BEATS: BEAmline for synchrotron X-ray microTomography at SESAME.

The ID10 beamline of the SESAME (Synchrotron-light for Experimental Science and Applications in the Middle East) synchrotron light source in Jordan was inaugurated in June 2023 and is now open to scientific users. The beamline, which was designed and installed within the European Horizon 2020 project BEAmline for Tomography at SESAME (BEATS), provides full-field X-ray radiography and microtomography imaging with monochromatic or polychromatic X-rays up to photon energies of 100 keV. The photon source generated by a 2.9 T wavelength shifter with variable gap, and a double-multilayer monochromator system allow versatile application for experiments requiring either an X-ray beam with high intensity and flux, and/or a partially spatial coherent beam for phase-contrast applications. Sample manipulation and X-ray detection systems are designed to allow scanning samples with different size, weight and material, providing image voxel sizes from 13 µm down to 0.33 µm. A state-of-the-art computing infrastructure for data collection, three-dimensional (3D) image reconstruction and data analysis allows the visualization and exploration of results online within a few seconds from the completion of a scan. Insights from 3D X-ray imaging are key to the investigation of specimens from archaeology and cultural heritage, biology and health sciences, materials science and engineering, earth, environmental sciences and more. Microtomography scans and preliminary results obtained at the beamline demonstrate that the new beamline ID10-BEATS expands significantly the range of scientific applications that can be targeted at SESAME.

Method for auto-alignment and determination of parameter space in dual-phase grating interferometry.

X-ray dual-phase grating interferometry provides quantitative micro-structural information beyond the optical resolution through its tunable correlation length. Ensuring optimal performance of the set-up requires accurate correlation length estimation and precise alignment of the gratings. This paper presents an automated procedure for determining the complete geometrical parameters of the interferometer set-up with a high degree of precision. The algorithm's effectiveness is then evaluated through a series of experimental tests, illustrating its accuracy and robustness.

Pixel-wise beam-hardening correction for dark-field signal in X-ray dual-phase grating interferometry.

The dark-field signal provided by X-ray grating interferometry is an invaluable tool for providing structural information beyond the direct spatial resolution and their variations on a macroscopic scale. However, when using a polychromatic source, the beam-hardening effect in the dark-field signal makes the quantitative sub-resolution structural information inaccessible. Especially, the beam-hardening effect in dual-phase grating interferometry varies with spatial location, inter-grating distance, and diffraction order. In this work, we propose a beam-hardening correction algorithm, taking into account all these factors. The accuracy and robustness of the algorithm are then validated by experimental results. This work contributes a necessary step toward accessing small-angle scattering structural information in dual-phase grating interferometry.

Detailed analysis of the interference patterns measured in lab-based X-ray dual-phase grating interferometry through wave propagation simulation.

In this work, we analyze the interference patterns measured in lab-based dual-phase grating interferometry and for the first time explain the spatial dependencies of the measured interference patterns and the large visibility deviations between the theoretical prediction and the experimental results. To achieve this, a simulator based on wave propagation is developed. This work proves that the experimental results can be simulated with high accuracy by including the effective grating thickness profile induced by the cone-beam geometry, the measured detector response function and a non-ideal grating shape. With the comprehensive understanding of dual-phase grating interferometry, this provides the foundations for a more efficient and accurate algorithm to retrieve sample's structure information, and the realistic simulator is a useful tool for optimizing the set-up.

Refractive axicon for X-ray microscopy applications: design, optimization, and experiment.

In a full-field transmission X-ray microscopy (TXM) setup, a condenser X-ray optical element is used to illuminate the sample by condensing the X-ray beam delivered by the synchrotron storage ring. On-going and future upgrades of synchrotron facilities to diffraction-limited storage rings will pose new challenges to these TXM setups, such as much smaller X-ray beams on the condenser. Here, we demonstrate that a refractive axicon can be used as an X-ray beam shaper to match the ring-shaped aperture of the condenser. Aiming at more efficient use of the incoming X-ray intensity, we explore several axicon designs both analytically and with numerical simulations. The axicons were produced by two-photon polymerization 3D printing on thin silicon nitride membrane substrates. The first characterization of the axicon was carried out at the TOMCAT beamline of the Swiss Light Source (Switzerland).

