Soft X-ray Imaging Research Articles

Sedimentary diversity of the 2011 Tohoku-oki tsunami deposits on the Sendai coastal plain and the northern coast of Fukushima Prefecture, Japan

This paper documents the sedimentary characteristics of the widespread deposits associated with the 2011 Tohoku-oki tsunami on the lowlands along the Pacific coast of the Sendai and Fukushima regions, northern Japan, and observed tsunami inundation depths. In eight areas of the region, field observation was carried out at a total of 123 locations and sampling at a total of 49 locations. Grain-size analysis and soft X-ray imaging reveal that the tsunami deposits are usually composed of sheetlike sandy beds and generally show landward-thinning and landward-fining trends and a landward increase in mud content, although site-specific distributional patterns are apparent along each transect. These thickness and grain-size patterns indicate a landward decrease in flow capacity. This information on the sedimentology of tsunami deposits and observed inundation depths will assist with the identification of paleo-tsunami deposits in the geological record and provide valuable constraints for mathematical analyses of tsunami hydraulic conditions related to sedimentary characteristics.

Non-Destructive Method for Estimating Seed Weights from Intact Peanut Pods Using Soft X-ray Imaging

In the U.S., peanut farmers receive premium prices for crops with high seed grades. One component of seed grade is the proportion of seed weight to that of pod hulls and other matter. Seed weight and size are also important traits for food processors. Current methods for evaluating peanut seed grade require the opening of the pod and are time-consuming and labor-intensive. In this study, a non-destructive and efficient method to determine peanut seed weights was investigated. X-ray images of a total of 513 peanut pods from three commercial cultivars, each representing three market types, were taken using a soft X-ray imaging system. The region of interest of each image, the seeds, was extracted two ways, manually and with a differential evolution segmentation algorithm. The comprehensive attenuation index (CAI) value was calculated from the segmented regions of interest. Lastly, linear regression models were established between peanut seed weights and the CAI. The results demonstrated that the X-ray imaging technology, coupled with the differential evolution segmentation algorithm, may be used to estimate seed weights efficiently from intact peanut pods.

Structural identification of multidimensional metal–organic frameworks using soft x‐ray tomography

AbstractThis paper mainly discusses the applicability of using soft x‐ray tomography technology to examine the multidimensional structure of metal–organic frameworks, such as their core‐shell and hollow framework, by visually observing their corresponding images in different energy bands by different excitation energies for different elements. The results show that the use of soft x‐ray tomography (SXT) can effectively observe the distribution of metals in the structure, as well as observe the type of hollow pores the metal–organic framework (MOF) possesses. This pioneering evaluation of MOFs via SXT shows excellent performance in the structure identification of multidimensional metal–organic frameworks.

The Relationship between Solar Wind Charge Exchange Soft X-ray Emission and the Tangent Direction of Magnetopause in an XMM–Newton Event

With the advent of soft X-ray imaging enabling global magnetopause detection, it is critical to use reconstruction techniques to derive the 3-dimensional magnetopause location from 2-dimensional X-ray images. One of the important assumptions adopted by most techniques is that the direction with maximum soft X-ray emission is the tangent direction of the magnetopause, which has not been validated in observation so far. This paper analyzes a magnetospheric solar wind charge exchange (SWCX) soft X-ray event detected by XMM–Newton during relatively stable solar wind and geomagnetic conditions. The tangent direction of the magnetopause is determined by an empirical magnetopause model. Observation results show that the maximum SWCX soft X-ray intensity gradient tends to be the tangent of the magnetopause’s inner boundary, while the maximum SWCX soft X-ray intensity tends to be the tangent of the magnetopause’s outer boundary. Therefore, it is credible to use the assumption that the tangent direction of the magnetopause is the maximum SWCX soft X-ray intensity or its gradient when reconstructing the 3-dimensional magnetopause location. In addition, since these two maxima tend to be the inner and outer boundaries of the magnetopause, the thickness of magnetopause can also be revealed by soft X-ray imaging.

