Showing 1–50 of 66 results for author: Morgan, K

Satellite-based emissions estimate indicates progress toward China's methane mitigation goals

Authors: Ziting Huang, Ao Chen, Leyang Feng, William S. Daniels, Dylan C. Gaeta, Kristan L. Morgan, Lee T. Murray, Xueying Yu, Benjamin F. Hobbs, Scot M. Miller

Abstract: China emits the most methane of any country worldwide, but there are large uncertainties in recent emissions trends, sources, and the potential impacts of policy actions. This study focuses on a period when the government initiated ambitious methane control efforts, linking sectoral policies with atmospheric evidence on sectoral, sub-national, and seasonal emissions during 2019--2024. We quantify… ▽ More China emits the most methane of any country worldwide, but there are large uncertainties in recent emissions trends, sources, and the potential impacts of policy actions. This study focuses on a period when the government initiated ambitious methane control efforts, linking sectoral policies with atmospheric evidence on sectoral, sub-national, and seasonal emissions during 2019--2024. We quantify daily methane emissions from China using a regional atmospheric inverse model with TROPOMI satellite observations. Our results reveal an average methane emissions increase rate of 0.3 Tg yr$^{-2}$ in Eastern & Central China, likely a milder trend than in the 2010s. Coal industry methane emissions intensity declined for the first time (-3.2% yr$^{-1}$) despite rising production, possibly associated with diverse policy instruments, mandates, and incentives. We further highlight two emerging challenges for future mitigation: leaks from expanding urban gas use amid the energy transition and rising agricultural emission yet with substantial uncertainty in estimates. Lastly, declining emissions intensity of coal mines points to the future role of targeted mandates and incentives in encouraging methane reduction for other sectors. △ Less

Submitted 18 July, 2026; originally announced July 2026.

A Systematic Evaluation of Molecular Mixture Behavior Prediction

Authors: Roel J. Leenhouts, Nathan K. Morgan, William Green, Jan G. Rittig, Florence H. Vermeire

Abstract: Machine learning for molecular property prediction has focused largely on pure compounds, even though many practical applications depend on mixtures with intermolecular interactions. Recent work has expanded the availability of mixture datasets, but evaluation still focuses mainly on absolute accuracy. However, absolute errors in mixtures conflate pure-component contributions with deviations from… ▽ More Machine learning for molecular property prediction has focused largely on pure compounds, even though many practical applications depend on mixtures with intermolecular interactions. Recent work has expanded the availability of mixture datasets, but evaluation still focuses mainly on absolute accuracy. However, absolute errors in mixtures conflate pure-component contributions with deviations from ideal mixing. We propose an evaluation framework that decomposes mixture-property error into pure-compound and interaction (non-ideal) components. The framework combines leakage-aware split protocols, ideal-mixture baselines, and excess-property metrics. To support reproducible benchmarking, we curate seven matched pure and mixture physicochemical property datasets. Across multiple mixture-property tasks and model families, we find that strong absolute accuracy can mask poor recovery of non-ideal mixture behavior, and that performance drops substantially under strict molecule splits. These results identify transfer to unseen molecules as a central challenge in molecular mixture machine learning and motivate evaluation beyond absolute accuracy alone. △ Less

Submitted 28 May, 2026; originally announced May 2026.

X-ray dark-field imaging from intensity flow: A Fokker-Planck approach to grating interferometry

Authors: Samantha J. Alloo, Florian Schaff, Regine Gradl, Benedikt Gunther, Franz Pfeiffer, Kaye S. Morgan

Abstract: Grating interferometry is a promising diagnostic technique that enables simultaneous acquisition of three complementary, synergistic X-ray images: transmission, differential phase, and dark-field. Its key advantage over other setups is its ability to use large pixels and, hence, large-area detectors, as well as its compatibility with low-coherence, compact X-ray sources, both of which are key fact… ▽ More Grating interferometry is a promising diagnostic technique that enables simultaneous acquisition of three complementary, synergistic X-ray images: transmission, differential phase, and dark-field. Its key advantage over other setups is its ability to use large pixels and, hence, large-area detectors, as well as its compatibility with low-coherence, compact X-ray sources, both of which are key factors for human-scale imaging. It has already demonstrated strong potential for chest imaging applications, including the diagnosis of pulmonary emphysema, fibrosis, and cancer. To retrieve transmission, differential phase, and dark-field images from data, an algorithm is required to separate the distinct mechanisms contributing to measured contrast. Since its realization, this image-retrieval step has remained fundamentally unchanged. In this work, we develop a novel transmission- and dark-field retrieval algorithm for grating-interferometry derived from the X-ray Fokker-Planck equation. To demonstrate and validate our Fokker-Planck algorithm, we apply it to experimental measurements of a test sample and to data from a mouse chest acquired with varying exposure times and added Poisson noise. The retrieved images were qualitatively and quantitatively compared with those retrieved using a conventional sinusoidal-fitting approach. Across both samples, the Fokker--Planck method produced images consistent with conventional retrieval, with a comparable signal-to-noise ratio. Notably, our Fokker-Planck method suppresses artefacts arising in the conventional approach under grating perturbations (e.g., structural defects like scratches) and reduced flux or visibility, yielding smoother and more reproducible images. Additionally, we demonstrate that our Fokker-Planck method has an advantage over the conventional dark-field retrieval method for fast sample imaging with short exposure times and high noise. △ Less

Submitted 2 May, 2026; originally announced May 2026.

Comments: Supplementary material is available upon request from the corresponding author (samantha.alloo@monash.edu)

Broad-band High-Energy Resolution Hard X-ray Spectroscopy using Transition Edge Sensors at SPring-8

Authors: Shinya Yamada, Yuto Ichinohe, Hideyuki Tatsuno, Ryota Hayakawa, Hirotaka Suda, Takaya Ohashi, Yoshitaka Ishisaki, Tomoya Uruga, Oki Sekizawa, Kiyofumi Nitta, Yoshio Takahashi, Takaaki Itai, Hiroki Suga, Makoto Nagasawa, Masato Tanaka, Minako Kurisu, Tadashi Hashimoto, Douglas Bennett, Ed Denison, William, Doriese, Malcolm Durkin, Joseph Fowler, Galen O'Neil, Kelsey Morgan , et al. (18 additional authors not shown)

Abstract: We have succeeded in operating a transition-edge sensor (TES) spectrometer and evaluating its performance at the SPring-8 synchrotron X-ray light source. The TES spectrometer consists of a 240 pixel National Institute of Standards and Technology (NIST) TES system, and 220 pixels are operated simultaneously with an energy resolution of $4$~eV at 6~keV at a rate of about 1~c/s/pixel. The tolerance f… ▽ More We have succeeded in operating a transition-edge sensor (TES) spectrometer and evaluating its performance at the SPring-8 synchrotron X-ray light source. The TES spectrometer consists of a 240 pixel National Institute of Standards and Technology (NIST) TES system, and 220 pixels are operated simultaneously with an energy resolution of $4$~eV at 6~keV at a rate of about 1~c/s/pixel. The tolerance for high count rates is evaluated in terms of energy resolution and live time fraction, leading to an empirical compromise of about 2 x 10^3 c/s/all pixels with an energy resolution of 5 eV at 6 keV. By utilizing the TES's wide-band spectroscopic capability, simultaneous multi-element analysis is demonstrated for a standard sample. We conducted X-ray absorption near-edge structure (XANES) analysis in fluorescence mode using the TES spectrometer. The excellent energy resolution of the TES enabled us to detect weak fluorescence lines from dilute samples and trace elements that have previously been difficult to resolve due to the nearly overlapping emission lines of other dominant elements. The neighboring lines of As K alpha and Pb L alpha2 of the standard sample were clearly resolved and the XANES of Pb L alpha2 was obtained. Moreover, the X-ray spectrum from the small amount of Fe in aerosols was distinguished from the spectrum of a blank target, which helps us to understand the targets and the environment. These results are the first important step for the application of high resolution TES-based spectroscopy at hard X-ray synchrotron facilities. △ Less

Submitted 23 April, 2026; originally announced April 2026.

Comments: Review of Scientific Instruments, Accepted: December 04 2020

Journal ref: Rev. Sci. Instrum. 1 January 2021; 92 (1): 013103

Imaging the Superconducting Proximity Effect in S-S'-S Transition Edge Sensors

Authors: Austin R. Kaczmarek, Samantha Walker, Jason Austermann, Douglas Bennett, W. Bertrand Doriese, Shannon M. Duff, Johannes Hubmayr, Kelsey Morgan, Michael D. Niemack, Dan Schmidt, Daniel Swetz, Joel Ullom, Joel Weber, Katja C. Nowack

Abstract: Proximity effects at superconducting interfaces, between different superconductors (S-S') or between superconductors and normal metals (S-N), are fundamental to the performance of superconducting electronics, yet only few experiments have directly probed the spatial structure of proximity effects within a device. This is particularly relevant for transition edge sensors (TESs), where the interplay… ▽ More Proximity effects at superconducting interfaces, between different superconductors (S-S') or between superconductors and normal metals (S-N), are fundamental to the performance of superconducting electronics, yet only few experiments have directly probed the spatial structure of proximity effects within a device. This is particularly relevant for transition edge sensors (TESs), where the interplay of direct and inverse proximity effects governs detector sensitivity. Here, we use scanning superconducting interference device (SQUID) susceptometry to directly image the local diamagnetic response in functional S-S'-S TES structures. We resolve long range proximity coupling extending over tens of micrometers, revealing that the local transition temperature is dramatically tuned by neighboring regions, being either enhanced by superconducting (S) leads or suppressed by normal metal (N) contacts. Our observations are quantitatively supported by Ginzburg Landau modeling of the device geometry and calculations of the temperature dependent diamagnetism based on self-consistent Usadel equations. By providing spatially resolved measurements of the interplay of proximity effects in TES devices, this work establishes a framework for understanding and controlling superconducting states in heterogeneous superconducting structures. △ Less

Submitted 22 February, 2026; originally announced February 2026.

Paraxial diffusion-field retrieval. II. Fokker-Planck generalization of the transport-of-intensity equation

Authors: David M. Paganin, Kaye S. Morgan

Abstract: The transport-of-intensity equation (TIE), namely the continuity equation associated with a coherent paraxial optical wavefield, is widely used for phase retrieval. It is a second-order partial differential equation which may be solved for the phase of a coherent paraxial field such as a monochromatic scalar optical beam, given the intensity and longitudinal intensity derivative in a plane perpend… ▽ More The transport-of-intensity equation (TIE), namely the continuity equation associated with a coherent paraxial optical wavefield, is widely used for phase retrieval. It is a second-order partial differential equation which may be solved for the phase of a coherent paraxial field such as a monochromatic scalar optical beam, given the intensity and longitudinal intensity derivative in a plane perpendicular to the optical axis. We show how the coherent flow associated with the TIE may be augmented by a diffusive flow associated with a scalar or tensor diffusion field. Such diffusive flow can arise via scattering from unresolved spatially random microstructure in an illuminated sample, blurring effects of an extended chaotic source that illuminates the sample, the resolution-reducing effect of shot noise in detected intensity images of the sample, and the sharpening effect (negative diffusion) associated with scattering from sharp sample edges. Augmenting the TIE's modeling of coherent flow with a diffuse-flow channel leads to a Fokker-Planck extension to this equation. Two different augmentations are obtained, using several complementary derivations. The inverse problems of phase retrieval and diffusion-field retrieval are then considered, for defocus-based imaging and mask-based imaging. When symmetric overfocus and underfocus images are used for phase retrieval, the diffusive term drops out and our Fokker-Planck formalism implies that any ensuing TIE-based phase-retrieval method needs no modification in light of our formalism. However, the same focal-series dataset---typically an infocus image, a weakly overfocused image, and a weakly underfocused image---may also be employed to access the additional channel of information associated with the Fokker-Planck diffusion field. Our formalism is applicable to visible light, x-ray, electron, and neutron imaging. △ Less

Submitted 17 August, 2026; v1 submitted 20 January, 2026; originally announced January 2026.

