Image quality and scan time optimisation for in situ phase contrast x-ray tomography of the intervertebral disc
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36 MATERIALS SCIENCE↗
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Results for “Image reconstruction”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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STORM Super-Resolution Visualization of Self-Assembled γPFD Chaperone Ultrastructures in Methanocaldococcus jannaschii
Gamma-prefoldin (γPFD), a unique chaperone found in the extremely thermophilic methanogen Methanocaldococcus jannaschii, self-assembles into filaments in vitro, which so far have been observed using transmission electron microscopy and cryo-electron microscopy. Utilizing three-dimensional stochastic optical reconstruction microscopy (3D-STORM), here we achieve ~20 nm resolution by precisely locating individual fluorescent molecules, hence resolving γPFD ultrastructure both in vitro and in vivo. Through CF647 NHS ester labeling, we first demonstrate the accurate visualization of filaments and bundles with purified γPFD. Next, by implementing immunofluorescence labeling after creating a 3xFLAG-tagged γPFD strain, we successfully visualize γPFD in M. jannaschii cells. Through 3D-STORM and two-color STORM imaging with DNA, we show the widespread distribution of filamentous γPFD structures within the cell. These findings provide valuable insights into the structure and localization of γPFD, opening up possibilities for studying intriguing nanoscale components not only in archaea but also in other microorganisms.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Particle hit clustering and identification using point set transformers in liquid argon time projection chambers
Liquid argon time projection chambers are often used in neutrino physics and dark-matter searches because of their high spatial resolution. The images generated by these detectors are extremely sparse, as the energy values detected by most of the detector are equal to 0, meaning that despite their high resolution, most of the detector is unused in a particular interaction. Instead of representing all of the empty detections, the interaction is usually stored as a sparse matrix, a list of detection locations paired with their energy values. Traditional machine learning methods that have been applied to particle reconstruction such as convolutional neural networks (CNNs), however, cannot operate over data stored in this way and therefore must have the matrix fully instantiated as a dense matrix. Operating on dense matrices requires a lot of memory and computation time, in contrast to directly operating on the sparse matrix. We propose a machine learning model using a point set neural network that operates over a sparse matrix, greatly improving both processing speed and accuracy over methods that instantiate the dense matrix, as well as over other methods that operate over sparse matrices. Compared to competing state-of-the-art methods, our method improves classification performance by 14%, segmentation performance by more than 22%, while taking 80% less time and using 66% less memory. Compared to state-of-the-art CNN methods, our method improves classification performance by more than 86%, segmentation performance by more than 71%, while reducing runtime by 91% and reducing memory usage by 61%.
calibration and fitting methods↗
Beyond Contrast Transfer: Spectral SNR as a Finite-Dose Metric for STEM Phase Retrieval
The contrast transfer function (CTF) is widely used to evaluate phase retrieval methods in scanning transmission electron microscopy (STEM), including center-of-mass imaging, parallax imaging, direct ptychography, and iterative ptychography. However, the CTF reflects only the maximum usable signal, neglecting the effects of finite electron fluence and the Poisson-limited nature of detection. As a result, it can significantly overestimate practical performance, especially in low-dose regimes. Here, we employ the spectral signal-to-noise ratio (SSNR), as a finite-dose statistical framework to evaluate the recoverable signal as a function of spatial frequency. Using numerical reconstructions of white-noise objects, we show that center-of-mass, parallax, and direct ptychography exhibit dose-independent SSNRs, with close-form analytic expressions. In contrast, iterative ptychography exhibits a surprising dose dependence: at low fluence, its SSNR converges to that of direct ptychography; at high fluence, it saturates at a value consistent with the maximum detective quantum efficiency predicted by recent quantum Fisher information bounds. The results highlight the limitations of CTF-based evaluation and motivate SSNR as a more accurate, finite-dose metric for assessing STEM phase retrieval methods.