Temporal and spatial association between microwaves and type III bursts in the upper corona

One of the most important tasks in solar physics is the study of particles and energy transfer from the lower corona to the outer layers of the solar atmosphere. The most sensitive methods for detecting fluxes of non-thermal electrons in the solar atmosphere is observing their radio emission using modern large radioheliographs. We analyzed joint observations from the 13 April 2019 event observed by LOw-Frequency ARray (LOFAR) at meter wavelengths, and the Siberian Radio Heliograph (SRH) and the Badary Broadband Microwave Spectropolarimeter (BBMS) spectropolarimeter in microwaves performed at the time of the second PSP perihelion. During a period without signatures of non-thermal energy release in X-ray emission, numerous type III and/or type J bursts were observed. During the same two hours we observed soft X-ray brightenings and the appearance of weak microwave emission in an abnormally narrow band around 6 GHz. At these frequencies the increasing flux is well above the noise level, reaching 9 sfu. In the LOFAR dynamic spectrum of 53−80 MHz a region is found that lasts about an hour whose emission is highly correlated with 6 GHz temporal profile. The flux peaks in the meter waves are well correlated with extreme UV (EUV) emission variations caused by repeated surges from the bright X-point. We argue that there is a common source of non-thermal electrons located in the tail of the active region, where two loop systems of very different sizes interacted. The frequencies of type III and/or type J bursts are in accordance with large loop heights around 400 Mm, obtained by the magnetic field reconstruction. The microwave coherent emission was generated in the low loops identified as bright X-ray points seen in soft X-ray and EUV images, produced by electrons with energies several tens of keV at about twice the plasma frequency.

Soft x-ray imaging of Earth's dayside using hybrid simulations

Soft x-ray imaging of Earth's dayside using hybrid simulations

Numerical modelling of micron particle inhalation in a realistic nasal airway with pediatric adenoid hypertrophy: A virtual comparison between pre- and postoperative models.

Adenoid hypertrophy (AH) is an obstructive condition due to enlarged adenoids, causing mouth breathing, nasal blockage, snoring and/or restless sleep. While reliable diagnostic techniques, such as lateral soft tissue x-ray imaging or flexible nasopharyngoscopy, have been widely adopted in general practice, the actual impact of airway obstruction on nasal airflow and inhalation exposure to drug aerosols remains largely unknown. In this study, the effects of adenoid hypertrophy on airflow and micron particle inhalation exposure characteristics were analysed by virtually comparing pre- and postoperative models based on a realistic 3-year-old nasal airway with AH. More specifically, detailed comparison focused on anatomical shape variations, overall airflow and olfactory ventilation, associated particle deposition in overall and local regions were conducted. Our results indicate that the enlarged adenoid tissue can significantly alter the airflow fields. By virtually removing the enlarged tissue and restoring the airway, peak velocity and wall shear stress were restored, and olfactory ventilation was considerably improved (with a 16∼63% improvement in terms of local ventilation speed). Furthermore, particle deposition results revealed that nasal airway with AH exhibits higher particle filtration tendency with densely packed deposition hot spots being observed along the floor region and enlarged adenoid tissue area. While for the postoperative model, the deposition curve was shifted to the right. The local deposition efficiency results demonstrated that more particles with larger inertia can be delivered to the targeted affected area following Adenoidectomy (Adenoid Removal). Research findings are expected to provide scientific evidence for adenoidectomy planning and aerosol therapy following Adenoidectomy, which can substantially improve present clinical treatment outcomes.

Initial Experimental Results of Three-Dimensional Plasma Structure Reconstructed from Seven Independent X-Ray Images on RELAX

In this study, we demonstrated the principle underlying the three-dimensional (3D) reconstruction of plasma structure by using a soft X-ray camera with multiple pinholes. Time evolutions of seven independent soft X-ray images were captured by the camera. The obtained data were used to reconstruct a 3D soft X-ray emission profile in the reversed-field pinch produced in the RELAX machine, which appeared to be consistent with the forecast in our feasibility study.

Investigating insulin vesicle maturation pathways using soft X-ray tomography.

Insulin secretion is a well-studied phenomenon consisting of an interplay between various cellular signaling pathways. Despite the importance of insulin in regulating blood glucose, little is known about the pathways governing insulin vesicle acidification and maturation. Proper maturation of vesicles is imperative for the processing of the active form of insulin and vesicle trafficking. Here, we use Soft X-ray Tomography (SXT) to investigate the effect of a variety of insulin secretagogues and chemical probes to determine pathways leading to maturation of insulin vesicles. SXT is an ideal approach to this problem as it enables high-throughput, three-dimensional organelle mapping of intact cells. This enables us to map and quantify the trafficking of vesicles, informing us about subcellular rearrangements and organelle contacts during the secretory process. In addition, SXT allows us to detect changes in molecular densities and in turn, changes in biochemical density and packaging efficiency of insulin vesicles. Our results indicate varied levels of insulin vesicle density and differences in organelle contacts, specifically insulin vesicle-mitochondria contacts, under the influence of compounds acting via orthogonal signaling pathways. Overall, our screening pipeline will be useful to allow for rapid and high throughput identification of cellular pathways involved in enhancing insulin packaging and maturation.

Correlative visible light and soft X-ray tomography of in-situ mesoscale heterochromatin organization.

