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At least 19 records

Interior soft x-ray tomography with sparse global sampling

To investigate the feasibility of interior imaging reconstruction in soft X-ray tomography for higher-resolution cellular imaging, including whole-cell imaging, we develop an alignment and reconstruction algorithm that combines a small number of sparse whole-cell images with a high-resolution local interior scan. Based on numerical simulations, we demonstrate that combined reconstructions mitigate the depth-of-field limitation in high-resolution scans, enable radiation dose optimization, and yield quantitative X-ray absorption values with sparse sampling. We further validate our numerical approach using experimental data from two different cell types and show that the combined reconstruction reliably provides high spatial resolution within an interior region of interest of a whole cell. The resulting sparse reconstruction framework offers robust, faithful visualization of cellular organelles in soft X-ray tomography. This mesoscale imaging strategy allows one to ‘scout’ and zoom into selected subcellular volumes of interest, enabling increased spatial resolution without sacrificing larger-volume imaging and providing information on the relative positions of all organelles within a cell.

3D imaging↗

Automated segmentation of soft X-ray tomography: Native cellular structure with submicron resolution at high-throughput for whole-cell quantitative imaging in yeast

Soft X-ray tomography (SXT) is an invaluable tool for quantitatively analyzing cellular structures at suboptical isotropic resolution. However, it has traditionally depended on manual segmentation, limiting its scalability for large datasets. Here, we leverage a deep learning-based autosegmentation pipeline to segment and label cellular structures in hundreds of cells across three Saccharomyces cerevisiae strains. This task-based pipeline uses manual iterative refinement to improve segmentation accuracy for key structures, including the cell body, nucleus, vacuole, and lipid droplets, enabling high-throughput and precise phenotypic analysis. Using this approach, we quantitatively compared the three-dimensional (3D) whole-cell morphometric characteristics of wild-type, VPH1-GFP, and vac14 strains, uncovering detailed strain-specific cell and organelle size and shape variations. We show the utility of SXT data for precise 3D curvature analysis of entire organelles and cells and detection of fine morphological features using surface meshes. Our approach facilitates comparative analyses with high spatial precision and statistical throughput, uncovering subtle morphological features at the single-cell and population level. This workflow significantly enhances our ability to characterize cell anatomy and supports scalable studies on the mesoscale, with applications in investigating cellular architecture, organelle biology, and genetic research across diverse biological contexts.

Chen, Jianhua [Lawrence Berkeley National Laborato↗

Initial in-orbit operation of the soft X-ray spectrometer Resolve onboard the X-ray imaging and spectroscopy mission satellite

The X-Ray Imaging and Spectroscopy Mission satellite was launched on September 6, 2023 (UT). Its Resolve instrument is a high-resolution X-ray spectrometer enabled by a microcalorimeter array thermally anchored to a 50-mK heat sink. Many sensitive, critical sub-systems comprise Resolve, including a multistage cryogenic cooling system, thin-film aperture filters, low-noise electronics, on-board signal processing, and several sources of X-rays for calibration. We summarize the initial on-orbit power-on and checkout of Resolve that commenced immediately after launch. Soon after launch, the cryocoolers were activated, and their operation was successfully established. On October 9, 2023, the first cycle of the adiabatic demagnetization refrigerator was carried out, bringing the sensors to their steady-state operational temperatures. Following this, the energy resolution at 5.9 keV was successfully measured. The energy scale of the system is highly sensitive to the thermal environment surrounding both the sensors and their analog electronics. Gain correction was performed using reference X-ray lines from onboard calibration sources. To optimize cooler frequency settings, noise spectra were collected across a range of frequencies, and the most suitable frequency pair was selected based on the in-orbit environment. During the final phase of the checkout, an attempt was made to open the gate valve, which is designed to protect the Dewar’s interior from external pressure during ground operations and launch. Unfortunately, this attempt was unsuccessful. As a result, the checkout process was temporarily paused, and a stable operational strategy was subsequently developed to enable Resolve to function effectively with the gate valve remaining closed.

