.

Role of threading dislocations on the growth of HgCdTe epilayers investigated using monochromatic X-ray Bragg diffraction imaging.

High-quality Hg1-xCdxTe (MCT) single crystals are essential for two-dimensional infrared detector arrays. Crystal quality plays an important role on the performance of these devices. Here, the dislocations present at the interface of CdZnTe (CZT) substrates and liquid-phase epitaxy grown MCT epilayers are investigated using X-ray Bragg diffraction imaging (XBDI). The diffraction contributions coming from the threading dislocations (TDs) of the CZT substrate and the MCT epilayers are separated using weak-beam conditions in projection topographs. The results clearly suggest that the lattice parameter of the growing MCT epilayer is, at the growth inception, very close to that of the CZT substrate and gradually departs from the substrate's lattice parameter as the growth advances. Moreover, the relative growth velocity of the MCT epilayer around the TDs is found to be faster by a factor of two to four compared with the matrix. In addition, a fast alternative method to the conventional characterization methods for probing crystals with low dislocation density such as atomic force microscopy and optical interferometry is introduced. A 1.5 mm × 1.5 mm area map of the epilayer defects with sub-micrometre spatial resolution is generated, using section XBDI, by blocking the diffraction contribution of the substrate and scanning the sample spatially.

Multilayer Laue lenses at high X-ray energies: performance and applications.

X-ray microscopy at photon energies above 15 keV is very attractive for the investigation of atomic and nanoscale properties of technologically relevant structural and bio materials. This method is limited by the quality of X-ray optics. Multilayer Laue lenses (MLLs) have the potential to make a major impact in this field because, as compared to other X-ray optics, they become more efficient and effective with increasing photon energy. In this work, MLLs were utilized with hard X-rays at photon energies up to 34.5 keV. The design, fabrication, and performance of these lenses are presented, and their application in several imaging configurations is described. In particular, two "full field" modes of imaging were explored, which provide various contrast modalities that are useful for materials characterisation. These include point projection imaging (or Gabor holography) for phase contrast imaging and direct imaging with both bright-field and dark-field illumination. With high-efficiency MLLs, such modes offer rapid data collection as compared with scanning methods as well as a large field of views.

Decoding entangled transitions: Polyamorphism and stressed rigidity.

There is much to learn from simulation studies of polyamorphism achieved for systems with different bonding environments. Chalcogenide glasses such as Ge-Se glasses undergo an elastic phase transition involving important changes in network connectivity. Stimulated by recent developments of topological constraint theory, we show that the concept of rigidity can be extended to a broader range of thermodynamic conditions including densified glasses. After having validated our structural first principles molecular dynamics models with experimental data over a broad pressure range for GeSe4, we show that the onset of polyamorphism is strongly related to the constraint density measuring the degree of rigidity of the network backbone, while voids and cavities in the structure collapse at very small pressures. This leads to the identification that the progressive onset of higher coordinated species typical of high pressure phases is responsible for the onset of stressed rigidity, although the constraint analysis also indicates progressive stiffening of bonding angles. Results are compared to stoichiometric and stressed rigid GeSe2 and to isostatic As2Se3 and then generalized to other compositions in the Ge-Se binary under pressure.

Self-Assembled Monolayers of Pseudo-C2v-Symmetric, Low-Band-Gap Areneoxazolethiolates on Gold Surfaces.

A series of three homologous arene[2,3-d]-oxazole-2-thiols (benzoxazole-2-thiol (BOxSH), naphthaleneoxazole-2-thiol (NOxSH), and anthraceneoxazole-2-thiol (AOxSH)) were deposited onto Au(111) to obtain surfaces suitable as injection layers for organic electronics. The guiding idea was that the increasingly extended conjugated system would lower the band gap of the films while the introduction of the annulated heteroaromatic ring would provide the opportunity for pseudosymmetric attachment of the sulfur anchor, what should lower the conformational freedom of the system. In fact, the annulation of the oxazole ring lowers the optical band gaps of the parent compounds to 3.1-4.0 eV, depending on the number of benzene rings. To characterize the respective monolayers, a variety of spectroscopic techniques such as ellipsometry, infrared reflection-absorption spectroscopy, X-ray photoelectron spectroscopy, and near-edge X-ray absorption fine structure spectroscopy have been utilized. The monolayers of BOxS exhibit a lower film quality than those of NOxS and AOxS, with enhanced molecular density and more upright molecular orientation with increasing molecular length. Infrared spectroscopy suggests that the nitrogen atoms of the oxazole rings are located more closely to the Au(111) surface than the oxygen atoms, although no hints for an electronic interaction between the N atoms and the gold surface could be found. This preferred orientation could be tentatively traced to packing effects, solving a conundrum of the literature.