Towards clinical-dose grating interferometry breast CT with fused intensity-based iterative reconstruction.

X-ray grating interferometry CT (GI-CT) is an emerging imaging modality which provides three complementary contrasts that could increase the diagnostic content of clinical breast CT: absorption, phase, and dark-field. Yet, reconstructing the three image channels under clinically compatible conditions is challenging because of severe ill-conditioning of the tomographic reconstruction problem. In this work we propose to solve this problem with a novel reconstruction algorithm that assumes a fixed relation between the absorption and the phase-contrast channel to reconstruct a single image by automatically fusing the absorption and phase channels. The results on both simulations and real data show that, enabled by the proposed algorithm, GI-CT outperforms conventional CT at a clinical dose.

A Novel Three-Dimensional Approach Towards Evaluating Endomyocardial Biopsies for Follow-Up After Heart Transplantation: X-Ray Phase Contrast Imaging and Its Agreement With Classical Histopathology.

Endomyocardial biopsies are the gold standard for surveillance of graft rejection following heart transplantation, and are assessed by classical histopathology using a limited number of previously stained slices from several biopsies. Synchrotron propagation-based X-ray phase contrast imaging is a non-destructive method to image biological samples without tissue preparation, enabling virtual 2D and 3D histopathology. We aimed to show the feasibility of this method to assess acute cellular rejection and its agreement to classical histopathology. Right ventricular biopsies were sampled from 23 heart transplantation recipients (20 males, mean age 54±14 years) as part of standard follow-up. The clinical diagnosis of potential rejection was made using classical histopathology. One additional study sample was harvested and imaged by X-ray phase contrast imaging, producing 3D datasets with 0.65 µm pixel size, and up to 4,320 images per sample. An experienced pathologist graded both histopathological and X-ray phase contrast images in a blinded fashion. The agreement between methods was assessed by weighted kappa, showing substantial agreement (kappa up to 0.80, p < 0.01) between X-ray phase contrast imaging and classical histopathology. X-ray phase contrast imaging does not require tissue processing, allows thorough analysis of a full myocardial sample and allows identification of acute cellular rejection.

Technical note: A collision prediction tool using Blender.

Non-coplanar radiotherapy treatment techniques on C-arm linear accelerators have the potential to reduce dose to organs-at-risk in comparison with coplanar treatment techniques. Accurately predicting possible collisions between gantry, table and patient during treatment planning is needed to ensure patient safety. We offer a freely available collision prediction tool using Blender, a free and open-source 3D computer graphics software toolset. A geometric model of a C-arm linear accelerator including a library of patient models is created inside Blender. Based on the model, collision predictions can be used both to calculate collision-free zones and to check treatment plans for collisions. The tool is validated for two setups, once with and once without a full body phantom with the same table position. For this, each gantry-table angle combination with a 2° resolution is manually checked for collision interlocks at a TrueBeam system and compared to simulated collision predictions. For the collision check of a treatment plan, the tool outputs the minimal distance between the gantry, table and patient model and a video of the movement of the gantry and table, which is demonstrated for one use case. A graphical user interface allows user-friendly input of the table and patient specification for the collision prediction tool. The validation resulted in a true positive rate of 100%, which is the rate between the number of correctly predicted collision gantry-table combinations and the number of all measured collision gantry-table combinations, and a true negative rate of 89%, which is the ratio between the number of correctly predicted collision-free combinations and the number of all measured collision-free combinations. A collision prediction tool is successfully created and able to produce maps of collision-free zones and to test treatment plans for collisions including visualisation of the gantry and table movement.

Intensity-based iterative reconstruction for helical grating interferometry breast CT with static grating configuration.

