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At least 721 records · Page 40

A Scalable Pipeline for Gigapixel Whole Slide Imaging Analysis on Leadership Class HPC Systems

Whole Slide Imaging (WSI) captures microscopic details of a patient's histopathological features at multiple res-olutions organized across different levels. Images produced by WSI are gigapixel-sized, and saving a single image in memory requires a few gigabytes which is scarce since a complicated model occupies tens of gigabytes. Performing a simple met-ric operation on these large images is also expensive. High-performance computing (HPC) can help us quickly analyze such large images using distributed training of complex deep learning models. One popular approach in analyzing these images is to divide a WSI image into smaller tiles (patches) and then train a simpler model with these reduced-sized but large numbers of patches. However, we need to solve three pre-processing challenges efficiently for pursuing this patch-based approach. 1) Creating small patches from a high-resolution image can result in a high number (hundreds of thousands per image) of patches. Storing and processing these images can be challenging due to a large number of I/O and arithmetic operations. To reduce I/Oand memory accesses, an optimal balance between the size and number of patches must exist to reduce I/O and memory accesses. 2) WSI images may have tiny annotated regions for cancer tissue and a significant portion with normal and fatty tissues; correct patch sampling should avoid dataset imbalance. 3) storing and retrieving many patches to and from disk storage might incur I/O latency while training a deep learning model. An efficient distributed data loader should reduce I/O latency during the training and inference steps. This paper explores these three challenges and provides empirical and algorithmic solutions deployed on the Summit supercomputer hosted at the Oak Ridge Leadership Computing Facility.

Dash, Sajal↗

Improving the astrometric solution of the Hyper Suprime-Cam with anisotropic Gaussian processes

Context. We study astrometric residuals from a simultaneous fit of Hyper Suprime-Cam images. Aims. We aim to characterize these residuals and study the extent to which they are dominated by atmospheric contributions for bright sources. Methods. We used Gaussian process interpolation with a correlation function (kernel) measured from the data to smooth and correct the observed astrometric residual field. Results. We find that a Gaussian process interpolation with a von Kármán kernel allows us to reduce the covariances of astrometric residuals for nearby sources by about one order of magnitude, from 30 mas 2 to 3 mas 2 at angular scales of ~1 arcmin. This also allows us to halve the rms residuals. Those reductions using Gaussian process interpolation are similar to recent result published with the Dark Energy Survey dataset. We are then able to detect the small static astrometric residuals due to the Hyper Suprime-Cam sensors effects. We discuss how the Gaussian process interpolation of astrometric residuals impacts galaxy shape measurements, particularly in the context of cosmic shear analyses at the Rubin Observatory Legacy Survey of Space and Time.

79 ASTRONOMY AND ASTROPHYSICS↗

Using double pulse laser ablation in air to enhance the strength of laser-driven shocks

In the process of multi-pulse laser ablation, inter-pulse delay time, Δ t , is known to be an important parameter for maximizing ablation efficiency as well as impulse imparted to the target. In this work, using photon Doppler velocimetry, we show that for single pairs of colinear pulses (1064 nm, 8 ns, ∼ 60 J cm -2 per pulse) in air, the peak free surface velocity of the back surface of an aluminum target (125 µm thick) is increased, by a factor of nearly 3, when Δ t = 10 microseconds, compared with both pulses arriving simultaneously (Δ t = 0). Fast imaging of the ablation process suggests this enhancement is due to rarefaction of the contiguous air in the passage of the leading shock produced by ablation, which then in turn allows a larger fraction of the energy of the second pulse to reach the target surface. This interpretation is strengthened by additional experiments in which the two pulses do not overlap on the target surface, but the shock strength is nevertheless enhanced. Given a fixed energy budget this work suggests a prescription for maximizing laser-driven shock strength by judicious choice of inter-pulse delay.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Foliar functional traits from imaging spectroscopy across biomes in eastern North America

Summary Foliar functional traits are widely used to characterize leaf and canopy properties that drive ecosystem processes and to infer physiological processes in Earth system models. Imaging spectroscopy provides great potential to map foliar traits to characterize continuous functional variation and diversity, but few studies have demonstrated consistent methods for mapping multiple traits across biomes. With airborne imaging spectroscopy data and field data from 19 sites, we developed trait models using partial least squares regression, and mapped 26 foliar traits in seven NEON (National Ecological Observatory Network) ecoregions (domains) including temperate and subtropical forests and grasslands of eastern North America. Model validation accuracy varied among traits (normalized root mean squared error, 9.1–19.4%; coefficient of determination, 0.28–0.82), with phenolic concentration, leaf mass per area and equivalent water thickness performing best across domains. Across all trait maps, 90% of vegetated pixels had reasonable values for one trait, and 28–81% provided high confidence for multiple traits concurrently. Maps of 26 traits and their uncertainties for eastern US NEON sites are available for download, and are being expanded to the western United States and tundra/boreal zone. These data enable better understanding of trait variations and relationships over large areas, calibration of ecosystem models, and assessment of continental‐scale functional diversity.

