Soft X-ray Imaging Research Articles

Correlative light and soft X-ray tomography of in situ mesoscale heterochromatin structure in intact cells.

Heterochromatin organization is critical to many genome-related programs including transcriptional silencing and DNA repair. While super-resolution imaging, electron microscopy, and multiomics methods have provided indirect insights into the heterochromatin organization, a direct measurement of mesoscale heterochromatin ultrastructure is still missing. We use a combination of correlative light microscopy and cryo-soft X-ray tomography (CLXT) to analyze heterochromatin organization in the intact hydrated state of human mammary fibroblast cells. Our analysis reveals that the heterochromatin ultra-structure has a typical mean domain size of approximately 80nm and a mean separation of approximately 120nm between domains. Functional perturbations yield further insights into the molecular density and alterations in the mesoscale organization of the heterochromatin regions. Furthermore, our polymer simulations provide a mechanistic basis for the experimentally observed size and separation distributions of the mesoscale chromatin domains. Collectively, our results provide direct, label-free observation of heterochromatin organization in the intact hydrated state of cells.

Investigating the effect of BT direction on W source-to-core pathways during the SAS-VW campaign on DIII-D

Experiments using the V-shaped closed slot tungsten (W) coated SAS-VW divertor in DIII-D studied the effects of the BT direction on core contamination of eroded tungsten from a closed slot divertor configuration. Core W content is inferred using soft-X ray tomography (SXR) and vacuum ultraviolet spectroscopy (SPRED), while W divertor erosion is inferred from visible spectroscopy of W emission (400.9 nm) measured by in-slot filterscopes (filtered photo-multipliers). Post-mortem analysis from the campaign discovered tile misalignment leading to suspected pronounced leading-edge erosion in the unfavorable BT direction (ion B→×∇B→ drift away from divertor) likely not captured by diagnostics. However, empirical findings show up to ∼ 2-3x larger core contamination in the favorable BT direction even considering no additional W erosion from leading edges. A “source-to-core efficiency factor” is derived to estimate the effects of leading-edge erosion and compare W contamination for two pairs of H-mode discharges in opposite BT directions. While having differing absolute parameters, similar core impurity density gradients suggest comparable core impurity transport. These results show that favorable BT may have stronger source-to-core pathways for W impurities sourced from the outer divertor region. Possible explanations could include the effects of E→×B→ drifts on W transport in the scrape-off-layer (SOL) as well as previously determined fast SOL inner target directed flows in favorable BT.

Flexible Soft X-Ray Image Sensors based on Metal Halide Perovskites With High Quantum Efficiency.

Soft X-ray imaging is a powerful tool to explore the structure of cells, probe material with nanometer resolution, and investigate the energetic phenomena in the universe. Conventional soft X-ray image sensors are by and large Si-based charge coupled devices that suffer from low frame rates, complex fabrication processes, mechanical inflexibility, and required cooling below -60°C. Here, a soft X-ray photodiode is reported based on low-cost metal halide perovskite with comparable performance to commercial Si-based device. Nanothrough network electrodeminimized the optical loss due to the shadowing of insensitive layers, while a multidimensional perovskite heterojunctionis generated to reduce the photo-generated carrier loss. This strategy promoted a record quantum efficiency of 8×103% without cooling, several orders of magnitude greater than the previously achieved. Flexible and curved soft X-ray imaging arrays are fabricated based on this high-performance device structure, demonstrating stable soft X-ray response and sharp imaging capabilities. This work highlights the low-cost and efficient perovskite photodiode as a strong candidate for the next-generation soft X-ray image sensors.