Grating interferometry breast computed tomography (GI-BCT) has the potential to provide enhanced soft tissue contrast and to improve visualization of cancerous lesions for breast imaging. However, with a conventional scanning protocol, a GI-BCT scan requires longer scanning time and higher operation complexity compared to conventional attenuation-based CT. This is mainly due to multiple grating movements at every projection angle, so-called phase stepping, which is used to retrieve attenuation, phase, and scattering (dark-field) signals. To reduce the measurement time and complexity and extend the field of view, we have adopted a helical GI-CT setup and present here the corresponding tomographic reconstruction algorithm. This method allows simultaneous reconstruction of attenuation, phase contrast, and scattering images while avoiding grating movements. Experiments on simulated phantom and real initial intensity, visibility and phase maps are provided to validate our method.

Fabrication of a fractal pattern device for focus characterizations of X-ray imaging systems by Si deep reactive ion etching and bottom-up Au electroplating.

Precisely aligned optical components are crucial prerequisites for X-ray tomography at high resolution. We propose a device with a fractal pattern for precise automatic focusing. The device is etched in a Si substrate by deep reactive ion etching and then filled by a self-terminating bottom-up Au electroplating process. The fractal nature of the device produces an X-ray transmission image with globally homogeneous macroscopic visibility and high local contrast for pixel sizes in the range of 0.165 µm to 11 µm, while the high absorption contrast provided between Au and Si enables its use for X-ray energies ranging from 12 keV to 40 keV.

Micrometer-resolution X-ray tomographic full-volume reconstruction of an intact post-mortem juvenile rat lung.

In this article, we present an X-ray tomographic imaging method that is well suited for pulmonary disease studies in animal models to resolve the full pathway from gas intake to gas exchange. Current state-of-the-art synchrotron-based tomographic phase-contrast imaging methods allow for three-dimensional microscopic imaging data to be acquired non-destructively in scan times of the order of seconds with good soft tissue contrast. However, when studying multi-scale hierarchically structured objects, such as the mammalian lung, the overall sample size typically exceeds the field of view illuminated by the X-rays in a single scan and the necessity for achieving a high spatial resolution conflicts with the need to image the whole sample. Several image stitching and calibration techniques to achieve extended high-resolution fields of view have been reported, but those approaches tend to fail when imaging non-stable samples, thus precluding tomographic measurements of large biological samples, which are prone to degradation and motion during extended scan times. In this work, we demonstrate a full-volume three-dimensional reconstruction of an intact rat lung under immediate post-mortem conditions and at an isotropic voxel size of (2.75 µm)3. We present the methodology for collecting multiple local tomographies with 360° extended field of view scans followed by locally non-rigid volumetric stitching. Applied to the lung, it allows to resolve the entire pulmonary structure from the trachea down to the parenchyma in a single dataset. The complete dataset is available online ( https://doi.org/10.16907/7eb141d3-11f1-47a6-9d0e-76f8832ed1b2 ).

High sensitivity X-ray phase contrast imaging by laboratory grating-based interferometry at high Talbot order geometry.

X-ray phase contrast imaging is a powerful analysis technique for materials science and biomedicine. Here, we report on laboratory grating-based X-ray interferometry employing a microfocus X-ray source and a high Talbot order (35th) asymmetric geometry to achieve high angular sensitivity and high spatial resolution X-ray phase contrast imaging in a compact system (total length <1 m). The detection of very small refractive angles (∼50 nrad) at an interferometer design energy of 19 keV was enabled by combining small period X-ray gratings (1.0, 1.5 and 3.0 µm) and a single-photon counting X-ray detector (75 µm pixel size). The performance of the X-ray interferometer was fully characterized in terms of angular sensitivity and spatial resolution. Finally, the potential of laboratory X-ray phase contrast for biomedical imaging is demonstrated by obtaining high resolution X-ray phase tomographies of a mouse embryo embedded in solid paraffin and a formalin-fixed full-thickness sample of human left ventricle in water with a spatial resolution of 21.5 µm.

Laboratory X-ray interferometry imaging with a fan-shaped source grating.

