High-resolution short-exposure small-animal laboratory x-ray phase-contrast tomography

Visualisation of gene expression within the context of tissues using an X-ray computed tomography-based multimodal approach

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.

Noncontact Respiratory Motion Detection in Anesthetized Rodents

Small animal physiology studies are often complicated, but the level of complexity is greatly increased when performing live-animal X-ray imaging studies at synchrotron radiation facilities. This is because these facilities are typically not designed specifically for biomedical research, and the animals and image detectors are located away from the researchers in a radiation enclosure. In respiratory X-ray imaging studies one challenge is the detection of respiration in free-breathing anaesthetised rodents, to enable images to be acquired at specific phases of the breath and for detecting changes in respiratory rate. We have previously used a Philtec RC60 sensor interfaced to a PowerLab data acquisition system and custom-designed timing hub to perform this task. Here we evaluated the Panasonic HL-G108 for respiratory sensing. The performance of the two sensors for accurate and reliable breath detection was directly compared using a single anesthetized rat. We also assessed how an infrared heat lamp used to maintain body temperature affected sensor performance. Based on positive results from these comparisons, the HL-G108 sensor was then used for respiratory motion detection in tracheal X-ray imaging studies of 21 rats at the SPring-8 Synchrotron, including its use for gated image acquisition. The results of that test were compared to a similar imaging study that used the RC60 for respiratory detection in 19 rats. Finally, the HL-G108 sensor was tested on 5 mice to determine its effectiveness on smaller species. The results showed that the HL-G108 is much more robust and easier to configure than the RC60 sensor and produces an analog signal that is amenable to stable peak detection. Furthermore, gated image acquisition produced sequences with substantially reduced motion artefacts, enabling the additional benefit of reduced radiation dose through the application of shuttering. Finally, the mouse experiments showed that the HL-G108 is equally capable of detecting respiration in this smaller species.

Optimization of phase contrast imaging with a nano-focus x-ray tube

Propagation-based phase contrast imaging with a laboratory x-ray source is a valuable tool for studying samples that show only low absorption contrast, either because of low density, elemental composition, or small feature size. If a propagation distance between sample and detector is introduced and the illumination is sufficiently coherent, the phase shift in the sample will cause additional contrast around interfaces, known as edge enhancement fringes. The strength of this effect depends not only on sample parameters and energy but also on the experimental geometry, which can be optimized accordingly. Recently, x-ray lab sources using transmission targets have become available, which provide very small source sizes in the few hundred nanometer range. This allows the use of a high-magnification geometry with a very short source-sample distance, while still achieving sufficient spatial coherence at the sample position. Moreover, the high geometrical magnification makes it possible to use detectors with a larger pixel size without reducing the image resolution. Here, we explore the influence of magnification on the edge enhancement fringes in such a geometry. We find experimentally and theoretically that the fringes become maximal at a magnification that is independent of the total source-detector distance. This optimal magnification only depends on the source size, the steepness of the sample feature, and the detector resolution. A stronger influence of the sample feature on the optimal magnification compared to low-magnification geometries is observed.

Brain virtual histology with X-ray phase-contrast tomography Part I: whole-brain myelin mapping in white-matter injury models

White-matter injury leads to severe functional loss in many neurological diseases. Myelin staining on histological samples is the most common technique to investigate white-matter fibers. However, tissue processing and sectioning may affect the reliability of 3D volumetric assessments. The purpose of this study was to propose an approach that enables myelin fibers to be mapped in the whole rodent brain with microscopic resolution and without the need for strenuous staining. With this aim, we coupled in-line (propagation-based) X-ray phase-contrast tomography (XPCT) to ethanol-induced brain sample dehydration. We here provide the proof-of-concept that this approach enhances myelinated axons in rodent and human brain tissue. In addition, we demonstrated that white-matter injuries could be detected and quantified with this approach, using three animal models: ischemic stroke, premature birth and multiple sclerosis. Furthermore, in analogy to diffusion tensor imaging (DTI), we retrieved fiber directions and DTI-like diffusion metrics from our XPCT data to quantitatively characterize white-matter microstructure. Finally, we showed that this non-destructive approach was compatible with subsequent complementary brain sample analysis by conventional histology. In-line XPCT might thus become a novel gold-standard for investigating white-matter injury in the intact brain. This is Part I of a series of two articles reporting the value of in-line XPCT for virtual histology of the brain; Part II shows how in-line XPCT enables the whole-brain 3D morphometric analysis of amyloid- β (A β ) plaques.