Wang, Zhihui↗

High-Magnification Faraday Rotation Imaging and Analysis of X-pinch Implosion Dynamics

An X-pinch load driven by an intense current pulse (>100 kA in ~100 ns) can result in the formation of a small radius, runaway compressional micro-pinch. A micro-pinch is characterized by a hot (>1 keV), current-driven (>100 kA), high-density plasma column (near solid density) with a small neck diameter (1–10 μm), a short axial extent (<1 mm), and a short duration (.1 ns). With material pressures often well into the multi-Mbar regime, a micro-pinch plasma often radiates an intense, sub-ns burst of sub-keV to multi-keV x-rays. A low-density coronal plasma immediately surrounding the dense plasma neck could potentially shunt current away from the neck and thus reduce the magnetic drive pressure applied to the neck. To study the current distribution in the coronal plasma throughout the implosion process, a Faraday rotation imaging diagnostic (1064 nm) capable of producing simultaneous high-magnification polarimetric and interferometric images has been developed for the 1-MA, 100-ns MAIZE facility at the University of Michigan. Designed with a variable magnification (1–10&times;), this diagnostic achieves a spatial resolution of approximately 35 μm, which is useful for resolving the ~100-μm-scale coronal plasma region immediately surrounding the dense core. Combined with the corresponding interferogram, which provides the radial density distribution in the low-density coronal plasma, the measured rotation can be used to diagnose the delivery of the driver current, and thus the magnetic drive pressure, to the micro-pinch plasma as it approaches minimal radius. Using this technique on MAIZE, we have measured

Dowhan, G. V.↗

What Can Plastic Flow Fields Tell Us About Heat Sources in Deformation Processing?

We characterize primary (shape-change) and secondary (friction) deformation, and associated temperature fields, in metal cutting and forming processes, using in situ imaging and simulation. The experimental configurations enable access to the deformation zones and die contact-interfaces, for measuring deformation, temperature, and frictional drag. Infra-red thermography reveals that the plastic strain-rate field is an excellent proxy for the deformation-induced heat sources. Both spatially confined and diffuse strain-rate fields occur, depending on the initial workpiece deformation state. When the strain rate is confined, as in pre-hardened material, the temperature modeling is much simplified, as the heat source is also now localized. However complex, microstructure-driven deformation modes, like sinuous flow in annealed metals, result in spatially diffuse strain-rate and body heat sources, more challenging to analyze. Furthermore, our unified measurements should be of value for accurately estimating the fraction of plastic dissipation that is converted into heat in large-strain deformation processes.

36 MATERIALS SCIENCE↗

Ultrafast electron microscopy for probing magnetic dynamics

Abstract The spatial features of ultrafast changes in magnetic textures carry detailed information on microscopic couplings and energy transport mechanisms. Electrons excel in imaging such picosecond or shorter processes at nanometer length scales. We review the range of physical interactions that produce ultrafast magnetic contrast with electrons, and specifically highlight the recent emergence of ultrafast Lorentz transmission electron microscopy. From the fundamental processes involved in demagnetization at extremely short timescales to skyrmion-based devices, we show that ultrafast electron imaging will be a vital tool in solving pressing problems in magnetism and magnetic materials where nanoscale inhomogeneity, microscopic field measurement, non-equilibrium behavior or dynamics are involved. Graphic abstract

36 MATERIALS SCIENCE↗

High speed PLIF study of the Richtmyer–Meshkov instability upon re-shock

The Richtmyer–Meshkov instability (RMI) of a twice-shocked gas interface is researched using high-speed planar-laser induced fluorescence (PLIF) in the Wisconsin Shock Tube Laboratory’s vertical shock tube. The initial condition (IC) is a shear layer with broadband diffuse perturbations at the interface between a helium-acetone mixture and argon. This IC is accelerated by a shock of nominal strength M = 1.8, and then accelerated again by the transmitted shock that reflects off the end wall of the tube. An estimate of the light gas mole fraction is extracted from high-speed imaging using an iterative process that accounts for the nonlinear temperature dependence of the acetone’s fluorescence quantum yield (FQY) and absorption cross-section. A vorticity deposition model for the initial growth rate after reshock is compared with the Mikaelian model for re-shock. Previously used in literature, the number of generations is shown to naturally arise from a normalisation of the scalar transport equation. A self-similar analysis is then further performed using the mole fraction data to explore the evolution of the RMI after reshock and the higher order moments of the light gas mole fraction are compared with a proposed model.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Laboratory Demonstration of Collisionless Blob Formation via Laser-Produced Plasma Self-Focusing

