X-ray Phase Contrast Research Articles

Investigating gut alterations in Alzheimer's disease: In-depth analysis with micro- and nano-3D X-ray phase contrast tomography.

Alzheimer's disease (AD), a debilitating neurodegenerative disorder, remains one of the foremost public health challenges affecting more than 30 million people worldwide with the etiology still largely enigmatic. The intricate gut-brain axis, serving as a vital communication network between the gut and the brain, appears to wield influence in the progression of AD. Our study showcases the remarkable precision of x-ray phase-contrast tomography (XPCT) in conducting an advanced three-dimensional examination of gut cellular composition and structure. The exploitation of micro- and nano-XPCT on various AD mouse models unveiled relevant alterations in villi and crypts, cellular transformations in Paneth and goblet cells, along with the detection of telocytes, neurons, erythrocytes, and mucus secretion by goblet cells within the gut cavity. The observed gut structural variations may elucidate the transition from dysbiosis to neurodegeneration and cognitive decline. Leveraging XPCT could prove pivotal in early detection and prognosis of the disease.

Efficient X-ray dark field contrast simulations using a condensed history approach.

Due to the growing interest in X-ray phase contrast imaging (XPCI), the development of XPCI simulators has become an active field of research. Efficient computer simulations are a prime tool for optimizing the XPCI setup and acquisition process. In addition to phase contrast, modern XPCI setups provide insight into the unresolvable sample micro structure distribution through the dark field signal. However, to accurately simulate XPCI dark field signals, the virtual sample model should contain many fine structures, considerably increasing the simulation time. Moreover, accurately modeling micro structure distributions is challenging and the micro structure distribution of one virtual sample cannot be easily transferred to another. In this work, we apply a condensed history approach to dark field simulations, removing the need to explicitly model the micro structures in the virtual sample. Instead, a tunable dark field material parameter, representing a measure of the material micro structure distribution, is attached to the sample. The condensed history simulation model offers a substantial increase in simulation speed and the dark field material parameter is easily transferable between samples. The implementation is validated using the edge illumination XPCI setup. Condensed history simulations are compared to real data, showing good agreement, and the simulation speed increase is presented for increasing sample thickness and field of view. The simulation model is shown to remain valid even for thick samples. Simulated computed tomography data sets, with and without explicit micro structure, are favorably compared to each other.

Three-dimensional structure of entire hydrated murine hearts at histological resolution

Imaging the entire cardiomyocyte network in entire small animal hearts at single cell resolution is a formidable challenge. Optical microscopy provides sufficient contrast and resolution in 2d, however fails to deliver non-destructive 3d reconstructions with isotropic resolution. It requires several invasive preparation steps, which introduce structural artefacts, namely dehydration, physical slicing and staining, or for the case of light sheet microscopy also clearing of the tissue. Our goal is to provide 3d reconstructions of the cardiomyocyte network in entire hydrated murine hearts, and to develop a methodology for quantitative analysis of heart pathologies based on X-ray phase contrast computed tomography (XPCT). We have used XPCT at two beamlines of the extremely brilliant source (EBS) at the European Synchrotron Radiation Facility (ESRF) to scan wild-type murine hearts at high resolution, as well as a series of murine hearts of different pathological models, at reduced resolution and higher throughput. All hearts were obtained from the small animal facility of the university medical center in Göttingen. The hearts were fixed in formalin, stored and measured non-destructively in phosphate buffer solution. The high resolution dataset allows to discern individual cardiomyocytes in the tissue. All datasets have been analyzed using semi-automated image segmentation of the ventricles, rotation into a common coordinate system, classification into different anatomical compartments, and finally the structure tensor approach. A 3d streamline representation of the cardiomyocyte orientation vector field is provided. The different cardiovascular disease models are analysed based on metrics derived from the 3d structure tensor. An entire hydrated murine heart has been covered at an isotropic voxel size of 1.6μm (distributed over several volumes). A binned and fused dataset of this heart is available at 3.2μm, and has been analyzed by the structure tensor approach to yield the ventricular cardiomyocyte network or mesh, i.e. the aggregation of the cardiomyocyte chains in particular in the ventricular wall. Semi-automatic determination of structural metrics is already achieved and the corresponding tools and resulting data are made publically available. XPCT using extremely brilliant undulator radiation is close to achieve single cell reconstruction in an entire small animal organ.

Optimising CPAP and oxygen levels to support spontaneous breathing in preterm rabbits.