Integration of multiple imaging platforms to uncover cardiovascular defects in adult zebrafish

Aims

Mammalian models have been instrumental in investigating adult heart function and human disease. However, electrophysiological differences with human hearts and high costs motivate the need for non-mammalian models. The zebrafish is a well-established genetic model to study cardiovascular development and function; however, analysis of cardiovascular phenotypes in adult specimens is particularly challenging as they are opaque.

Methods and results

Here, we optimized and combined multiple imaging techniques including echocardiography, magnetic resonance imaging, and micro-computed tomography to identify and analyse cardiovascular phenotypes in adult zebrafish. Using alk5a/tgfbr1a mutants as a case study, we observed morphological and functional cardiovascular defects that were undetected with conventional approaches. Correlation analysis of multiple parameters revealed an association between haemodynamic defects and structural alterations of the heart, as observed clinically.

Conclusion

We report a new, comprehensive, and sensitive platform to identify otherwise indiscernible cardiovascular phenotypes in adult zebrafish.

Zernike phase-contrast full-field transmission X-ray nanotomography for 400 micrometre-sized samples

Full-field X-ray nanotomography based on a Fresnel zone plate offers a promising and intuitive approach to acquire high-quality phase-contrast images with a spatial resolution of tens of nanometres, and is applicable to both synchrotron radiation and laboratory sources. However, its small field of view (FOV) of tens of micrometres provides limited volume information, which primarily limits its application fields. This work proposes a method for expanding the FOV as the diameter of the objective zone plate, which provides a 400 µm FOV at below 500 nm resolution with Zernike phase contrast. General applications of large-volume nanotomography are demonstrated in integrated circuit microchips and Artemia cysts. This method can be useful for imaging/analyzing industrial and biological samples where bulk properties are important or the sample is difficult to section.

BriXS, a new X-ray inverse Compton source for medical applications

MariX is a research infrastructure conceived for multi-disciplinary studies, based on a cutting-edge system of combined electron accelerators at the forefront of the world-wide scenario of X-ray sources. The generation of X-rays over a large photon energy range will be enabled by two unique X-ray sources: a Free Electron Laser and an inverse Compton source, called BriXS (Bright compact X-ray Source). The X-ray beam provided by BriXS is expected to have an average energy tunable in the range 20-180 keV and intensities between 10¹¹ and 10¹³ photon/s within a relative bandwidth ΔE/E=1-10%. These characteristics, together with a very small source size (~20 μm) and a good transverse coherence, will enable a wide range of applications in the bio-medical field. An additional unique feature of BriXS will be the possibility to make a quick switch of the X-ray energy between two values for dual-energy and K-edge subtraction imaging. In this paper, the expected characteristics of BriXS will be presented, with a particular focus on the features of interest to its possible medical applications.

A phase-retrieval toolbox for X-ray holography and tomography

Propagation-based phase-contrast X-ray imaging is by now a well established imaging technique, which - as a full-field technique - is particularly useful for tomography applications. Since it can be implemented with synchrotron radiation and at laboratory micro-focus sources, it covers a wide range of applications. A limiting factor in its development has been the phase-retrieval step, which was often performed using methods with a limited regime of applicability, typically based on linearization. In this work, a much larger set of algorithms, which covers a wide range of cases (experimental parameters, objects and constraints), is compiled into a single toolbox - the HoloTomoToolbox - which is made publicly available. Importantly, the unified structure of the implemented phase-retrieval functions facilitates their use and performance test on different experimental data.