Anomalous diffusion and non-monotonic relaxation processes in Ge-Se liquids.

We investigate the dynamical properties of liquid GexSe100-x as a function of Ge content by first-principles molecular dynamic simulations for a certain number of temperatures in the liquid state. The focus is set on ten compositions (where x ≤ 33%) encompassing the reported flexible to rigid and rigid to stressed-rigid transitions. We examine diffusion coefficients, diffusion activation energies, glassy relaxation behavior, and viscosity of these liquids from Van Hove correlation and intermediate scattering functions. At fixed temperature, all properties/functions exhibit an anomalous behavior with Ge content in the region 18%-22%, and provide a direct and quantitative link to the network rigidity.

Multiscale in-situ characterization of static recrystallization using dark-field X-ray microscopy and high-resolution X-ray diffraction.

Dark-field X-ray microscopy (DFXM) is a high-resolution, X-ray-based diffraction microstructure imaging technique that uses an objective lens aligned with the diffracted beam to magnify a single Bragg reflection. DFXM can be used to spatially resolve local variations in elastic strain and orientation inside embedded crystals with high spatial (~ 60 nm) and angular (~ 0.001°) resolution. However, as with many high-resolution imaging techniques, there is a trade-off between resolution and field of view, and it is often desirable to enrich DFXM observations by combining it with a larger field-of-view technique. Here, we combine DFXM with high-resolution X-ray diffraction (HR-XRD) applied to an in-situ investigation of static recrystallization in an 80% hot-compressed Mg-3.2Zn-0.1Ca wt.% (ZX30) alloy. Using HR-XRD, we track the relative grain volume of > 8000 sub-surface grains during annealing in situ. Then, at several points during the annealing process, we "zoom in" to individual grains using DFXM. This combination of HR-XRD and DFXM enables multiscale characterization, used here to study why particular grains grow to consume a large volume fraction of the annealed microstructure. This technique pairing is particularly useful for small and/or highly deformed grains that are often difficult to resolve using more standard diffraction microstructure imaging techniques.

Extensive 3D mapping of dislocation structures in bulk aluminum.

Thermomechanical processing such as annealing is one of the main methods to tailor the mechanical properties of materials, however, much is unknown about the reorganization of dislocation structures deep inside macroscopic crystals that give rise to those changes. Here, we demonstrate the self-organization of dislocation structures upon high-temperature annealing in a mm-sized single crystal of aluminum. We map a large embedded 3D volume ([Formula: see text] [Formula: see text]m[Formula: see text]) of dislocation structures using dark field X-ray microscopy (DFXM), a diffraction-based imaging technique. Over the wide field of view, DFXM's high angular resolution allows us to identify subgrains, separated by dislocation boundaries, which we identify and characterize down to the single-dislocation level using computer-vision methods. We demonstrate how even after long annealing times at high temperatures, the remaining low density of dislocations still pack into well-defined, straight dislocation boundaries (DBs) that lie on specific crystallographic planes. In contrast to conventional grain growth models, our results show that the dihedral angles at the triple junctions are not the predicted 120[Formula: see text], suggesting additional complexities in the boundary stabilization mechanisms. Mapping the local misorientation and lattice strain around these boundaries shows that the observed strain is shear, imparting an average misorientation around the DB of [Formula: see text] 0.003 to 0.006[Formula: see text].

Study of GaN coalescence by dark-field X-ray microscopy at the nanoscale.

This work illustrates the potential of dark-field X-ray microscopy (DFXM), a 3D imaging technique of nanostructures, in characterizing novel epitaxial structures of gallium nitride (GaN) on top of GaN/AlN/Si/SiO2 nano-pillars for optoelectronic applications. The nano-pillars are intended to allow independent GaN nanostructures to coalesce into a highly oriented film due to the SiO2 layer becoming soft at the GaN growth temperature. DFXM is demonstrated on different types of samples at the nanoscale and the results show that extremely well oriented lines of GaN (standard deviation of 0.04°) as well as highly oriented material for zones up to 10 × 10 µm2 in area are achieved with this growth approach. At a macroscale, high-intensity X-ray diffraction is used to show that the coalescence of GaN pyramids causes misorientation of the silicon in the nano-pillars, implying that the growth occurs as intended (i.e. that pillars rotate during coalescence). These two diffraction methods demonstrate the great promise of this growth approach for micro-displays and micro-LEDs, which require small islands of high-quality GaN material, and offer a new way to enrich the fundamental understanding of optoelectronically relevant materials at the highest spatial resolution.