An Adaptive X‐Ray Dynamic Image Estimation Method Based on OMNI Solar Wind Parameters and SXI Simulated Observations

AbstractObservations of the overall interactions between solar wind and the Earth's magnetosphere are crucial for space weather monitoring. Upcoming missions like the Solar Wind Magnetosphere Ionosphere Link Explorer (SMILE) and the Lunar Environment heliosphere X‐ray Imager (LEXI) aim to make comprehensive global imaging of Earth's magnetosphere using soft X‐ray imager (SXI) in order to understand its dynamic response to solar wind impact. Short‐duration X‐ray images have a low signal‐to‐noise ratio (SNR), limited by cosmic background and Poisson noise. Longer integration times provide better SNR of magnetospheric structures but fail to capture the short‐term dynamics during the integration. Our study introduces a neural network method which is able to estimate the short‐term dynamics during a long integration, driven by OMNI solar wind data and simulated soft X‐ray images. Specifically, an adaptive X‐ray image estimator and a spatio‐temporal discriminator are used. It leverages X‐ray models like Magnetohydrodynamic (MHD) and Jorgensen & Sun model, driven by OMNI data to provide high‐temporal‐resolution prior information on magnetosphere motion, with SXI observation images acting as a posterior constraint on the magnetosphere's state. Experimental validation demonstrates apparent improvements in Peak signal‐to‐noise ratio (PSNR) and Structural Similarity (SSIM) compared to traditional linear and optical flow interpolation methods. The method's flexibility, considering input‐output consistency, enables easy extension to any interval (>3 min), meeting diverse application needs. In conclusion, our study presents a new approach to soft X‐ray image estimation based on neural networks, providing insights into magnetospheric dynamics as observed in soft X‐rays.

Soft x-ray tomography on the high field spherical tokamak ST40.

As part of its roadmap to developing commercial fusion plants, Tokamak Energy Ltd. operates the high field spherical tokamak ST40. Studies on this device will help to expand the high field spherical tokamak physics basis by characterizing confinement and the fusion triple product. In support of this, bolometers and broadband and x-ray sensitive diodes can provide information on key energy loss mechanisms of the plasma. These mechanisms include core magnetohydrodynamic activity that deteriorates confinement, such as sawtooth crashes that can be used to characterize relaxations in the q-profile. In addition, combinations of these diagnostics can be used to infer the total radiated power losses and plasma composition. Here, we present results from a new, midplane, tangential, Be-filtered diode with 16 channels spanning the radial extent of the plasma. The system is shown to resolve magnetohydrodynamic instabilities (up to 100kHz) and be able to provide radiation profiles through tomography. The tomographic inversion routine is compared against other diagnostics on ST40 and provides emissivity measurements across a variety of operating scenarios. Finally, we look ahead to implementing multiple soft x-ray cameras on ST40 and the improvements this will have on the diagnostic capabilities.

Preoperative abaloparatide plus zoledronate treatment accelerates femoral bone healing in rats following osteotomy.

Purpose: We investigated the potential efficacy of abaloparatide (Abalo) and zoledronate (ZA) combination therapy for accelerating femoral union in a rat osteotomy model. Methods: Nine-week-old male Sprague-Dawley rats were randomly divided into four groups (n = 14 per group): control, abaloparatide (Abalo, 30μg/kg via subcutaneous injection [s.c.] 5 times per week for 6weeks), zoledronate (ZA; 0.1mg/kg via s.c., single dose), and Abalo + ZA. Rats were then subjected to unilateral osteotomy of the femoral shaft, followed by osteosynthesis with intramedullary nailing to establish bone healing models. At 2 and 4weeks after osteotomy, both femurs were removed from seven rats per group for soft X-ray imaging to evaluate bone union and microcomputed tomography (micro-CT) for bone morphometric evaluation. Blood samples were collected from all rats every 2week starting 6weeks pre- to 4weeks postosteotomy. Toluidine blue staining was used for histopathological evaluation of the undecalcified specimens. Results: Soft X-ray imaging revealed accelerated callus formation, callus maturation, and fracture line closure in Abalo and Abalo + ZA groups compared to ZA and control groups. Micro-CT demonstrated greater cortical bone and trabecular bone to total volume ratios in contralateral (left) femurs of the Abalo + ZA group compared to the Abalo group. Both trabecular and cortical bone mineral densities were also greater in contralateral femurs of the Abalo + ZA group compared to Abalo and ZA groups. Conclusion: These findings suggest substantial additive or synergistic efficacy of abaloparatide plus zoledronate combination therapy for accelerating bone healing following osteotomy and for maintaining normal bone health.