X-ray micro-calorimeter↗

Resolve instrument onboard the X-Ray Imaging and Spectroscopy Mission

We present an overview of the design and in-flight performance of the Resolve soft X-ray spectrometer on the X-Ray Imaging and Spectroscopy Mission that was successfully launched on September 7, 2023, on a JAXA H-IIA rocket from the Tanegashima Space Center of Japan. The instrument has a 36-pixel array of microcalorimeters, 35 of which are at the focus of a high-throughput grazing-incidence X-ray mirror. The instrument has achieved its required operational base temperature of 0.05 K and a spectral resolution of 4.5 eV (FWHM) at 6 keV. The cooling chain was designed to provide a lifetime of at least 3 years in orbit and operate with and without liquid helium to provide redundancy and the longest operational lifetime for the instrument. Early indications are that the cryogen lifetime may reach 6 years with a cryogen-free mode thereafter. A series of onboard X-ray calibration sources produces energy scale calibration lines simultaneously while observing celestial sources. The overall design and in-flight performance of Resolve are described.

Astronomy and AstroPhysics↗

Soft X-ray reflection ptychography

Scanning transmission X-ray microscopy and ptychography have become mature tools for high-resolution, element-specific imaging of nanoscale structures. However, transmission geometries impose stringent constraints on sample thickness and preparation, thereby limiting investigations of extended or bulk specimens, especially in the soft X-ray region. Here, we demonstrate reflection-geometry soft X-ray ptychography as a robust imaging mode. Instrumental feasibility and spatial resolution are established using a lithographically defined Siemens star and barcode test pattern on a multilayer substrate. We empirically demonstrate a full-pitch spatial resolution of ca. 45 nm from Fourier ring correlation analysis of the reconstructed object. The results highlight the potential of the reflection geometry for nondestructive X-ray studies of materials without the need for transmissive samples.

Guenzing, Damian [Lawrence Berkeley National Labor↗

Three-dimensional high-content imaging of unstained soft tissue with subcellular resolution using a laboratory-based X-ray microscope

With increasing interest in studying biological systems across spatial scales—from centimeters down to nanometers—histology continues to be the gold standard for tissue imaging at cellular resolution, providing an essential bridge between macroscopic and nanoscopic analysis. However, its inherently destructive and two-dimensional nature limits its ability to capture the full three-dimensional complexity of tissue architecture. Here, we show that phase-contrast X-ray microscopy can enable three-dimensional virtual histology with subcellular resolution. This technique provides direct quantification of electron density without restrictive assumptions, allowing for direct characterization of cellular nuclei in a standard laboratory setting. By combining high spatial resolution and soft tissue contrast, with automated segmentation of cell nuclei, we demonstrated virtual Hematoxylin and Eosin (H&E) staining using machine learning-based style transfer, yielding volumetric datasets compatible with existing histopathological analysis tools. Furthermore, by integrating electron density and the sensitivity to nanometric features of the dark field contrast channel, we achieve stain-free, high-content imaging capable of distinguishing nuclei and extracellular matrix.

3D virtual histology↗

In-orbit operation of Resolve Filter Wheel and modulated X-ray source

The Resolve soft X-ray spectrometer is a high spectral resolution microcalorimeter spectrometer for the X-ray Imaging and Spectroscopy Mission. In the beam of Resolve, there is a filter wheel containing X-ray filters. In the beam, there is also an active calibration source, the modulated X-ray source (MXS), which can provide pulsed X-rays to facilitate gain calibration. The filter wheel consists of six filter positions. Two open positions, one 55 Fe source to aid in spectrometer characterization during the commissioning phase, and three transmission filters: a neutral density filter, an optical blocking filter, and a beryllium filter. The X-ray intensity, pulse period, and pulse separation of an MXS are highly configurable. Furthermore, the switch-on time is synchronized with the spacecraft’s internal clock to give accurate start and end times of the pulses. One of the issues raised during ground testing was the susceptibility of an MXS at high voltage to ambient light. Although measures were taken to mitigate the light leak, the efficacy of those measures must be verified in orbit. Along with an overview of issues raised during ground testing, we will discuss the calibration source and the filter performance in-flight and compare with the transmission curves present in the Resolve calibration database.