Simultaneous bright- and dark-field X-ray microscopy at X-ray free electron lasers.

The structures, strain fields, and defect distributions in solid materials underlie the mechanical and physical properties across numerous applications. Many modern microstructural microscopy tools characterize crystal grains, domains and defects required to map lattice distortions or deformation, but are limited to studies of the (near) surface. Generally speaking, such tools cannot probe the structural dynamics in a way that is representative of bulk behavior. Synchrotron X-ray diffraction based imaging has long mapped the deeply embedded structural elements, and with enhanced resolution, dark field X-ray microscopy (DFXM) can now map those features with the requisite nm-resolution. However, these techniques still suffer from the required integration times due to limitations from the source and optics. This work extends DFXM to X-ray free electron lasers, showing how the [Formula: see text] photons per pulse available at these sources offer structural characterization down to 100 fs resolution (orders of magnitude faster than current synchrotron images). We introduce the XFEL DFXM setup with simultaneous bright field microscopy to probe density changes within the same volume. This work presents a comprehensive guide to the multi-modal ultrafast high-resolution X-ray microscope that we constructed and tested at two XFELs, and shows initial data demonstrating two timing strategies to study associated reversible or irreversible lattice dynamics.

Alpha-lipoic acid reduces peridural fibrosis after laminectomy of lumbar vertebrae in rabbits.

BACKGROUND: Peridural fibrosis is an inevitable healing process causing failed back surgery syndrome after lumbar spinal operations. In this study, alpha-lipoic acid (ALA), reported to reduce fibrosis in liver, oral mucosa, and peritoneum, investigated as a potential candidate for prevention of peridural fibrosis. METHOD: Twelve adult New Zealand white male rabbits were divided into control (n = 5) and ALA groups (n = 7). Laminectomy of lumbar spine was performed and ALA was applied on the exposed dura mater topically in ALA group. RESULTS: According to histological peridural grading, the ALA group (median grade 1) showed significantly less peridural fibrosis than the control group (median grade 3, p = 0.005). CONCLUSIONS: ALA is a promising substance in the prevention of peridural fibrosis, especially in early preoperative and postoperative period.

Simulating dark-field X-ray microscopy images with wavefront propagation techniques.

Dark-field X-ray microscopy is a diffraction-based synchrotron imaging technique capable of imaging defects in the bulk of extended crystalline samples. Numerical simulations are presented of image formation in such a microscope using numerical integration of the dynamical Takagi-Taupin equations and wavefront propagation. The approach is validated by comparing simulated images with experimental data from a near-perfect single crystal of diamond containing a single stacking-fault defect in the illuminated volume.

Postoperative cerebellar mutism and autistic spectrum disorder.

PURPOSE: I read the article "An Inside View of Autism" written by a 44-year-old autistic woman who had a successful international career designing livestock equipment. In this article, she wrote about her life, disease, and experiences as an autistic individual. She stated that "It is interesting that my speech resembled the stressed speech in young children who have had tumors removed from the cerebellum". METHODS: In this article, we intend to review and extensively document both postoperative cerebellar mutism and autistic spectrum disorder. RESULTS: We reviewed the clinical and neurological findings, etio-pathogenesis, neuroanatomy, mechanisms of development, and similarities between the etio-pathogenesis of both diseases. CONCLUSIONS: Cerebellar lesions can produce mutism and dysarthria, symptoms sometimes seen in autistic spectrum disorder. In mammals, cerebellar lesions disturb motivated behavior and reduce social interactions, functions that are disturbed in autistic spectrum disorder and cerebellar mutism. The cerebellum and two regions within the frontal lobes are active in certain language tasks. Language is abnormal in autistic spectrum disorder and cerebellar mutism.