Comments: 45 pages, 9 figures, revised and significantly extended paper to be resubmitted to Physical Review A

Characterization of Silicon-Membrane TES Microcalorimeters for Large-Format X-ray Spectrometers with Integrated Microwave SQUID Readout

Authors: Avirup Roy, Robinjeet Singh, Joel C. Weber, W. B. Doriese, Johnathon Gard, Mark W. Keller, John A. B. Mates, Kelsey M. Morgan, Nathan J. Ortiz, Daniel S. Swetz, Daniel R. Schmidt, Joel N. Ullom, Evan P. Jahrman, Thomas C. Allison, Sasawat Jamnuch, John Vinson, Charles J. Titus, Cherno Jaye, Daniel A. Fischer, Galen C. O'Neil

Abstract: We present the electro-thermal characterization of transition-edge sensor (TES) detectors suspended on Si membranes fabricated using a silicon-on-insulator (SOI) wafer. The use of an all-silicon fabrication platform, in contrast to the more commonly used silicon nitride membranes, is compatible with monolithic fabrication of integrated TES and SQUID circuits. The all-silicon architecture additiona… ▽ More We present the electro-thermal characterization of transition-edge sensor (TES) detectors suspended on Si membranes fabricated using a silicon-on-insulator (SOI) wafer. The use of an all-silicon fabrication platform, in contrast to the more commonly used silicon nitride membranes, is compatible with monolithic fabrication of integrated TES and SQUID circuits. The all-silicon architecture additionally allows efficient use of focal plane area; the readout circuitry may be positioned out of the focal plane by bending a thinned portion of the chip. Compatibility with integrated fabrication and efficient use of focal plane area provide a path to an efficient soft X-ray spectrometer. This work is motivated by our goal to develop a 10,000-pixel TES spectrometer to overcome critical measurement limitations in catalysis research. The characterization of fragile, carbon-based intermediates via techniques like Resonant Inelastic X-ray Scattering (RIXS) is often precluded by the slow, high-flux nature of existing technologies. The new instrument will allow for fast RIXS measurements to be made without causing sample damage. We verify the detector models and measure the energy resolution using a pulsed optical laser, demonstrating the viability of this approach for the final instrument to be deployed at the National Synchrotron Light Source II (NSLS-II). △ Less

Submitted 14 January, 2026; originally announced January 2026.

Comments: Accepted for publication in IEEE: Transactions on Applied Superconductivity

Lithographic integration of TES microcalorimeters with SQUID multiplexer circuits for large format spectrometers

Authors: Robinjeet Singh, Avirup Roy, Daniel Becker, Johnathan D. Gard, Mark W. Keller, John A. B. Mates, Kelsey M. Morgan, Nathan J. Ortiz, Daniel R. Schmidt, Daniel S. Swetz, Joel N. Ullom, Leila R. Vale, Michael Vissers, Galen C. O'Neil, Joel C. Weber

Abstract: Arrays of hundreds or thousands of low temperature detectors have been deployed for many experiments, both bolometers for long wavelength applications and calorimeters for shorter wavelength applications. One challenge that is common to many of these arrays is the efficient use of focal plane area to achieve a large fill fraction of absorbers coupled to detectors. We are developing an integrated f… ▽ More Arrays of hundreds or thousands of low temperature detectors have been deployed for many experiments, both bolometers for long wavelength applications and calorimeters for shorter wavelength applications. One challenge that is common to many of these arrays is the efficient use of focal plane area to achieve a large fill fraction of absorbers coupled to detectors. We are developing an integrated fabrication of soft X-ray transition edge sensors (TES) and microwave SQUID multiplexers ($μ$MUX) with the goal of maximizing the fill fraction of the focal plane area on a scale of many thousand pixel detectors. We will utilize lithographically defined high density interconnects to circumvent limitations in existing solutions that use wirebonds or flip-chip bonds. Here we report the first demonstration of combining TES and $μ$MUX processes into a single TES-System-on-a-Chip (TES-SoC) fabrication on a silicon wafer. The $μ$MUX SQUIDs and TES electrothermal feedback circuits are microfabricated first and protected with passivating SiO$_2$, then the TES devices and TES-to-SQUID interconnects are fabricated, and finally the protective layer is removed before the fabrication of the microwave resonators. We show that the microwave SQUIDs are functional and have reasonable yield, and that we are able to read out the transition temperature of the connected TESs using those SQUIDs. △ Less

Submitted 8 October, 2025; originally announced October 2025.

Comments: 7 pages including citations, 7 figures

Quantitative Stain Mapping in X-ray Virtual Histology

Authors: Dominik John, David M. Paganin, Marie-Christine Zdora, Lisa Marie Petzold, Patrick Ilg, Junan Chen, Sara Baggio, Johannes B. Thalhammer, Sami Wirtensohn, Julian Moosmann, Jörg U. Hammel, Felix Beckmann, Samantha J. Alloo, Jannis Ahlers, Madleen Busse, Julia Herzen, Kaye S. Morgan

Abstract: Virtual histology is an emerging field in biomedicine that enables three-dimensional tissue visualization using X-ray micro-computed tomography. However, the method still lacks the specificity of conventional histology, in which parts of the tissue are selectively highlighted using targeted stains. Though some first X-ray stains have been developed to address this issue, their precise location and… ▽ More Virtual histology is an emerging field in biomedicine that enables three-dimensional tissue visualization using X-ray micro-computed tomography. However, the method still lacks the specificity of conventional histology, in which parts of the tissue are selectively highlighted using targeted stains. Though some first X-ray stains have been developed to address this issue, their precise location and quantity inside the tissue volume remain largely unknown. In this work, we present a novel approach to virtual histology that simultaneously captures electron number density and X-ray attenuation values through modulation-based X-ray imaging with a structured phase modulator. These complementary measurements enable decomposition of tissue volumes into basis materials, which allows the extraction of three-dimensional maps of molar contrast agent distribution alongside morphological details on the micrometer scale -- here demonstrated on murine kidneys. The concentration values are validated against the established method of K-edge subtraction imaging. We also create a direct bridge from X-ray to visible light imaging by detecting the same stain both using classical histology and our proposed X-ray approach. Our methodology opens new possibilities for biomedical research into disease progression by providing quantitative three-dimensional stain mapping across entire tissue volumes alongside high-contrast morphology, enabling deeper insights into disease mechanisms. △ Less

Submitted 18 September, 2025; originally announced September 2025.

Demonstrating a family of X-ray dark-field retrieval approaches on a common set of samples

Authors: Samantha J. Alloo, Ying Ying How, Jannis N. Ahlers, David M. Paganin, Michelle K. Croughan, Kaye S. Morgan

Abstract: Sensitive to scattering from unresolved sample structures, the dark-field channel in full-field X-ray imaging provides complementary information to that offered by conventional attenuation and phase-contrast methods. A range of experimental dark-field techniques and retrieval algorithms have been recently developed to extract this signal by directly resolving dark-field-associated local image blur… ▽ More Sensitive to scattering from unresolved sample structures, the dark-field channel in full-field X-ray imaging provides complementary information to that offered by conventional attenuation and phase-contrast methods. A range of experimental dark-field techniques and retrieval algorithms have been recently developed to extract this signal by directly resolving dark-field-associated local image blurring with a high-resolution camera. While the underlying physical mechanism that generates dark-field contrast is generally defined similarly across the methods, no comparison of these dark-field techniques using identical samples has been conducted. In this paper, dark-field imaging data from two samples were acquired using three emerging dark-field setups at a synchrotron: propagation-based, single-grid, and speckle-based X-ray imaging. Dark-field images were then reconstructed using a variety of retrieval algorithms--some requiring only a single sample exposure, others multiple; some performing local, pixel-wise analysis, and others operating globally on entire images. We find that the dominant contribution to dark-field contrast--arising from diffuse scattering from unresolved microstructures or multiple refractions through larger, potentially resolved structures--is consistently recovered across all approaches, demonstrating mutual agreement. However, some differences emerge for structures that are spatially varying. We attribute these differences to the idea that each technique has a different internal ruler, a sensitivity scale for dark-field retrieval influenced by both the experimental design and algorithmic assumptions of the technique. This study is intended to guide dark-field imaging users in selecting the most appropriate technique for their imaging goals and to motivate future research into dark-field sensitivity and sources of dark-field contrast across different methods. △ Less

Submitted 3 September, 2025; originally announced September 2025.

High-energy X-ray phase-contrast CT of an adult human chest phantom

Authors: Jannis N. Ahlers, Lorenzo D'Amico, Henriette Bast, Lucy F. Costello, Martin Donnelley, Samantha J. Alloo, Stephanie A. Harker, Ying Ying How, Michelle K. Croughan, James A. Pollock, Daniel Hausermann, Anton Maksimenko, Christopher Hall, Timur E. Gureyev, Yakov I. Nesterets, Marcus J. Kitchen, Konstantin M. Pavlov, Kaye S. Morgan

Abstract: Propagation-based phase-contrast X-ray imaging is a promising technique for in~vivo medical imaging, offering lower radiation doses than traditional attenuation-based imaging. Previous studies have focused on X-ray energies below 50 keV for small-animal imaging and mammography. Here, we investigate the feasibility of high-energy propagation-based computed tomography for human adult-scale lung imag… ▽ More Propagation-based phase-contrast X-ray imaging is a promising technique for in~vivo medical imaging, offering lower radiation doses than traditional attenuation-based imaging. Previous studies have focused on X-ray energies below 50 keV for small-animal imaging and mammography. Here, we investigate the feasibility of high-energy propagation-based computed tomography for human adult-scale lung imaging at the Australian Synchrotron's Imaging and Medical Beamline. This facility is uniquely positioned for human lung imaging, offering a large field of view, high X-ray energies, and supporting clinical infrastructure. We imaged an anthropomorphic chest phantom (LungMan) between 50 keV and 80 keV across the range of possible sample-to-detector distances, with a photon-counting and an integrating detector. Strong phase-contrast fringes were observed with the photon-counting detector, even at high X-ray energies and a large pixel size relative to previous work, whereas the integrating detector with lower spatial resolution showed no clear phase effects. Measured X-ray phase-shifting properties of LungMan aligned well with reference soft tissue values, validating the phantom for phase-contrast studies. Imaging quality assessments suggest an optimal configuration at approximately 70 keV and the longest available propagation distance of 7.5 m, indicating potential benefit in positioning the patient in an upstream hutch. This study represents the first step towards clinical adult lung imaging at the Australian Synchrotron. △ Less

Submitted 20 May, 2025; originally announced May 2025.

Comments: 19 pages, 10 figures

Journal ref: Scientific Reports 15, 29314 (2025)

Estimations of lung structural properties from a single propagation-based dark-field X-ray image

Authors: Dylan W. O'Connell, Kaye S. Morgan, Linda C. P. Croton, James A. Pollock, Gary Ruben, Kelly J. Crossley, Megan J. Wallace, Erin. V. McGillick, Stuart B. Hooper. Marcus J. Kitchen

Abstract: In this investigation, we applied a single-projection dark-field imaging technique to gain statistical information on the smallest airway structures within the lung$\unicode{x2014}$the alveoli$\unicode{x2014}$focusing on their size and number as key indicators of lung health. The algorithm employed here retrieves the projected thickness of the sample from a propagation-based phase contrast image u… ▽ More In this investigation, we applied a single-projection dark-field imaging technique to gain statistical information on the smallest airway structures within the lung$\unicode{x2014}$the alveoli$\unicode{x2014}$focusing on their size and number as key indicators of lung health. The algorithm employed here retrieves the projected thickness of the sample from a propagation-based phase contrast image using the transport-of-intensity equation. The first Born approximation is then used to isolate the dark-field signal associated with edge scattering, which increases the visibility of microstructure boundaries. PMMA spheres of known sizes were imaged first as an idealised alveolar model. The dark-field signal was then recovered from propagation-based phase-contrast X-ray images of the lungs of small mammals using this method. The retrieved dark-field signal was found to be proportional to both the alveolar size ($R^2 = 0.85$) and the number in projection ($R^2 = 0.69$), and these measurements could be combined to provide an estimate of the total surface area of the alveolar interfaces ($R^2 = 0.78$). This demonstrates the approach's ability to indicate lung health using the dark-field signal retrieved from a single-phase-contrast X-ray image. △ Less

Submitted 9 May, 2025; v1 submitted 5 May, 2025; originally announced May 2025.

