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At least 271 records · Page 15

TomoPyUI : a user-friendly tool for rapid tomography alignment and reconstruction

The management and processing of synchrotron and neutron computed tomography data can be a complex, labor-intensive and unstructured process. Users devote substantial time to both manually processing their data ( i.e. organizing data/metadata, applying image filters etc. ) and waiting for the computation of iterative alignment and reconstruction algorithms to finish. In this work, we present a solution to these problems: TomoPyUI , a user interface for the well known tomography data processing package TomoPy . This highly visual Python software package guides the user through the tomography processing pipeline from data import, preprocessing, alignment and finally to 3D volume reconstruction. The TomoPyUI systematic intermediate data and metadata storage system improves organization, and the inspection and manipulation tools (built within the application) help to avoid interrupted workflows. Notably, TomoPyUI operates entirely within a Jupyter environment. Herein, we provide a summary of these key features of TomoPyUI , along with an overview of the tomography processing pipeline, a discussion of the landscape of existing tomography processing software and the purpose of TomoPyUI , and a demonstration of its capabilities for real tomography data collected at SSRL beamline 6-2c.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

The magnetic structure of long-wavelength magnetohydrodynamic modes in current-carrying stellarator plasmas

Magnetic field fluctuations are observed in current-carrying stellarator plasmas when the rotational transform is close to a rational value at the edge of the plasma. At low plasma pressure, these fluctuations are associated with perturbed currents parallel to the equilibrium magnetic field lines. A model for these magnetohydrodynamic modes in a low-β, three-dimensional stellarator equilibria has been developed. A set of helical current filaments are constrained to mimic the structure of magnetic field lines on rational surfaces derived from three-dimensional (3D) equilibrium reconstructions. Transformation to straight field line coordinates then allows fitting of the poloidal magnetic sensor data to a single harmonic function, which fixes the modeled toroidal mode structure via the field line flow geometry. The developed procedure accurately captures phase and amplitude variation for m/n = 3/2, 3/1, and 4/1 modes in the 3D equilibria of the compact toroidal hybrid experiment.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Cosmic Ray Background Rejection with Wire-Cell LArTPC Event Reconstruction in the MicroBooNE Detector

For a large liquid-argon time-projection chamber (LArTPC) operating on or near the Earth’s surface to detect neutrino interactions, the rejection of cosmogenic background is a critical and challenging task because of the large cosmic-ray flux and the long drift time of the time-projection chamber. We introduce a superior cosmic background rejection procedure based on the Wire-Cell three-dimensional (3D) event reconstruction for LArTPCs. From an initial 1:20 000 neutrino to cosmic-ray background ratio, we demonstrate these tools on data from the MicroBooNE experiment and create a high-performance generic neutrino event selection with a cosmic contamination of 14.9% (9.7%) for a visible energy region greater than O(200) MeV. The neutrino interaction selection efficiency is 80.4% and 87.6% for inclusive ν μ charged-current and ν e charged-current interactions, respectively. Here, this significantly improved performance compared with existing reconstruction algorithms marks a major milestone toward reaching the scientific goals of LArTPC neutrino oscillation experiments operating near the Earth’s surface.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Reconstructing the Position and Intensity of Multiple Gamma-Ray Point Sources with a Sparse Parametric Algorithm

IEEE We present an experimental demonstration of Additive Point Source Localization (APSL), a sparse parametric imaging algorithm that reconstructs the 3D positions and activities of multiple gamma-ray point sources. Using a handheld gamma-ray detector array and up to four 8 μCi 137 Cs gamma-ray sources, we performed both source-search and source-separation experiments in an indoor laboratory environment. In the majority of the source-search measurements, APSL reconstructed the correct number of sources with position accuracies of ~20 cm and activity accuracies (unsigned) of ~20%, given measurement times of two to three minutes and distances of closest approach (to any source) of ~20 cm. In source-separation measurements where the detector could be moved freely about the environment, APSL was able to resolve two sources separated by 75 cm or more given only ~60 s of measurement time. In these source-separation measurements, APSL produced larger total activity errors of ~40%, but obtained source separation distances accurate to within 15 cm. We also compare our APSL results against traditional Maximum Likelihood-Expectation Maximization (ML-EM) reconstructions, and demonstrate improved image accuracy and interpretability using APSL over ML-EM. These results indicate that APSL is capable of accurately reconstructing gamma-ray source positions and activities using measurements from existing detector hardware.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