The orientation mismatch between the cone beam of an X-ray tube and the grating lines in a flat substrate remains a big challenge for laboratory grating-based X-ray interferometry, since it severely limits the imaging field of view. Here, we fabricated fan-shaped G0 source gratings by modulating the electric field during the deep reactive ion etching of silicon. The gold electroplated fan-shaped G0 grating (3.0 µm pitch) in a 20 keV interferometer improves the uniformity of the field of view with an increase of average visibility from 16.2% to 18.5% and a better angular sensitivity (by a factor 5.8) at the edges.

Exceptional preservation of tiny embryos documents seed dormancy in early angiosperms.

The rapid diversification of angiosperms through the Early Cretaceous period, between about 130-100 million years ago, initiated fundamental changes in the composition of terrestrial vegetation and is increasingly well understood on the basis of a wealth of palaeobotanical discoveries over the past four decades and their integration with improved knowledge of living angiosperms. Prevailing hypotheses, based on evidence both from living and from fossil plants, emphasize that the earliest angiosperms were plants of small stature with rapid life cycles that exploited disturbed habitats in open, or perhaps understorey, conditions. However, direct palaeontogical data relevant to understanding the seed biology and germination ecology of Early Cretaceous angiosperms are sparse. Here we report the discovery of embryos and their associated nutrient storage tissues in exceptionally well-preserved angiosperm seeds from the Early Cretaceous. Synchrotron radiation X-ray tomographic microscopy of the fossil embryos from many taxa reveals that all were tiny at the time of dispersal. These results support hypotheses based on extant plants that tiny embryos and seed dormancy are basic for angiosperms as a whole. The minute size of the fossil embryos, and the modest nutrient storage tissues dictated by the overall small seed size, is also consistent with the interpretation that many early angiosperms were opportunistic, early successional colonizers of disturbance-prone habitats.

Impact of lossy compression of X-ray projections onto reconstructed tomographic slices.

Modern detectors used at synchrotron tomographic microscopy beamlines typically have sensors with more than 4-5 mega-pixels and are capable of acquiring 100-1000 frames per second at full frame. As a consequence, a data rate of a few TB per day can easily be exceeded, reaching peaks of a few tens of TB per day for time-resolved tomographic experiments. This data needs to be post-processed, analysed, stored and possibly transferred, imposing a significant burden onto the IT infrastructure. Compression of tomographic data, as routinely done for diffraction experiments, is therefore highly desirable. This study considers a set of representative datasets and investigates the effect of lossy compression of the original X-ray projections onto the final tomographic reconstructions. It demonstrates that a compression factor of at least three to four times does not generally impact the reconstruction quality. Potentially, compression with this factor could therefore be used in a transparent way to the user community, for instance, prior to data archiving. Higher factors (six to eight times) can be achieved for tomographic volumes with a high signal-to-noise ratio as it is the case for phase-retrieved datasets. Although a relationship between the dataset signal-to-noise ratio and a safe compression factor exists, this is not simple and, even considering additional dataset characteristics such as image entropy and high-frequency content variation, the automatic optimization of the compression factor for each single dataset, beyond the conservative factor of three to four, is not straightforward.

NRStitcher: non-rigid stitching of terapixel-scale volumetric images.

SUMMARY: In modern microscopy, the field of view is often increased by obtaining an image mosaic, where multiple sub-images are taken side-by-side and combined post-acquisition. Mosaic imaging often leads to long imaging times that can increase the probability of sample deformation during the acquisition due to, e.g. changes in the environment, damage caused by the radiation used to probe the sample or biologically induced deterioration. Here we propose a technique, based on local phase correlation, to detect the deformations and construct an artifact-free image mosaic from deformed sub-images. The implementation of the method supports distributed computing and can be used to generate teravoxel-size mosaics. We demonstrate its capabilities by assembling a 5.6 teravoxel tomographic image mosaic of microvasculature in whole mouse brain. The method is compared to existing rigid stitching implementations designed for very large datasets, and observed to create artifact-free image mosaics in comparable runtime with the same hardware resources. AVAILABILITY AND IMPLEMENTATION: The stitching software and C++/Python source code are available at GitHub (https://github.com/arttumiettinen/pi2) along with an example dataset and user instructions.