STEM phase retrieval↗
Design of Electrostatic Aberration Correctors for Scanning Transmission Electron Microscopy
Abstract In a scanning transmission electron microscope (STEM), producing a high-resolution image generally requires an electron beam focused to the smallest point possible. However, the magnetic lenses used to focus the beam are unavoidably imperfect, introducing aberrations that limit resolution. Modern STEMs overcome this by using hardware aberration correctors comprised of many multipole elements, but these devices are complex, expensive, and can be difficult to tune. We demonstrate a design for an electrostatic phase plate that can act as an aberration corrector. The corrector is comprised of annular segments, each of which is an independent two-terminal device that can apply a constant or ramped phase shift to a portion of the electron beam. We show the improvement in image resolution using an electrostatic corrector. Engineering criteria impose that much of the beam within the probe-forming aperture be blocked by support bars, leading to large probe tails for the corrected probe that sample the specimen beyond the central lobe. We also show how this device can be used to create other STEM beam profiles such as vortex beams and probes with a high degree of phase diversity, which improve information transfer in ptychographic reconstructions.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
An intergalactic medium temperature from a giant radio galaxy
ABSTRACT The warm–hot intergalactic medium (warm–hot IGM, or WHIM) pervades the filaments of the Cosmic Web and harbours half of the Universe’s baryons. The WHIM’s thermodynamic properties are notoriously hard to measure. Here we estimate a galaxy group–WHIM boundary temperature using a new method. In particular, we use a radio image of the giant radio galaxy (giant RG, or GRG) created by NGC 6185, a massive nearby spiral. We analyse this extraordinary object with a Bayesian 3D lobe model and deduce an equipartition pressure Peq = 6 × 10−16 Pa – among the lowest found in RGs yet. Using an X-ray-based statistical conversion for Fanaroff–Riley II RGs, we find a true lobe pressure $P = 1.5\substack{+1.7\\ -0.4}\times 10^{-15}\ \mathrm{Pa}$. Cosmic Web reconstructions, group catalogues, and MHD simulations furthermore imply an Mpc–scale IGM density $1 + \delta _\mathrm{IGM} = 40\substack{+30\\ -10}$. The buoyantly rising lobes are crushed by the IGM at their inner side, where an approximate balance between IGM and lobe pressure occurs: PIGM ≈ P. The ideal gas law then suggests an IGM temperature $T_\mathrm{IGM} = 11\substack{+12\\-5} \times 10^6\ \mathrm{K}$, or $k_\mathrm{B}T_\mathrm{IGM} = 0.9\substack{+1.0\\-0.4}\ \mathrm{keV}$, at the virial radius – consistent with X-ray-derived temperatures of similarly massive groups. Interestingly, the method is not performing at its limit: in principle, estimates TIGM ∼ 4 × 106 K are already possible – rivalling the lowest X-ray measurements available. The technique’s future scope extends from galaxy group outskirts to the WHIM. In conclusion, we demonstrate that observations of GRGs in Cosmic Web filaments are finally sensitive enough to probe the thermodynamics of galaxy groups and beyond.