High-resolution cryo-EM reconstructions in the presence of substantial aberrations

Here, an analysis is performed of how uncorrected antisymmetric aberrations, such as coma and trefoil, affect cryo-EM single-particle reconstruction (SPR) results, and an analytical formula quantifying information loss owing to their presence is inferred that explains why Fourier-shell coefficient-based statistics may report significantly overestimated resolution if these aberrations are not fully corrected. The analysis is validated with reference-based aberration refinement for two cryo-EM SPR data sets acquired with a 200 kV microscope in the presence of coma exceeding 40 µm, and 2.3 and 2.7 Å reconstructions for 144 and 173 kDa particles, respectively, were obtained. The results provide a description of an efficient approach for assessing information loss in cryo-EM SPR data acquired in the presence of higher order aberrations, and address inconsistent guidelines regarding the level of aberrations that is acceptable in cryo-EM SPR experiments.

3D reconstruction and image processing↗

Super-resolution model for overlapping peak detection and improved spatial resolution in high-energy diffraction microscopy

Reconstruction quality in Far-field High-Energy Diffraction Microscopy (FF-HEDM) is limited by the spatial resolution of area detectors and the frequent occurrence of overlapping diffraction spots. To address these challenges, we developed a super-resolution (SR) framework using convolutional neural networks (CNNs) to recreate 2D diffraction peaks at up to ×8 resolution from raw detector data. A specialized simulation tool was created to generate synthetic training datasets with varying degrees of peak overlap. Integrated into the Microstructural Imaging using Diffraction Analysis Software (MIDAS), the SR model improves the spatial accuracy and precision of 3D grain reconstruction by an order of magnitude. This approach provides a robust solution for investigation of complex micromechanical states and material classes where the analysis is limited by the presence of overlapping peaks. Furthermore, the methodology developed here can potentially be extended to other techniques that require sub-pixel accuracy for high-fidelity data analysis.

High-energy diffraction microscopy↗

Relation Between the 3D-Geometry of the Coronal Wave and Associated CME During the 26 April 2008 Event

We study the kinematical characteristics and 3D geometry of a large-scale coronal wave that occurred in association with the 26 April 2008 flare-CME event. The wave was observed with the EUVI instruments aboard both STEREO spacecraft (STEREO-A and STEREO-B) with a mean speed of approx 240 km/s. The wave is more pronounced in the eastern propagation direction, and is thus, better observable in STEREO-B images. From STEREO-B observations we derive two separate initiation centers for the wave, and their locations fit with the coronal dimming regions. Assuming a simple geometry of the wave we reconstruct its 3D nature from combined STEREO-A and STEREO-B observations. We find that the wave structure is asymmetric with an inclination toward East. The associated CME has a deprojected speed of approx 750 +/- 50 km/s, and it shows a non-radial outward motion toward the East with respect to the underlying source region location. Applying the forward fitting model developed by Thernisien, Howard, and Vourlidas we derive the CME flux rope position on the solar surface to be close to the dimming regions. We conclude that the expanding flanks of the CME most likely drive and shape the coronal wave.

CMEs↗

Scintillation light in SBND: simulation, reconstruction, and expected performance of the photon detection system

SBND is the near detector of the Short-Baseline Neutrino program at Fermilab. Its location near to the Booster Neutrino Beam source and relatively large mass will allow the study of neutrino interactions on argon with unprecedented statistics. This paper describes the expected performance of the SBND photon detection system, using a simulated sample of beam neutrinos and cosmogenic particles. Its design is a dual readout concept combining a system of 120 photomultiplier tubes, used for triggering, with a system of 192 X-ARAPUCA devices, located behind the anode wire planes. Furthermore, covering the cathode plane with highly-reflective panels coated with a wavelength-shifting compound recovers part of the light emitted towards the cathode, where no optical detectors exist. We show how this new design provides a high light yield and a more uniform detection efficiency, an excellent timing resolution and an independent 3D-position reconstruction using only the scintillation light. Finally, the whole reconstruction chain is applied to recover the temporal structure of the beam spill, which is resolved with a resolution on the order of nanoseconds.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