SPARC x-ray diagnostics: Technical and functional overview.

An overview is given of SPARC's three main x-ray diagnostics, with a focus on the functions they fulfill with respect to tokamak operation. The first is an in-vessel soft x-ray tomography diagnostic, aimed at providing early campaign information on plasma position, MHD activity, and impurity content. The second is an ex-vessel set of hard x-ray scintillators aimed at detecting the presence of runaway electrons, in particular during plasma startup phases. The third is a set of x-ray Bragg spectrometers, located outside of the tokamak hall, aimed at informing on the ion temperature as an indirect constraint to reduce uncertainties on the fusion power, on providing plasma rotation velocity estimates, and on observing impurity emission. Finally, more technical details are given on the beamlines at the end of which the spectrometers are located. It explains how their design allows us to ensure tritium containment and limit neutron radiation while providing a straight view into the plasma that can also be used for testing new innovative sensors.

Two-Dimensional Plasma Soft X-ray Radiation Imaging System: Optimization of Amplification Stage Based on Gas Electron Multiplier Technology.

The objective of the proposed research is to develop plasma soft X-ray (SXR) radiation imaging that includes spectral information in addition to standard SXR tomography for the purpose of studying, for example, tungsten transport and its interplay with magnetohydrodynamics (MHD) in tokamak plasmas in an ITER-relevant approach. The SXR radiation provides valuable information about both aspects, particularly when measured with high spatial and temporal resolution and when tomographic reconstructions are performed. The spectral data will facilitate the tracking of both light and high-Z impurities. This approach is pertinent to both the advancement of a detailed understanding of physics and the real-time control of plasma, thereby preventing radiative collapses. The significance of this development lies in its ability to provide three-dimensional plasma tomography, a capability that extends beyond the scope of conventional tomography. The utilization of two-dimensional imaging capabilities inherent to Gas Electron Multiplier (GEM) detectors in a toroidal view, in conjunction with the conventional poloidal tomography, allows for the acquisition of three-dimensional information, which should facilitate the study of, for instance, the interplay between impurities and MHD activities. Furthermore, this provides a valuable opportunity to investigate the azimuthal asymmetry of tokamak plasmas, a topic that has rarely been researched. The insights gained from this research could prove invaluable in understanding other toroidal magnetically confined plasmas, such as stellarators, where comprehensive three-dimensional measurements are essential. To illustrate, by attempting to gain access to anisotropic radiation triggered by magnetic reconnection or massive gas injections, such diagnostics will provide the community with enhanced experimental tools to understand runaway electrons (energy distribution and spatial localization) and magnetic reconnection (spatial localization, speed…). This work forms part of the optimization studies of a detecting unit proposed for use in such a diagnostic system, based on GEM technology. The detector is currently under development with the objective of achieving the best spatial resolution feasible with this technology (down to approximately 100 µm). The diagnostic design focuses on the monitoring of photons within the 2-15 keV range. The findings of the optimization studies conducted on the amplification stage of the detector, particularly with regard to the geometrical configuration of the GEM foils, are presented herein. The impact of hole shape and spacing in the amplifying foils on the detector parameters, including the spatial size of the avalanches and the electron gain/multiplication, has been subjected to comprehensive numerical analysis through the utilization of Degrad (v. 3.13) and Garfield++ (v. bd8abc76) software. The results obtained led to the identification of two configurations as the most optimal geometrical configurations of the amplifying foil for the three-foil GEM system for the designed detector. The first configuration comprises cylindrical holes with a diameter of 70 μm, while the second configuration comprises biconical holes with diameters of 70/50/70 μm. Both configurations had a hole spacing of 120 μm.

