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The size of 4D tomography datasets acquired at synchrotron or neutron imaging facilities can reach several terabytes, which presents a significant challenge for their evaluation. This paper presents a framework that allows a compressed dataset to be kept in memory and makes it possible to evaluate and manipulate the dataset without requiring enough memory to decompress the entire dataset. The framework enables the compensation of imaging artifacts, including the compression artifacts of the 4D dataset, through the integration of neural networks. The reduction of imaging artifacts can be performed at the imaging facility or at the user's home institution. This framework reduces the computational burden on the computing infrastructure of large synchrotron and neutron facilities by allowing end users to process datasets on their institution's computers. This is made possible by compressing TBs of data to less than 128 GB, allowing powerful PCs to process TBs of 4D tomography data.

Abstract The development of an organism is orchestrated by the spatial and temporal expression of genes. Accurate visualisation of gene expression patterns in the context of the surrounding tissues offers a glimpse into the mechanisms that drive morphogenesis. We developed correlative light-sheet fluorescence microscopy and X-ray computed tomography approach to map gene expression patterns to the whole organism`s 3D anatomy. We show that this multimodal approach is applicable to gene expression visualized by protein-specific antibodies and fluorescence RNA in situ hybridisation offering a detailed understanding of individual phenotypic variations in model organisms. Furthermore, the approach offers a unique possibility to identify tissues together with their 3D cellular and molecular composition in anatomically less-defined in vitro models, such as organoids. We anticipate that the visual and quantitative insights into the 3D distribution of gene expression within tissue architecture, by multimodal approach developed here, will be equally valuable for reference atlases of model organisms development, as well as for comprehensive screens, and morphogenesis studies of in vitro models.

In situ X-ray reciprocal space mapping was performed during the interval heating and cooling of InGaN/GaN quantum wells (QWs) grown via metal–organic vapor phase epitaxy (MOVPE). Our detailed in situ X-ray analysis enabled us to track changes in the peak intensities and radial and angular broadenings of the reflection. By simulating the radial diffraction profiles recorded during the thermal cycle treatment, we demonstrate the presence of indium concentration distributions (ICDs) in the different QWs of the heterostructure (1. QW, bottom, 2. QW, middle, and 3. QW, upper). During the heating process, we found that the homogenization of the QWs occurred in the temperature range of 850 °C to 920 °C, manifesting in a reduction in ICDs in the QWs. Furthermore, there is a critical temperature (T = 940 °C) at which the mean value of the indium concentration starts to decrease below 15% in 1. QW, indicating the initiation of decomposition in 1. QW. Moreover, further heating up to 1000 °C results in extended diffuse scattering along the angular direction of the diffraction spot, confirming the propagation of the decomposition and the formation of trapezoidal objects, which contain voids and amorphous materials (In-Ga). Heating InGaN QWs up to T = 1000 °C led to a simultaneous decrease in the indium content and ICDs. During the cooling phase, there was no significant variation in the indium concentrations in the different QWs but rather an increase in the defect area, which contributes to the amplification of diffuse scattering. A comparison of ex situ complementary high-resolution transmission microscopy (Ex-HRTEM) measurements performed at room temperature before and after the thermal cycle treatment provides proof of the formation of four different types of defects in the QWs, which result from the decomposition of 1. QW during the heating phase. This, in turn, has strongly influenced the intensity of the photoluminescence emission spectra without any detectable shift in the emission wavelength λMQWs.

Compound semiconductors are playing a major role in the production of X-ray pixel detectors for the application in laboratories and beamlines at photon sources. The performance of these detectors has constantly been improved for the last decades but experiments are still limited by the properties of the detector material, especially under high flux illumination. The fast development of perovskite crystals opens the possibility for new materials to be used as highly efficient X-ray pixel detectors. The published data until now, of the transport properties, demonstrate the large potential of perovskite semiconductors. The achieved values are comparable with the ones of CdTe-based detectors. This paper presents potential perovskite-based detector materials and compares their performance with the state-of-the-art CdTe-based detectors. The perspectives of perovskite semiconductors are promising for the production of large area X-ray detectors but still some challenges remain.