Real-time in vivo imaging of regional lung function in a mouse model of cystic fibrosis on a laboratory X-ray source

Most measures of lung health independently characterise either global lung function or regional lung structure. The ability to measure airflow and lung function regionally would provide a more specific and physiologically focused means by which to assess and track lung disease in both pre-clinical and clinical settings. One approach for achieving regional lung function measurement is via phase contrast X-ray imaging (PCXI), which has been shown to provide highly sensitive, high-resolution images of the lungs and airways in small animals. The detailed images provided by PCXI allow the application of four-dimensional X-ray velocimetry (4DxV) to track lung tissue motion and provide quantitative information on regional lung function. However, until recently synchrotron facilities were required to produce the highly coherent, high-flux X-rays that are required to achieve lung PCXI at a high enough frame rate to capture lung motion. This paper presents the first translation of 4DxV technology from a synchrotron facility into a laboratory setting by using a liquid-metal jet microfocus X-ray source. This source can provide the coherence required for PCXI and enough X-ray flux to image the dynamics of lung tissue motion during the respiratory cycle, which enables production of images compatible with 4DxV analysis. We demonstrate the measurements that can be captured in vivo in live mice using this technique, including regional airflow and tissue expansion. These measurements can inform physiological and biomedical research studies in small animals and assist in the development of new respiratory treatments.

Visualization of internal 3D structure of small live seed on germination by laboratory-based X-ray microscopy with phase contrast computed tomography

BACKGROUND

The visualization of internal 3D-structure of tissues at micron resolutions without staining by contrast reagents is desirable in plant researches, and it can be achieved by an X-ray computed tomography (CT) with a phase-retrieval technique. Recently, a laboratory-based X-ray microscope adopting the phase contrast CT was developed as a powerful tool for the observation of weakly absorbing biological samples. Here we report the observation of unstained pansy seeds using the laboratory-based X-ray phase-contrast CT.

RESULTS

A live pansy seed within 2 mm in size was simply mounted inside a plastic tube and irradiated by in-house X-rays to collect projection images using a laboratory-based X-ray microscope. The phase-retrieval technique was applied to enhance contrasts in the projection images. In addition to a dry seed, wet seeds on germination with the poorer contrasts were tried. The phase-retrieved tomograms from both the dry and the wet seeds revealed a cellular level of spatial resolutions that were enough to resolve cells in the seeds, and provided enough contrasts to delineate the boundary of embryos manually. The manual segmentation allowed a 3D rendering of embryos at three different stages in the germination, which visualized an overall morphological change of the embryo upon germination as well as a spatial arrangement of cells inside the embryo.

CONCLUSIONS

Our results confirmed an availability of the laboratory-based X-ray phase-contrast CT for a 3D-structural study on the development of small seeds. The present method may provide a unique way to observe live plant tissues at micron resolutions without structural perturbations due to the sample preparation.

An interactive and intuitive visualisation method for X-ray computed tomography data of biological samples in 3D Portable Document Format

3D imaging approaches based on X-ray microcomputed tomography (microCT) have become increasingly accessible with advancements in methods, instruments and expertise. The synergy of material and life sciences has impacted biomedical research by proposing new tools for investigation. However, data sharing remains challenging as microCT files are usually in the range of gigabytes and require specific and expensive software for rendering and interpretation. Here, we provide an advanced method for visualisation and interpretation of microCT data with small file formats, readable on all operating systems, using freely available Portable Document Format (PDF) software. Our method is based on the conversion of volumetric data into interactive 3D PDF, allowing rotation, movement, magnification and setting modifications of objects, thus providing an intuitive approach to analyse structures in a 3D context. We describe the complete pipeline from data acquisition, data processing and compression, to 3D PDF formatting on an example of craniofacial anatomical morphology in the mouse embryo. Our procedure is widely applicable in biological research and can be used as a framework to analyse volumetric data from any research field relying on 3D rendering and CT-biomedical imaging.

Quantification of image texture in X-ray phase-contrast-enhanced projection images of in vivo mouse lungs observed at varied inflation pressures