3D Geolocation of Simulated Lightning Sources from Low-Earth Orbit

The recent removal of the Lightning Imaging Sensor from the International Space Station has left an observational gap in lightning detection from low-Earth orbit (LEO). However, new studies have demonstrated the potential for 3D geolocation of lightning sources using orbiting sensors. The Cubespark mission concept aims to take advantage of these developments by deploying a constellation of satellites with radio frequency (RF) sensors and optical imagers to not only map lightning locations, but also to collect bi-spectral flash images. These new capabilities include mapping storm charge structure, flash channel structure, and distinguishing microphysical processes throughout flash development, helping link microphysics and convective processes with overall flash and storm structure around the globe from LEO. In this study, we simulate lightning RF sources in the very high frequency (VHF) band, extrapolate their signals to space-based detection using an improved ionospheric model, and reconstruct their 3D locations using a time-of-arrival (TOA) minimization algorithm. Various constellation configurations, locations, and atmospheric conditions are considered in order to identify and quantify the three main sources of geolocation error: geometric, ionospheric, and instrumental effects. The promising results of this study emphasize the potential of space-based 3D lightning mapping under diverse conditions. 3D resolution is shown to be better than 1-2 km in many cases, enabling new global applications in meteorology and climate sciences. Here we present a selection of these geolocation results as seen from space alongside recent advancements, paving the way for a future generation of LEO lightning mappers.

CubeSpark↗

Orthographic Stereo Correlator on the Terrain Model for Apollo Metric Images

A stereo correlation method on the object domain is proposed to generate the accurate and dense Digital Elevation Models (DEMs) from lunar orbital imagery. The NASA Ames Intelligent Robotics Group (IRG) aims to produce high-quality terrain reconstructions of the Moon from Apollo Metric Camera (AMC) data. In particular, IRG makes use of a stereo vision process, the Ames Stereo Pipeline (ASP), to automatically generate DEMs from consecutive AMC image pairs. Given camera parameters of an image pair from bundle adjustment in ASP, a correlation window is defined on the terrain with the predefined surface normal of a post rather than image domain. The squared error of back-projected images on the local terrain is minimized with respect to the post elevation. This single dimensional optimization is solved efficiently and improves the accuracy of the elevation estimate.

Terrain Model↗

Three-dimensional bubble reconstruction in high burnup UO 2

In light water reactor (LWR) UO 2 fuels, the evolution of volatile fission products is one of the critical areas of fuel behavior that is yet to be fully understood. In UO 2 irradiated to high burnups, it is well known that most released fission gases come from the central region of the fuel as opposed to the highly porous high burnup structure (HBS) on the periphery of the pellets. However, fuels with and without interconnected bubble networks at the fuel center showed high to moderate release fractions, which conceals the mechanisms responsible for the gas release in the latter scenario. In this work, focused ion beam tomography was used to investigate the three-dimensional bubble structure in an irradiated LWR UO 2 fuel pellet with high degree of fission gas retention so that the degree of bubble interconnection could be assessed. Six radial locations with different burnups and temperatures were serially sectioned and imaged to reconstruct the three-dimensional bubble structure. As expected, the highest porosity was observed at the periphery of the fuel (HBS). Here, the porosity then decreased towards the pellet center, except for the centermost location. This location had a slightly higher porosity than its adjacent mid-radial location, which was attributed to the temperature difference between the two locations. This study provides a first-time volumetric evaluation of the porosity at different radial locations on a UO 2 fuel pellet. During this investigation, no significant bubble interconnection was noted at any of the six radial locations.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Mafic explosive volcanism at Llaima Volcano: 3D x-ray microtomography reconstruction of pyroclasts to constrain shallow conduit processes