X-ray Imaging and Spectroscopy Mission/Resolve↗

Soft x-ray high-harmonic generation in an anti-resonant hollow core fiber driven by a 3 μ m ultrafast laser

High-harmonic upconversion driven by a mid-infrared femtosecond laser can generate coherent soft x-ray beams in a tabletop-scale setup. Here, we report on a compact ytterbium-pumped optical parametric chirped pulse amplifier (OPCPA) laser system seeded by an all-fiber front-end and employing periodically poled lithium niobate (PPLN) nonlinear media operated near the pulse fluence limits of current commercially available PPLN crystals. The OPCPA delivers 3 µm wavelength pulses with 775 µJ energy at 1 kHz repetition rate, with transform-limited 120 fs pulse duration, diffraction-limited beam quality, and ultrahigh 0.33% rms energy stability over >18 h. Using this laser, we generate soft x-ray high harmonics (HHG) in argon gas by focusing into a low-loss, high-pressure gas-filled anti-resonant hollow core fiber (ARHCF), generating coherent light at photon energies up to the argon L-edge (250 eV) and carbon K-edge (284 eV), with high beam quality and ∼1% rms energy stability. This work demonstrates soft x-ray HHG in a high-efficiency guided-wave phase matched geometry, overcoming the high losses inherent to mid-IR propagation in unstructured waveguides, or the short interaction lengths of gas cells or jets. The ARHCF can operate in the long term without damage and with the repetition rate, stability, and robustness required for demanding applications in spectromicroscopy and imaging. Finally, we discuss routes for further optimizing the soft x-ray HHG flux by driving He at higher laser intensities using either the signal (1.5 μm) or idler wavelengths (3 μm).

Femtosecond lasers↗

Energy gain scale calibration of the XRISM Resolve microcalorimeter spectrometer: ground calibration results and on-orbit comparison

The Resolve instrument aboard the X-ray Imaging and Spectroscopy Mission (XRISM) is a 36-pixel microcalorimeter spectrometer that provides nondispersive spectroscopy with ∼ 5 eV spectral resolution in the soft X-ray waveband. Resolve has a requirement to provide an absolute energy-scale calibration of ± 2 eV from 0.3 to 12 keV. We describe our ground calibration strategy and results of a subset of the ground calibration campaigns, including a discussion of improvements in the energy scale ground calibration compared with Hitomi’s. These improvements include calibration of the low-energy band below 4 keV with the instrument in the flight dewar and the dewar aperture door open, which was not performed for Hitomi, and thorough measurements over an extended high-energy waveband to 22 keV. We also developed an improved technique for gain calibration of “mid-res” secondary events, which have suppressed gain due to proximity to a preceding X-ray event (18 to 70 ms) on the same pixel. We provide a discussion of the on-orbit energy scale monitoring campaigns and an assessment of the Resolve energy scale uncertainties, a key parameter for astrophysics analysis. Energy-scale calibration approaches for future space-based instruments, including the X-ray Integral Field Unit on Athena and microcalorimeter spectrometers proposed or under discussion for future X-ray observatory concepts, have heritage in the calibration of XRISM. We briefly comment on lessons learned from Resolve calibration that are relevant for these future instruments.

Aluminum↗

Classifying biophysical subpopulations of insulin secretory granules using quantitative whole-cell structure analysis

Pancreatic beta cells contain insulin secretory granules (ISGs), organelles where proinsulin is converted into insulin. As ISGs mature, they undergo extensive biophysical remodeling, producing a spectrum of subpopulations with heterogeneous molecular and spatial characteristics. However, systematic methods to define ISG subpopulations remain underdeveloped. To address this gap in knowledge, we employed soft X-ray tomography (SXT), which can quantitatively measure the biochemical density of ISGs within whole beta cells. Using unsupervised clustering, we classified subpopulations based on molecular density, size, and spatial positioning. Across different insulin secretory stimuli, we observed shifts toward mature and releasable subtypes, demonstrating that exogenous signals can dynamically remodel ISG subpopulation distributions. We extended this methodology to primary beta cells characterized using volume electron microscopy (vEM). Integrating subpopulations from SXT and vEM uncovered insights inaccessible by a single method in isolation. This strategy establishes a framework for defining therapeutic approaches aimed at enriching physiologically beneficial ISG subpopulations.