Unilateral Phthiriasis Palpebrarum: A Case Study

Phthiriasis palpebrarum is a rare eyelid infestation caused by Phthirus pubis (pubic lice) that is often confused with other causes of blepharoconjunctivitis. In this study, we report the case of a 49-year-old male patient with phthiriasis palpebrarum who presented with itching and eye irritation in the left eye and had undergone treatment for conjunctivitis in the past month. Biomicroscopic examination revealed a dense population of motile and translucent lice and eggs, more intensely on the upper lid. For treatment, the lice were first cleaned mechanically, eyelashes were cut from the bottom, and eggs and lice were removed from the eye, after which petrolatum jelly (vsaseline) was applied to the lids for 10 days. In the control examination, no lice and eggs were observed.

In situ visualization of long-range defect interactions at the edge of melting.

Connecting a bulk material's microscopic defects to its macroscopic properties is an age-old problem in materials science. Long-range interactions between dislocations (line defects) are known to play a key role in how materials deform or melt, but we lack the tools to connect these dynamics to the macroscopic properties. We introduce time-resolved dark-field x-ray microscopy to directly visualize how dislocations move and interact over hundreds of micrometers deep inside bulk aluminum. With real-time movies, we reveal the thermally activated motion and interactions of dislocations that comprise a boundary and show how weakened binding forces destabilize the structure at 99% of the melting temperature. Connecting dynamics of the microstructure to its stability, we provide important opportunities to guide and validate multiscale models that are yet untested.

Dislocation-toughened ceramics.

Functional and structural ceramics have become irreplaceable in countless high-tech applications. However, their inherent brittleness tremendously limits the application range and, despite extensive research efforts, particularly short cracks are hard to combat. While local plasticity carried by mobile dislocations allows desirable toughness in metals, high bond strength is widely believed to hinder dislocation-based toughening of ceramics. Here, we demonstrate the possibility to induce and engineer a dislocation microstructure in ceramics that improves the crack tip toughness even though such toughening does not occur naturally after conventional processing. With modern microscopy and simulation techniques, we reveal key ingredients for successful engineering of dislocation-based toughness at ambient temperature. For many ceramics a dislocation-based plastic zone is not impossible due to some intrinsic property (e.g. bond strength) but limited by an engineerable quantity, i.e. the dislocation density. The impact of dislocation density is demonstrated in a surface near region and suggested to be transferrable to bulk ceramics. Unexpected potential in improving mechanical performance of ceramics could be realized with novel synthesis strategies.

Quantifying microscale drivers for fatigue failure via coupled synchrotron X-ray characterization and simulations.

During cyclic loading, localization of intragranular deformation due to crystallographic slip acts as a precursor for crack initiation, often at coherent twin boundaries. A suite of high-resolution synchrotron X-ray characterizations, coupled with a crystal plasticity simulation, was conducted on a polycrystalline nickel-based superalloy microstructure near a parent-twin boundary in order to understand the deformation localization behavior of this critical, 3D microstructural configuration. Dark-field X-ray microscopy was spatially linked to high energy X-ray diffraction microscopy and X-ray diffraction contrast tomography in order to quantify, with cutting-edge resolution, an intragranular misorientation and high elastic strain gradients near a twin boundary. These observations quantify the extreme sub-grain scale stress gradients present in polycrystalline microstructures, which often lead to fatigue failure.

Imaging microstructural dynamics and strain fields in electro-active materials in situ with dark field x-ray microscopy.

The electric-field-induced and temperature induced dynamics of domains, defects, and phases play an important role in determining the macroscopic functional response of ferroelectric and piezoelectric materials. However, distinguishing and quantifying these phenomena remains a persistent challenge that inhibits our understanding of the fundamental structure-property relationships. In situ dark field x-ray microscopy is a new experimental technique for the real space mapping of lattice strain and orientation in bulk materials. In this paper, we describe an apparatus and methodology for conducting in situ studies of thermally and electrically induced structural dynamics and demonstrate their use on ferroelectric BaTiO3 single crystals. The stable temperature and electric field apparatus enables simultaneous control of electric fields up to ≈2 kV/mm at temperatures up to 200 °C with a stability of ΔT = ±0.01 K and a ramp rate of up to 0.5 K/min. This capability facilitates studies of critical phenomena, such as phase transitions, which we observe via the microstructural change occurring during the electric-field-induced cubic to tetragonal phase transition in BaTiO3 at its Curie temperature. With such systematic control, we show how the growth of the polar phase front and its associated ferroelastic domains fall along unexpected directions and, after several cycles of electric field application, result in a non-reversible lattice strain at the electrode-crystal interface. These capabilities pave the way for new insights into the temperature and electric field dependent electromechanical transitions and the critical influence of subtle defects and interfaces.