To date, there are very limited noninvasive, regional assays of in vivo lung microstructure near the alveolar level. It has been suggested that x-ray phase-contrast enhanced imaging reveals information about the air volume of the lung; however, the image texture information in these images remains underutilized. Projection images of in vivo mouse lungs were acquired via a tabletop, propagation-based, X-ray phase-contrast imaging system. Anesthetized mice were mechanically ventilated in an upright position. Consistent with previously published studies, a distinct image texture was observed uniquely within lung regions. Lung regions were automatically identified using supervised machine learning applied to summary measures of the image texture data. It was found that an unsupervised clustering within predefined lung regions colocates with expected differences in anatomy along the cranial-caudal axis in upright mice. It was also found that specifically selected inflation pressures-here, a purposeful surrogate of distinct states of mechanical expansion-can be predicted from the lung image texture alone, that the prediction model itself varies from apex to base and that prediction is accurate regardless of overlap with nonpulmonary structures such as the ribs, mediastinum, and heart. Cross-validation analysis indicated low inter-animal variation in the image texture classifications. Together, these results suggest that the image texture observed in a single X-ray phase-contrast-enhanced projection image could be used across a range of pressure states to study regional variations in regional lung function.

A new in-line X-ray phase-contrast computed tomography reconstruction algorithm based on adaptive-weighted anisotropic TpV regularization for insufficient data

In-line X-ray phase-contrast computed tomography (IL-PCCT) is a valuable tool for revealing the internal detailed structures in weakly absorbing objects (e.g. biological soft tissues), and has a great potential to become clinically applicable. However, the long scanning time for IL-PCCT will result in a high radiation dose to biological samples, and thus impede the wider use of IL-PCCT in clinical and biomedical imaging. To alleviate this problem, a new iterative CT reconstruction algorithm is presented that aims to decrease the radiation dose by reducing the projection views, while maintaining the high quality of reconstructed images. The proposed algorithm combines the adaptive-weighted anisotropic total p-variation (AwaTpV, 0 < p < 1) regularization technique with projection onto convex sets (POCS) strategy. Noteworthy, the AwaTpV regularization term not only contains the horizontal and vertical image gradients but also adds the diagonal image gradients in order to enforce the directional continuity in the gradient domain. To evaluate the effectiveness and ability of the proposed algorithm, experiments with a numerical phantom and synchrotron IL-PCCT were performed, respectively. The results demonstrated that the proposed algorithm had the ability to significantly reduce the artefacts caused by insufficient data and effectively preserved the edge details under noise-free and noisy conditions, and thus could be used as an effective approach to decrease the radiation dose for IL-PCCT.

Rigid Embedding of Fixed and Stained, Whole, Millimeter-Scale Specimens for Section-free 3D Histology by Micro-Computed Tomography

For over a hundred years, the histological study of tissues has been the gold standard for medical diagnosis because histology allows all cell types in every tissue to be identified and characterized. Our laboratory is actively working to make technological advances in X-ray micro-computed tomography (micro-CT) that will bring the diagnostic power of histology to the study of full tissue volumes at cellular resolution (i.e., an X-ray Histo-tomography modality). Toward this end, we have made targeted improvements to the sample preparation pipeline. One key optimization, and the focus of the present work, is a straightforward method for rigid embedding of fixed and stained millimeter-scale samples. Many of the published methods for sample immobilization and correlative micro-CT imaging rely on placing the samples in paraffin wax, agarose, or liquids such as alcohol. Our approach extends this work with custom procedures and the design of a 3-dimensional printable apparatus to embed the samples in an acrylic resin directly into polyimide tubing, which is relatively transparent to X-rays. Herein, sample preparation procedures are described for the samples from 0.5 to 10 mm in diameter, which would be suitable for whole zebrafish larvae and juveniles, or other animals and tissue samples of similar dimensions. As proof of concept, we have embedded the specimens from Danio, Drosophila, Daphnia, and a mouse embryo; representative images from 3-dimensional scans for three of these samples are shown. Importantly, our methodology leads to multiple benefits including rigid immobilization, long-term preservation of laboriously-created resources, and the ability to re-interrogate samples.