Structures of Liquid-Liquid Interfaces in Partially Miscible Systems Revealed by Soft X-ray Imaging.

The properties of liquid-liquid interfaces are intricately linked to its structure, with a particular focus on the concentration distribution within the interface. To obtain precise information regarding the concentration distribution, we have developed a high-resolution soft X-ray imaging method for liquid-liquid interfaces. This work focused on representative partially miscible systems, analyzing the interfacial concentration distribution profiles of water-alkanols under both steady-state and dynamic processes, and obtaining the diffusion coefficients of different water concentrations in alkanols. Significant disparities in concentration distributions and the concentration-related diffusion coefficients were observed despite comparable diffusion distances within the same system across different states. Meanwhile, it was found that alkanols exhibit adsorption phenomena at the interface. This newfound knowledge serves as a crucial stepping stone toward a deeper understanding of partially miscible systems. Our study opens a way to explore liquid-liquid interface information with high-resolution.

Crucial future observations and directions for unveiling magnetopause dynamics and their geospace impacts

The dynamics of Earth’s magnetopause, driven by several different external/internal physical processes, plays a major role in the geospace energy budget. Given magnetopause motion couples across many space plasma regions, numerous forms of observations may provide valuable information in understanding these dynamics and their impacts. In-situ multi-point spacecraft measurements measure the local plasma environment, dynamics and processes; with upcoming swarms providing the possibility of improved spatiotemporal reconstruction of dynamical phenomena, and multi-mission conjunctions advancing understanding of the “mesoscale” coupling across the geospace “system of systems.” Soft X-ray imaging of the magnetopause should enable boundary motion to be directly remote sensed for the first time. Indirect remote sensing capabilities might be enabled through the field-aligned currents associated with disturbances to the magnetopause; by harnessing data from satellite mega-constellations in low-Earth orbit, and taking advantage of upgraded auroral imaging and ionospheric radar technology. Finally, increased numbers of closely-spaced ground magnetometers in both hemispheres may help discriminate between high-latitude processes in what has previously been a “zone of confusion.” Bringing together these multiple modes of observations for studying magnetopause dynamics is crucial. These may also be aided by advanced data processing techniques, such as physics-based inversions and machine learning methods, along with comparisons to increasingly sophisticated geospace assimilative models and simulations.

Characterization of similar Marshak waves observed at the LMJ

We detail results of two experiments performed at the Laser Mégajoule (LMJ) facility aimed at studying similar supersonic Marshak waves propagating in a low-density SiO2 aerogel enclosed in metallic tubes. Similar means here that these two experiments, driven by the same input radiation temperature history, use purposely very different tubes in terms of length (L = 1200 or 2000 μm), diameter (2R = 1000 or 2000 μm), nature of the wall (gold or copper), and aerogel densities (ρ = 30 or 20 mg/cm3), yet the transit time and the radiation temperature of the fronts at the tube exit are the same for both shots. Marshak waves are characterized at the exit using simultaneously for the first time to our knowledge, a one dimensional soft x-ray imager from which the radiation front transit time and curvature are measured and also a broadband x-ray spectrometer to infer its temperature history. These constraining results are then successfully compared to those from simple analytical models [Cohen et al., Phys. Rev. Res. 2, 023007 (2020) and Hurricane et al., Phys. Plasmas 13, 113303 (2006)] and from the three dimensional Lagrangian radiation-hydrodynamics code TROLL to get information on x-ray energy losses. Controlled compensation effects between the length, diameter, and nature of the tubes (governing these losses) are such that the radiation temperature drop along the tubes is eventually the same for these two similar shots.

A 1D imaging soft X-ray spectrometer for the small quantum systems instrument at the European XFEL.