dense-core granules↗

Novel soft x-ray multi-energy camera to study thermal plasmas on WEST

A multi-energy soft x-ray (SXR) pinhole camera has been built, calibrated and deployed on the WEST tokamak to aid the study of thermal plasmas. This novel imaging diagnostic technique employs a 2D pixelated x-ray detector in which the lower energy threshold for photon detection can be adjusted independently on each pixel. This innovation allows the simultaneous measurement of x-rays with space, time and energy resolution. Measurements at lower energy (2–6 keV) dominated by tungsten line emission are used to estimate the tungsten concentration and the plasma ΔZ eff . Measurements at higher energy (11–18 keV), where only continuum emission is present, are employed to infer the plasma electron temperature. Other applications of this powerful diagnostic include the determination of the plasma SXR centroid vertical position, characterization of tungsten UFOs and various real-time measurements.

electron temperature↗

Strain-associated nanoscale fluctuating lithium transport within single-crystalline LiNi 1/3 Mn 1/3 Co 1/3 O 2 cathode particles

Solid-state lithium diffusion dynamics are critical for the rate capability and longevity of Li-ion batteries. Conventionally, nanoscale lithium diffusion within individual battery particles has been simplified as being primarily driven by concentration gradients, despite the associated processes inducing local lattice expansion, contraction, and strain fields. Using operando scanning transmission soft X-ray microscopy with high spatial resolution and chemical sensitivity to track nanoscale intraparticle lithium transport, and post-cycling Bragg coherent diffraction X-ray imaging to directly reveal three-dimensional intraparticle strain fields, we uncover strain-associated lithium transport dynamics within single-crystalline LiNi 1/3 Mn 1/3 Co 1/3 O 2 (scNMC) particles during cycling. Contrary to the expected thermodynamic solid-solution behavior of scNMC, our observations reveal near-uniform but fluctuating regions of lithium-dense and lithium-dilute areas during cycling. These fluctuations suggest that nanoscale lithium diffusion can proceed counter to concentration gradients. Additionally, we demonstrate that an increased presence of lithium-dilute regions near the surface enhances lithium surface insertion kinetics, emphasizing the importance of controlling surface lithium distribution to improve rate performance. Our study provides insights into nanoscale solid-state ion transport, with potential applications in batteries, solid-state fuel cells, and memristors.

Lee, Danwon [Seoul National Univ. (Korea, Republic↗

The scientific case for concurrent neutron and X-ray scattering and spectroscopy

The interrogation of materials with X-rays or neutrons to determine structure, energetics, and dynamics is fundamental to advancing physical and chemical materials science and enabling innovative material technologies. A persistent challenge in materials development is that progress depends on understanding structure and dynamics across multiple length and time scales in increasingly complex, multicomponent systems featuring interfaces, heterogeneity, and hierarchical organization. Despite rapidly growing demands on materials characterization, current experimental approaches are almost exclusively based on isolated X-ray or neutron scattering and spectroscopy, reflecting a paradigm largely unchanged for decades. To assess the scientific need for a new experimental paradigm, a 3-day workshop sponsored by the U.S. National Science Foundation (NSF) was held at the SpringHill Suites, San Jose, California, from June 2 to 4, 2022. The workshop brought together 70 national and international experts who critically evaluated opportunities enabled by concurrent neutron and X-ray (NeX) scattering, spectroscopy, and imaging experiments. The participants reached a clear consensus that establishing NeX capabilities is crucial for advancing the science of complex materials in the United States. This report illustrates the scientific drivers for NeX experiments through representative examples spanning biomaterials, energy materials, soft matter, nanomaterials, quantum materials, geoscience, and applied materials research. The complementarity of neutrons and X-rays is essential for robust model development and refinement, particularly in multiphase and multicomponent systems. While joint refinement of data from separate experiments is valuable, concurrent measurements uniquely eliminate uncertainties arising from sample evolution, environmental drift, and irreproducibility associated with experiments performed at different locations and times. Realizing NeX capabilities will require the development of new instrumentation, data analysis frameworks, and robust sample environments compatible with both neutron and X-ray probes. Addressing these challenges will enable unambiguous interpretation of complex materials behavior and open new frontiers in materials research.