A quantitative analysis of 3D-cell distribution in regenerating muscle-skeletal system with synchrotron X-ray computed microtomography

One of the greatest enigmas of modern biology is how the geometry of muscular and skeletal structures are created and how their development is controlled during growth and regeneration. Scaling and shaping of vertebrate muscles and skeletal elements has always been enigmatic and required an advanced technical level in order to analyse the cell distribution in 3D. In this work, synchrotron X-ray computed microtomography (µCT) and chemical contrasting has been exploited for a quantitative analysis of the 3D-cell distribution in tissues of a developing salamander (Pleurodeles waltl) limb – a key model organism for vertebrate regeneration studies. We mapped the limb muscles, their size and shape as well as the number and density of cells within the extracellular matrix of the developing cartilage. By using tomographic approach, we explored the polarity of the cells in 3D, in relation to the structure of developing joints. We found that the polarity of chondrocytes correlates with the planes in joint surfaces and also changes along the length of the cartilaginous elements. Our approach generates data for the precise computer simulations of muscle-skeletal regeneration using cell dynamics models, which is necessary for the understanding how anisotropic growth results in the precise shapes of skeletal structures.

An iterative image reconstruction algorithm combined with forward and backward diffusion filtering for in-line X-ray phase-contrast computed tomography

In-line X-ray phase-contrast computed tomography (IL-PCCT) can reveal fine inner structures for low-Z materials (e.g. biological soft tissues), and shows high potential to become clinically applicable. Typically, IL-PCCT utilizes filtered back-projection (FBP) as the standard reconstruction algorithm. However, the FBP algorithm requires a large amount of projection data, and subsequently a large radiation dose is needed to reconstruct a high-quality image, which hampers its clinical application in IL-PCCT. In this study, an iterative reconstruction algorithm for IL-PCCT was proposed by combining the simultaneous algebraic reconstruction technique (SART) with eight-neighbour forward and backward (FAB8) diffusion filtering, and the reconstruction was performed using the Shepp-Logan phantom simulation and a real synchrotron IL-PCCT experiment. The results showed that the proposed algorithm was able to produce high-quality computed tomography images from few-view projections while improving the convergence rate of the computed tomography reconstruction, indicating that the proposed algorithm is an effective method of dose reduction for IL-PCCT.

Application of a novel in vivo imaging approach to measure pulmonary vascular responses in mice

Noninvasive imaging of the murine pulmonary vasculature is challenging due to the small size of the animal, limits of resolution of the imaging technology, terminal nature of the procedure, or the need for intravenous contrast. We report the application of laboratory-based high-speed, high-resolution x-ray imaging, and image analysis to detect quantitative changes in the pulmonary vascular tree over time in the same animal without the need for intravenous contrast. Using this approach, we detected an increased number of vessels in the pulmonary vascular tree of animals after 30 min of recovery from a brief exposure to inspired gas with 10% oxygen plus 5% carbon dioxide (mean ± standard deviation: 2193 ± 382 at baseline vs. 6177 ± 1171 at 30 min of recovery; P < 0.0001). In a separate set of animals, we showed that the total pulmonary blood volume increased (P = 0.0412) while median vascular diameter decreased from 0.20 mm (IQR: 0.15-0.28 mm) to 0.18 mm (IQR: 0.14-0.26 mm; P = 0.0436) over the respiratory cycle from end-expiration to end-inspiration. These findings suggest that the noninvasive, nonintravenous contrast imaging approach reported here can detect dynamic responses of the murine pulmonary vasculature and may be a useful tool in studying these responses in models of disease.

High-spatial-resolution x-ray fluorescence tomography with spectrally matched nanoparticles

Present macroscopic biomedical imaging methods provide either morphology with high spatial resolution (e.g. CT) or functional/molecular information with lower resolution (e.g. PET). X-ray fluorescence (XRF) from targeted nanoparticles allows molecular or functional imaging but sensitivity has so far been insufficient resulting in low spatial resolution, despite long exposure times and high dose. In the present paper, we show that laboratory XRF tomography with metal-core nanoparticles (NPs) provides a path to functional/molecular biomedical imaging with ~100 µm resolution in living rodents. The high sensitivity and resolution rely on the combination of a high-brightness liquid-metal-jet x-ray source, pencil-beam optics, photon-counting energy-dispersive detection, and spectrally matched NPs. The method is demonstrated on mice for 3D tumor imaging via passive targeting of in-house-fabricated molybdenum NPs. Exposure times, nanoparticle dose, and radiation dose agree well with in vivo imaging.