A 1D imaging soft X-ray spectrometer installed on the small quantum systems (SQS) scientific instrument of the European XFEL is described. It uses movable cylindrical constant-line-spacing gratings in the Rowland configuration for energy dispersion in the vertical plane, and Wolter optics for simultaneous 1D imaging of the source in the horizontal plane. The soft X-ray fluorescence spectro-imaging capability will be exploited in pump-probe measurements and in investigations of propagation effects and other nonlinear phenomena.

Integrating Cryo Soft X-ray Tomography into Light and Electron Microscopy Workflows

Integrating Cryo Soft X-ray Tomography into Light and Electron Microscopy Workflows

Soft X-ray performance of an optimised charge-coupled device for astronomy

For the upcoming European Space agency (ESA)/Chinese Academy of Sciences (CAS) SMILE mission, launching in 2025, large-format soft X-ray optimised CCDs have been manufactured by Teledyne e2v, named the CCD370. The CCDs are approximately 8 cm × 8 cm and are comprised of 4510 × 4510 18 μm pitch pixels, with a store shield covering approximately 1/7th of the active imaging area to facilitate frame-transfer operation mode. To optimise quantum efficiency within the soft X-ray energy band, the device is 16 μm thick, back illuminated, and has an additional back surface passivation process. The focal plane of the soft X-ray imager (SXI) on the SMILE spacecraft will be comprised of 2 CCD370s, operating with 6 × 6 on-chip binning to mitigate against CTI-induced charge transfer losses and charge spreading throughout the 3-year mission lifetime.As part of the pre-flight testing and calibration, a CCD370 was characterised at the PTB beamline at the BESSY 2 synchrotron in Berlin, and key metrics such as quantum efficiency and energy resolution in the 0.2–1.8 keV energy band were assessed. The quantum efficiency measurements show expected performance within specification for the instrument, and also match a transmission-layer QE model. The energy resolution is 68 ± 2 eV FWHM @ 1.2 keV, which is an improvement over the current generation of X-ray telescopes such as XMM-Newton, Chandra, and the Swift X-ray Telescope. Although competing technologies such as DEPFETs and scientific CMOS image sensors now have similar performance to CCDs, the performance shown here can still easily satisfy requirements for novel X-ray instruments, and can still be useful in future astronomy missions given the rich heritage, high technology-readiness-level, and maturity of the technology.

On-line correlative imaging of cryo-PALM and soft X-ray tomography for identification of subcellular structures.

Correlative imaging of fluorescence microscopy and soft X-ray microscopy plays a crucial role in exploring the relationship between structure and function in cellular biology. However, the current correlative imaging methods are limited either to off-line or low-resolution fluorescence imaging. In this study, we developed an integrated on-line cryogenic photoactivated localization microscopy (cryo-PALM) system at a soft X-ray microscopy station. This design eliminates some critical issues such as sample damage and complex post-correlation arising from transferring samples between different cryostages. Furthermore, we successfully achieved correlative imaging of cryopreserved near-native cells, with a resolution of about 50 nm of cryo-PALM. Therefore, the developed on-line correlation imaging platform provides a powerful tool for investigating the intricate relationship between structure and function in biological and molecular interactions, as well as in other life science disciplines.

Deep Learning Based Surrogate Model a fast Soft X-ray (SXR) Tomography on HL-2 a Tokamak

Deep Learning Based Surrogate Model a fast Soft X-ray (SXR) Tomography on HL-2 a Tokamak

Observation of mammalian living cells with femtosecond single pulse illumination generated by a soft X-ray free electron laser

Soft X-ray transmission microscopy is a powerful tool for visualizing cellular structures due to the natural contrast between organic material and water, but radiation damage has hindered its application to living cells. We have developed a soft X-ray microscope using femtosecond pulse illumination generated by a soft X-ray free electron laser, with which structural change of cells caused by radiation damage is negligible. Employing Wolter mirrors for illumination and objective optics allowed us to perform soft X-ray imaging with a large field of view, enabling observation of mammalian cells. We successfully captured images of living cells in a culture medium visualizing their carbon distribution. The broad wavelength-tunability of soft X-ray free electron lasers, in conjunction with the achromaticity of Wolter mirrors, enabled wavelength resolved cellular imaging.