Strongly localized, propagating plasma density structures that are capable of crossing magnetic field lines are known as “blobs.” Here we demonstrate a novel mechanism for the formation and propagation of an ion gyroradius-scale blob-cavity structure at the interface between a super-Alfvénic laser-produced plasma (LPP) and an ambient magnetized plasma. The LPP self-focuses along the edge of the diamagnetic cavity which results in a dense, jetlike structure as compared to ballistic motion. This collimated flow couples momentum to the ambient plasma through a collisionless process known as Larmor coupling. The Larmor electric fields locally displace the ambient ions forming a blob above the LPP flow. In the region between a gyrating blob and collimated LPP flow, a secondary cavity of expelled magnetic field forms. In conclusion, these findings are supported by particle-in-cell simulations that replicate the blob formation mechanism and provide insight to similar processes in space, astrophysical, and laboratory settings characterized by ion kinetic scales.

Fluorescence spectroscopy↗

Anion exchange and extraction chromatography tandem column isolation of zirconium-89 ( 89 Zr) from cyclotron bombarded targets using an automated fluidic platform

The long-lived positron emitter 89 Zr is a highly promising nuclide employed in diagnostic Positron Emission Tomography (PET) imaging. Methods of radiochemical processing to obtain 89 Zr for clinical use are traditionally performed with a single hydroxamate resin column. In this work, we present a tandem column purification method for the preparation of high-purity 89 Zr from cyclotron bombarded Y metal foils. The primary column is a macroporous, strongly basic anion exchange resin on styrene divinylbenzene co-polymer. The secondary microcolumn, with an internal volume of 33 µL, is packed with an extraction chromatography resin (ExCR) loaded with HDEHP. A condition of “inverted selectivity” is presented, wherein the 89 Zr elution from the primary column is synonymous with the load condition on the secondary column. The ability to transfer 89 Zr from one column to the next allows two sequential column clean-up methods to be performed prior to the final elution of the 89 Zr product. This approach assures delivery of very high purity 89 Zr . The tandem column purification process has been implemented into a prototype automated fluidic system. Optimization of the method is presented, followed by evaluation of the process using seven cyclotron bombarded Y metal foil targets. Once optimized, we found that 93.7±2.3% of the 89 Zr present in the foils was recovered in the secondary column elution fraction (0.8 M oxalic acid). Radiochromatograms of the product elution peaks enabled determination of full width at half-maximum (FWHM) and 89 Zr collection yields as a function of volume. Because of the small size of the secondary microcolumn, a 89 Zr product volume of ~0.28 mL is reported, which provides a substantially increased nuclide concentration over traditional methods. Finally, we evaluated the transchelation of the resulting 89 Zr oxalate product to deferoxamine mesylate (DFOM) salt. We observed effective specific activities (ESA) and bindable metals concentrations ([M B ]) that exceed those reported by the traditional single hydroxamate column method.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Mirostructure Characterization of Friction Consolidated Copper-Nickel using a Machine Learning Approach: Developing Process to Microstructure Associations

Friction consolidation (FC) is a solid phase processing approach where discrete material forms such as powders, chips, nuggets, etc. are densified via shear deformation. The precursors are placed in a billet container and brought in contact with a rotating tool that applying the desirable amount of normal force. Under the combined action of the rotation and normal pressure, the discrete precursor is consolidated through porosity reduction and shear deformation. FC is increasingly being studied as an attractive approach to manufacturing fully dense parts from powder forms owing to its ability to mix, alloy and consolidate difficult-to-process precursors in minimal number of process steps. Material consolidation and deformation in shear consolidation processes have been studied extensively previously for different material combinations previously. However, despite the extensive research in this area, understanding of the mechanistic processes in pore consolidation, deformation-induced mixing and material solubility during FC is still evolving. Material development using solid phase processing approaches such as FC is often performed based on research experience/education, which can be biased. Conventional analysis and simulation tools in this area tend to be successful only when material thermodynamic pathways and microstructural evolution sequences resulting from processing are clearly defined or known. They are not as effective for emerging advanced manufacturing technologies where material evolution pathways are not well established. The ability to predict optimal process parameters based on material chemistry and bulk properties is essential to accelerate materials design and processing, as are an understanding of the relevant structure-processing-property relationships. These structure-processing-property-performance relationships are at the core of materials science research. Microstructure characterization provides the link to these four core areas, often through visualizing material microstructure using imaging techniques. However, linking microstructure image data (i.e., micrographs) to variables of interest (e.g., processing parameters, material chemistry) in a reproducible, generalizable, and quantitative manner is a significant challenge. Typically, quantitatively linking image data to processing history relies on significant domain knowledge and manual or subject matter expert (SME)-heuristic based image analysis. Such an approach to image analysis has the potential to be biased, inefficient, and difficult to replicate.