Cellular-resolution 3D virtual histology of human coronary arteries using x-ray phase tomography

High-spatial-resolution histology of coronary artery autopsy samples play an important role for understanding heart disease such as myocardial infarction. Unfortunately, classical histology is often destructive, has thick slicing, requires extensive sample preparation, and is time-consuming. X-ray micro-CT provides fast nondestructive 3D imaging but absorption contrast is often insufficient, especially for observing soft-tissue features with high resolution. Here we show that propagation-based x-ray phase-contrast tomography has the resolution and contrast to image clinically relevant soft-tissue features in intact coronary artery autopsy samples with cellular resolution. We observe microscopic lipid-rich plaques, individual adipose cells, ensembles of few foam cells, and the thin fibrous cap. The method relies on a small-spot laboratory x-ray microfocus source, and provides high-spatial resolution in all three dimensions, fast data acquisition, minimum sample distortion and requires no sample preparation.

High-resolution μCT of a mouse embryo using a compact laser-driven X-ray betatron source

In the field of X-ray microcomputed tomography (μCT) there is a growing need to reduce acquisition times at high spatial resolution (approximate micrometers) to facilitate in vivo and high-throughput operations. The state of the art represented by synchrotron light sources is not practical for certain applications, and therefore the development of high-brightness laboratory-scale sources is crucial. We present here imaging of a fixed embryonic mouse sample using a compact laser-plasma-based X-ray light source and compare the results to images obtained using a commercial X-ray μCT scanner. The radiation is generated by the betatron motion of electrons inside a dilute and transient plasma, which circumvents the flux limitations imposed by the solid or liquid anodes used in conventional electron-impact X-ray tubes. This X-ray source is pulsed (duration <30 fs), bright (>1010 photons per pulse), small (diameter <1 μm), and has a critical energy >15 keV. Stable X-ray performance enabled tomographic imaging of equivalent quality to that of the μCT scanner, an important confirmation of the suitability of the laser-driven source for applications. The X-ray flux achievable with this approach scales with the laser repetition rate without compromising the source size, which will allow the recording of high-resolution μCT scans in minutes.

Three-dimensional virtual histology of human cerebellum by X-ray phase-contrast tomography

The complex cytoarchitecture of human brain tissue is traditionally studied by histology, providing structural information in 2D planes. This can be partly extended to 3D by inspecting many parallel slices, however, at nonisotropic resolution. This work shows that propagation-based X-ray phase-contrast tomography, both at the synchrotron and even at a compact laboratory source, can be used to perform noninvasive 3D virtual histology on unstained paraffin-embedded human cerebellum at isotropic subcellular resolution. The resulting data quality is high enough to visualize and automatically locate ∼10⁶ neurons within the different layers of the cerebellum, providing unprecedented data on its 3D cytoarchitecture and spatial organization.

To quantitatively evaluate brain tissue and its corresponding function, knowledge of the 3D cellular distribution is essential. The gold standard to obtain this information is histology, a destructive and labor-intensive technique where the specimen is sliced and examined under a light microscope, providing 3D information at nonisotropic resolution. To overcome the limitations of conventional histology, we use phase-contrast X-ray tomography with optimized optics, reconstruction, and image analysis, both at a dedicated synchrotron radiation endstation, which we have equipped with X-ray waveguide optics for coherence and wavefront filtering, and at a compact laboratory source. As a proof-of-concept demonstration we probe the 3D cytoarchitecture in millimeter-sized punches of unstained human cerebellum embedded in paraffin and show that isotropic subcellular resolution can be reached at both setups throughout the specimen. To enable a quantitative analysis of the reconstructed data, we demonstrate automatic cell segmentation and localization of over 1 million neurons within the cerebellar cortex. This allows for the analysis of the spatial organization and correlation of cells in all dimensions by borrowing concepts from condensed-matter physics, indicating a strong short-range order and local clustering of the cells in the granular layer. By quantification of 3D neuronal “packing,” we can hence shed light on how the human cerebellum accommodates 80% of the total neurons in the brain in only 10% of its volume. In addition, we show that the distribution of neighboring neurons in the granular layer is anisotropic with respect to the Purkinje cell dendrites.

