X-ray Phase Contrast Research Articles

3D imaging of SARS-CoV-2 infected hamster lungs by X-ray phase contrast tomography enables drug testing

X-ray Phase Contrast Tomography (XPCT) based on wavefield propagation has been established as a high resolution three-dimensional (3D) imaging modality, suitable to reconstruct the intricate structure of soft tissues, and the corresponding pathological alterations. However, for biomedical research, more is needed than 3D visualisation and rendering of the cytoarchitecture in a few selected cases. First, the throughput needs to be increased to cover a statistically relevant number of samples. Second, the cytoarchitecture has to be quantified in terms of morphometric parameters, independent of visual impression. Third, dimensionality reduction and classification are required for identification of effects and interpretation of results. To address these challenges, we here design and implement a novel integrated and high throughput XPCT imaging and analysis workflow for 3D histology, pathohistology and drug testing. Our approach uses semi-automated data acquisition, reconstruction and statistical quantification. We demonstrate its capability for the example of lung pathohistology in Covid-19. Using a small animal model, different Covid-19 drug candidates are administered after infection and tested in view of restoration of the physiological cytoarchitecture, specifically the alveolar morphology. To this end, we then use morphometric parameter determination followed by a dimensionality reduction and classification based on optimal transport. This approach allows efficient discrimination between physiological and pathological lung structure, thereby providing quantitative insights into the pathological progression and partial recovery due to drug treatment. Finally, we stress that the XPCT image chain implemented here only used synchrotron radiation for validation, while the data used for analysis was recorded with laboratory μ\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mu$$\\end{document}CT radiation, more easily accessible for pre-clinical research.

Progressive Weakening of Granite by Piezoelectric Excitation of Quartz with Alternating Current

A promising solution to reduce energy usage and mitigate the wear of drilling and comminution tools during mining operations involves inducing vibrations within the piezoelectric phases dispersed in the structure of rocks using alternating current (AC). This paper presents experimental evidence of AC-induced weakening of Kuru granite, manifested as improvements in rock drillability and reductions of strength. Sievers’ J-miniature drill tests were used to assess surface drillability. The impact of AC treatment on the quasi-static strength of granite was assessed via three-point bending and indirect tension Brazilian disk tests. The influence of AC treatment on the dynamic tensile strength of the rock was determined using split Hopkinson bar tests, with the fragmentation process captured using in situ ultra-fast synchrotron X-ray phase contrast imaging. The quasi-static tests revealed no reduction in rock strength after the AC treatment. In contrast, reductions of 25% in hardness and 18% in dynamic tensile strength were observed. Fragmentation patterns differed between treated and non-treated rocks, with treated specimens exhibiting reduced macrocrack formation during loading.

Characterization of spring and durum wheat using non-destructive synchrotron phase contrast X-ray microtomography during storage

Post-harvest losses during cereal grain storage are a big concern in both developing and developed countries, where spring and durum wheat are staple food grains. Varieties under these classes behave differently under storage, which affects their end storage life. High resolution imaging data of dry as well as spoiled seed are not available for any class of wheat; therefore, an attempt was made to generate 3D data for better understanding of seed structure and changes due to spoilage. Six wheat varieties (3 varieties for each class of wheat) were stored for 5 week at 17% moisture content (wb) before scanning. Seeds were also stored in a freezer (-18 °C) for further scanning to determine if any changes occur in the structure of seeds due to freezing. Spring varieties of wheat performed better than durum varieties and freezing did not affect seed structure. Data could also help plant breeders to develop varieties that do not easily spoil, adjust grain processing techniques, and develop post-harvest recommendations for other wheat varieties.

Phase contrast micro-CT with adjustable in-slice spatial resolution at constant magnification

Objective. To report on a micro computed tomography (micro-CT) system capable of x-ray phase contrast imaging and of increasing spatial resolution at constant magnification. Approach. The micro-CT system implements the edge illumination (EI) method, which relies on two absorbing masks with periodically spaced transmitting apertures in the beam path; these split the beam into an array of beamlets and provide sensitivity to the beamlets’ directionality, i.e. refraction. In EI, spatial resolution depends on the width of the beamlets rather than on the source/detector point spread function (PSF), meaning that resolution can be increased by decreasing the mask apertures, without changing the source/detector PSF or the magnification. Main results. We have designed a dedicated mask featuring multiple bands with differently sized apertures and used this to demonstrate that resolution is a tuneable parameter in our system, by showing that increasingly small apertures deliver increasingly detailed images. Phase contrast images of a bar pattern-based resolution phantom and a biological sample (a mouse embryo) were obtained at multiple resolutions. Significance. The new micro-CT system could find application in areas where phase contrast is already known to provide superior image quality, while the added tuneable resolution functionality could enable more sophisticated analyses in these applications, e.g. by scanning samples at multiple scales.