Subcellular Feature-Based Classification of α and β Cells Using Soft X-ray Tomography.

The dysfunction of α and β cells in pancreatic islets can lead to diabetes. Many questions remain on the subcellular organization of islet cells during the progression of disease. Existing three-dimensional cellular mapping approaches face challenges such as time-intensive sample sectioning and subjective cellular identification. To address these challenges, we have developed a subcellular feature-based classification approach, which allows us to identify α and β cells and quantify their subcellular structural characteristics using soft X-ray tomography (SXT). We observed significant differences in whole-cell morphological and organelle statistics between the two cell types. Additionally, we characterize subtle biophysical differences between individual insulin and glucagon vesicles by analyzing vesicle size and molecular density distributions, which were not previously possible using other methods. These sub-vesicular parameters enable us to predict cell types systematically using supervised machine learning. We also visualize distinct vesicle and cell subtypes using Uniform Manifold Approximation and Projection (UMAP) embeddings, which provides us with an innovative approach to explore structural heterogeneity in islet cells. This methodology presents an innovative approach for tracking biologically meaningful heterogeneity in cells that can be applied to any cellular system.

Dark matter search in the Perseus cluster with simultaneous analysis of Hitomi and Suzaku data

Abstract The reported detection of a 3.5 keV emission line in the Perseus cluster, possibly originating from dark matter decay, is still under scrutiny. Despite extensive observations, the detection has not yet been confirmed, and its origin remains a topic of active debate. Most of the previous searches relied on spectroscopy with X-ray charge-coupled devices, such as the X-ray Imaging Spectrometer on Suzaku. Although this provided a large amount of observational data, it only offered moderate spectral resolution. The X-ray astronomy satellite Hitomi offers new results using its high-resolution X-ray spectrometer (Soft X-ray Spectrometer). However, the data gathered were somewhat limited in terms of statistics. In this work, we present the results of a new spectral analysis of the Perseus cluster that combines the spectra from the XIS and SXS, along with the Soft X-ray Imager on Hitomi, thereby complementing each other’s capability. Our search was conducted for a line emission or absorption in the energy range of 2.6–5.9 keV assuming the Navarro–Frenk–White mass distribution with a concentration parameter of 5.0 and virial radius, r200, of 1.79 Mpc. We also considered the instrumental systematic uncertainty caused by the effective area calibration, which we empirically evaluated using the Crab Nebula spectra. On combining these results, we found no significant line features above the baryonic thermal emission from the intra-cluster medium. The upper limit at 3.5 keV, at a 3σ confidence level, is tightly constrained to 4.2 × 10−5 photons cm−2 s−1 for the $15^{\prime }$ circular sky region, which encloses a dark matter mass of $1.67\times 10^{14}\, M_{\odot }$, assuming a line velocity dispersion of 180 km s−1. This constraint is three times tighter than the previous one, which only used the SXS. On the basis of these findings, we provide the upper limit of the dark matter decay rate and the mixing angle for the sterile neutrino origin.

A model for photon counting X-ray event reconstruction uncertainty

Evaluation of detectors for a soft X-ray imaging spectrometer has resulted in the need to understand the effect of charge spreading on apparent detector noise properties, and therefore achievable energy resolution. This paper presents a mathematical model for the processes leading to increased uncertainty within a simplified X-ray reconstruction process. This is a description for additional uncertainty introduced by the process of collecting X-ray generated electrons into a region of noisy pixels and reconstructing the recorded pixels values back into an estimated X-ray energy value. The predictions of the model, and preliminary experimental verification are shown.