Very preterm infants often require respiratory support after birth with current recommendations suggesting the use of continuous positive airway pressure (CPAP) of 4-8 cmH2O and an initial fraction of inspired oxygen (FiO2) of 0.21-0.3. We have examined the interaction of high and low CPAP and FiO2 levels on breathing rates and lung aeration in preterm rabbits. Prematurely delivered rabbits (29/32 days gestation) received CPAP of either 5cmH2O (5CPAP; n = 12) or 15 cmH2O (15CPAP; n = 14), and a FiO2 of either 0.3 (5CPAP/0.3, n = 6 or 15CPAP/0.3, n = 7) or 0.6 (5CPAP/0.6, n = 6 or 15CPAP/0.6, n = 7). Breathing rates, lung aeration (functional residual capacity; FRC), lung bulging and air accumulation in the stomach were measured using phase-contrast X-ray imaging. Kittens receiving 0.6 FiO2 had higher breathing rates (5CPAP/0.6: 32.6±6.4 breaths/min; p = 0.0064 and 15CPAP/0.6: 36.9±3.5breaths/min; p = 0.0010) than 5CPAP/0.3 kittens (11.8±4.1breaths/min). Kittens receiving 15CPAP/0.6 tended to have higher FRC volumes (34.9±4 mL/kg) than kittens receiving 5 cmH2O CPAP (5CPAP/0.3: 13.1±6mL/kg; p = 0.0675 and 5CPAP/0.6: 13.5±6 mL/kg; p = 0.1720) and 15CPAP/0.3 (22.5 ± 6.6 mL/kg; p = 0.4245). Lung bulging and air accumulation in the stomach were not different between groups. Preterm rabbits supported with both 15 cmH2O CPAP and 0.6 FiO2 increased spontaneous breathing rates and lung aeration without increasing the risk of air in the stomach or lung bulging. While current guidelines recommend the use of low CPAP (4-8 cmH2O) and low FiO2 levels (0.21-0.3 FiO2) to support preterm infants at birth, the optimum levels are unknown. This study has shown that 15 cmH2O of CPAP and FiO2 of 0.6 improved lung aeration and breathing in preterm rabbits, compared with a CPAP of 4 cmH2O and FiO2 of 0.3. These results add to the evidence indicating that initial high CPAP and high FiO2 levels, followed by titration of both, enhance respiratory support for preterm newborns.

External negative pressure improves lung aeration in near-term rabbit kittens at risk of developing respiratory distress.

As airway liquid is cleared into lung interstitial tissue after birth, the chest wall must expand to accommodate this liquid and the incoming air. We examined the effect of applying external positive and negative pressures to the chest wall on lung aeration in near-term rabbit kittens at risk of developing respiratory distress. Rabbit kittens (30 days; term ∼31 days) were randomised into Control and Elevated Liquid (EL) groups. Lung liquid was drained in Control kittens to simulate expected volumes following vaginal delivery. EL kittens had lung liquid drained before 30 ml/kg was returned to simulate expected volumes after caesarean section. Kittens were delivered, placed in a water-filled plethysmograph and the external pressure was adjusted to -6 (negative), 0 (atmospheric), or +6 (positive) cmH2O. Kittens were ventilated with an 8 ml/kg tidal volume and PEEP of 0 cmH2O and lungs imaged using phase contrast x-ray imaging. Compared to external atmospheric pressures, external negative pressures expanded the chest (by 2100 ± 43 vs. 1805 ± 59 mm2; Control kittens; P = 0.028), directed tidal ventilation into lower, larger lung regions and increased functional residual capacity (FRC) levels in both Control (26.7 ± 2.0 vs. 12.6 ± 2.2 ml/kg; P < 0.001) and EL (19.6 ± 1.6 vs. 10.0 ± 2.9 ml/kg; P < 0.01) kittens. External positive pressures reduced FRC levels in Control (6.3 ± 0.8 vs. 12.6 ± 2.2 ml/kg; P < 0.05), but not in EL kittens, and directed tidal ventilation into upper lung regions. External negative pressures increased lung aeration and resulted in a more evenly distributed tidal ventilation immediately after birth in near-term rabbit kittens, whereas external positive pressures reduced lung aeration and compliance.

Laboratory-based x-ray phase contrast microscopy system for targeting in unstained soft-tissue samples

Laboratory-based x-ray phase contrast microscopy system for targeting in unstained soft-tissue samples

The use of ethanol as contrast enhancer in synchrotron X-ray phase-contrast imaging leads to heterogeneous myocardial tissue shrinkage: a case report.