Comments: 15 pages, 11 figures

Towards Precision Spectroscopy of Antiprotonic Atoms for Probing Strong-field QED

Authors: Gonçalo Baptista, Shikha Rathi, Michael Roosa, Quentin Senetaire, Jonas Sommerfeldt, Toshiyuki Azuma, Daniel Becker, Francois Butin, Ofir Eizenberg, Joseph Fowler, Hiroyuki Fujioka, Davide Gamba, Nabil Garroum, Mauro Guerra, Tadashi Hashimoto, Takashi Higuchi, Paul Indelicato, Jorge Machado, Kelsey Morgan, Francois Nez, Jason Nobles, Ben Ohayon, Shinji Okada, Daniel Schmidt, Daniel Swetz , et al. (4 additional authors not shown)

Abstract: PAX (antiProtonic Atom X-ray spectroscopy) is a new experiment with the aim to test strong-field quantum electrodynamics (QED) effects by performing high-precision x-ray spectroscopy of antiprotonic atoms. By utilizing advanced microcalorimeter detection techniques and a low-energy antiproton beam provided by the ELENA ring at CERN, gaseous targets will be used for the creation of antiprotonic ato… ▽ More PAX (antiProtonic Atom X-ray spectroscopy) is a new experiment with the aim to test strong-field quantum electrodynamics (QED) effects by performing high-precision x-ray spectroscopy of antiprotonic atoms. By utilizing advanced microcalorimeter detection techniques and a low-energy antiproton beam provided by the ELENA ring at CERN, gaseous targets will be used for the creation of antiprotonic atoms, and the measurement of transitions between circular Rydberg states will be conducted with up to two orders of magnitude improved accuracy over previous studies using high-purity germanium detectors. Our approach eliminates the longstanding issue of nuclear uncertainties that have hindered prior studies using highly charged ions, thus enabling direct and purely QED-focused measurements. By precisely probing atomic systems with electric fields up to two orders of magnitude above the Schwinger limit, PAX will test vacuum polarization and second-order QED corrections, opening new frontiers in fundamental physics and uncovering potential pathways to physics beyond the Standard Model. △ Less

Submitted 15 January, 2025; originally announced January 2025.

Data-driven methods to discover stable linear models of the helicity injectors on HIT-SIU

Authors: Zachary L. Daniel, Alan A. Kaptanoglu, Christopher J. Hansen, Kyle D. Morgan, Steven L. Brunton, J. Nathan Kutz

Abstract: Accurate and efficient circuit models are necessary to control the power electronic circuits found on plasma physics experiments. Tuning and controlling the behavior of these circuits is inextricably linked to plasma performance. Linear models are greatly preferred for control applications due to their well-established performance guarantees, but they typically fail to capture nonlinear dynamics a… ▽ More Accurate and efficient circuit models are necessary to control the power electronic circuits found on plasma physics experiments. Tuning and controlling the behavior of these circuits is inextricably linked to plasma performance. Linear models are greatly preferred for control applications due to their well-established performance guarantees, but they typically fail to capture nonlinear dynamics and changes in experimental parameters. Data-driven system identification can help mitigate these shortcomings by learning interpretable and accurate reduced-order models of a complex system, in this case the injector circuits of the Helicity Injected Torus - Steady Inductive Upgrade (HIT-SIU) experiment. Specifically, the Bagging Optimized Dynamic Mode Decomposition (BOP-DMD), is leveraged to learn stable, reduced order models of the interaction between the spheromak plasma formed in the confinement volume, and the injector circuits of the device. BOP-DMD is trained and evaluated on an analytic model of the vacuum dynamics of the injector circuits of HIT-SIU, as well as an analytic linear reduced-order model for the injector dynamics when a plasma is present. BOP-DMD is then fit on experimental data, both on shots with and without a plasma in the confinement volume. In doing so, we demonstrate the capability of data-driven methods to produce stable, linear models for control and uncertainty quantification in plasma experiments. △ Less

Submitted 6 January, 2026; v1 submitted 9 January, 2025; originally announced January 2025.

Comments: Corrected a missing figure reference

A high-speed, high-resolution Transition Edge Sensor spectrometer for soft X-rays at the Advanced Photon Source

Authors: Orlando Quaranta, Don Jensen, Kelsey Morgan, Joel C. Weber, Jessica L. McChesney, Hao Zheng, Tejas Guruswamy, Jonathan Baldwin, Ben Mates, Nathan Ortiz, Johnathon Gard, Doug Bennet, Dan Schmidt, Lisa Gades, Antonino Miceli

Abstract: This project explores the design and development of a transition edge sensor (TES) spectrometer for resonant soft X- ray scattering (RSXS) measurements developed in collaboration between Argonne National Laboratory (ANL) and the National Institute of Standards and Technology (NIST). Soft X-ray scattering is a powerful technique for studying the electronic and magnetic properties of materials on a… ▽ More This project explores the design and development of a transition edge sensor (TES) spectrometer for resonant soft X- ray scattering (RSXS) measurements developed in collaboration between Argonne National Laboratory (ANL) and the National Institute of Standards and Technology (NIST). Soft X-ray scattering is a powerful technique for studying the electronic and magnetic properties of materials on a microscopic level. However, the lack of high-performance soft X-ray spectrometers has limited the potential of this technique. TES spectrometers have the potential to overcome these limitations due to their high energy resolution, high efficiency, and broad energy range. This project aims to optimize the design of a TES spectrometer for RSXS measurements and more generally soft X-ray spectroscopy at the Advanced Photon Source (APS) 29-ID, leading to improved understanding of advanced materials. We will present a detailed description of the instrument design and implementation. The spectrometer consists of a large array of approximately 250 high-speed and high-resolution pixels. The pixels have saturation energies of approximately 1 keV, sub-ms pulse duration and energy resolution of approximately 1 eV. The array is read out using microwave multiplexing chips with MHz bandwidth per channel, enabling efficient data throughput. To facilitate measurement of samples in situ under ultra-high vacuum conditions at the beamline, the spectrometer is integrated with an approximately 1 m long snout. △ Less

Submitted 3 January, 2025; originally announced January 2025.

Stabilizing Laplacian Inversion in Fokker-Planck Image Retrieval using the Transport-of-Intensity Equation

Authors: Samantha J Alloo, Kaye S Morgan

Abstract: X-ray attenuation, phase, and dark-field images provide complementary information. Different experimental techniques can capture these contrast mechanisms, and the corresponding images can be retrieved using various theoretical algorithms. Our previous works developed the Multimodal Intrinsic Speckle-Tracking (MIST) algorithm, which is suitable for multimodal image retrieval from speckle-based X-r… ▽ More X-ray attenuation, phase, and dark-field images provide complementary information. Different experimental techniques can capture these contrast mechanisms, and the corresponding images can be retrieved using various theoretical algorithms. Our previous works developed the Multimodal Intrinsic Speckle-Tracking (MIST) algorithm, which is suitable for multimodal image retrieval from speckle-based X-ray imaging (SBXI) data. MIST is based on the X-ray Fokker-Planck equation, requiring the inversion of derivative operators that are often numerically unstable. These instabilities can be addressed by employing regularization techniques, such as Tikhonov regularization. The regularization output is highly sensitive to the choice of the Tikhonov regularization parameter, making it crucial to select this value carefully and optimally. Here, we present an automated iterative algorithm to optimize the regularization of the inverse Laplacian operator in our most recently published MIST variant, addressing the operator's instability near the Fourier-space origin. Our algorithm leverages the inherent stability of the phase solution obtained from the transport-of-intensity equation for SBXI, using it as a reliable ground truth for the more complex Fokker-Planck-based algorithms that incorporate the dark-field signal. We applied the algorithm to an SBXI dataset collected using synchrotron light of a four-rod sample. The four-rod sample's phase and dark-field images were optimally retrieved using our developed algorithm, eliminating the tedious and subjective task of selecting a suitable Tikhonov regularization parameter. The developed regularization-optimization algorithm makes MIST more user-friendly by eliminating the need for manual parameter selection. We anticipate that our optimization algorithm can also be applied to other image retrieval approaches derived from the Fokker-Planck equation. △ Less

Submitted 19 December, 2024; originally announced December 2024.

Single-exposure X-ray dark-field imaging via a dual-energy propagation-based setup

Authors: Jannis N. Ahlers, Konstantin M. Pavlov, Marcus J. Kitchen, Stephanie A. Harker, Emily J. Pryor, James A. Pollock, Michelle K. Croughan, Ying Ying How, Marie-Christine Zdora, Lucy F. Costello, Dylan W. O'Connell, Christopher Hall, Kaye S. Morgan

Abstract: X-ray dark-field imaging visualises scattering from sample microstructure, and has found application in medical and security contexts. While most X-ray dark-field imaging techniques rely on masks, gratings, or crystals, recent work on the Fokker--Planck model of diffusive imaging has enabled dark-field imaging in the propagation-based geometry. Images captured at multiple propagation distances or… ▽ More X-ray dark-field imaging visualises scattering from sample microstructure, and has found application in medical and security contexts. While most X-ray dark-field imaging techniques rely on masks, gratings, or crystals, recent work on the Fokker--Planck model of diffusive imaging has enabled dark-field imaging in the propagation-based geometry. Images captured at multiple propagation distances or X-ray energies can be used to reconstruct dark-field from propagation-based images but have previously required multiple exposures. Here, we show single-exposure dark-field imaging by exploiting the harmonic content in a monochromatised synchrotron beam and utilising an energy-discriminating photon-counting detector to capture dual-energy propagation-based images. The method is validated by filming time-varying samples, showing the advantage of the dark-field contrast in analysing dynamic evolution. We measure and adjust for the impact of detector charge-sharing on the images. This work opens the way for low-dose and dynamic dark-field X-ray imaging without the need for a high-stability set-up and precision optics. △ Less

Submitted 17 December, 2024; originally announced December 2024.

Comments: 9 pages, 7 figures

Journal ref: Optics Letters 50(7), 2171-2174 (2025)

In vivo 4D x-ray dark-field lung imaging in mice

Authors: Ying Ying How, Nicole Reyne, Michelle K. Croughan, Patricia Cmielewski, Daniel Batey, Lucy F. Costello, Ronan Smith, Jannis N. Ahlers, Marian Cholewa, Magdalena Kolodziej, Julia Duerr, Marcus A. Mall, Marcus J. Kitchen, Marie-Liesse Asselin-Labat, David M. Paganin, Martin Donnelley, Kaye S. Morgan

Abstract: X-ray dark-field imaging is well-suited to visualizing the health of the lungs because the alveoli create a strong dark-field signal. However, time-resolved and tomographic (i.e., 4D) dark-field imaging is challenging, since most x-ray dark-field techniques require multiple sample exposures, captured while scanning the position of crystals or gratings. Here, we present the first in vivo 4D x-ray d… ▽ More X-ray dark-field imaging is well-suited to visualizing the health of the lungs because the alveoli create a strong dark-field signal. However, time-resolved and tomographic (i.e., 4D) dark-field imaging is challenging, since most x-ray dark-field techniques require multiple sample exposures, captured while scanning the position of crystals or gratings. Here, we present the first in vivo 4D x-ray dark-field lung imaging in mice. This was achieved by synchronizing the data acquisition process of a single-exposure grid-based imaging approach with the breath cycle. The short data acquisition time per dark-field projection made this approach feasible for 4D x-ray dark-field imaging by minimizing the motion-blurring effect, the total time required and the radiation dose imposed on the sample. Images were captured from a control mouse and from mouse models of muco-obstructive disease and lung cancer, where a change in the size of the alveoli was expected. This work demonstrates that the 4D dark-field signal provides complementary information that is inaccessible from conventional attenuation-based CT images, in particular, how the size of the alveoli from different parts of the lungs changes throughout a breath cycle, with examples shown across the different models. By quantifying the dark-field signal and relating it to other physical properties of the alveoli, this technique could be used to perform functional lung imaging that allows the assessment of both global and regional lung conditions where the size or expansion of the alveoli is affected. △ Less

Submitted 21 November, 2024; originally announced November 2024.