Recent evidence has revealed that cellular aging is accompanied by alterations in DNA methylation and histone modifications leading to a decrease in nucleosome packing density and heterochromatin remodeling. While these observations were obtained with multi-omics data (eg. Hi-C, ATAC-seq), the underlying ultrastructural mechanisms of mesoscale heterochromatin reorganization during cellular aging are still unclear. Towards this, we developed correlative light microscopy and cryo-soft X-ray tomography to analyze the alterations in heterochromatin organization in human mammary fibroblast cells. Our analysis revealed the micro-domain organization of heterochromatin structure with the mean domain size of 115 nm in the intact and hydrated state of cells. Upon addition of histone deacetylase inhibitor, that phenocopied aging, we observed a marked decrease in the heterochromatin density distribution, disruption of microdomains, and decrease in chromatin compaction length scales. To validate these observations, we also developed a bidisperse copolymer model in a confined volume using Brownian dynamics simulations. Collectively, our results provide direct evidence of mesoscale domains in heterochromatin packing and their alterations during cellular aging

On-Line Fluorescence Microscopy for Identification and Imaging of Apoptotic Cell with Synchrotron-Based Soft X-ray Tomography.

Synchrotron-based soft X-ray tomography (SXT), providing three-dimensional morphology and quantitative distribution of linear absorption coefficient (LAC) of the imaged objects, is widely used in many fields to obtain ultra-structure images, especially in cellular imaging. Off-line fluorescence microscopies (FMs) are combined to identify the type of organelles and status of cells. However, deformation and displacement usually occur during the transfer and loading process, which decreases the precision of two-modal images' registration. In this paper, we report on an on-line FM, at the SXT station (BL07W) of the National Synchrotron Radiation Laboratory (NSRL), which avoids deformation and displacement. Therefore, researchers can easily find the sample and take the useful data without tedious post-processing. Combining SXT with on-line FM, we achieved the identification and high-resolution imaging of an apoptotic cell. The experiments revealed that the LAC of the nucleus of the apoptotic cell was larger than that of a normal cell, which could be explained by nucleus pyknosis of the apoptotic cell.

Correlative Cryo-imaging Using Soft X-Ray Tomography for the Study of Virus Biology in Cells and Tissues.

Viruses are obligate intracellular pathogens that depend on their host cell machinery and metabolism for their replicative life cycle. Virus entry, replication, and assembly are dynamic processes that lead to the reorganisation of host cell components. Therefore, a complete understanding of the viral processes requires their study in the cellular context where advanced imaging has been proven valuable in providing the necessary information. Among the available imaging techniques, soft X-ray tomography (SXT) at cryogenic temperatures can provide three-dimensional mapping to 25 nm resolution and is ideally suited to visualise the internal organisation of virus-infected cells. In this chapter, the principles and practices of synchrotron-based cryo-soft X-ray tomography (cryo-SXT) in virus research are presented. The potential of the cryo-SXT in correlative microscopy platforms is also demonstrated through working examples of reovirus and hepatitis research at Beamline B24 (Diamond Light Source Synchrotron, UK) and BL09-Mistral beamline (ALBA Synchrotron, Spain), respectively.

Magnetic correlations in the magnetic topological insulator (Cr,Sb)2Te3

Chromium-doped ${\mathrm{Sb}}_{2}{\mathrm{Te}}_{3}$ is a magnetic topological insulator (MTI), which belongs to the $(\mathrm{Sb},{\mathrm{Bi})}_{2}(\mathrm{Se},{\mathrm{Te})}_{3}$ family. When doped with the transition metals V, Cr, and Mn this family displays long-range ferromagnetic order above liquid nitrogen temperature and is currently intensely explored for quantum device applications. Despite the large magnetic ordering temperature, the experimental observation of dissipationless electrical transport channels, i.e., the quantum anomalous Hall effect, is limited in these materials to temperatures below $\ensuremath{\approx}2$ K. Inhomogeneities in the MTI have been identified as a major concern, affecting the coupling between the Dirac states and the magnetic dopants. Nevertheless, details on the local magnetic order in these materials are not well understood. Here, we report the study of the magnetic correlations in thin films using a combination of muon spin relaxation $(\ensuremath{\mu}\mathrm{SR})$, and magnetic soft x-ray spectroscopy and imaging. $\ensuremath{\mu}\mathrm{SR}$ provides two key quantities for understanding the microscopic magnetic behavior: The magnetic volume fraction, i.e., the percentage of the material that is ferromagnetically ordered, and the relaxation rate, which is sensitive to the magnetic static $(\ensuremath{\approx}\ensuremath{\mu}\mathrm{s})$ and dynamic disorder. By choosing different implantation depths for the muons, one can further discriminate between near-surface and bulk properties. No evidence for a surface enhancement of the magnetic ordering is observed, but, instead, we find evidence of small magnetically ordered clusters in a paramagnetic background, which are coupled. The significant magnetic field shift that is present in all samples indicates a percolation transition that proceeds through the formation and growth of magnetically ordered spin clusters. We further find that fluctuations are present even at low temperatures, and that there appears to be a transition between superparamagnetism and superferromagnetism.