One of the main limitations of conventional absorption-based X-ray micro-computed tomography imaging of biological samples is the low inherent X-ray contrast of soft tissue. To overcome this limitation, the use of ethanol as contrast agent has been proposed to enhance image contrast of soft tissues through dehydration. Some authors have shown that ethanol shrinks and hardens the tissue too much, also causing small tissue ruptures due to fast dehydration. However, the local tissue deformation occurring as a consequence of tissue dehydration and whether tissue shrinkage can modify myocardial architecture has not been quantified yet. The aim of this paper is to quantify the local myocardial tissue deformation due to ethanol dehydration based on 3D non-rigid registration and perform a detailed characterization of its myocardial tissue organization, before and after ethanol dehydration. A rat adult heart was imaged with synchrotron-radiation-based X-ray phase contrast imaging (X-PCI) three times: before, 9 h after and 342 h after ethanol immersion. The total volume shrinkage as well as changes in the left ventricular myocardial thickness were computed. Then, to determine local deformation of the heart caused by ethanol dehydration, the related 3D tomographic datasets were registered by means of a non-rigid registration algorithm. Finally, changes on the orientation and organization of myocytes were assessed. Our results show that the use of ethanol in synchrotron X-PCI can improve image contrast, but the tissue shrinkage is not homogeneous thus changing the local myocardial organization.

Development of MHz X-ray phase contrast imaging at the European XFEL.

We report on recent developments that enable megahertz hard X-ray phase contrast imaging (MHz XPCI) experiments at the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument of the European XFEL facility (EuXFEL). We describe the technical implementation of the key components, including an MHz fast camera and a modular indirect X-ray microscope system based on fast scintillators coupled through a high-resolution optical microscope, which enable full-field X-ray microscopy with phase contrast of fast and irreversible phenomena. The image quality for MHz XPCI data showed significant improvement compared with a pilot demonstration of the technique using parallel beam illumination, which also allows access to up to 24 keV photon energies at the SPB/SFX instrument of the EuXFEL. With these developments, MHz XPCI was implemented as a new method offered for a broad user community (academic and industrial) and is accessible via standard user proposals. Furthermore, intra-train pulse diagnostics with a high few-micrometre spatial resolution and recording up to 128 images of consecutive pulses in a train at up to 1.1 MHz repetition rate is available upstream of the instrument. Together with the diagnostic camera upstream of the instrument and the MHz XPCI setup at the SPB/SFX instrument, simultaneous two-plane measurements for future beam studies and feedback for machine parameter tuning are now possible.

Review and experimental comparison of speckle-tracking algorithms for X-ray phase contrast imaging.

X-ray speckles have been used in a wide range of experiments, including imaging (and tomography), wavefront sensing, spatial coherence measurements, X-ray photon correlation spectroscopy and ptychography. In this review and experimental comparison, we focus on using X-ray near-field speckle grains as wavefront markers and numerical methods for retrieving the phase information they contain. We present the most common tracking methods, introducing the existing algorithms with their specifications and comparing their performances under various experimental conditions. This comparison includes applications to different types of samples: phantoms for quantitative analysis and complex samples for assessing image quality. Our goal is to unify concepts from several speckle tracking methods using consistent terminology and equation formalism, while keeping the discussion didactic and accessible to a broad audience.

In situ characterisation of dynamic fracture in Al2O3 using ultra-fast X-ray phase contrast radioscopy: effects of porosity and crack speed

The dynamic fracture properties of porous ceramics were studied using single bunch synchrotron X-ray phase contrast imaging. The modified brazilian geometry was used to initiate and propagate a pure mode I crack. The specimen was compressed using the Split Hopkinson bars at strain rates of the order of 102 s-1. Main cracks were isolated for four different grades of Al2O3, one dense alumina, and three porous grades with 20% to 60% porosity. The maximum measured crack velocities for three grades is of the order of 0.6cR and 0.4cR for the most porous. The fracture energy was estimated using a FE numerical simulation to quantify the influence of inertial effects induced by crack propagation. The results show that these inertial effects are far from negligible (up to 80% of the stored energy) and that the dynamic correction factors known from the literature tend to overestimate the fracture energy. The values obtained vary from 22 J/m2 for the densest to 5 J/m2 for the most porous.