Comments: 11 pages, 5 figures, supplementary information available

Primary activity measurement of an Am-241 solution using microgram inkjet gravimetry and decay energy spectrometry

Authors: Ryan P. Fitzgerald, Bradley Alpert, Denis E. Bergeron, Max Carlson, Richard Essex, Sean Jollota, Kelsey Morgan, Shin Muramoto, Svetlana Nour, Galen O`Neil, Daniel R. Schmidt, Gordon Shaw, Daniel Swetz, R. Michael Verkouteren

Abstract: We demonstrate a method for radionuclide assay that is spectroscopic with 100 % counting efficiency for alpha decay. Advancing both cryogenic decay energy spectrometry (DES) and drop-on-demand inkjet metrology, a solution of Am-241 was assayed for massic activity (of order 100 kBq/g) with a relative combined standard uncertainty less than 1 %. We implement live-timed counting, spectroscopic analys… ▽ More We demonstrate a method for radionuclide assay that is spectroscopic with 100 % counting efficiency for alpha decay. Advancing both cryogenic decay energy spectrometry (DES) and drop-on-demand inkjet metrology, a solution of Am-241 was assayed for massic activity (of order 100 kBq/g) with a relative combined standard uncertainty less than 1 %. We implement live-timed counting, spectroscopic analysis, validation by liquid scintillation (LS) counting, and confirmation of quantitative solution transfer. Experimental DES spectra are well modeled with a Monte Carlo simulation. The model was further used to simulate Pu-238 and Pu-240 impurities, calculate detection limits, and demonstrate the potential for tracer-free multi-nuclide analysis, which will be valuable for new cancer therapeutics based on decay chains, Standard Reference Materials (SRMs) containing impurities, and more widely in nuclear energy, environmental monitoring, security, and forensics. △ Less

Submitted 30 June, 2025; v1 submitted 4 November, 2024; originally announced November 2024.

Comments: Revision includes clarifications in the text and graph axes

Journal ref: Metrologia, 62, 4, 2005

Separating edges from microstructure in X-ray dark-field imaging: Evolving and devolving perspectives via the X-ray Fokker-Planck equation

Authors: Samantha J. Alloo, David M. Paganin, Michelle K. Croughan, Jannis N. Ahlers, Konstantin M. Pavlov, Kaye S. Morgan

Abstract: A key contribution to X-ray dark-field (XDF) is X-ray diffusion by sample structures smaller than the imaging system's spatial resolution. However, some XDF techniques report that resolvable sample edges also generate XDF. Speckle-based X-ray imaging (SBXI) extracts XDF by analyzing sample-imposed changes to a reference speckle pattern's visibility. We present an algorithm for SBXI (a variant of o… ▽ More A key contribution to X-ray dark-field (XDF) is X-ray diffusion by sample structures smaller than the imaging system's spatial resolution. However, some XDF techniques report that resolvable sample edges also generate XDF. Speckle-based X-ray imaging (SBXI) extracts XDF by analyzing sample-imposed changes to a reference speckle pattern's visibility. We present an algorithm for SBXI (a variant of our Multimodal Intrinsic Speckle-Tracking (MIST) algorithm) capable of separating these two distinct XDF contrast mechanisms. The algorithm uses the 'devolving' X-ray Imaging Fokker-Planck equation as its forward model and then solves the associated multimodal inverse problem, to retrieve sample attenuation, phase, and XDF. Previous MIST variants were based on the evolving Fokker-Planck equation, which considers how a reference-speckle image is modified by introducing a sample. The devolving perspective instead considers how the image collected in the presence of the sample and speckle membrane optically flows in reverse, to generate the reference-speckle image when the sample is removed from the system. We compare single- and multiple-exposure multimodal retrieval algorithms from the two Fokker-Planck perspectives. We demonstrate that the devolving perspective can distinguish between two physically different XDF contrast mechanisms; unresolved microstructure- and sharp-edge-induced XDF. This was verified by applying the retrieval algorithms to two experimental data sets. We anticipate that this work will be useful in: Yielding a pair of complementary XDF images that separate sharp-edge diffuse scatter from unresolved microstructure diffuse scatter. XDF computed tomography, where the strong edge XDF can lead to tainting streaking artefacts. Sample preparation, as samples will not need to be embedded since the strong XDF edge signal seen between the sample and air can be separated out. △ Less

Submitted 23 October, 2024; originally announced October 2024.

Comments: 21 pages and 7 figures

Few-electron highly charged muonic Ar atoms verified by electronic $K$ x rays

Authors: T. Okumura, T. Azuma, D. A. Bennett, W. B. Doriese, M. S. Durkin, J. W. Fowler, J. D. Gard, T. Hashimoto, R. Hayakawa, Y. Ichinohe, P. Indelicato, T. Isobe, S. Kanda, D. Kato, M. Katsuragawa, N. Kawamura, Y. Kino, N. Kominato, Y. Miyake, K. M. Morgan, H. Noda, G. C. O'Neil, S. Okada, K. Okutsu, N. Paul , et al. (18 additional authors not shown)

Abstract: Electronic $K$ x rays emitted by muonic Ar atoms in the gas phase were observed using a superconducting transition-edge-sensor microcalorimeter. The high-precision energy spectra provided a clear signature of the presence of muonic atoms accompanied by a few electrons, which have never been observed before. One-, two-, and three-electron bound, i.e., H-like, He-like, and Li-like, muonic Ar atoms w… ▽ More Electronic $K$ x rays emitted by muonic Ar atoms in the gas phase were observed using a superconducting transition-edge-sensor microcalorimeter. The high-precision energy spectra provided a clear signature of the presence of muonic atoms accompanied by a few electrons, which have never been observed before. One-, two-, and three-electron bound, i.e., H-like, He-like, and Li-like, muonic Ar atoms were identified from electronic $K$ x rays and hyper-satellite $K$ x rays. These $K$ x rays are emitted after the charge transfer process by the collisions with surrounding Ar atoms. With the aid of theoretical calculations, we confirmed that the peak positions are consistent with the x-ray energies from highly charged Cl ions, and the intensities reflecting deexcitation dynamics were successfully understood by taking into account the interaction between the muon and bound electrons. △ Less

Submitted 10 July, 2024; originally announced July 2024.

Low-dose, high-resolution CT of infant-sized lungs via propagation-based phase contrast

Authors: James A. Pollock, Kaye Morgan, Linda C. P. Croton, Emily J. Pryor, Kelly J. Crossley, Christopher J. Hall, Daniel Hausermann, Anton Maksimenko, Stuart B. Hooper, Marcus J. Kitchen

Abstract: Many lung diseases require detailed visualisation for accurate diagnosis and treatment. High-resolution computed tomography (CT) is the gold-standard technique for non-invasive lung disease detection, but it presents a risk to the patient through the relatively high ionising radiation dose required. Utilising the X-ray phase information may allow improvements in image resolution at equal or lower… ▽ More Many lung diseases require detailed visualisation for accurate diagnosis and treatment. High-resolution computed tomography (CT) is the gold-standard technique for non-invasive lung disease detection, but it presents a risk to the patient through the relatively high ionising radiation dose required. Utilising the X-ray phase information may allow improvements in image resolution at equal or lower radiation levels than current clinical imaging. Propagation-based phase-contrast imaging requires minimal adaption of existing medical systems, and is well suited to lung imaging due to the strong phase gradients introduced by the lung-air material interfaces. Herein, propagation-based phase contrast CT is demonstrated for large animals, namely lambs, as a model for paediatric patients, using monochromatic radiation and a photon-counting detector at the Imaging and Medical Beamline of the Australian Synchrotron. Image quality, normalised against radiation dose, was optimised as a function of the beam energy and propagation distance, with the optimal conditions used to test the available image quality at very low radiation dose. The resulting CT images demonstrate superior resolution to existing high-resolution CT systems, pushing dose to the quantum limit to comply with current Australian guidelines for infant chest CT exposure of $<2.5\:\text{mSv}$ effective dose. Constituent raw projections are shown to have significant proportions of pixels with zero photon counts that would create severe information loss in conventional CT. Phase retrieval enabled clear visualisation of minor lung airways at doses up to 1,225$\pm$31\% times lower than conventional CT reconstruction, at a voxel size of just 75$\mathrmμ$m. △ Less

Submitted 13 May, 2026; v1 submitted 8 July, 2024; originally announced July 2024.

Comments: Updated to match published version

Correcting directional dark-field x-ray imaging artefacts using position-dependent image deblurring and attenuation removal

Authors: Michelle K Croughan, David M Paganin, Samantha J Alloo, Jannis N Ahlers, Ying Ying How, Stephanie A Harker, Kaye S. Morgan

Abstract: In recent years, a novel x-ray imaging modality has emerged that reveals unresolved sample microstructure via a "dark-field image", which provides complementary information to conventional "bright-field" images, such as attenuation and phase-contrast modalities. This x-ray dark-field signal is produced by unresolved microstructures scattering the x-ray beam resulting in localised image blur. Dark-… ▽ More In recent years, a novel x-ray imaging modality has emerged that reveals unresolved sample microstructure via a "dark-field image", which provides complementary information to conventional "bright-field" images, such as attenuation and phase-contrast modalities. This x-ray dark-field signal is produced by unresolved microstructures scattering the x-ray beam resulting in localised image blur. Dark-field retrieval techniques extract this blur to reconstruct a dark-field image. Unfortunately, the presence of non-dark-field blur such as source-size blur or the detector point-spread-function can affect the dark-field retrieval as they also blur the experimental image. In addition, dark-field images can be degraded by the artefacts induced by large intensity gradients from attenuation and propagation-based phase contrast, particularly around sample edges. By measuring any non-dark-field blurring across the image plane and removing it from experimental images, as well as removing attenuation and propagation-based phase contrast, we show that a directional dark-field image can be retrieved with fewer artefacts and more consistent quantitative measures. We present the details of these corrections and provide "before and after" directional dark-field images of samples imaged at a synchrotron source. This paper utilises single-grid directional dark-field imaging, but these corrections have the potential to be broadly applied to other x-ray imaging techniques. △ Less

Submitted 6 May, 2024; v1 submitted 26 April, 2024; originally announced April 2024.

X-ray phase and dark-field computed tomography without optical elements

Authors: T. A. Leatham, D. M. Paganin, K. S. Morgan

Abstract: X-ray diffusive dark-field imaging, which allows spatially unresolved microstructure to be mapped across a sample, is an increasingly popular tool in an array of settings. Here, we present a new algorithm for phase and dark-field computed tomography based on the x-ray Fokker-Planck equation. Needing only a coherent x-ray source, sample, and detector, our propagation-based algorithm can map the sam… ▽ More X-ray diffusive dark-field imaging, which allows spatially unresolved microstructure to be mapped across a sample, is an increasingly popular tool in an array of settings. Here, we present a new algorithm for phase and dark-field computed tomography based on the x-ray Fokker-Planck equation. Needing only a coherent x-ray source, sample, and detector, our propagation-based algorithm can map the sample density and dark-field/diffusion properties of the sample in 3D. Importantly, incorporating dark-field information in the density reconstruction process enables a higher spatial resolution reconstruction than possible with previous propagation-based approaches. Two sample exposures at each projection angle are sufficient for the successful reconstruction of both the sample density and dark-field Fokker-Planck diffusion coefficients. We anticipate that the proposed algorithm may be of benefit in biomedical imaging and industrial settings. △ Less

Submitted 5 December, 2023; v1 submitted 14 October, 2023; originally announced October 2023.