Implementation of a double-grating interferometer for phase-contrast computed tomography in a conventional system nanotom® m

Visualizing the internal architecture of large soft tissue specimens within the laboratory environment in a label-free manner is challenging, as the conventional absorption-contrast tomography yields a poor contrast. In this communication, we present the integration of an X-ray double-grating interferometer (XDGI) into an advanced, commercially available micro computed tomography system nanotom® m with a transmission X-ray source and a micrometer-sized focal spot. The performance of the interferometer is demonstrated by comparing the registered three-dimensional images of a human knee joint sample in phase- and conventional absorption-contrast modes. XDGI provides enough contrast (1.094 ± 0.152) to identify the cartilage layer, which is not recognized in the conventional mode (0.287 ± 0.003). Consequently, the two modes are complementary, as the present XDGI set-up only reaches a spatial resolution of (73 ± 6) μm, whereas the true micrometer resolution in the absorption-contrast mode has been proven. By providing complimentary information, XDGI is especially a supportive quantitative method for imaging soft tissues and visualizing weak X-ray absorbing species in the direct neighborhood of stronger absorbing components at the microscopic level.

Novel imaging approaches for small animal models of lung disease (2017 Grover Conference series)

Imaging in small animal models of lung disease is challenging, as existing technologies are limited either by resolution or by the terminal nature of the imaging approach. Here, we describe the current state of small animal lung imaging, the technological advances of laboratory-sourced phase contrast X-ray imaging, and the application of this novel technology and its attendant image analysis techniques to the in vivo imaging of the large airways and pulmonary vasculature in murine models of lung health and disease.

Coherence-resolution relationship in holographic and coherent diffractive imaging

We study by numerical simulation how spatial coherence affects the reconstruction quality of images in coherent diffractive x-ray imaging. Using a conceptually simple, but computationally demanding approach, we have simulated diffraction data recorded under partial coherence, and then use the data for iterative reconstruction algorithms using a support constraint. By comparison of experimental regimes and parameters, we observe a significantly higher robustness against partially coherent illumination in the near-field compared to the far-field setting.

Removal of ring artifacts in microtomography by characterization of scintillator variations

Ring artifacts reduce image quality in tomography, and arise from faulty detector calibration. In microtomography, we have identified that ring artifacts can arise due to high-spatial frequency variations in the scintillator thickness. Such variations are normally removed by a flat-field correction. However, as the spectrum changes, e.g. due to beam hardening, the detector response varies non-uniformly introducing ring artifacts that persist after flat-field correction. In this paper, we present a method to correct for ring artifacts from variations in scintillator thickness by using a simple method to characterize the local scintillator response. The method addresses the actual physical cause of the ring artifacts, in contrary to many other ring artifact removal methods which rely only on image post-processing. By applying the technique to an experimental phantom tomography, we show that ring artifacts are strongly reduced compared to only making a flat-field correction.

Propagation-based Phase-Contrast X-ray Imaging at a Compact Light Source

We demonstrate the applicability of propagation-based X-ray phase-contrast imaging at a laser-assisted compact light source with known phantoms and the lungs and airways of a mouse. The Munich Compact Light Source provides a quasi-monochromatic beam with partial spatial coherence, and high flux relative to other non-synchrotron sources (up to 10¹⁰ ph/s). In our study we observe significant edge-enhancement and quantitative phase-retrieval is successfully performed on the known phantom. Furthermore the images of a small animal show the potential for live bio-imaging research studies that capture biological function using short exposures.

Reconstructing mode mixtures in the optical near-field

We propose a reconstruction scheme for hard x-ray inline holography, a variant of propagation imaging, which is compatible with imaging conditions of partial (spatial) coherence. This is a relevant extension of current full-field phase contrast imaging, which requires full coherence. By the ability to reconstruct the coherent modes of the illumination (probe), as demonstrated here, the requirements of coherence filtering could be relaxed in many experimentally relevant settings. The proposed scheme is built on the mixed-state approach introduced in [Nature494, 68 (2013)], combined with multi-plane detection of extended wavefields [Opt. Commun.199, 65 (2001), Opt. Express22, 16571 (2014)]. Notably, the diversity necessary for the reconstruction is generated by acquiring measurements at different defocus positions of the detector. We show that we can recover the coherent mode structure and occupancy numbers of the partial coherent probe. Practically relevant quantities as the transversal coherence length can be computed from the reconstruction in a straightforward way.