Abstract Mafic volcanic activity is dominated by effusive to mildly explosive eruptions. Plinian and ignimbrite-forming mafic eruptions, while rare, are also possible; however, the conditions that promote such explosivity are still being explored. Eruption style is determined by the ability of gas to escape as magma ascends, which tends to be easier in low-viscosity, mafic magmas. If magma permeability is sufficiently high to reduce bubble overpressure during ascent, volatiles may escape from the magma, inhibiting violent explosive activity. In contrast, if the permeability is sufficiently low to retain the gas phase within the magma during ascent, bubble overpressure may drive magma fragmentation. Rapid ascent may induce disequilibrium crystallization, increasing viscosity and affecting the bubble network with consequences for permeability, and hence, explosivity. To explore the conditions that promote strongly explosive mafic volcanism, we combine microlite textural analyses with synchrotron x-ray computed microtomography of 10 pyroclasts from the 12.6 ka mafic Curacautín Ignimbrite (Llaima Volcano, Chile). We quantify microlite crystal size distributions (CSD), microlite number densities, porosity, bubble interconnectivity, bubble number density, and geometrical properties of the porous media to investigate the role of magma degassing processes at mafic explosive eruptions. We use an analytical technique to estimate permeability and tortuosity by combing the Kozeny-Carman relationship, tortuosity factor, and pyroclast vesicle textures. The groundmass of our samples is composed of up to 44% plagioclase microlites, > 85% of which are < 10 µm in length. In addition, we identify two populations of vesicles in our samples: (1) a convoluted interconnected vesicle network produced by extensive coalescence of smaller vesicles (> 99% of pore volume), and (2) a population of very small and completely isolated vesicles (< 1% of porosity). Computed permeability ranges from 3.0 × 10 −13 to 6.3 × 10 −12 m 2 , which are lower than the similarly explosive mafic eruptions of Tarawera (1886; New Zealand) and Etna (112 BC; Italy). The combination of our CSDs, microlite number densities, and 3D vesicle textures evidence rapid ascent that induced high disequilibrium conditions, promoting rapid syn-eruptive crystallization of microlites within the shallow conduit. We interpret that microlite crystallization increased viscosity while simultaneously forcing bubbles to deform as they grew together, resulting in the permeable by highly tortuous network of vesicles. Using the bubble number densities for the isolated vesicles (0.1-3 −3 × 10 4 bubbles per mm 3 ), we obtain a minimum average decompression rate of 1.4 MPa/s. Despite the textural evidence that the Curacautín magma reached the percolation threshold, we propose that rapid ascent suppressed outgassing and increased bubble overpressures, leading to explosive fragmentation. Further, using the porosity and permeability of our samples, we estimated that a bubble overpressure > 5 MPa could have been sufficient to fragment the Curacautín magma. Other mafic explosive eruptions report similar disequilibrium conditions induced by rapid ascent rate, implying that syn-eruptive disequilibrium conditions may control the explosivity of mafic eruptions more generally.

Valdivia, Pedro↗

From irregular to regular eutectic growth in the Al-Al 3 Ni system: In situ observations during directional solidification

Here we investigate the irregular eutectic growth dynamics of the Al-Al 3 Ni alloy, in which one of the solid phases (Al 3 Ni) grows faceted from the liquid. Leveraging in situ optical microscopy and synchrotron transmission x-ray microscopy, we address the question of the degree of coupling between Al and Al 3 Ni at the growth front and that of the shape of the microstructures left behind in the bulk solid during directional solidification. Real-time optical observations bring evidence for a morphological transition from a eutectic-grain dependent, irregular eutectic growth at low solidification velocity V (typically 1 μm s -1 ), to a weakly anisotropic, regular growth at higher V ( reaching 10 μm s -1 ). Unprecedented x-ray nano-imaging of the solid–liquid interface, and 3D characterization of the growth patterns, were made possible by a new DS setup at Brookhaven National Laboratory’s NSLS-II. At low V, the leading tips of partly faceted Al 3 Ni crystals are observed to grow not far ahead of the Al growth front. Correlating in situ images and postmortem 3D tomographic reconstructions reveals that the presence of faceted and non-faceted regions of Al 3 Ni crystals in the solid is a direct consequence of coupling and decoupling during DS, respectively. Upon increasing V, the lead distance of Al 3 Ni vanishes, and the shape of Al 3 Ni ceases to be governed by faceted growth. These observations cast light onto the basic mechanisms (faceted growth, diffusive coupling, and the dynamics of trijunctions) governing a faceted to rod-like transition upon increasing V in the Al 3 Ni system, with broad implications to a large class of irregular eutectics.