Comments: 15 pages, 5 figures

X-ray dark-field via spectral propagation-based imaging

Authors: Jannis N. Ahlers, Konstantin M. Pavlov, Marcus J. Kitchen, Kaye S. Morgan

Abstract: Dark-field X-ray imaging is a novel modality which visualises scattering from unresolved microstructure. Most dark-field imaging techniques rely on crystals or structured illumination, but recent work has shown that dark-field effects are observable in straightforward propagation-based imaging (PBI). Based on the single-material X-ray Fokker--Planck equation with an a priori dark-field energy depe… ▽ More Dark-field X-ray imaging is a novel modality which visualises scattering from unresolved microstructure. Most dark-field imaging techniques rely on crystals or structured illumination, but recent work has shown that dark-field effects are observable in straightforward propagation-based imaging (PBI). Based on the single-material X-ray Fokker--Planck equation with an a priori dark-field energy dependence, we propose an algorithm to extract phase and dark-field effects from dual-energy PBI images. We successfully apply the dark-field retrieval algorithm to simulated and experimental dual-energy data, and show that by accounting for dark-field effects, projected thickness reconstruction is improved compared to the classic Paganin algorithm. With the emergence of spectral detectors, the method could enable single-exposure dark-field imaging of dynamic and living samples. △ Less

Submitted 8 July, 2024; v1 submitted 27 September, 2023; originally announced September 2023.

Comments: 21 pages, 17 figures

Journal ref: Optica 11(8), 1182-1191 (2024)

Multimodal Intrinsic Speckle-Tracking (MIST) to extract rapidly-varying diffuse X-ray scatter

Authors: Samantha J. Alloo, Kaye S. Morgan, David M. Paganin, Konstantin M. Pavlov

Abstract: Speckle-based phase-contrast X-ray imaging (SB-PCXI) can reconstruct high-resolution images of weakly-attenuating materials that would otherwise be indistinguishable in conventional attenuation-based imaging. The experimental setup of SB-PCXI requires only a sufficiently coherent source and spatially random mask, positioned between the source and detector. The technique can extract sample informat… ▽ More Speckle-based phase-contrast X-ray imaging (SB-PCXI) can reconstruct high-resolution images of weakly-attenuating materials that would otherwise be indistinguishable in conventional attenuation-based imaging. The experimental setup of SB-PCXI requires only a sufficiently coherent source and spatially random mask, positioned between the source and detector. The technique can extract sample information at length scales smaller than the imaging system's spatial resolution; this enables multimodal signal reconstruction. ``Multimodal Intrinsic Speckle-Tracking'' (MIST) is a rapid and deterministic formalism derived from the paraxial-optics form of the Fokker-Planck equation. MIST simultaneously extracts attenuation, refraction, and small-angle scattering (diffusive-dark-field) signals from a sample and is more computationally efficient compared to alternative speckle-tracking approaches. Hitherto, variants of MIST have assumed the diffusive-dark-field signal to be spatially slowly varying. Although successful, these approaches have been unable to well-describe unresolved sample microstructure whose statistical form is not spatially slowly varying. Here, we extend the MIST formalism such that there is no such restriction, in terms of a sample's rotationally-isotropic diffusive-dark-field signal. We reconstruct multimodal signals of two samples, each with distinct X-ray attenuation and scattering properties. The reconstructed diffusive-dark-field signals have superior image quality compared to our previous approaches which assume the diffusive-dark-field to be a slowly varying function of transverse position. Our generalisation may assist increased adoption of SB-PCXI in applications such as engineering and biomedical disciplines, forestry, and palaeontology, and is anticipated to aid the development of speckle-based diffusive-dark-field tensor tomography. △ Less

Submitted 4 February, 2023; v1 submitted 25 January, 2023; originally announced February 2023.

Comments: 18 pages, 7 figures

Journal ref: Scientific Reports 13, 5424 (2023)

3DMPR -- A robust morphological approach for applying phase retrieval in proximity to highly-attenuating objects in CT

Authors: J. A. Pollock, L. C. P. Croton, K. S. Morgan, K. J. Crossley, M. J. Wallace, G. A. Buckley, S. B. Hooper, M. J. Kitchen

Abstract: X-ray imaging is a fast, precise and non-invasive method of imaging which, when combined with computed tomography, provides detailed 3D rendering of samples. Incorporating propagation-based phase contrast can vastly improve data quality for weakly attenuating samples via phase retrieval, allowing radiation exposure to be reduced. However, applying phase retrieval to multi-material samples commonly… ▽ More X-ray imaging is a fast, precise and non-invasive method of imaging which, when combined with computed tomography, provides detailed 3D rendering of samples. Incorporating propagation-based phase contrast can vastly improve data quality for weakly attenuating samples via phase retrieval, allowing radiation exposure to be reduced. However, applying phase retrieval to multi-material samples commonly requires choice of which material boundary to tune the reconstruction. Selecting the boundary with strongest phase contrast increases noise suppression, but at the detriment of over-blurring other interfaces and potentially removing quantitative sample information. Additionally, conventional phase-retrieval algorithms cannot be used for regions bounded by more than one material, requiring alternative methods. Here we present a computationally-efficient, non-iterative nor AI-mediated method for applying strong phase retrieval, whilst preserving sharp boundaries for all materials within the sample. 3D phase retrieval is combined with morphological operations to prevent over-blurring artefacts from being introduced, while avoiding the potentially long convergence times required by iterative approaches. This technique, entitled 3DMPR, was tested on phase contrast images of a rabbit kitten brain encased by the surrounding dense skull. Using 24kVp synchrotron radiation with a 5m propagation distance, 3DMPR provided a 6.8-fold improvement in the signal-to-noise ratio (SNR) of brain tissue over the standard phase retrieval procedure, without over-smoothing the images. △ Less

Submitted 12 May, 2026; v1 submitted 29 January, 2023; originally announced January 2023.

Comments: Updated to match published version

Paraxial diffusion-field retrieval

Authors: David M. Paganin, Daniele Pelliccia, Kaye S. Morgan

Abstract: Unresolved spatially-random microstructure, in an illuminated sample, can lead to position-dependent blur when an image of that sample is formed. For a small propagation distance, between the exit surface of the sample and the entrance surface of a position-sensitive detector, the paraxial approximation implies that the blurring influence of the sample may be modeled using an anomalous-diffusion f… ▽ More Unresolved spatially-random microstructure, in an illuminated sample, can lead to position-dependent blur when an image of that sample is formed. For a small propagation distance, between the exit surface of the sample and the entrance surface of a position-sensitive detector, the paraxial approximation implies that the blurring influence of the sample may be modeled using an anomalous-diffusion field. This diffusion field may have a scalar or tensor character, depending on whether the random microstructure has an autocorrelation function that is rotationally isotropic or anisotropic, respectively. Partial differential equations are written down and then solved, in a closed-form manner, for several variants of the inverse problem of diffusion-field retrieval given suitable intensity images. Both uniform-illumination and structured-illumination schemes are considered. Links are made, between the recovered diffusion field and certain statistical properties of the unresolved microstructure. The developed theory -- which may be viewed as a crudely parallel form of small-angle scattering under the Guinier approximation -- is applicable to a range of paraxial radiation and matter fields, such as visible light, x rays, neutrons, and electrons. △ Less

Submitted 13 July, 2023; v1 submitted 21 January, 2023; originally announced January 2023.

Comments: Numerous very minor corrections and clarifications throughout, compared to the previous version

Journal ref: Physical Review A 108, 013517 (2023)

A tabletop x-ray tomography instrument for nanometer-scale imaging: demonstration of the 1,000-element transition-edge sensor subarray

Authors: Paul Szypryt, Nathan Nakamura, Daniel T. Becker, Douglas A. Bennett, Amber L. Dagel, W. Bertrand Doriese, Joseph W. Fowler, Johnathon D. Gard, J. Zachariah Harris, Gene C. Hilton, Jozsef Imrek, Edward S. Jimenez, Kurt W. Larson, Zachary H. Levine, John A. B. Mates, D. McArthur, Luis Miaja-Avila, Kelsey M. Morgan, Galen C. O'Neil, Nathan J. Ortiz, Christine G. Pappas, Daniel R. Schmidt, Kyle R. Thompson, Joel N. Ullom, Leila Vale , et al. (6 additional authors not shown)

Abstract: We report on the 1,000-element transition-edge sensor (TES) x-ray spectrometer implementation of the TOMographic Circuit Analysis Tool (TOMCAT). TOMCAT combines a high spatial resolution scanning electron microscope (SEM) with a highly efficient and pixelated TES spectrometer to reconstruct three-dimensional maps of nanoscale integrated circuits (ICs). A 240-pixel prototype spectrometer was recent… ▽ More We report on the 1,000-element transition-edge sensor (TES) x-ray spectrometer implementation of the TOMographic Circuit Analysis Tool (TOMCAT). TOMCAT combines a high spatial resolution scanning electron microscope (SEM) with a highly efficient and pixelated TES spectrometer to reconstruct three-dimensional maps of nanoscale integrated circuits (ICs). A 240-pixel prototype spectrometer was recently used to reconstruct ICs at the 130 nm technology node, but to increase imaging speed to more practical levels, the detector efficiency needs to be improved. For this reason, we are building a spectrometer that will eventually contain 3,000 TES microcalorimeters read out with microwave superconducting quantum interference device (SQUID) multiplexing, and we currently have commissioned a 1,000 TES subarray. This still represents a significant improvement from the 240-pixel system and allows us to begin characterizing the full spectrometer performance. Of the 992 maximimum available readout channels, we have yielded 818 devices, representing the largest number of TES x-ray microcalorimeters simultaneously read out to date. These microcalorimeters have been optimized for pulse speed rather than purely energy resolution, and we measure a FWHM energy resolution of 14 eV at the 8.0 keV Cu K$α$ line. △ Less

Submitted 22 December, 2022; originally announced December 2022.

Comments: 5 pages, 4 figures, submitted to IEEE Transactions on Applied Superconductivity

Journal ref: IEEE Transactions on Applied Superconductivity, vol. 33, no. 5, pp. 1-5, Aug. 2023, Art no. 2100705

Nanoscale Three-Dimensional Imaging of Integrated Circuits using a Scanning Electron Microscope and Transition-Edge Sensor Spectrometer

Authors: Nathan Nakamura, Paul Szypryt, Amber L. Dagel, Bradley K. Alpert, Douglas A. Bennett, W. Bertrand Doriese, Malcolm Durkin, Joseph W. Fowler, Dylan T. Fox, Johnathon D. Gard, Ryan N. Goodner, J. Zachariah Harris, Gene C. Hilton, Edward S. Jimenez, Burke L. Kernen, Kurt W. Larson, Zachary H. Levine, Daniel McArthur, Kelsey M. Morgan, Galen C. O'Neil, Nathan J. Ortiz, Christine G. Pappas, Carl D. Reintsema, Daniel R. Schmidt, Peter A. Schultz , et al. (8 additional authors not shown)

Abstract: X-ray nanotomography is a powerful tool for the characterization of nanoscale materials and structures, but is difficult to implement due to competing requirements on X-ray flux and spot size. Due to this constraint, state-of-the-art nanotomography is predominantly performed at large synchrotron facilities. We present a laboratory-scale nanotomography instrument that achieves nanoscale spatial res… ▽ More X-ray nanotomography is a powerful tool for the characterization of nanoscale materials and structures, but is difficult to implement due to competing requirements on X-ray flux and spot size. Due to this constraint, state-of-the-art nanotomography is predominantly performed at large synchrotron facilities. We present a laboratory-scale nanotomography instrument that achieves nanoscale spatial resolution while changing the limitations of conventional tomography tools. The instrument combines the electron beam of a scanning electron microscope (SEM) with the precise, broadband X-ray detection of a superconducting transition-edge sensor (TES) microcalorimeter. The electron beam generates a highly focused X-ray spot in a metal target held micrometers away from the sample of interest, while the TES spectrometer isolates target photons with high signal-to-noise. This combination of a focused X-ray spot, energy-resolved X-ray detection, and unique system geometry enable nanoscale, element-specific X-ray imaging in a compact footprint. The proof-of-concept for this approach to X-ray nanotomography is demonstrated by imaging 160 nm features in three dimensions in 6 layers of a Cu-SiO2 integrated circuit, and a path towards finer resolution and enhanced imaging capabilities is discussed. △ Less

Submitted 4 March, 2024; v1 submitted 20 December, 2022; originally announced December 2022.