Effect of temperature on high strain-rate damage evolving in CFRP studied by synchrotron-based MHz X-ray phase contrast imaging

The present study demonstrates experimental evidence of subsurface mesoscale damage initiation and evolution in angle-ply CFRP laminates under high strain-rate loading at low temperatures using synchrotron-based X-ray MHz radiography. A bespoke set of loading, temperature control and in-situ X-ray imaging systems were applied to simultaneously correlate high strain-rate mechanical response with observed subsurface damage in a time-resolved manner. The results demonstrate that independent of temperature, damage evolved following a specific sequence; firstly intra-ply shear cracking along the fibre direction, developing into multi-layer cracking with continued deformation, and finally culminating in inter-ply delamination and complete failure of the specimen. The timescale for this sequence, however, was observed to strongly depend upon temperature, with low temperatures resulting in more rapid damage evolution and loss of mechanical strength.

Model-driven CT reconstruction algorithm for nano-resolution x-ray phase contrast imaging

Abstract The low-density imaging performance of a zone plate-based nano-resolution hard x-ray computed tomography (CT) system can be significantly improved by incorporating a grating-based Lau interferometer. Due to the diffraction, however, the acquired nano-resolution phase signal may suffer splitting problem, which impedes the direct reconstruction of phase contrast CT (nPCT) images. To overcome, a new model-driven nPCT image reconstruction algorithm is developed in this study. In it, the diffraction procedure is mathematically modeled into a matrix B , from which the projections without signal splitting can be generated invertedly. Furthermore, a penalized weighted least-square model with total variation (PWLS-TV) is employed to denoise these projections, from which nPCT images with high accuracy are directly reconstructed. Numerical experiments demonstrate that this new algorithm is able to work with phase projections having any splitting distances. Moreover, results also reveal that nPCT images of higher signal-to-noise-ratio (SNR) could be reconstructed from projections having larger splitting distances. In summary, a novel model-driven nPCT image reconstruction algorithm with high accuracy and robustness is verified for the Lau interferometer-based hard x-ray nano-resolution phase contrast imaging.

Transport-of-intensity model for single-mask x-ray differential phase contrast imaging

X-ray phase contrast imaging holds great promise for improving the visibility of light-element materials such as soft tissues and tumors. The single-mask differential phase contrast imaging method stands out as a simple and effective approach to yield differential phase contrast. In this work, we introduce a model for a single-mask phase imaging system based on the transport-of-intensity equation. Our model provides an accessible understanding of signal and contrast formation in single-mask x-ray phase imaging, offering a clear perspective on the image formation process, for example, the origin of alternate bright and dark fringes in phase contrast intensity images. Aided by our model, we present an efficient retrieval method that yields differential phase contrast imagery in a single acquisition step. Our model gives insight into the contrast generation and its dependence on the system geometry and imaging parameters in both the initial intensity image as well as retrieved images. The model validity as well as the proposed retrieval method are demonstrated via both experimental results on a system developed in house as well as Monte Carlo simulations. In conclusion, our work not only provides a model for an intuitive visualization of image formation but also offers a method to optimize differential phase imaging setups, holding tremendous promise for advancing medical diagnostics and other applications.

Detection of early pulmonary emphysema by multi-contrast x-ray Talbot-Lau interferometer.

Pulmonary emphysema is a part of chronic obstructive pulmonary disease, which is an irreversible chronic respiratory disease. In order to avoid further damage to lung tissue, early diagnosis and treatment of pulmonary emphysema is essential. Early pulmonary emphysema diagnosis is difficult with conventional radiographic imaging. Recently, x-ray phase contrast imaging has proved to be an effective and promising imaging strategy for soft tissue, due to its high sensitivity and multi-contrast. The aim of this study is to diagnose pulmonary emphysema early utilizing an x-ray Talbot-Lau interferometer (TLI). We successfully established the mouse model of emphysema by porcine pancreatic elastase treatment, and then used the established x-ray TLI to perform imaging experiments on the mice with different treatment time. The traditional absorption CT and phase contrast CT were obtained simultaneously through TLI. The CT results and histopathology of mice lung in different treatment time were quantitatively analyzed. By imaging mice lungs, it can be found that phase contrast has higher sensitivity than absorption contrast in early pulmonary emphysema. The results show that the phase contrast signal could distinguish the pulmonary emphysema earlier than the conventional attenuation signal, which can be consistent with histological images. Through the quantitative analysis of pathological section and phase contrast CT, it can be found that there is a strong linear correlation. In this study, we quantitatively analyze mean linear intercept of histological sections and CT values of mice. The results show that the phase contrast signal has higher imaging sensitivity than the attenuation signal. X-ray TLI multi-contrast imaging is proved as a potential diagnostic method for early pulmonary emphysema in mice.