X-ray↗

Fragmentation dynamics of CS 2 dications and trications following S 2p ionization

Here, we present the results from a detailed study of the fragmentation dynamics of CS$_2^{2+}$ and CS$_2^{3+}$, formed in intense femtosecond soft x-ray pulses above the sulfur 2p edge, primarily through single core photoionization from the S 2p site, and subsequent Auger–Meitner decay(s). By combining three-dimensional velocity map imaging with covariance analysis, we determine the relative momenta of the ions produced in each two- and three-body fragmentation channel, at significantly higher ion count rates than conventional coincidence measurements. We shed new light on the wide range of fragmentation channels observed from the CS 2 dication and trication, including channels that involve ionization-induced bond formation and fragmentations producing undetected neutral cofragments. In the latter case, a “native frames” approach is used to isolate contributions from concerted and sequential fragmentations and extract dynamical information about each step of a concerted fragmentation process. While dications often fragment sequentially, the trication is dominated by concerted fragmentation. The main trication fragmentation channel into S + + C + + S + can be well-approximated by classical Coulombic simulations of the ground-state geometry distribution, reflecting both the nature of the trication potential energy surface and the rapid multiple ionization prior to substantial structural dynamics. This study demonstrates ways in which fundamental insights into the fragmentation dynamics of polycations following x-ray ionization may be extracted, which will be beneficial to future studies that employ time-resolved x-ray Coulomb explosion imaging to study ultrafast photochemistry.

Allum, Felix [Deutsches Elektronen-Synchrotron (DE↗

Imaging Three-Dimensional Molecular Structure and Dynamics with Multiparticle Covariance and Cumulant Coulomb Explosion Analysis

Coulomb explosion imaging (CEI) provides a direct means of imaging molecular geometry by correlating fragment ion momenta following the fragmentation of a molecular polycation. Here, we demonstrate the use of three-body covariance and four-body cumulant analysis to extract three-dimensional (3D) structural information from the X-ray-induced Coulomb explosion of tert-butyl iodide (C4H9I). Site-selective ionization at the iodine 4d edge with intense femtosecond soft X-ray pulses from an X-ray free-electron laser (XFEL) enables rapid charge buildup and molecular breakup. By correlating ionic fragments in the molecular frame, we isolate complete dissociation channels and reveal subtle structural changes, such as umbrella-type motion of the branched alkyl chain, during the ionization process. Comparison with point-charge simulations of the Coulomb explosion shows close agreement, validating the approach. Furthermore, these results establish covariance/cumulant mapping as a powerful strategy for imaging complex three-dimensional molecular structures and point the way toward time-resolved CEI using both XFEL and tabletop sources for capturing ultrafast structural dynamics.

Imaging↗

Pair Cascades in Magnetar Magnetospheres

Resonant inverse Compton scattering (RICS) of soft thermal photons by relativistic particles on closed magnetic field loops has been proposed to explain the hard emission observed up to and beyond 200 keV from magnetars. If particles injected at the base of the loops have Lorentz factors ≳10 2 , the RICS spectra will be attenuated by both one-photon pair production and photon splitting in the ultrastrong magnetar fields, producing additional spectral components from pair synchrotron radiation and split photons that produce further generations of pairs and split photons. We investigate such cascades initiated by the primary injected electrons through a Monte Carlo simulation, and study the cascade spectra and pair distributions. For most observer angles, the pair synchrotron and split-photon spectra dominate the RICS primary spectra and produce complex polarization signals. In particular, the synchrotron spectra are highly polarized with degree 40%–80%, are softer than the RICS spectra, and may account for the high polarization of some magnetar spectra observed by the Imaging X-ray Polarimetry Explorer above 3 keV.