X-ray phase contrast imaging and diffraction in the laser-heated diamond anvil cell: A case study on the high-pressure melting of Pt

X-ray phase contrast imaging and diffraction in the laser-heated diamond anvil cell: A case study on the high-pressure melting of Pt

Evaluation Image Quality of Self-produced Phantom for Nano Electromagnetic Wave X-ray Phase Contrast Imaging

Evaluation Image Quality of Self-produced Phantom for Nano Electromagnetic Wave X-ray Phase Contrast Imaging

Combined speckle- and propagation-based single shot two-dimensional phase retrieval method

Single-shot two-dimensional (2D) phase retrieval (PR) can recover the phase shift distribution within an object from a single 2D x-ray phase contrast image (XPCI). Two competing XPCI imaging modalities often used for single-shot 2D PR to recover material properties critical for predictive performance capabilities are: speckle-based (SP-XPCI) and propagation-based (PB-XPCI) XPCI imaging. However, PR from SP-XPCI and PB-XPCI images are, respectively, limited to reconstructing accurately slowly and rapidly varying features due to noise and differences in their contrast mechanisms. Herein, we consider a combined speckle- and propagation-based XPCI (SPB-XPCI) image by introducing a mask to generate a reference pattern and imaging in the near-to-holographic regime to induce intensity modulations in the image. We develop a single-shot 2D PR method for SPB-XPCI images of pure phase objects without imposing restrictions such as object support constraints. It is compared against PR methods inspired by those developed for SP-XPCI and PB-XPCI on simulated and experimental images of a thin glass shell before and during shockwave compression. Reconstructed phase maps show improvements in quantitative scores of root-mean-square error and structural similarity index measure using our proposed method.

Self-supervised Resolution Enhancement for Anisotropic Volumes in Edge Illumination X-ray Phase Contrast Micro-Computed Tomography

Self-supervised Resolution Enhancement for Anisotropic Volumes in Edge Illumination X-ray Phase Contrast Micro-Computed Tomography

Fabrication and X-ray microtomography of sandwich-structured PEEK implants for skull defect repair

Bone defects pose a significant risk to human health. Medical polyetheretherketone (PEEK) is an excellent implant material for bone defect repair, but it faces the challenge of bone osteoconduction and osseointegration. Osteoconduction describes the process by which bone grows on the surface of the implant, while osseointegration is the stable anchoring of the implant achieved by direct contact between the bone and the implant. Bone defects repair depends on the implant’s three-dimensional spatial structure, including pore size, porosity, and interconnections to a great extent. However, it is challenging to fabricate the porous structures to meet specific requirements and to characterize them without causing damage. In this study, we designed and fabricated sandwich-like PEEK implants mimicking the three-layer structures of the skull, whose defects imposes a significant burden on young adulthood and paediatric populations, and performed in-line phase-contrast synchrotron X-ray microtomography to non-destructively investigate the internal porous microstructures. The sandwich-like three-layer microstructure, comprising a dense layer, a loose layer and a dense layer in succession, exhibits structural similarity to that in a natural skull. This work demonstrated the fabrication of the sandwich-like PEEK implant that could potentially enhance osteoconduction and osseointegration. Furthermore, the interior structures and residual porogen sodium chloride particles were observed within the PEEK implant, which cannot be realized by other microscopic methods without destroying the sample. It highlights the advantages and potential of using synchrotron X-ray microtomography to analyze the structure of biomedical materials. This study provides theoretical guidance for the further design and fabrication of PEEK bone repair materials and will advance the clinical application of innovative bioactive bone repair materials.

Study of shocks and ablation front in diamond ablator during a capsule implosion experiment at the National Ignition Facility

An X-ray phase contrast imaging platform using streaked refraction enhanced radiography (RER) was recently developed for capsule implosions at the National Ignition Facility. RER was demonstrated to image in-flight capsule density gradients such as the fuel-ablator interface that is not visible in traditional absorption only radiography. The latest experiments probing the early time evolution of the implosion allowed the precise measurement of the density gradients. An iterative analysis method has been applied to the RER radiograph to allow the reconstruction of temporal evolution of the radial density distribution from the ice-ablator interface to the ablation front. The estimated density reconstruction precision is ±2.4% with a density gradient sensitivity threshold of 1023cm−3 over a 2μm scale length. This enabled the study of shocks velocity and density gradients as well as ablation front scale length and shape.