Abstract Hierarchical guidance is developed for three-dimensional (3D) nanoscale X-ray imaging, enabling identification, refinement, and tracking of regions of interest (ROIs) within specimens considerably exceeding the field of view. This opens up new possibilities for in situ investigations. Experimentally, the approach takes advantage of rapid multiscale measurements based on magnified projection microscopy featuring continuous zoom capabilities. Immediate and continuous feedback on the subsequent experimental progress is enabled by suitable on-the-fly data processing. For this, by theoretical justification and experimental validation, so-called quasi-particle phase-retrieval is generalised to conical-beam conditions, being key for sufficiently fast computation without significant loss of imaging quality and resolution compared to common approaches for holographic microscopy. Exploiting 3D laminography, particularly suited for imaging of ROIs in laterally extended plate-like samples, the potential of hierarchical guidance is demonstrated by the in situ investigation of damage nucleation inside alloy sheets under engineering-relevant boundary conditions, providing novel insight into the nanoscale morphological development of void and particle clusters under mechanical load. Combined with digital volume correlation, we study deformation kinematics with unprecedented spatial resolution. Correlation of mesoscale (i.e. strain fields) and nanoscale (i.e. particle cracking) evolution opens new routes for the understanding of damage nucleation within sheet materials with application-relevant dimensions.

The hexagonal ferrite h-YbFeO3 grown on YSZ(111) by pulsed laser deposition is foreseen as a promising single multiferroic candidate where ferroelectricity and antiferromagnetism coexist for future applications at low temperatures. We studied in detail the microstructure as well as the temperature dependence of the magnetic properties of the devices by comparing the heterostructures grown directly on YSZ(111) (i.e., YbPt_Th0nm) with h-YbFeO3 films deposited on substrates buffered with platinum Pt/YSZ(111) and in dependence on the Pt underlayer film thickness (i.e., YbPt_Th10nm, YbPt_Th40nm, YbPt_Th55nm, and YbPt_Th70nm). The goal was to deeply understand the importance of the crystal quality and morphology of the Pt underlayer for the h-YbFeO3 layer crystal quality, surface morphology, and the resulting physical properties. We demonstrate the relevance of homogeneity, continuity, and hillock formation of the Pt layer for the h-YbFeO3 microstructure in terms of crystal structure, mosaicity, grain boundaries, and defect distribution. The findings of transmission electron microscopy and X-ray diffraction reciprocal space mapping characterization enable us to conclude that an optimum film thickness for the Pt bottom electrode is ThPt = 70 nm, which improves the crystal quality of h-YbFeO3 films grown on Pt-buffered YSZ(111) in comparison with h-YbFeO3 films grown on YSZ(111) (i.e., YbPt_Th0nm). The latter shows a disturbance in the crystal structure, in the up-and-down atomic arrangement of the ferroelectric domains, as well as in the Yb–Fe exchange interactions. Therefore, an enhancement in the remanent and in the total magnetization was obtained at low temperatures below 50 K for h-YbFeO3 films deposited on Pt-buffered substrates Pt/YSZ(111) when the Pt underlayer reached ThPt = 70 nm.