79 ASTRONOMY AND ASTROPHYSICS↗

Pulsed laser synthesis of mesoporous metal chalcogenide thin films

Mesoporous films of the metal chalcogenide B-FeSe were grown on MgO substrates by KrF pulsed laser deposition (PLD) in an argon background. At 100 mTorr, gated intensified charge-coupled device imaging and ion probe measurements showed that the plasma plume responsible for crystal growth initially comprised three components, with distinct expansion velocities. Plume interactions with the substrate heater and ablation target gave rise to complex dynamics, including collisions between the charged leading edge—rebounding between the substrate and the target—and slower-moving species in the plume interior. Film growth was dominated by species with kinetic energies ≤0.5 eV/atom. X-ray reflectivity revealed that films grown in this environment—with a substrate temperature of 350 ° C, a laser fluence of 1.0 J cm −2 , and a 7.5 mm 2 spot area—formed a porous framework with 15% porosity. Atomic force microscopy showed surface features that suggest pore sizes below 100 nm. X-ray diffraction indicated that the porous films were epitaxial with respect to the substrate and likely grew by oriented-attachment of gas-phase molecular clusters or very small nanoparticles, in contrast to the conventional epitaxy of vacuum films from atomic constituents. The in-plane orientation of the mesoporous films was B-FeSe [100]||[110] MgO, attributed to the soft landing of pre-formed crystallites on the MgO substrates, where protruding Se rows of B-FeSe aligned with corrugations of the MgO surface. In conclusion, this work implies that growth of candidate electrocatalyst materials by PLD in inert gas background may allow mesoporous frameworks with a single crystallographic orientation that expose specific crystal facets for electrochemical reactions and active site engineering.

cluster epitaxy↗

Thermal and kinematic properties of ejecta in SN1987A revealed by XRISM

We present an analysis of high-resolution spectra from the shock-heated plasmas in SN 1987A, based on an observation using the Resolve instrument onboard the X-Ray Imaging and Spectroscopy Mission (XRISM). The 1.7–10 keV Resolve spectra are accurately represented by a single-component, plane-parallel shock plasma model, with a temperature of $2.84_{-0.08}^{+0.09}$ keV and an ionization parameter of $2.64_{-0.45}^{+0.58}$ × $10^{11}\,\,{\rm s\,\, cm}^{-3}$. The Resolve spectra are also well reproduced by the 3D magneto-hydrodynamic simulation presented by Orlando et al. (2020, A&A, 636, A22) suggesting substantial contribution from the ejecta. The metal abundances obtained with Resolve align with the Large Magellanic Cloud value, indicating that the X-rays in 2024 originate from “non-metal-rich” shock-heated ejecta and the reverse shock has not reached the inner metal-rich region of ejecta. Doppler widths of the atomic lines from Si, S, and Fe correspond to velocities of 1500–1700 km s$^{-1}$, where the thermal broadening effects in this non-metal-rich plasma are negligible. Therefore, the line broadening seen in Resolve spectra is determined by the large bulk motion of ejecta. For reference, we determined a $90\%$ upper limit on non-thermal emission from a pulsar wind nebula at $4.3 \times 10^{-13}$ erg cm$^{-2}$ s$^{-1}$ in the 2–10 keV range, aligning with NuSTAR findings by Greco et al. (2022, ApJ, 931, 132). Additionally, we searched for the $^{44}$Sc K line feature and found a $1\sigma$ upper limit of $1.0 \times 10^{-6}$ photons cm$^{-2}$ s$^{-1}$, which translates to an initial $^{44}$Ti mass of approximately $2 \times 10^{-4}\, M_{\odot }$, consistent with previous X-ray to soft gamma-ray observations (Boggs et al. 2015, Science, 348, 670; Grebenev et al. 2012, Nature, 490, 373; Leising 2006, ApJ, 651, 1019).

ISM: supernova remnants↗