Design of a 3000-pixel transition-edge sensor x-ray spectrometer for microcircuit tomography

Authors: Paul Szypryt, Douglas A. Bennett, William J. Boone, Amber L. Dagel, Gabriella Dalton, W. Bertrand Doriese, Joseph W. Fowler, Edward J. Garboczi, Johnathon D. Gard, Gene C. Hilton, Jozsef Imrek, Edward S. Jimenez, Vincent Y. Kotsubo, Kurt Larson, Zachary H. Levine, John A. B. Mates, Daniel McArthur, Kelsey M. Morgan, Nathan Nakamura, Galen C. O'Neil, Nathan J. Ortiz, Christine G. Pappas, Carl D. Reintsema, Daniel R. Schmidt, Daniel S. Swetz , et al. (6 additional authors not shown)

Abstract: Feature sizes in integrated circuits have decreased substantially over time, and it has become increasingly difficult to three-dimensionally image these complex circuits after fabrication. This can be important for process development, defect analysis, and detection of unexpected structures in externally sourced chips, among other applications. Here, we report on a non-destructive, tabletop approa… ▽ More Feature sizes in integrated circuits have decreased substantially over time, and it has become increasingly difficult to three-dimensionally image these complex circuits after fabrication. This can be important for process development, defect analysis, and detection of unexpected structures in externally sourced chips, among other applications. Here, we report on a non-destructive, tabletop approach that addresses this imaging problem through x-ray tomography, which we uniquely realize with an instrument that combines a scanning electron microscope (SEM) with a transition-edge sensor (TES) x-ray spectrometer. Our approach uses the highly focused SEM electron beam to generate a small x-ray generation region in a carefully designed target layer that is placed over the sample being tested. With the high collection efficiency and resolving power of a TES spectrometer, we can isolate x-rays generated in the target from background and trace their paths through regions of interest in the sample layers, providing information about the various materials along the x-ray paths through their attenuation functions. We have recently demonstrated our approach using a 240 Mo/Cu bilayer TES prototype instrument on a simplified test sample containing features with sizes of $\sim$1 $μ$m. Currently, we are designing and building a 3000 Mo/Au bilayer TES spectrometer upgrade, which is expected to improve the imaging speed by factor of up to 60 through a combination of increased detector number and detector speed. △ Less

Submitted 14 December, 2022; originally announced December 2022.

Comments: 5 pages, 3 figures, published in IEEE Transactions on Applied Superconductivity

Journal ref: in IEEE Transactions on Applied Superconductivity, vol. 31, no. 5, pp. 1-5, Aug. 2021, Art no. 2100405

Single-exposure x-ray dark-field imaging: quantifying sample microstructure using a single-grid setup

Authors: Ying Ying How, David M. Paganin, Kaye S. Morgan

Abstract: The size of the smallest detectable sample feature in an x-ray imaging system is usually restricted by the spatial resolution of the system. This limitation can now be overcome using the diffusive dark-field signal, which is generated by unresolved phase effects or the ultra-small-angle x-ray scattering from unresolved sample microstructures. A quantitative measure of this dark-field signal can be… ▽ More The size of the smallest detectable sample feature in an x-ray imaging system is usually restricted by the spatial resolution of the system. This limitation can now be overcome using the diffusive dark-field signal, which is generated by unresolved phase effects or the ultra-small-angle x-ray scattering from unresolved sample microstructures. A quantitative measure of this dark-field signal can be useful in revealing the microstructure size or material for medical diagnosis, security screening and materials science. Recently, we derived a new method to quantify the diffusive dark-field signal in terms of a scattering angle using a single-exposure grid-based approach. In this manuscript, we look at the problem of quantifying the sample microstructure size from this single-exposure dark-field signal. We do this by quantifying the diffusive dark-field signal produced by 5 different sizes of polystyrene microspheres, ranging from 1.0 $μ$m to 10.8 $μ$m, to investigate how the strength of the dark-field signal changes with the sample microstructure size, $S$. We also explore the feasibility of performing single-exposure dark-field imaging with a simple equation for the optimal propagation distance given microstructure with a specific size and thickness, and successfully verify this equation with experimental data. Our theoretical model predicts that the dark-field scattering angle is inversely proportional to $\sqrt{S}$, which is consistent with our experimental data. △ Less

Submitted 1 December, 2022; originally announced December 2022.

Comments: 20 pages, 11 figures

Directional dark-field retrieval with single-grid x-ray imaging

Authors: Michelle K Croughan, Ying Ying How, Allan Pennings, Kaye S Morgan

Abstract: Directional dark-field imaging is an emerging x-ray modality that is sensitive to unresolved anisotropic scattering from sub-pixel sample microstructures. A single-grid imaging set-up can be used to capture dark-field images by looking at changes in a grid pattern projected upon the sample. By creating analytical models for the experiment, we have developed a single-grid directional dark field ret… ▽ More Directional dark-field imaging is an emerging x-ray modality that is sensitive to unresolved anisotropic scattering from sub-pixel sample microstructures. A single-grid imaging set-up can be used to capture dark-field images by looking at changes in a grid pattern projected upon the sample. By creating analytical models for the experiment, we have developed a single-grid directional dark field retrieval algorithm that can extract dark-field parameters such as the dominant scattering direction, and the semi-major and -minor scattering angles. We show that this method is effective even in the presence of high image noise, allowing for low dose and time sequence imaging. △ Less

Submitted 6 April, 2023; v1 submitted 20 November, 2022; originally announced November 2022.

Journal ref: Optics Express Vol. 31, Issue 7, pp. 11578-11597 (2023)

Fast implicit diffusive dark-field retrieval for single-exposure, single-mask x-ray imaging

Authors: Mario A. Beltran, David M. Paganin, Michelle K. Croughan, Kaye S. Morgan

Abstract: Complementary to conventional and phase X-ray radiography, dark-field imaging has become central in visualizing diffusive scattering signal due to the spatially-unresolved texture within an object. To date most diffusive-dark-field retrieval methods require either the acquisition of multiple images at the cost of higher radiation dose or significant amounts of computational memory and time. In thi… ▽ More Complementary to conventional and phase X-ray radiography, dark-field imaging has become central in visualizing diffusive scattering signal due to the spatially-unresolved texture within an object. To date most diffusive-dark-field retrieval methods require either the acquisition of multiple images at the cost of higher radiation dose or significant amounts of computational memory and time. In this work, a simple method of X-ray diffusive dark-field retrieval is presented, applicable to any single-mask imaging setup, with only one exposure of the sample. The approach, which is based on a model of geometric and diffusive reverse-flow conservation, is implicit and non-iterative. This numerically fast methodology is applied to experimental X-ray images acquired using both a random mask and a grid mask, giving high quality reconstructions that are very stable in the presence of noise. The method should be useful for high-speed imaging and/or imaging with low-flux sources. △ Less

Submitted 17 March, 2023; v1 submitted 11 November, 2022; originally announced November 2022.

Absolute Energy Measurements with Superconducting Transition-Edge Sensors for Muonic X-ray Spectroscopy at 44 keV

Authors: Daikang Yan, Joel C. Weber, Tejas Guruswamy, Kelsey M. Morgan, Galen C. O'Neil, Abigail L. Wessels, Douglas A. Bennett, Christine G. Pappas, John A. Mates, Johnathon D. Gard, Daniel T. Becker, Joseph W. Fowler, Daniel S. Swetz, Daniel R. Schmidt, Joel N. Ullom, Takuma Okumura, Tadaaki Isobe, Toshiyuki Azuma, Shinji Okada, Shinya Yamada, Tadashi Hashimoto, Orlando Quaranta, Antonino Miceli, Lisa M. Gades, Umeshkumar M. Patel , et al. (3 additional authors not shown)

Abstract: Superconducting transition-edge sensor (TES) microcalorimeters have great utility in x-ray applications owing to their high energy resolution, good collecting efficiency and the feasibility of being multiplexed into large arrays. In this work, we develop hard x-ray TESs to measure the absolute energies of muonic-argon ($μ$-Ar) transition lines around 44 keV and 20 keV. TESs with sidecar absorbers… ▽ More Superconducting transition-edge sensor (TES) microcalorimeters have great utility in x-ray applications owing to their high energy resolution, good collecting efficiency and the feasibility of being multiplexed into large arrays. In this work, we develop hard x-ray TESs to measure the absolute energies of muonic-argon ($μ$-Ar) transition lines around 44 keV and 20 keV. TESs with sidecar absorbers of different heat capacities were fabricated and characterized for their energy resolution and calibration uncertainty. We achieved ~ 1 eV absolute energy measurement accuracy at 44 keV, and < 12 eV energy resolution at 17.5 keV. △ Less

Submitted 21 July, 2022; originally announced July 2022.

Scalable, Highly Crystalline, 2D Semiconductor Atomic Layer Deposition Process for High Performance Electronic Applications

Authors: Nikolaos Aspiotis, Katrina Morgan, Benjamin März, Knut Müller-Caspary, Martin Ebert, Chung-Che Huang, Daniel W. Hewak, Sayani Majumdar, Ioannis Zeimpekis

Abstract: This work demonstrates a large area process for atomically thin 2D semiconductors to unlock the technological upscale required for their commercial uptake. The new atomic layer deposition (ALD) and conversion technique yields large area performance uniformity and tunability. Like graphene, 2D Transition Metal Dichalcogenides (TMDCs) are prone to upscaling challenges limiting their commercial uptak… ▽ More This work demonstrates a large area process for atomically thin 2D semiconductors to unlock the technological upscale required for their commercial uptake. The new atomic layer deposition (ALD) and conversion technique yields large area performance uniformity and tunability. Like graphene, 2D Transition Metal Dichalcogenides (TMDCs) are prone to upscaling challenges limiting their commercial uptake. They are challenging to grow uniformly on large substrates and to transfer on alternative substrates while they often lack in large area electrical performance uniformity. The scalable ALD process of this work enables uniform growth of 2D TMDCs on large area with independent control of layer thickness, stoichiometry and crystallinity while allowing chemical free transfers to application substrates. Field effect transistors (FETs) fabricated on flexible substrates using the process present a field effect mobility of up to 55 cm^2/Vs, subthreshold slope down to 80 mV/dec and on/off ratios of 10^7. Additionally, non-volatile memory transistors using ferroelectric FETs (FeFETs) operating at +-5 V with on/off ratio of 107 and a memory window of 3.25 V are demonstrated. These FeFETs demonstrate state-of-the-art performance with multiple state switching, suitable for one-transistor non-volatile memory and for synaptic transistors revealing the applicability of the process to flexible neuromorphic applications. △ Less

Submitted 19 March, 2022; originally announced March 2022.

Comments: 16 pages, 9 figures

Accurate measures of regional lung air volumes from chest X-rays of small animals

Authors: D. W. O'Connell, K. S. Morgan, G. Ruben, L. C. P. Croton, J. A. Pollock, M. K. Croughan, E. V. McGillick, M. J. Wallace, K. J. Crossley, E. J. Pryor, R. A. Lewis, S. B. Hooper, M. J. Kitchen

Abstract: We present a robust technique for calculating regional volume changes within the lung from X-ray radiograph sequences captured during ventilation, without the use of computed tomography (CT). This technique is based on the change in transmitted X-ray intensity that occurs for each lung region as air displaces the attenuating lung tissue. Lung air volumes calculated from X-ray intensity changes sho… ▽ More We present a robust technique for calculating regional volume changes within the lung from X-ray radiograph sequences captured during ventilation, without the use of computed tomography (CT). This technique is based on the change in transmitted X-ray intensity that occurs for each lung region as air displaces the attenuating lung tissue. Lung air volumes calculated from X-ray intensity changes showed a strong correlation ($R^2$=0.98) against the true volumes, measured from high-resolution CT. This correlation enables us to accurately convert projected intensity data into relative changes in lung air volume. We have applied this technique to measure changes in regional lung volumes from X-ray image sequences of mechanically ventilated, recently-deceased newborn rabbits, without the use of CT. This method is suitable for biomedical research studies and shows potential for clinical application. △ Less

Submitted 7 April, 2022; v1 submitted 16 February, 2022; originally announced February 2022.