Referenceless, grating-based, single shot X-ray phase contrast imaging with optimized laser-driven K-𝛼 sources

Referenceless, grating-based, single shot X-ray phase contrast imaging with optimized laser-driven K-𝛼 sources

Edge illumination x-ray phase contrast simulations using the CAD-ASTRA toolbox.

Edge illumination x-ray phase contrast imaging (XPCI) provides increased contrast for low absorbing materials compared to attenuation images and sheds light on the material microstructure through dark field contrast. To apply XPCI in areas such as non-destructive testing and inline inspection, where scanned samples are increasingly compared to simulated reference images, accurate and efficient simulation software is required. However, currently available simulators rely on expensive Monte Carlo techniques or wave-optics frameworks, resulting in long simulation times. Furthermore, these simulators are often not optimized to work with computer-aided design (CAD) models, a common and memory-efficient method to represent manufactured objects, hindering their integration in an inspection pipeline. In this work, we address these shortcomings by introducing an edge illumination XPCI simulation framework built upon the recently developed CAD-ASTRA toolbox. CAD-ASTRA allows for the efficient simulation of x-ray projections from CAD models through GPU-accelerated ray tracing and supports ray refraction in a geometric optics framework. The edge illumination implementation is validated and its performance is benchmarked against GATE, a state-of-the-art Monte Carlo simulator, revealing a simulation speed increase of up to three orders of magnitude, while maintaining high accuracy in the resulting images.

Bottom-up Gold Filling of Trenches in Curved Wafers

A Bi3+ -stimulated Au electrodeposition process in slightly alkaline Na3AuSO32+Na2SO3 electrolytes has been previously demonstrated for void-free extreme bottom-up filling of high aspect ratio trenches in gratings that are key to advanced X-ray imaging technologies. Effective use of the full area of the gratings with conventional X-ray sources requires they have a finite radius of curvature to align the high aspect ratio Au-filled trenches with divergent X-rays. With that in mind, this work demonstrates bottom-up Au filling in gratings that are attached to curved holders. Contactless mapping of the Au-filled gratings captures residual curvature that is retained after their release from the curved holders (i.e., intrinsic curvature). X-ray diffraction captures the elastic strains in the Si underlying the Au-filled trenches of the grating. Complementary measurements on the surfaces of unpatterned Si wafers mounted on curved holders capture the actual curvatures and strains imposed in the mounted gratings. The gratings, either intrinsically curved or re-bent, provide high visibility across the entire field of view of an X-ray phase contrast imaging system with elastic strains substantially below those in planar gratings bent to the same radius.

Increase in the Resolution of Hard X-Ray Phase-Contrast Imaging in a Device Based on a Triple Laue-Case Interferometer

The possibility of increasing the resolution of X-ray phase-contrast imaging with a device based on a triple Laue-case interferometer is considered. To address one of the drawbacks of this scheme—the distortion of the interference pattern during diffraction of the object wave on the interferometer analyzer—it is proposed to replace the analyzer with two crystalline blocks of equal thickness. These blocks act as a diffraction lens, suppressing the mentioned distortions. Numerical simulations demonstrate that the low coherence of the initial radiation increases the quality of phase-contrast imaging using this method.

Monte Carlo simulation of phase-contrast X-ray imaging with a single-grid setup

Phase-contrast X-ray imaging is widely used to visualize the internal structures of samples that cannot be seen with conventional X-ray imaging. Among various phase-sensitive imaging techniques available—propagation-based, grating-interferometry, edge-illumination, and speckle-based—single-grid-based imaging, a variant of the speckle-based technique, provides benefits like single exposure and a simple setup. In this study, we developed a Monte Carlo (MC) simulator based on Geant4 for phase-contrast imaging with a single-grid setup. We then validated the MC simulations of single-grid imaging against theoretical predictions. Our results demonstrate that the phase-contrast images obtained using the simulator align well with the theoretical predictions. Moreover, we quantitatively investigated the effects of imaging parameters, such as X-ray focal spot size and grid period, on image quality using the MC simulator. This confirmed the viability of the simulator. We expect that this simulator will be useful in designing an optimal single-grid-based imaging setup.