36 MATERIALS SCIENCE↗

Tracking nickel oxide reduction in solid oxide cells via ex-situ ptychographic nano-tomography

In solid oxide cell (SOC) electrodes, nickel oxide reduction is a fundamental step occurring during the initial stages of cell operation. The reduction procedure is considered to be crucial in producing the final fuel electrode microstructure. This work studies the reduction reaction occurring in a SOC fuel electrode by means of X-ray ptychographic nanotomography. The same microstructure is analyzed in its pristine state and after 1 h of reduction at 850 °C, in dry hydrogen. The microstructure evolution is discussed in terms of changes in volume fractions, surface areas, and connectivity of the different constituent materials. The pore network in the unreduced cermet is revealed to be fully isolated, implying that reduction proceeds inwards from the edges of the sample towards the center. For the given experimental conditions we report that reduction is complete after 1 h of treatment but the resulting nickel network is not yet percolated and detached from the yttria-stabilized zirconia.

25 ENERGY STORAGE↗

Calculating the grain boundary inclination of voxelated grain structures using a smoothing algorithm

We have developed a flexible method for calculating the grain boundary (GB) inclinations of voxelated grain structure data using smoothing algorithms. We compared the performance of four algorithms: the linear interpolation, Allen–Cahn, level-set, and vertex algorithms. We assessed their accuracy using 2D and 3D cases with known inclinations. The vertex algorithm provided the best balance between accuracy and efficiency for 2D structures while the linear interpolation algorithm provided the best balance for 3D structures. We compared the GB inclinations calculated using our smoothing method on a 3D high energy X-ray diffraction microscopy (HEDM) dataset to those determined by meshing the GBs. The two approaches determined similar GB plane distributions, though they varied significantly at triple junctions. In conclusion, the smoothing method was demonstrated for two sources of 3D voxelated grain structures: HEDM data and results from Monte Carlo Potts grain growth simulations.

36 MATERIALS SCIENCE↗

Shining light on nanoscale ‘vine-on-stick’ eutectic structures in the Al-Ce-Ni system

Multiphase eutectics often comprise entangled solid phases with nanoscale periodicity, making it difficult to unravel their 3D connectivity using conventional 2D techniques. Among such systems, the three-phase eutectic Al-Al 11 Ce 3 -Al 3 Ni stands out for its ultrafine (∼100 nm) interphase spacing and promising creep resistance, yet its microstructure remains relatively unexplored despite its potential for high-temperature applications. Here, we use scanning hard X-ray microscopy with an unprecedented ∼10 nm pixel size to resolve its 3D morphology. Reconstructions reveal a novel “vine-on-stick” motif, wherein Al 11 Ce 3 wraps around Al 3 Ni pillars. Analysis of phase tortuosities confirms that Al 11 Ce 3 exhibits more convoluted morphologies than Al 3 Ni. No orientation relationship was observed between the two intermetallics, suggesting that growth is controlled by local solute gradients rather than epitaxy. Fragmentation of intermetallics along their longitudinal axis suggests a Rayleigh-type breakup mechanism in solid state. The “vine-on-stick” pattern may generalize to other alloy systems with variable interfacial anisotropies and low mutual solubilities.

36 MATERIALS SCIENCE↗

Multibeam Electron Diffraction

One of the primary uses for transmission electron microscopy (TEM) is to measure diffraction pattern images in order to determine a crystal structure and orientation. In nanobeam electron diffraction (NBED), we scan a moderately converged electron probe over the sample to acquire thousands or even millions of sequential diffraction images, a technique that is especially appropriate for polycrystalline samples. However, due to the large Ewald sphere of TEM, excitation of Bragg peaks can be extremely sensitive to sample tilt, varying strongly for even a few degrees of sample tilt for crystalline samples. In this paper, we present multibeam electron diffraction (MBED), where multiple probe-forming apertures are used to create multiple scanning transmission electron microscopy (STEM) probes, all of which interact with the sample simultaneously. We detail designs for MBED experiments, and a method for using a focused ion beam to produce MBED apertures. We show the efficacy of the MBED technique for crystalline orientation mapping using both simulations and proof-of-principle experiments. We also show how the angular information in MBED can be used to perform 3D tomographic reconstruction of samples without needing to tilt or scan the sample multiple times. Finally, we also discuss future opportunities for the MBED method.

47 OTHER INSTRUMENTATION↗