Comments: 12 Pages, 10 Figures

Low energy switching of phase change materials using a 2D thermal boundary layer

Authors: Jing Ning, Yunzheng Wang, Ting Yu Teo, Chung-Che Huang, Ioannis Zeimpekis, Katrina Morgan, Siew Lang Teo, Daniel W. Hewak, Michel Bosman, Robert E. Simpson

Abstract: The switchable optical and electrical properties of phase change materials (PCMs) are finding new applications beyond data storage in reconfigurable photonic devices. However, high power heat pulses are needed to melt-quench the material from crystalline to amorphous. This is especially true in silicon photonics, where the high thermal conductivity of the waveguide material makes heating the PCM e… ▽ More The switchable optical and electrical properties of phase change materials (PCMs) are finding new applications beyond data storage in reconfigurable photonic devices. However, high power heat pulses are needed to melt-quench the material from crystalline to amorphous. This is especially true in silicon photonics, where the high thermal conductivity of the waveguide material makes heating the PCM energy inefficient. Here, we improve the energy efficiency of the laser-induced phase transitions by inserting a layer of two-dimensional (2D) material, either MoS2 or WS2, between the silica or silicon and the PCM. The 2D material reduces the required laser power by at least 40% during the amorphization (RESET) process, depending on the substrate. Thermal simulations confirm that both MoS2 and WS2 2D layers act as a thermal barrier, which efficiently confines energy within the PCM layer. Remarkably, the thermal insulation effect of the 2D layer is equivalent to a ~100 nm layer of SiO2. The high thermal boundary resistance induced by the van der Waals (vdW)-bonded layers limits the thermal diffusion through the layer interfaces. Hence, 2D materials with stable vdW interfaces can be used to improve the thermal efficiency of PCM-tuned Si photonic devices. Furthermore, our waveguide simulations show that the 2D layer does not affect the propagating mode in the Si waveguide, thus this simple additional thin film produces a substantial energy efficiency improvement without degrading the optical performance of the waveguide. Our findings pave the way for energy-efficient laser-induced structural phase transitions in PCM-based reconfigurable photonic devices. △ Less

Submitted 9 February, 2022; originally announced February 2022.

Comments: 34 pages, 12 figures

Quantifying the x-ray dark-field signal in single-grid imaging

Authors: Ying Ying How, Kaye Morgan

Abstract: X-ray dark-field imaging reveals the sample microstructure that is unresolved when using conventional methods of x-ray imaging. In this paper, we derive a new method to extract and quantify the x-ray dark-field signal collected using a single-grid imaging set-up, and relate the signal strength to the number of sample microstructures, $N$. This was achieved by modelling sample-induced changes to th… ▽ More X-ray dark-field imaging reveals the sample microstructure that is unresolved when using conventional methods of x-ray imaging. In this paper, we derive a new method to extract and quantify the x-ray dark-field signal collected using a single-grid imaging set-up, and relate the signal strength to the number of sample microstructures, $N$. This was achieved by modelling sample-induced changes to the shadow of the upstream grid, and fitting experimental data to this model. Our results suggested that the dark-field scattering angle from our spherical microstructures is proportional to $^{2.19}\sqrt{N}$, which deviated from the theoretical model of $\sqrt{N}$, but was not inconsistent with results from other experimental methods. We believe the approach outlined here can equip quantitative dark-field imaging of small samples, particularly in cases where only one sample exposure is possible, either due to sample movement or radiation dose limitations. Future directions include an extension into directional dark-field imaging. △ Less

Submitted 27 December, 2021; originally announced December 2021.

Comments: 20 pages, 9 figures

X-ray dark-field and phase retrieval without optics, via the Fokker-Planck equation

Authors: T. A. Leatham, D. M. Paganin, K. S. Morgan

Abstract: Emerging methods of x-ray imaging that capture phase and dark-field effects are equipping medicine with complementary sensitivity to conventional radiography. These methods are being applied over a wide range of scales, from virtual histology to clinical chest imaging, and typically require the introduction of optics such as gratings. Here, we consider extracting x-ray phase and dark-field signals… ▽ More Emerging methods of x-ray imaging that capture phase and dark-field effects are equipping medicine with complementary sensitivity to conventional radiography. These methods are being applied over a wide range of scales, from virtual histology to clinical chest imaging, and typically require the introduction of optics such as gratings. Here, we consider extracting x-ray phase and dark-field signals from bright-field images collected using nothing more than a coherent x-ray source and detector. Our approach is based on the Fokker--Planck equation for paraxial imaging, which is the diffusive generalization of the transport-of-intensity equation. Specifically, we utilize the Fokker--Planck equation in the context of propagation-based phase-contrast imaging, where we show that two intensity images are sufficient for successful retrieval of the projected thickness and dark-field signals associated with the sample. We show the results of our algorithm using both a simulated dataset and an experimental dataset. These demonstrate that the x-ray dark-field signal can be extracted from propagation-based images, and that x-ray phase can be retrieved with better spatial resolution when dark-field effects are taken into account. We anticipate the proposed algorithm will be of benefit in biomedical imaging, industrial settings, and other non-invasive imaging applications. △ Less

Submitted 7 November, 2022; v1 submitted 21 December, 2021; originally announced December 2021.

Comments: 16 pages, 8 figures

Journal ref: IEEE Transactions on Medical Imaging 42, 1681-1695 (2023)

Tomographic phase and attenuation extraction for a sample composed of unknown materials using X-ray propagation-based phase-contrast imaging

Authors: Samantha J. Alloo, David M. Paganin, Kaye S. Morgan, Timur E. Gureyev, Sherry C. Mayo, Sara Mohammadi, Darren Lockie, Ralf Hendrik Menk, Fulvia Arfelli, Fabrizio Zanconati, Giuliana Tromba, Konstantin M. Pavlov

Abstract: Propagation-based phase-contrast X-ray imaging (PB-PCXI) generates image contrast by utilizing sample-imposed phase-shifts. This has proven useful when imaging weakly-attenuating samples, as conventional attenuation-based imaging does not always provide adequate contrast. We present a PB-PCXI algorithm capable of extracting the X-ray attenuation, $β$, and refraction, $δ$, components of the complex… ▽ More Propagation-based phase-contrast X-ray imaging (PB-PCXI) generates image contrast by utilizing sample-imposed phase-shifts. This has proven useful when imaging weakly-attenuating samples, as conventional attenuation-based imaging does not always provide adequate contrast. We present a PB-PCXI algorithm capable of extracting the X-ray attenuation, $β$, and refraction, $δ$, components of the complex refractive index of distinct materials within an unknown sample. The method involves curve-fitting an error-function-based model to a phase-retrieved interface in a PB-PCXI tomographic reconstruction, which is obtained when Paganin-type phase-retrieval is applied with incorrect values of $δ$ and $β$. The fit parameters can then be used to calculate true $δ$ and $β$ values for composite materials. This approach requires no a priori sample information, making it broadly applicable. Our PB-PCXI reconstruction is single distance, requiring only one exposure per tomographic angle, which is important for radiosensitive samples. We apply this approach to a breast-tissue sample, recovering the refraction component, $δ$, with 0.6 - 2.4\% accuracy compared to theoretical values. △ Less

Submitted 14 October, 2021; v1 submitted 12 October, 2021; originally announced October 2021.

Comments: 8 pages, 4 figures and 1 table

Journal ref: Optics Letters 47, 1945-1948 (2022)

Precise phase retrieval for propagation-based images using discrete mathematics

Authors: J. A. Pollock, K. S. Morgan, L. C. P. Croton, M. K. Croughan, G. Ruben, N. Yagi, H. Sekiguchi, M. J. Kitchen

Abstract: The ill-posed problem of phase retrieval in optics, using one or more intensity measurements, has a multitude of applications using electromagnetic or matter waves. Many phase retrieval algorithms are computed on pixel arrays using discrete Fourier transforms due to their high computational efficiency. However, the mathematics underpinning these algorithms is typically formulated using continuous… ▽ More The ill-posed problem of phase retrieval in optics, using one or more intensity measurements, has a multitude of applications using electromagnetic or matter waves. Many phase retrieval algorithms are computed on pixel arrays using discrete Fourier transforms due to their high computational efficiency. However, the mathematics underpinning these algorithms is typically formulated using continuous mathematics, which can result in a loss in spatial resolution in the reconstructed images. Herein we investigate how phase retrieval algorithms for propagation-based phase-contrast X-ray imaging can be rederived using discrete mathematics and result in more precise retrieval for single- and multi-material objects and for spectral image decomposition. We validate this theory through experimental measurements of spatial resolution using computed tomography (CT) reconstructions of plastic phantoms and biological tissue, using detectors with a range of imaging system point spread functions (PSFs). We demonstrate that if the PSF substantially suppresses high spatial frequencies, the potential improvement from utilising the discrete derivation is limited. However, with detectors characterised by a single pixel PSF (e.g. direct, photon-counting X-ray detectors), a significant improvement in spatial resolution can be obtained, demonstrated here at up to 17%. △ Less

Submitted 20 September, 2022; v1 submitted 14 June, 2021; originally announced June 2021.

Directional dark-field implicit x-ray speckle tracking using an anisotropic-diffusion Fokker-Planck equation

Authors: Konstantin M. Pavlov, David M. Paganin, Kaye S. Morgan, Heyang, Li, Sebastien Berujon, Laurène Quénot, Emmanuel Brun

Abstract: When a macroscopic-sized non-crystalline sample is illuminated using coherent x-ray radiation, a bifurcation of photon energy flow may occur. The coarse-grained complex refractive index of the sample may be considered to attenuate and refract the incident coherent beam, leading to a coherent component of the transmitted beam. Spatially-unresolved sample microstructure, associated with the fine-gra… ▽ More When a macroscopic-sized non-crystalline sample is illuminated using coherent x-ray radiation, a bifurcation of photon energy flow may occur. The coarse-grained complex refractive index of the sample may be considered to attenuate and refract the incident coherent beam, leading to a coherent component of the transmitted beam. Spatially-unresolved sample microstructure, associated with the fine-grained components of the complex refractive index, introduces a diffuse component to the transmitted beam. This diffuse photon-scattering channel may be viewed in terms of position-dependent fans of ultra-small-angle x-ray scatter. These position-dependent fans, at the exit surface of the object, may under certain circumstances be approximated as having a locally-elliptical shape. By using an anisotropic-diffusion Fokker-Planck approach to model this bifurcated x-ray energy flow, we show how all three components (attenuation, refraction and locally-elliptical diffuse scatter) may be recovered. This is done via x-ray speckle tracking, in which the sample is illuminated with spatially-random x-ray fields generated by coherent illumination of a spatially-random membrane. The theory is developed, and then successfully applied to experimental x-ray data. △ Less

Submitted 26 September, 2021; v1 submitted 22 May, 2021; originally announced May 2021.

Comments: To be published in Physical Review A; accepted version with minor revisions compared to the previous version

Journal ref: Phys. Rev. A 104, 053505 (2021)

The structure of global conservation laws in Galerkin plasma models

Authors: Alan A. Kaptanoglu, Kyle D. Morgan, Christopher J. Hansen, Steven L. Brunton

Abstract: Plasmas are highly nonlinear and multi-scale, motivating a hierarchy of models to understand and describe their behavior. However, there is a scarcity of plasma models of lower fidelity than magnetohydrodynamics (MHD). Galerkin models, obtained by projection of the MHD equations onto a truncated modal basis, can furnish this gap in the lower levels of the model hierarchy. In the present work, we d… ▽ More Plasmas are highly nonlinear and multi-scale, motivating a hierarchy of models to understand and describe their behavior. However, there is a scarcity of plasma models of lower fidelity than magnetohydrodynamics (MHD). Galerkin models, obtained by projection of the MHD equations onto a truncated modal basis, can furnish this gap in the lower levels of the model hierarchy. In the present work, we develop low-dimensional Galerkin plasma models which preserve global conservation laws by construction. This additional model structure enables physics-constrained machine learning algorithms that can discover these types of low-dimensional plasma models directly from data. This formulation relies on an energy-based inner product which takes into account all of the dynamic variables. The theoretical results here build a bridge to the extensive Galerkin literature in fluid mechanics, and facilitate the development of physics-constrained reduced-order models from plasma data. △ Less

Submitted 9 January, 2021; originally announced January 2021.