36 MATERIALS SCIENCE↗

A thermally-limited bubble growth model for the relaxation time of superheated fuels

Here, we propose a novel approach to evaluate the relaxation time of vapor bubble growth in the context of the flash boiling of a superheated liquid. In alternative to the empirical correlation derived from superheated water experiments almost fifty years ago, the new model describes the thermally-dominated growth of vapor bubbles in terms that are dependent on the local Jakob number (the ratio of sensible heat to latent heat during phase change) and the number density of vapor bubbles. The model is tested by plugging the resulting relaxation time into the Homogenous Relaxation Model (HRM). Flash-boiling simulations carried out with HRM are compared with n-pentane (C 5 H 12 ) injection and boil-off experiments conducted with a real-size, axial-hole, transparent gasoline injector discharging into a constant-pressure vessel. The long-distance microscopy images from the experiments, processed to derive the projected liquid volume (PLV) of the spray, provide a unique set of time-resolved validation data for direct fuel injection simulations. At conditions ranging from flaring to mild and minimal flash boiling, we show that switching to the new relaxation time improves the agreement with the measured PLV profiles with respect to the standard empirical model. Particularly at flaring conditions, the predicted increase in gas cooling caused by rapid vapor production is shown to be more consistent with the observed boil-off.

42 ENGINEERING↗

Pointing stabilization of a 1 Hz high-power laser via machine learning

Abstract High-power lasers are vital for particle acceleration, imaging, fusion and materials processing, requiring precise control and high-energy delivery. Laser plasma accelerators (LPAs) demand laser positional stability at focus to ensure consistent electron beams in applications such as X-ray free-electron lasers and high-energy colliders. Achieving this stability is especially challenging for the low-repetition-rate lasers in current LPAs. We present a machine learning method that predicts and corrects laser pointing instabilities in real-time using a high-frequency pilot beam. By preemptively adjusting a correction mirror, this approach overcomes traditional feedback limits. Demonstrated on the BELLA petawatt laser operating at the terawatt level (30 mJ amplification), our method achieved root mean square pointing stabilization of 0.34 and 0.59 $\unicode{x3bc} \mathrm{rad}$ in the x and y directions, reducing jitter by 65% and 47%, respectively. This is the first successful application of predictive control for shot-to-shot stabilization in low-repetition-rate laser systems, paving the way for full-energy petawatt lasers and transformative advances across science, industry and security.

Amodio, Alessio↗

Nanomaterial Synthesis Insights from Machine Learning of Scientific Articles by Extracting, Structuring, and Visualizing Knowledge

Nanomaterials of varying compositions and morphologies are of interest for many applications from catalysis to optics, but the synthesis of nanomaterials and their scale-up are most often time-consuming and Edisonian processes. Information gleaned from the scientific literature can help inform and accelerate nanomaterials development, but again, searching the literature and digesting the information are time-consuming manual processes for researchers. To help address these challenges, here we developed scientific article-processing tools that extract and structure information from the text and figures of nanomaterials articles, thereby enabling the creation of a personalized knowledgebase for nanomaterials synthesis that can be mined to help inform further nanomaterials development. Starting with a corpus of ~35k nanomaterials-related articles, we developed models to classify articles according to the nanomaterial composition and morphology, extract synthesis protocols from within the articles’ text, and extract, normalize, and categorize chemical terms within synthesis protocols. We demonstrate the efficiency of the proposed pipeline on an expert-labeled set of nanomaterials synthesis articles, achieving 100% accuracy on composition prediction, 95% accuracy on morphology prediction, 0.99 AUC on protocol identification, and up to a 0.87 F1-score on chemical entity recognition. In addition to processing articles’ text, microscopy images of nanomaterials within the articles are also automatically identified and analyzed to determine the nanomaterials’ morphologies and size distributions. To enable users to easily explore the database, we developed a complementary browser-based visualization tool that provides flexibility in comparing across subsets of articles of interest. We use these tools and information to identify trends in nanomaterials synthesis, such as the correlation of certain reagents with various nanomaterial morphologies, which is useful in guiding hypotheses and reducing the potential parameter space during experimental design.