A combination of soft X-ray and laser light sources offer 3D high content information on the native state of the cellular environment

Beamline B24 is a life sciences correlative cryo-imaging beamline at Diamond Light Source. B24 uses a combination of conventional and super-resolution visible-light fluorescence microscopy and soft X-ray tomography (cryoSXT) to provide 3D imaging of the cellular landscape at a resolution up to 25 nm in cryo-preserved biological samples up to 12 μm thick. B24 offers user-friendly, semi-automated 3D correlative cryo-imaging through an integrated platform of methods that encompass (a) sample preparation and evaluation, (b) data collection and processing and (c) data analysis and correlation. CryoSXT fills the current resolution gap between fluorescence and electron microscopy while cryo-structured illumination microscopy provides the additional dimension of chemical localization within the same cellular ultrastructure captured by cryoSXT. Beamline instruments can be accessed biannually by academics and industry globally through peer-reviewed standard and rapid access proposal processes. The B24 user base is primarily academic research groups studying cell function and cytopathology in biological systems ranging from viruses and algae to mammalian cells and proto-tissue complexes. Future work will consolidate development efforts and experiences gained thus far to enable high-throughput data collection. Special emphasis is placed on the delivery of other integrated advanced imaging methods such as X-ray absorption near-edge spectroscopy and phase contrast.

Finding Magnetopause Standoff Distance Using a Soft X‐ray Imager: 2. Methods to Analyze 2‐D X‐ray Images

AbstractThe Earth's magnetosheath and cusps are the sources of soft X‐rays. In the accompanying paper (Part 1) and this paper, we discuss the methods of finding the magnetopause position by analyzing the X‐ray images. We use the software developed for the Soft X‐ray Imager (SXI) on board the forthcoming Solar wind Magnetosphere Ionosphere Link Explorer (SMILE) mission. We show how to find the maximum SXI count rate in noisy count maps. We verify the assumption that the maximum of the X‐ray emissivity integrated along the Line‐of‐Sight (Ix) is tangent to the magnetopause. We consider two cases using two MHD models and apply different methods of magnetospheric masking. Overall, the magnetopause is located close to the maximum Ix gradient or between the maximum Ix gradient and the maximum Ix depending on the method used. But since the angular distance between the maximum Ix gradient and the maximum Ix is relatively small (about 3°), the maximum Ix might be used as an indicator of the outer boundary of a wide magnetopause layer usually obtained in MHD simulations.

Design of a plane grating with multilayer coating for the soft X-ray tomography beamline

An alternate multilayer plane grating has been designed for the soft X-ray tomography beamline. At this beamline, a grating with 600 line/mm and Au coating has already been set up to serve the energy range from 260 eV to 1200 eV. To fit the original optical design, a varied-line-spacing plane grating optimized at 2473 eV will be used in this beamline. The groove depth is 2.5 nm and its duty cycle is 0.5. The B4C/Mo alternate layers with period 30 are selected to enhance diffraction efficiency in the energy range 1100 eV -- 2600 eV. The varied-line-spacing plane grating paired with a matched multilayer plane mirror constitutes a monochromator to provide energetic photons. Based on the designed multilayer conditions, the calculated diffraction efficiency of alternate multilayer varied-line-spacing plane grating is about 0.24 at 2473 eV; the calculated photon flux is about 2.3 × 1011 photons/s. The resolving power is about 1670; the openings of the entrance and exit slits are 25 and 50 μm respectively.