79 ASTRONOMY AND ASTROPHYSICS↗
Fast and noise-tolerant determination of the center of rotation in tomography
High-quality tomographic reconstruction is not possible without the accurate localization of the center of rotation. Poor localization leads to artifacts in the data and can even cause reconstructions to fail. There are many approaches to solving this problem, some of which involve the collection of full sinograms, or even provisional tomographic reconstructions, in order to determine the center of rotation. Here, a simple method based on the expected symmetry of the Fourier transform of summed projections approximately 180° apart is presented; unlike cross-correlation methods, it requires only a single Fourier transform to compute, and uses mainly low spatial frequency information which is less susceptible to noise. This approach is shown to be fast, and robust against poor signal-to-noise as well as to projection images acquired at angles that are not exactly 180° apart. This rapid method can be useful as a first step in the processing of tomographic data.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
A Parameterization of the Cloud Scattering Polarization Signal Derived From GPM Observations for Microwave Fast Radative Transfer Models
Microwave cloud polarized observations have shown the potential to improve precipitation retrievals since they are linked to the orientation and shape of ice habits. Stratiform clouds show larger brightness temperature (TB) polarization differences (PDs), defined as the vertically polarized TB (TBV) minus the horizontally polarized TB (TBH), with ~10 K PD values at 89 GHz due to the presence of horizontally aligned snowflakes, while convective regions show smaller PD signals, as graupel and/or hail in the updraft tend to become randomly oriented. The launch of the global precipitation measurement (GPM) microwave imager (GMI) has extended the availability of microwave polarized observations to higher frequencies (166 GHz) in the tropics and midlatitudes, previously only available up to 89 GHz. This study analyzes one year of GMI observations to explore further the previously reported stable relationship between the PD and the observed TBs at 89 and 166 GHz, respectively. The latitudinal and seasonal variability is analyzed to propose a cloud scattering polarization parameterization of the PD-TB relationship, capable of reconstructing the PD signal from simulated TBs. Given that operational radiative transfer (RT) models do not currently simulate the cloud polarized signals, this is an alternative and simple solution to exploit the large number of cloud polarized observations available. Finally, the atmospheric radiative transfer simulator (ARTS) is coupled with the weather research and forecasting (WRF) model, in order to apply the proposed parameterization to the RT simulated TBs and hence infer the corresponding PD values, which show to reproduce the observed GMI PDs well.
54 ENVIRONMENTAL SCIENCES↗
Neutron-antineutron oscillation search with MicroBooNE and DUNE
The Deep Underground Neutrino Experiment (DUNE) is an international project aiming at neutrino physics and astrophysics and a search for phenomena predicted by theories beyond the standard model (BSM). The excellent imaging capability of Liquid Argon Time Projection Chamber (LArTPC) technology, particle tracking and identification utilized in the Far Detector, as well as the Far Detector size and underground placement, allow the experiment to achieve high sensitivity to various rare processes. BSM theories predict the existence of baryon number non-conservation effects, in particular when the baryon number changes by 2. Here we discuss the sensitivity of DUNE to neutron-antineutron oscillation. With full event simulation and reconstruction using the LArSoft package, we have investigated the background to potential signal events from atmospheric neutrino interactions and particle misidentification, and utilized machine learning techniques to enhance the discrimination between signal and background. The methodologies being developed for a high-sensitivity search for neutron-antineutron oscillation in DUNE can also be demonstrated with the currently running MicroBooNE LArTPC. We discuss progress on demonstrating the developed techniques with the first-ever search for neutron-antineutron oscillation in a LArTPC using MicroBooNE data.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Evolution of eggshell structure in relation to nesting ecology in non-avian reptiles
Amniotic eggs are multifunctional structures that enabled early tetrapods to colonize the land millions of years ago, and are now the reproductive mode of over 70% of all terrestrial amniotes. Eggshell morphology is at the core of animal survival, mediating the interactions between embryos and their environment, and has evolved into a massive diversity of forms and functions in modern reptiles. These functions are critical to embryonic survival and may serve as models for new antimicrobial and/or breathable membranes. However, we still lack critical data on the basic structural and functional properties of eggs, particularly of reptiles. Here, we first characterized egg shape, shell thickness, porosity, and mineralization of eggs from 91 reptile species using optical images, scanning electron microscopy, and micro computed tomography, and collected data on nesting ecology from the literature. We then used comparative analyses to test hypotheses on the selective pressures driving their evolution. We hypothesized that eggshell morphology has evolved to protect shells from physical damage and desiccation, and, in support, found a positive relationship between thickness and precipitation, and a negative relationship between porosity and temperature. Although mineralization varied extensively, it was not correlated with nesting ecology variables. Ancestral state reconstructions show thinning and increased porosity over evolutionary time in squamates, but the opposite in turtles and crocodilians. Egg shape, size, porosity and calcification were correlated, suggesting potential structural or developmental tradeoffs. This study provides new data and insights into the morphology and evolution of reptile eggs, and raises numerous questions for additional research.