Restoration of X-ray phase-contrast imaging based on generative adversarial networks

For light-element materials, X-ray phase contrast imaging provides better contrast compared to absorption imaging. While the Fourier transform method has a shorter imaging time, it typically results in lower image quality; in contrast, the phase-shifting method offers higher image quality but is more time-consuming and involves a higher radiation dose. To rapidly reconstruct low-dose X-ray phase contrast images, this study developed a model based on Generative Adversarial Networks (GAN), incorporating custom layers and self-attention mechanisms to recover high-quality phase contrast images. We generated a simulated dataset using Kaggle’s X-ray data to train the GAN, and in simulated experiments, we achieved significant improvements in Peak Signal-to-Noise Ratio (PSNR) and Structural Similarity Index (SSIM). To further validate our method, we applied it to fringe images acquired from three phase contrast systems: a single-grating phase contrast system, a Talbot-Lau system, and a cascaded grating system. The current results demonstrate that our method successfully restored high-quality phase contrast images from fringe images collected in experimental settings, though it should be noted that these results were achieved using relatively simple sample configurations.

The osteohistology of Orthosuchus stormbergi using synchrotron radiation microcomputed tomography.

Orthosuchus stormbergi was a small-bodied crocodyliform, representative of a diverse assemblage of Early Jurassic, early branching crocodylomorph taxa from the upper Elliot Formation of South Africa. The life history of these early branching taxa remains poorly understood, with only sparse investigations into their osteohistology, yet species like Orthosuchus have potential to inform about the macroevolution of growth strategies on the stem leading to crown crocodilians. In order to elucidate the growth patterns of Orthosuchus, we used propagation phase contrast X-ray synchrotron micro-computed tomography to virtually image the osteohistology of the postcrania of two specimens, including multiple elements from the type (SAM-PK-K409), and the femur of a referred specimen (BP/1/4242). In total, we scanned nine mid-diaphyseal sections of the humerus, radius, ulna, radiale, femur, tibia, fibula, and a rib. We then compared our results to osteohistological sections of crocodylomorph taxa from the published literature. Our results show that the most predominant bone tissue type in Orthosuchus is lamellar, with a few patches of woven and parallel-fibred bone. The type specimen contains four to five lines of arrested growth and the hindlimb elements present outer circumferential lamellae, whereas the referred specimen contains six to seven. Both specimens grew at similar rates, reaching adult skeletal body size at year four or five. The sectioned bones, most notably the radius and ulna, are comparatively thick walled and compact. Our virtual osteohistological sections are one of the first for an early branching crocodyliform, and the broad sample of skeletal elements makes Orthosuchus a key anchor point for understanding the plesiomorphic life history traits of the clade.

Advanced three-dimensional X-ray imaging unravels structural development of the human thymus compartments

BackgroundThe thymus, responsible for T cell-mediated adaptive immune system, has a structural and functional complexity that is not yet fully understood. Until now, thymic anatomy has been studied using histological thin sections or confocal microscopy 3D reconstruction, necessarily for limited volumes.MethodsWe used Phase Contrast X-Ray Computed Tomography to address the lack of whole-organ volumetric information on the microarchitecture of its structural components. We scanned 15 human thymi (9 foetal and 6 postnatal) with synchrotron radiation, and repeated scans using a conventional laboratory x-ray system. We used histology, immunofluorescence and flow cytometry to validate the x-ray findings.ResultsApplication to human thymi at pre- and post-natal stages allowed reliable tracking and quantification of the evolution of parameters such as size and distribution of Hassall’s Bodies and medulla-to-cortex ratio, whose changes reflect adaptation of thymic activity. We show that Hassall’s bodies can occupy 25% of the medulla volume, indicating they should be considered a third thymic compartment with possible implications on their role. Moreover, we demonstrate compatible results can be obtained with standard laboratory-based x-ray equipment, making this research tool accessible to a wider community.ConclusionsOur study allows overcoming the resolution and/or volumetric limitations of existing approaches for the study of thymic disfunction in congenital and acquired disorders affecting the adaptive immune system.

Synchrotron X-ray imaging of soft biological tissues - principles, applications and future prospects.

Synchrotron-based tomographic phase-contrast X-ray imaging (SRµCT or SRnCT) is a versatile isotropic three-dimensional imaging technique that can be used to study biological samples spanning from single cells to human-sized specimens. SRµCT and SRnCT take advantage of the highly brilliant and coherent X-rays produced by a synchrotron light source. This enables fast data acquisition and enhanced image contrast for soft biological samples owing to the exploitation of phase contrast. In this Review, we provide an overview of the basics behind the technique, discuss its applications for biologists and provide an outlook on the future of this emerging technique for biology. We introduce the latest advances in the field, such as whole human organs imaged with micron resolution, using X-rays as a tool for virtual histology and resolving neuronal connections in the brain.