Modeling of beam hardening effects in a dual-phase X-ray grating interferometer for quantitative dark-field imaging.

X-ray grating interferometry (XGI) can provide access to unresolved sub-pixel information by utilizing the so-called dark-field or visibility reduction contrast. A recently developed variant of conventional XGI named dual-phase grating interferometer, based only on phase-shifting structures, has allowed for straightforward micro-structural investigations over multiple length scales with conventional X-ray sources. Nonetheless, the theoretical framework of the image formation for the dark-field signal has not been fully developed yet, thus hindering the quantification of unresolved micro-structures. In this work, we expand the current theoretical formulation of dual-phase grating interferometers taking into account polychromatic sources and beam hardening effects. We propose a model that considers the contribution of beam hardening to the visibility reduction and accounts for it. Finally, the method is applied to previously acquired and new experimental data showing that discrimination between actual micro-structures and beam hardening effects can be achieved.

Towards clinical grating-interferometry mammography.

OBJECTIVES: Grating-interferometry-based mammography (GIM) might facilitate breast cancer detection, as several research works have demonstrated in a pre-clinical setting, since it is able to provide attenuation, differential phase contrast, and scattering images simultaneously. In order to translate this technique to the clinics, it has to be adapted to cover a large field-of-view within a clinically acceptable exposure time and radiation dose. METHODS: We set up a grating interferometer that fits into a standard mammography system and fulfilled the aforementioned conditions. Here, we present the first mastectomy images acquired with this experimental device. RESULTS AND CONCLUSION: Our system performs at a mean glandular dose of 1.6 mGy for a 5-cm-thick, 18%-dense breast, and a field-of-view of 26 × 21 cm2. It seems to be well-suited as basis for a clinical-environment device. Further, dark-field signals seem to support an improved lesion visualization. Evidently, the effective impact of such indications must be evaluated and quantified within the context of a proper reader study. KEY POINTS: • Grating-interferometry-based mammography (GIM) might facilitate breast cancer detection, since it is sensitive to refraction and scattering and thus provides additional tissue information. • The most straightforward way to do grating-interferometry in the clinics is to modify a standard mammography device. • In a first approximation, the doses given with this technique seem to be similar to those of conventional mammography.

Correction to: Towards clinical grating-interferometry mammography.

The article Towards clinical grating-interferometry mammography, written by Carolina Arboleda, Zhentian Wang, Konstantins Jefimovs, Thomas Koehler, Udo Van Stevendaal, Norbert Kuhn, Bernd David, Sven Prevrhal, Kristina Lång, Serafino Forte, Rahel Antonia Kubik-Huch, Cornelia Leo.

High-numerical-aperture macroscope optics for time-resolved experiments.

A novel high-quality custom-made macroscope optics, dedicated to high-resolution time-resolved X-ray tomographic microscopy at the TOMCAT beamline at the Swiss Light Source (Paul Scherrer Institut, Switzerland), is introduced. The macroscope offers 4× magnification, has a very high numerical aperture of 0.35 and it is modular and highly flexible. It can be mounted both in a horizontal and vertical configuration, enabling imaging of tall samples close to the scintillator, to avoid edge-enhancement artefacts. The macroscope performance was characterized and compared with two existing in-house imaging setups, one dedicated to high spatial and one to high temporal resolution. The novel macroscope shows superior performance for both imaging settings compared with the previous systems. For the time-resolved setup, the macroscope is 4 times more efficient than the previous system and, at the same time, the spatial resolution is also increased by a factor of 6. For the high-spatial-resolution setup, the macroscope is up to 8.5 times more efficient with a moderate spatial resolution improvement (factor of 1.5). This high efficiency, increased spatial resolution and very high image quality offered by the novel macroscope optics will make 10-20 Hz high-resolution tomographic studies routinely possible, unlocking unprecedented possibilities for the tomographic investigations of dynamic processes and radiation-sensitive samples.