59 BASIC BIOLOGICAL SCIENCES↗
Austenitic parent grain reconstruction in martensitic steel using deep learning
In this work we develop a deep convolutional architecture to estimate the prior austenite structure from observed martensite electron backscatter diffraction micrographs. A novel data augmentation strategy randomizes the global reference coordinate system which makes it possible to train our model from only four micrographs. The model is much faster than algorithmic approaches and generalizes well when applied to micrographs of a different material. Empirical evidence suggests the efficacy of the model depends on the scale of the microstructure and receptive field of the vision model. Furthermore, this work demonstrates that modern computer vision approaches are well suited for capturing complex spatial-orientation patterns present in orientation imaging micrographs.
36 MATERIALS SCIENCE↗
Intrinsic and induced quantum quenches for enhancing qubit-based quantum noise spectroscopy
Quantum sensing protocols that exploit the dephasing of a probe qubit are powerful and ubiquitous methods for interrogating an unknown environment. They have a variety of applications, ranging from noise mitigation in quantum processors, to the study of correlated electron states. Here, we discuss a simple strategy for enhancing these methods, based on the fact that they often give rise to an inadvertent quench of the probed system: there is an effective sudden change in the environmental Hamiltonian at the start of the sensing protocol. These quenches are extremely sensitive to the initial environmental state, and lead to observable changes in the sensor qubit evolution. We show how these new features give access to environmental response properties. This enables methods for direct measurement of bath temperature, and for detecting non-thermal equilibrium states. We also discuss how to deliberately control and modulate this quench physics, which enables reconstruction of the bath spectral function. Extensions to non-Gaussian quantum baths are also discussed, as is the application of our ideas to a range of sensing platforms (e.g., nitrogen-vacancy (NV) centers in diamond, semiconductor quantum dots, and superconducting circuits).
59 BASIC BIOLOGICAL SCIENCES↗
Angularly resolved spectral reconstruction of x rays via filter pack attenuation
We have designed a new filter pack array to measure angular variations in x-ray spectra during a single shot. The filter pack was composed of repeating identical columns of aluminum and copper filters of varying thicknesses. These columns were located at different positions to measure the spectrum at each corresponding angle. This array was utilized in an experiment to measure the energy evolution of betatron x rays in a laser wakefield accelerator by curving the wakefield with a transverse density gradient, streaking the x rays across the array in front of an x-ray charge-coupled device (CCD) camera. After subtracting the background and “flattening” the image to remove spatial nonuniformities, a critical energy was calculated for each position that produced the best agreement with the measured signal. There was a clear change in critical energy with angle, shedding light on the dynamics of the electrons that traveled through the accelerator. Furthermore, these angles correspond to distinct emission times, covering a timescale of tens of picoseconds. The filter pack was capable of recovering these angular details without the impact of errors introduced by shot-to-shot variability.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Novel imaging technique for thermal neutrons using a fast optical camera
A novel imaging technique for thermal neutrons using a fast optical camera is presented. Thermal neutrons are reacted with 6 Lithium to produce a pair of 2.73 MeV tritium and 2.05 MeV alpha particles, which in turn interact in a thin layer of LYSO crystal scintillator to produce a localized flash of light. These photons are directed by a pair of lenses to a micro-channel plate intensifier, and its output is connected to the optical camera, TPX3CAM. The results from the camera are reconstructed through a custom algorithm. Various cutting parameters were found through data analysis to eliminate the background, and they were shown effective in matching the simulated rate of the neutron source. The system is fast with 40 ns decay time and allows free-space light collection, both vastly enhances flexibility of neutron detection.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Mutual modulation between surface chemistry and bulk microstructure within secondary particles of nickel-rich layered oxides
Abstract Surface lattice reconstruction is commonly observed in nickel-rich layered oxide battery cathode materials, causing unsatisfactory high-voltage cycling performance. However, the interplay of the surface chemistry and the bulk microstructure remains largely unexplored due to the intrinsic structural complexity and the lack of integrated diagnostic tools for a thorough investigation at complementary length scales. Herein, by combining nano-resolution X-ray probes in both soft and hard X-ray regimes, we demonstrate correlative surface chemical mapping and bulk microstructure imaging over a single charged LiNi 0.8 Mn 0.1 Co 0.1 O 2 (NMC811) secondary particle. We reveal that the sub-particle regions with more micro cracks are associated with more severe surface degradation. A mechanism of mutual modulation between the surface chemistry and the bulk microstructure is formulated based on our experimental observations and finite element modeling. Such a surface-to-bulk reaction coupling effect is fundamentally important for the design of the next generation battery cathode materials.