On rapid compaction of granular materials: Combining experiments with in-situ imaging and mesoscale modeling

Grain and pore kinematics are important features of the response of granular materials to impact loading and rapid compaction. These kinematics and the associated material-phase stresses control solidification processes in shock-driven manufacturing and ignition in energetic materials. Diagnostics used in traditional gas-gun experiments cannot resolve spatially-heterogeneous grain and pore kinematics during granular compaction. Similarly, continuum models of the granular compaction process do not account for this spatial heterogeneity, making predictions of solidification or ignition challenging. Here, we propose a method of accessing spatially-heterogeneous grain and pore behaviors during rapid compaction which involves x-ray tomography, in-situ x-ray phase contrast imaging, and mesoscale numerical modeling. We use this method to study heterogeneous grain and pore kinematics and local stresses in a ductile aluminum powder impacted at velocities up to 800 m/s. We first validate the mesoscale model by comparing its predictions with x-ray measurements from an impact experiment on a sample that was used to generate a numerical microstructure. We then quantify the evolution of variables such as 3D pore sizes and local stresses. We comment on the role of microstructure on the granular material’s response and the sensitivity of the material response to changes in structure, impact velocity, and sample size.

The effect of vibrotactile stimulation on hypoxia-induced irregular breathing and apnea in preterm rabbits.

Manual tactile stimulation is used to counteract apnea in preterm infants, but it is unknown when this intervention should be applied. We compared an anticipatory to a reactive approach using vibrotactile stimulation to prevent hypoxia induced apneas. Preterm rabbit kittens were prematurely delivered and randomized to either group. All kittens breathed spontaneously with a positive airway pressure of 8 cmH2O while they were imaged using phase contrast X-ray. Irregular breathing (IB) was induced using gradual hypoxia. The anticipatory group received stimulation at the onset of IB and the reactive group if IB transitioned into apnea. Breathing rate (BR), heart rate (HR) and functional residual capacity (FRC) were compared. Anticipatory stimulation significantly reduced apnea incidence and maximum inter-breath intervals and increased BR following IB, compared to reactive stimulation. Recovery in BR but not HR was more likely with anticipatory stimulation, although both BR and HR were significantly higher at 120 s after stimulation onset. FRC values and variability were not different. Anticipated vibrotactile stimulation is more effective in preventing apnea and enhancing breathing when compared to reactive stimulation in preterm rabbits. Stimulation timing is likely to be a key factor in reducing the incidence and duration of apnea. Anticipated vibrotactile stimulation can prevent apnea and stimulate breathing effort in preterm rabbits. Anticipated vibrotactile stimulation increases the likelihood of breathing rate recovery following hypoxia induced irregular breathing, when compared to reactive stimulation. Automated stimulation in combination with predictive algorithms may improve the treatment of apnea in preterm infants.

Combining Wave and Particle Effects in the Simulation of X-ray Phase Contrast—A Review

X-ray phase-contrast imaging (XPCI) is a family of imaging techniques that makes contrast visible due to phase shifts in the sample. Phase-sensitive techniques can potentially be several orders of magnitude more sensitive than attenuation-based techniques, finding applications in a wide range of fields, from biomedicine to materials science. The accurate simulation of XPCI allows for the planning of imaging experiments, potentially reducing the need for costly synchrotron beam access to find suitable imaging parameters. It can also provide training data for recently proposed machine learning-based phase retrieval algorithms. The simulation of XPCI has classically been carried out using wave optics or ray optics approaches. However, these approaches have not been capable of simulating all the artifacts present in experimental images. The increased interest in dark-field imaging has also prompted the inclusion of scattering in XPCI simulation codes. Scattering is classically simulated using Monte Carlo particle transport codes. The combination of the two perspectives has proven not to be straightforward, and several methods have been proposed. We review the available literature on the simulation of XPCI with attention given to particular methods, including the scattering component, and discuss the possible future directions for the simulation of both wave and particle effects in XPCI.