36 MATERIALS SCIENCE↗

Transforming microseismic clouds into near real-time visualization of the growing hydraulic fracture

SUMMARY Microseismic observations during unconventional reservoir stimulation are typically seen as a proxy for clusters of hydraulic fractures and the extent of the stimulated reservoir. Such straightforward interpretation is often misleading and fails to provide a physically reasonable image of the fracturing process. This paper demonstrates the application of a physics-based machine learning algorithm which enables a rapid and accurate fracture mapping from the microseismic data. Our training and validation data set relies on a history-matched geomechanical modelling workflow implemented in GEOS software for the Hydraulic Fracturing Test Site 1 (HFTS-1) project. For this study we augmented the simulated fracture growth through geostatistical modelling of induced seismicity, so that the synthetic microseismic catalogue matches the main statistical properties of the field observations. We formulated the problem of mapping the actual fracture in the clutter of events to parallel common video segmentation workflows: several past video frames (microseismic density snapshots) are passed through a deep convolutional network to classify whether a given voxel is associated with a fracture or intact rock. We found that for accurate fracture mapping, the network’s input and architecture must be augmented to incorporate the fluid injection parameters (pressure, rate, concentration of proppant, and location of the perforation within the cluster). The error rate for the network reached as little as 10 per cent of the fracture area, while a conventional microseismic interpretation approach yielded ∼300 per cent. Our approach also yields must faster predictions than conventional methods (minutes instead of weeks), and could enable engineers to make rapid decisions regarding engineering parameters (pumping rate, viscosity) in real time during stimulation.

58 GEOSCIENCES↗

MaNGA galaxy properties – II. A detailed comparison of observed and simulated spiral galaxy scaling relations

ABSTRACT We present a catalogue of dynamical properties for 2368 late-type galaxies from the MaNGA survey. The latter complements the catalogue of photometric properties for the same sample based on deep optical dark energy sky instrument legacy imaging survey (DESI) photometry processed with autoprof . Rotation curves (RCs), extracted by model-fitting H α velocity maps from the MaNGA Data Analysis Pipeline, extend out to 1.4 (1.9) Re for the primary (secondary) MaNGA samples, respectively. The RCs and ancillary MaNGA Pipe3D data products were used to construct various fundamental galaxy scaling relations that are also compared uniformly with similar relations from numerical investigation of a hundred astrophysical object (NIHAO) zoom-in simulations. Simulated NIHAO galaxies were found to broadly reproduce the observed MaNGA galaxy population for $\log (M_*/{\rm {\rm M}_{\odot })\, \gt\, 8.5}$. Some discrepancies remain, such as those pertaining to central stellar densities and the diversity of RCs due to strong feedback schemes. Also presented are spatially resolved scatters for the velocity-size-stellar mass (VRM*) structural relations using MaNGA and NIHAO samples. The scatter for these relations in the galaxian interiors is a consequence of the diversity of inner RC shapes, while scatter in the outskirts is dictated by the large range of stellar surface densities, which is itself driven by sporadic star formation. The detailed, spatially resolved scatter analysis highlights the complex interplay between local and global astrophysical processes and provides a strong constraint to numerical simulations.

Astronomy & Astrophysics↗

Ray-tracing image simulations of transparent objects with complex shape and inhomogeneous refractive index

Optical images of transparent three-dimensional objects can be different from a replica of the object’s cross section in the image plane, due to refraction at the surface or in the body of the object. Simulations of the object’s image are thus needed for the visualization and validation of physical models. We report ray tracing image simulations that achieved high physical fidelity, reproducing optical behaviors and image features not rendered in previous studies. We replicated brightfield microscopy images of drops with complex shapes, and images of pressure and shock waves traveling inside them. For high physical fidelity, the simulations must replicate the spatial and angular distribution of illumination rays, and both the experiment and the simulation must be designed for accurate optical modeling. The simulations are highly sensitive to the properties of the drops and can be used to diagnose and refine fluid dynamics models. The simulated images can also be optimized to extract multiple 3D properties from experimental images. Compared to specialized single-shot 3D imaging methods, this approach has the advantage that it preserves the experimental simplicity, the high resolution, and the visual interpretability characteristic to basic optical imaging. The techniques introduced here are directly applicable to optical microscopy, so they can be used in other fields, such as microfluidics and biology, to expand the type and the accuracy of three-dimensional information that can be extracted from basic optical images.

Cavitation↗