Comments: arXiv admin note: text overlap with arXiv:2004.10389

Absolute energies and emission line shapes of the L x-ray transitions of lanthanide metals

Authors: Joseph W. Fowler, Galen C. O'Neil, Bradley K. Alpert, Douglas A. Bennett, Ed V. Denison, W. B. Doriese, Gene C. Hilton, Lawrence T. Hudson, Young-Il Joe, Kelsey M. Morgan, Daniel R. Schmidt, Daniel S. Swetz, Csilla I. Szabo, Joel N. Ullom

Abstract: We use an array of transition-edge sensors, cryogenic microcalorimeters with 4 eV energy resolution, to measure L x-ray emission-line profiles of four elements of the lanthanide series: praseodymium, neodymium, terbium, and holmium. The spectrometer also surveys numerous x-ray standards in order to establish an absolute-energy calibration traceable to the International System of Units for the ener… ▽ More We use an array of transition-edge sensors, cryogenic microcalorimeters with 4 eV energy resolution, to measure L x-ray emission-line profiles of four elements of the lanthanide series: praseodymium, neodymium, terbium, and holmium. The spectrometer also surveys numerous x-ray standards in order to establish an absolute-energy calibration traceable to the International System of Units for the energy range 4 keV to 10 keV. The new results include emission line profiles for 97 lines, each expressed as a sum of one or more Voigt functions; improved absolute energy uncertainty on 71 of these lines relative to existing reference data; a median uncertainty on the peak energy of 0.24 eV, four to ten times better than the median of prior work; and 6 lines that lack any measured values in existing reference tables. The 97 lines comprise nearly all of the most intense L lines from these elements under broad-band x-ray excitation. The work improves on previous measurements made with a similar cryogenic spectrometer by the use of sensors with better linearity in the absorbed energy and a gold x-ray absorbing layer that has a Gaussian energy-response function. It also employs a novel sample holder that enables rapid switching between science targets and calibration targets with excellent gain balancing. Most of the results for peak energy values shown here should be considered as replacements for the currently tabulated standard reference values, while the line shapes given here represent a significant expansion of the scope of available reference data. △ Less

Submitted 30 November, 2020; originally announced December 2020.

Journal ref: Metrologia 58 (2021) 015016

A Transition-edge Sensor-based X-ray Spectrometer for the Study of Highly Charged Ions at the National Institute of Standards and Technology Electron Beam Ion Trap

Authors: P. Szypryt, G. C. O'Neil, E. Takacs, J. N. Tan, S. W. Buechele, A. S. Naing, D. A. Bennett, W. B. Doriese, M. Durkin, J. W. Fowler, J. D. Gard, G. C. Hilton, K. M. Morgan, C. D. Reintsema, D. R. Schmidt, D. S. Swetz, J. N. Ullom, Yu. Ralchenko

Abstract: We report on the design, commissioning, and initial measurements of a Transition-edge Sensor (TES) x-ray spectrometer for the Electron Beam Ion Trap (EBIT) at the National Institute of Standards and Technology (NIST). Over the past few decades, the NIST EBIT has produced numerous studies of highly charged ions in diverse fields such as atomic physics, plasma spectroscopy, and laboratory astrophysi… ▽ More We report on the design, commissioning, and initial measurements of a Transition-edge Sensor (TES) x-ray spectrometer for the Electron Beam Ion Trap (EBIT) at the National Institute of Standards and Technology (NIST). Over the past few decades, the NIST EBIT has produced numerous studies of highly charged ions in diverse fields such as atomic physics, plasma spectroscopy, and laboratory astrophysics. The newly commissioned NIST EBIT TES Spectrometer (NETS) improves the measurement capabilities of the EBIT through a combination of high x-ray collection efficiency and resolving power. NETS utilizes 192 individual TES x-ray microcalorimeters (166/192 yield) to improve upon the collection area by a factor of ~30 over the 4-pixel neutron transmutation doped germanium-based microcalorimeter spectrometer previously used at the NIST EBIT. The NETS microcalorimeters are optimized for the x-ray energies from roughly 500 eV to 8,000 eV and achieve an energy resolution of 3.7 eV to 5.0 eV over this range, a more modest (<2X) improvement over the previous microcalorimeters. Beyond this energy range NETS can operate with various trade-offs, the most significant of which are reduced efficiency at lower energies and being limited to a subset of the pixels at higher energies. As an initial demonstration of the capabilities of NETS, we measured transitions in He-like and H-like O, Ne, and Ar as well as Ni-like W. We detail the energy calibration and data analysis techniques used to transform detector counts into x-ray spectra, a process that will be the basis for analyzing future data. △ Less

Submitted 11 May, 2020; originally announced May 2020.

Physics-constrained, low-dimensional models for MHD: First-principles and data-driven approaches

Authors: Alan A. Kaptanoglu, Kyle D. Morgan, Chris J. Hansen, Steven L. Brunton

Abstract: Plasmas are highly nonlinear and multi-scale, motivating a hierarchy of models to understand and describe their behavior. However, there is a scarcity of plasma models of lower fidelity than magnetohydrodynamics (MHD), although these reduced models hold promise for understanding key physical mechanisms, efficient computation, and real-time optimization and control. Galerkin models, obtained by pro… ▽ More Plasmas are highly nonlinear and multi-scale, motivating a hierarchy of models to understand and describe their behavior. However, there is a scarcity of plasma models of lower fidelity than magnetohydrodynamics (MHD), although these reduced models hold promise for understanding key physical mechanisms, efficient computation, and real-time optimization and control. Galerkin models, obtained by projection of the MHD equations onto a truncated modal basis, and data-driven models, obtained by modern machine learning and system identification, can furnish this gap in the lower levels of the model hierarchy. This work develops a reduced-order modeling framework for compressible plasmas, leveraging decades of progress in projection-based and data-driven modeling of fluids. We begin by formalizing projection-based model reduction for nonlinear MHD systems. To avoid separate modal decompositions for the magnetic, velocity, and pressure fields, we introduce an energy inner product to synthesize all of the fields into a dimensionally-consistent, reduced-order basis. Next, we obtain an analytic model by Galerkin projection of the Hall-MHD equations onto these modes. We illustrate how global conservation laws constrain the model parameters, revealing symmetries that can be enforced in data-driven models, directly connecting these models to the underlying physics. We demonstrate the effectiveness of this approach on data from high-fidelity numerical simulations of a 3D spheromak experiment. This manuscript builds a bridge to the extensive Galerkin literature in fluid mechanics, and facilitates future principled development of projection-based and data-driven models for plasmas. △ Less

Submitted 15 July, 2021; v1 submitted 22 April, 2020; originally announced April 2020.

Journal ref: Phys. Rev. E 104, 015206 (2021)

Advanced modeling for the HIT-SI Experiment

Authors: Alan A. Kaptanoglu, Thomas E. Benedett, Kyle D. Morgan, Chris J. Hansen, Thomas R. Jarboe

Abstract: A two-temperature magnetohydrodynamic (MHD) model, which evolves the electron and ion temperatures separately, is implemented in the PSI-Tet code and used to model plasma dynamics in the HIT-SI experiment. When compared with single-temperature Hall-MHD, the two-temperature Hall-MHD model demonstrates improved qualitative agreement with experimental measurements, including: far-infrared interferome… ▽ More A two-temperature magnetohydrodynamic (MHD) model, which evolves the electron and ion temperatures separately, is implemented in the PSI-Tet code and used to model plasma dynamics in the HIT-SI experiment. When compared with single-temperature Hall-MHD, the two-temperature Hall-MHD model demonstrates improved qualitative agreement with experimental measurements, including: far-infrared interferometry, ion Doppler spectroscopy, Thomson scattering, and magnetic probe measurements. The two-temperature model is utilized for HIT-SI simulations in both the PSI-Tet and NIMROD codes at a number of different injector frequencies in the 14.5-68.5 kHz range. At all frequencies the two-temperature models result in increased toroidal current, lower chord-averaged density, and symmetrization of the current centroid, relative to single-temperature simulations. Both codes produce higher average temperatures and toroidal currents as the injector frequency is increased. Power balance and heat fluxes to the wall are calculated for the two-temperature PSI-Tet model and indicate considerable viscous and compressive heating, particularly at high injector frequency. Parameter scans are also presented for the artificial diffusivity, and Dirichlet wall temperature and density. Artificial diffusivity and the density boundary condition both significantly modify the plasma density profiles, leading to larger average temperatures, higher toroidal current, and increased relative density fluctuations at low diffusivity and low wall density. High power, low density simulations at 14.5 kHz achieve sufficiently high gain (G = 5) to generate significant volumes of closed flux lasting 1-2 injector periods. △ Less

Submitted 1 March, 2020; originally announced March 2020.

Material decomposition from a single x-ray projection via single-grid phase contrast imaging

Authors: Celebrity F. Groenendijk, Florian Schaff, Linda C. P. Croton, Marcus J. Kitchen, Kaye S. Morgan

Abstract: This study describes a new approach for material decomposition in x-ray imaging, utilising phase contrast to both increase sensitivity to weakly-attenuating samples and to act as a complementary measurement to attenuation, therefore allowing two overlaid materials to be separated. The measurements are captured using the single-exposure, single-grid x-ray phase contrast imaging technique, with a no… ▽ More This study describes a new approach for material decomposition in x-ray imaging, utilising phase contrast to both increase sensitivity to weakly-attenuating samples and to act as a complementary measurement to attenuation, therefore allowing two overlaid materials to be separated. The measurements are captured using the single-exposure, single-grid x-ray phase contrast imaging technique, with a novel correction that aims to remove propagation-based phase effects seen at sharp edges in the attenuation image. The use of a single-exposure technique means that images could be collected in a high-speed sequence. Results are shown for both a known two-material sample and for a biological specimen. △ Less

Submitted 8 February, 2020; originally announced February 2020.

Characterizing Magnetized Plasmas with Dynamic Mode Decomposition

Authors: Alan A. Kaptanoglu, Kyle D. Morgan, Chris J. Hansen, Steven L. Brunton

Abstract: Accurate and efficient plasma models are essential to understand and control experimental devices. Existing magnetohydrodynamic or kinetic models are nonlinear, computationally intensive, and can be difficult to interpret, while often only approximating the true dynamics. In this work, data-driven techniques recently developed in the field of fluid dynamics are leveraged to develop interpretable r… ▽ More Accurate and efficient plasma models are essential to understand and control experimental devices. Existing magnetohydrodynamic or kinetic models are nonlinear, computationally intensive, and can be difficult to interpret, while often only approximating the true dynamics. In this work, data-driven techniques recently developed in the field of fluid dynamics are leveraged to develop interpretable reduced-order models of plasmas that strike a balance between accuracy and efficiency. In particular, dynamic mode decomposition (DMD) is used to extract spatio-temporal magnetic coherent structures from the experimental and simulation datasets of the HIT-SI experiment. Three-dimensional magnetic surface probes from the HIT-SI experiment are analyzed, along with companion simulations with synthetic internal magnetic probes. A number of leading variants of the DMD algorithm are compared, including the sparsity-promoting and optimized DMD. Optimized DMD results in the highest overall prediction accuracy, while sparsity-promoting DMD yields physically interpretable models that avoid overfitting. These DMD algorithms uncover several coherent magnetic modes that provide new physical insights into the inner plasma structure. These modes were subsequently used to discover a previously unobserved three-dimensional structure in the simulation, rotating at the second injector harmonic. Finally, using data from probes at experimentally accessible locations, DMD identifies a resistive kink mode, a ubiquitous instability seen in magnetized plasmas. △ Less

Submitted 15 November, 2019; originally announced November 2019.