Shock compression of a low-density carbon foam

Porous polymer foams are found in numerous applications where they may be subjected to dynamic compression. The shockwave properties of polymer foams have several features that make shock Hugoniot measurements and interpretation challenging. Here, we present a comparison of dynamic X-ray phase contrast imaging and traditional optical velocimetry approaches to measuring the shocked states for a low-density carbon foam. Overall, dynamic X-ray phase contrast imaging was found to reduce errors associated with the measured Hugoniot states. The foam exhibits anomalous compression as expected due to its high initial porosity arising from shock heating.

CAD-ASTRA: a versatile and efficient mesh projector for X-ray tomography with the ASTRA-toolbox.

Accurate and fast simulation of X-ray projection data from mesh models has many applications in academia and industry, ranging from 3D X-ray computed tomography (XCT) reconstruction algorithms to radiograph-based object inspection and quality control. While software tools for the simulation of X-ray projection data from mesh models are available, they lack either performance, public availability, flexibility to implement non-standard scanning geometries, or easy integration with existing 3D XCT software. In this paper, we propose CAD-ASTRA, a highly versatile toolbox for fast simulation of X-ray projection data from mesh models. While fully functional as standalone software, it is also compatible with the ASTRA toolbox, an open-source toolbox for flexible tomographic reconstruction. CAD-ASTRA provides three specialized GPU projectors based on state-of-the-art algorithms for 3D rendering, implemented using the NVIDIA CUDA Toolkit and the OptiX engine. First, it enables X-ray phase contrast simulations by modeling refraction through ray tracing. Second, it allows the back-propagation of projective errors to mesh vertices, enabling immediate application in mesh reconstruction, deep learning, and other optimization routines. Finally, CAD-ASTRA allows simulation of polychromatic X-ray projections from heterogeneous objects with a source of finite focal spot size. Use cases on a CAD-based inspection task, a phase contrast experiment, a combined mesh-volumetric data projection, and a mesh reconstruction demonstrate the wide applicability of CAD-ASTRA.

X-ray phase contrast reveals soft tissue and shell growth lines in mollusks

High-resolution 3D imaging of species with exoskeletons such as shell-bearing mollusks typically involves destructive steps. Nondestructive alternatives are desirable since samples can be rare and valuable, and destructive steps are time-consuming and may distort the tissue. Here, we show for the first time that propagation-based phase-contrast X-ray imaging can significantly increase contrast in mollusks with intact shells. By using the recently upgraded monochromator at the SPring-8 BL20B2 synchrotron beamline, we imaged six species of mollusks, showing that X-ray phase contrast enhances soft-tissue contrast. Features that are almost invisible in conventional attenuation-based micro-computed tomography (micro-CT) are clearly reproduced with phase-contrast imaging under the same scan conditions. Furthermore, this method can reveal features such as growth rings in the shell and differentiate between calcite and aragonite crystal forms. Phase-contrast imaging can thus serve as a compelling alternative when destructive methods are not an option.

Deep learning to overcome Zernike phase-contrast nanoCT artifacts for automated micro-nano porosity segmentation in bone.

Bone material contains a hierarchical network of micro- and nano-cavities and channels, known as the lacuna-canalicular network (LCN), that is thought to play an important role in mechanobiology and turnover. The LCN comprises micrometer-sized lacunae, voids that house osteocytes, and submicrometer-sized canaliculi that connect bone cells. Characterization of this network in three dimensions is crucial for many bone studies. To quantify X-ray Zernike phase-contrast nanotomography data, deep learning is used to isolate and assess porosity in artifact-laden tomographies of zebrafish bones. A technical solution is proposed to overcome the halo and shade-off domains in order to reliably obtain the distribution and morphology of the LCN in the tomographic data. Convolutional neural network (CNN) models are utilized with increasing numbers of images, repeatedly validated by `error loss' and `accuracy' metrics. U-Net and Sensor3D CNN models were trained on data obtained from two different synchrotron Zernike phase-contrast transmission X-ray microscopes, the ANATOMIX beamline at SOLEIL (Paris, France) and the P05 beamline at PETRA III (Hamburg, Germany). The Sensor3D CNN model with a smaller batch size of 32 and a training data size of 70 images showed the best performance (accuracy 0.983 and error loss 0.032). The analysis procedures, validated by comparison with human-identified ground-truth images, correctly identified the voids within the bone matrix. This proposed approach may have further application to classify structures in volumetric images that contain non-linear artifacts that degrade image quality and hinder feature identification.