An Improved Magnetohydrodynamic Simulation of the 2006 December 13 Coronal Mass Ejection of NOAA Active Region 10930

We present a magnetohydrodynamic simulation of the coronal mass ejection on 2006 December 13 in the emerging δ-sunspot NOAA Active Region 10930, improving upon a previous simulation by Fan as follows. (1) Incorporate an ambient solar wind instead of using a static potential magnetic field extrapolation as the initial state. (2) In addition to imposing the emergence of a twisted flux rope, also impose at the lower boundary a random electric field that represents the effect of turbulent convection, which drives field-line braiding and produces resistive and viscous heating in the corona. With the inclusion of this heating, which depends on the magnetic field topology, we are able to model the synthetic soft X-ray images that would be observed by the X-Ray Telescope (XRT) of the Hinode satellite, produced by the simulated coronal magnetic field. We find that the simulated preeruption magnetic field with the buildup of a twisted magnetic flux rope produces synthetic soft X-ray emission that shows qualitatively similar morphology as that observed by the Hinode/XRT for both the ambient coronal loops of the active region and the central inverse S-shaped “sigmoid“ that sharpens just before the onset of the eruption. The synthetic postflare loop brightening also shows similar morphology to that seen in the Hinode/XRT image during the impulsive phase of the eruption. It is found that the kinematics of the erupting flux rope is significantly affected by the open magnetic fields and fast solar wind streams adjacent to the active region.

Extensive characterization of Marshak waves observed at the LIL laser facility

We detail results of an experiment performed at the Ligne d'Intégration Laser facility aimed at studying supersonic and diffusive radiation front propagation in low-density SiO2 aerogel (20 and 40 mg/cm3) enclosed in a gold tube, driven by thermal emission from a laser-heated spherical gold cavity. The evolution of the front is studied continuously by measuring its self-emission with a 1D (one-dimensional) time-resolved soft x-ray imager. Measurement is performed along (through a 200-μm-wide observation slit) and at the exit of the tube giving access to the dynamics and the curvature of the front. Experimental results are then compared successfully to results from the 3D (three-dimensional) radiation hydrodynamics code TROLL, which shows that if continuous tracking of the front position is accessible with this experimental scheme, measurement of its maximum radiation temperature is on the contrary affected by radiation closure of the observation slit. 3D simulations also indicate that this effect can even be worsened if one includes pointing errors of the x-ray imager. Radiation temperature along the tube was then inferred by combining results from the imager to a wall shock breakout time measurement using a velocity interferometer system for any reflector and results from a broadband x-ray spectrometer used to determine the temperature at the exit of the tube. A decrease in the radiation temperature along the tube is observed, the decrease being more important for the higher SiO2 aerogel density.

Soft X-ray Tomography Reveals HSV-1-Induced Remodeling of Human B Cells.

Upon infection, viruses hijack the cell machinery and remodel host cell structures to utilize them for viral proliferation. Since viruses are about a thousand times smaller than their host cells, imaging virus-host interactions at high spatial resolution is like looking for a needle in a haystack. Scouting gross cellular changes with fluorescent microscopy is only possible for well-established viruses, where fluorescent tagging is developed. Soft X-ray tomography (SXT) offers 3D imaging of entire cells without the need for chemical fixation or labeling. Here, we use full-rotation SXT to visualize entire human B cells infected by the herpes simplex virus 1 (HSV-1). We have mapped the temporospatial remodeling of cells during the infection and observed changes in cellular structures, such as the presence of cytoplasmic stress granules and multivesicular structures, formation of nuclear virus-induced dense bodies, and aggregates of capsids. Our results demonstrate the power of SXT imaging for scouting virus-induced changes in infected cells and understanding the orchestration of virus-host remodeling quantitatively.

Inconspicuous Solar Polar Coronal X-Ray Jets as the Source of Conspicuous Hinode/EUV Imaging Spectrometer Doppler Outflows

We examine in greater detail five events previously identified as being sources of strong transient coronal outflows in a solar polar region in Hinode/Extreme Ultraviolet (EUV) Imaging Spectrometer (EIS) Doppler data. Although relatively compact or faint and inconspicuous in Hinode/X-ray Telescope (XRT) soft-X-ray (SXR) images and in Solar Dynamics Observatory (SDO)/Atmospheric Imaging Assembly (AIA) EUV images, we find that all of these events are consistent with being faint coronal X-ray jets. The evidence for this is that the events result from eruption of minifilaments of projected sizes spanning 5000–14,000 km and with erupting velocities spanning 19–46 km s−1, which are in the range of values observed in cases of confirmed X-ray polar coronal hole jets. In SXR images, and in some EUV images, all five events show base brightenings, and faint indications of a jet spire that (in four of five cases where determinable) moves away from the brightest base brightening; these properties are common to more obvious X-ray jets. For a comparatively low-latitude event, the minifilament erupts from near (≲few arcsec) a location of near-eruption-time opposite-polarity magnetic-flux-patch convergence, which again is consistent with many observed coronal jets. Thus, although too faint to be identified as jets a priori, otherwise all five events are identical to typical coronal jets. This suggests that jets may be more numerous than recognized in previous studies, and might contribute substantially to solar wind outflow, and to the population of magnetic switchbacks observed in Parker Solar Probe (PSP) data.