The structure and the chemical composition of individual layers as well as of interfaces belonging to the two heterostructures M1 (BaFe12O19/YbFeO3/YSZ) and M2 (YbFeO3/BaFe12O19/YSZ) grown by pulsed laser deposition on yttria-stabilized zirconia (YSZ) substrates are deeply characterized by using a combination of methods such as high-resolution X-ray diffraction, transmission electron microscopy (TEM), and atomic-resolution scanning TEM with energy-dispersive X-ray spectroscopy. The temperature-dependent magnetic properties demonstrate two distinct heterostructures with different coercivity, anisotropy fields, and first anisotropy constants, which are related to the defect concentrations within the individual layers and to the degree of intermixing at the interface. The heterostructure with the stacking order BaFe12O19/YbFeO3, i.e., M1, exhibits a distinctive interface without any chemical intermixture, while an Fe-rich crystalline phase is observed in M2 both in atomic-resolution EDX maps and in mass density profiles. Additionally, M1 shows high c-axis orientation, which induces a higher anisotropy constant K1 as well as a larger coercivity due to a high number of phase boundaries. Despite the existence of a canted antiferromagnetic/ferromagnetic combination (T < 140 K), both heterostructures M1 and M2 do not reveal any detectable exchange bias at T = 50 K. Additionally, compressive residual strain on the BaM layer is found to be suppressing the ferromagnetism, thus reducing the Curie temperature (Tc) in the case of M1. These findings suggest that M1 (BaFe12O19/YbFeO3/YSZ) is suitable for magnetic storage applications.

The morphology and crystal structure of Pt films grown by pulsed laser deposition (PLD) on yttria-stabilized zirconia (YSZ)at high temperatures Tg = 900 °C was studied for four different film thicknesses varying between 10 and 70 nm. During the subsequent growth of the capping layer, the thermal stability of the Pt was strongly influenced by the Pt film’s thickness. Furthermore, these later affected the film morphology, the crystal structure and hillocks size, and distribution during subsequent growth at Tg = 900 °C for a long duration. The modifications in the morphology as well as in the structure of the Pt film without a capping layer, named also as the as-grown and encapsulated layers in the bilayer system, were examined by a combination of microscopic and scattering methods. The increase in the thickness of the deposited Pt film brought three competitive phenomena into occurrence, such as 3D–2D morphological transition, dewetting, and hillock formation. The degree of coverage, film continuity, and the crystal quality of the Pt film were significantly improved by increasing the deposition time. An optimum Pt film thickness of 70 nm was found to be suitable for obtaining a hillock-free Pt bottom electrode which also withstood the dewetting phenomena revealed during the subsequent growth of capping layers. This achievement is crucial for the deposition of functional bottom electrodes in ferroelectric and multiferroic heterostructure systems.

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.

Abstract Atomistic processes during pulsed-laser deposition (PLD) growth influence the physical properties of the resulting films. We investigated the PLD of epitaxial layers of hexagonal LuFeO $$_3$$ 3 by measuring the X-ray diffraction intensity in the quasiforbidden reflection 0003 in situ during deposition. From measured X-ray diffraction intensities we determined coverages of each layer and studied their time evolution which is described by scaling exponent $$\beta$$ β directly connected to the surface roughness. Subsequently we modelled the growth using kinetic Monte Carlo simulations. While the experimentally obtained scaling exponent $$\beta$$ β decreases with the laser frequency, the simulations provided the opposite behaviour. We demonstrate that the increase of the surface temperature caused by impinging ablated particles satisfactorily explains the recorded decrease in the scaling exponent with the laser frequency. This phenomena is often overlooked during the PLD growth.

The aim of this study was to investigate the biocompatibility and osteoinductive properties of fibrous scaffolds implanted in the bone tissue of white rats in vivo. The effect of various concentrations of conductive PANi (2 and 3 wt%) and rGO (0.2 and 1 wt%) in the PHB scaffolds on the reparative processes of bone callus formation in white rats was studied. On the 28th day after implantation, a histomorphological study of the preparations of the transverse section of the diaphysis of the femur of the implantation area was performed. The results of implantation tests in the femur revealed that all the studied scaffolds are biocompatible and the most pronounced stimulating effect on bone formation was observed for hybrid PHB scaffolds doped with 3 wt% PANi and 0.2 wt% rGO compared with pure PHB scaffolds, thus determining further prospects to study the osteoinductive features of hybrid PHB scaffolds.