25 ENERGY STORAGE↗
Ptychographic wavefront characterization for single-particle imaging at x-ray lasers
A well-characterized wavefront is important for many x-ray free-electron laser (XFEL) experiments, especially for single-particle imaging (SPI), where individual biomolecules randomly sample a nanometer region of highly focused femtosecond pulses. We demonstrate high-resolution multiple-plane wavefront imaging of an ensemble of XFEL pulses, focused by Kirkpatrick–Baez mirrors, based on mixed-state ptychography, an approach letting us infer and reduce experimental sources of instability. From the recovered wavefront profiles, we show that while local photon fluence correction is crucial and possible for SPI, a small diversity of phase tilts likely has no impact. Our detailed characterization will aid interpretation of data from past and future SPI experiments and provides a basis for further improvements to experimental design and reconstruction algorithms.
47 OTHER INSTRUMENTATION↗
Spatially resolved X-ray imaging and molecular characterisation of sulfur and iron in organic- and sulfur-rich hydrocarbon source mudstones
Sulfurisation of organic matter (OM) is a prominent preservation mechanism, however iron sulfide precipitation, particularly pyrite (FeS2), can counteract this mechanism. There is a dearth of high-resolution, spatially-resolved spectroscopic (redox) information on sulfur and iron inventories within organic-rich rocks that would improve our understanding of prevailing environmental conditions during deposition. Here, state-of-the-art synchrotron-based X-ray absorption and fluorescence analyses of key organic- and sulfur-rich mudstones demonstrate the potential of these techniques to non-destructively map and produce detailed spectroscopic information. Detailed high-resolution analyses (μm- to mm-scale) reveal the presence of widespread sulfurised OM in the Blackstone Band of the Kimmeridge Clay Formation, in line with a persistence of euxinia over a long temporal span and low reactive iron input, facilitating the preservation of OM through sulfurisation. In contrast, the presence of sulfurised OM was transitional in the Monterey Formation, consistent with fluctuating water column redox conditions, and is less significant in the Whitby Mudstone Formation, likely due to the high reactive iron concentrations outcompeting sulfurised OM formation. Analyses of sulfur species using model compounds further indicate that the Whitby Formation is strongly enriched in inorganic reduced sulfur minerals, while both the Kimmeridge Clay and Monterey Formations are dominated by organic sulfur species. These synchrotron-based observations improve our understanding of environmental conditions during the time of deposition of these mudstones and thus show great promise in the study of organic-rich sediments, especially in allowing their depositional settings to be more accurately reconstructed.
Kimmeridge Clay Formation↗
CAMIS: A Cylindrical Active Mask Imaging System
Detecting and locating radiological and nuclear materials at distances of 10 m or more in urban and cluttered environments continues to pose challenges in nuclear security and proliferation detection. Previous approaches have focused on large-area radiation imaging using planar configurations of detectors and passive masks. However, these approaches suffer from limitations such as limited field-of-view (FOV) and reduced detection efficiency due to absorption in the mask. To address these limitations, we have developed the cylindrical active mask imaging system (CAMIS). This system comprises 128 NaI(Tl) (10 cm)3 detectors. These detectors are arranged in a cylindrical configuration, enabling gamma-ray imaging with a full 360° azimuthal FOV. The active mask elements within the system are arranged in a pseudorandom configuration, providing unique encoding for all incident directions within the FOV. CAMIS offers an effective detection area of approximately 1 m2 across the entire 360° FOV in the horizontal plane, achieving a mean angular resolution of 10.9° in the azimuthal direction and 12.9° in the polar direction measured by taking the full-width at half-maximum (FWHM) of a cross-section at the maximum reconstructed intensity.
Lamb, C↗