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At least 613 records · Page 34

Comparison of automated chemical-guided segmentation and human annotation of soil organic matter in X-ray microcomputed tomography imaging in contrasted soil types

Soil organic matter (OM) formation and persistence is strongly influenced by the spatial distribution of organic substrates and microscale soil heterogeneity by dictating OM accessibility to microorganisms. However, traditional size and/or density fractionation techniques disrupt aggregate architecture, eliminating spatial information needed to fully understand intra-aggregate OM distribution. To quantify three-dimensional OM spatial distribution and automate segmentation in X-ray microcomputed tomography (µCT) imaging without human annotation bias, we developed an iodine gas vapor (I2) based staining workflow that eliminates labor-intensive manual annotation while maintaining segmentation accuracy, using aggregates from four taxonomically diverse soils (Xerofluvent, Haploxeroll Sphagnofibrist, Palehumult) with an 8-fold range of soil organic carbon. Human annotation of 10 µCT slices by the experienced and inexperienced annotators resulted in variations up to 3% in the Dice similarity coefficient (DSC), reflecting a degree of inherent subjectivity of manual labeling. Such inconsistencies are expected to compound as the number of manually annotated slices increases. Dual-energy µCT imaging at 33.1 keV (below the iodine (I) K-edge) and 33.2 keV (above the I K-edge) was used to resolve aggregate microstructure following I2 staining. The automated image subtraction pipeline identified OM regions by the I Kedge induced brightness increases, achieving DSC values of 0.58–0.83 relative to an experienced annotator. Sensitivity analyses revealed that the reconstruction alpha value—optimized via the open-source tool TomocuPy—and the 3D registration slice count were the primary determinants of accuracy, providing a novel benchmark for dual-energy soil imaging. The pipeline without GPU acceleration achieved 9.6 to 43.2 times faster than manual annotation. Using GPU-accelerated image post-processing and affine transformation matrices, the pipeline successfully segmented OM elements for large-scale datasets (3232×3232 pixel, 2048 slices) within ~5200 s from raw file acquisition to segmented output. The high-throughput approach enables the quantification of OM spatial distribution across diverse and heterogeneous soil.

Soil microbial biomass↗

Foundations of machine learning for low-temperature plasmas: methods and case studies

Abstract Machine learning (ML) and artificial intelligence have proven to be an invaluable tool in tackling a vast array of scientific, engineering, and societal problems. The main drivers behind the recent proliferation of ML in practically all aspects of science and technology can be attributed to: (a) improved data acquisition and inexpensive data storage; (b) exponential growth in computing power; and (c) availability of open-source software and resources that have made the use of state-of-the-art ML algorithms widely accessible. The impact of ML on the field of low-temperature plasmas (LTPs) could be particularly significant in the emerging applications that involve plasma treatment of complex interfaces in areas ranging from the manufacture of microelectronics and processing of quantum materials, to the LTP-driven electrification of the chemical industry, and to medicine and biotechnology. This is primarily due to the complex and poorly-understood nature of the plasma-surface interactions in these applications that pose unique challenges to the modeling, diagnostics, and predictive control of LTPs. As the use of ML is becoming more prevalent, it is increasingly paramount for the LTP community to be able to critically analyze and assess the concepts and techniques behind data-driven approaches. To this end, the goal of this paper is to provide a tutorial overview of some of the widely-used ML methods that can be useful, amongst others, for discovering and correlating patterns in the data that may be otherwise impractical to decipher by human intuition alone, for learning multivariable nonlinear data-driven prediction models that are capable of describing the complex behavior of plasma interacting with interfaces, and for guiding the design of experiments to explore the parameter space of plasma-assisted processes in a systematic and resource-efficient manner. We illustrate the utility of various supervised, unsupervised and active learning methods using LTP datasets consisting of commonly-available, information-rich measurements (e.g. optical emission spectra, current–voltage characteristics, scanning electron microscope images, infrared surface temperature measurements, Fourier transform infrared spectra). All the ML demonstrations presented in this paper are carried out using open-source software; the datasets and codes are made publicly available. The FAIR guiding principles for scientific data management and stewardship can accelerate the adoption and development of ML in the LTP community.

Physics↗

Using onset times from frequent seismic surveys to understand fluid flow at the Peace River Field, Canada

With our limited knowledge of the relationship between changes in the state of an aquifer or reservoir and the corresponding changes in the elastic moduli, that is the rock physics model, hampers the effective use of time-lapse seismic observations for estimating flow properties within the Earth. A central problem is the complicated dependence of the magnitude of time-lapse changes on the saturation, pressure, and temperature changes within an aquifer or reservoir. We describe an inversion methodology for reservoir characterization that uses onset times, the calendar time of the change in seismic attributes, rather than the magnitude of the changes. We find that onset times are much less sensitive than magnitudes to the rock physics model used to relate time-lapse observations to changes in saturation, temperature and fluid pressure. We apply the inversion scheme to observations from daily monitoring of enhanced oil recovery at the Peace River field in Canada. An array of 1492 buried hydrophones record seismic signals from 49 buried sources. Time-shifts for elastic waves traversing the reservoir are extracted from the daily time-lapse cubes. In our analysis 175 images of time-shifts are transformed into a single map of onset times, leading to a substantial reduction in the volume of data. These observations are used in conjunction with bottom hole pressure data to infer the initial conditions prior to the injection, and to update the reservoir permeability model. The combination of a global and local inversion scheme produces a collection of reservoir models that are best described by three clusters. The updated model leads to a nearly 70 percent reduction in seismic data misfit. The final set of solutions successfully predict the observed normalized pressure history during the soak and flow-back into the wells between 82 and 175 days into the cyclic steaming operation.

58 GEOSCIENCES↗

Rapid detection of rare events from in situ X-ray diffraction data using machine learning

High-energy X-ray diffraction methods can non-destructively map the 3D microstructure and associated attributes of metallic polycrystalline engineering materials in their bulk form. These methods are often combined with external stimuli such as thermo-mechanical loading to take snapshots of the evolving microstructure and attributes over time. However, the extreme data volumes and the high costs of traditional data acquisition and reduction approaches pose a barrier to quickly extracting actionable insights and improving the temporal resolution of these snapshots. This article presents a fully automated technique capable of rapidly detecting the onset of plasticity in high-energy X-ray microscopy data. The technique is computationally faster by at least 50 times than the traditional approaches and works for data sets that are up to nine times sparser than a full data set. This new technique leverages self-supervised image representation learning and clustering to transform massive data sets into compact, semantic-rich representations of visually salient characteristics ( e.g. peak shapes). These characteristics can rapidly indicate anomalous events, such as changes in diffraction peak shapes. It is anticipated that this technique will provide just-in-time actionable information to drive smarter experiments that effectively deploy multi-modal X-ray diffraction methods spanning many decades of length scales.

Zheng, Weijian↗

Spatial Heterodyne Raman Spectrometer (SHRS) for In Situ Chemical Sensing Using Sapphire and Silica Optical Fiber Raman Probes

A spatial heterodyne Raman spectrometer (SHRS), constructed using a modular optical cage and lens tube system, is described for use with a commercial silica and a custom single-crystal (SC) sapphire fiber Raman probe. The utility of these fiber-coupled SHRS chemical sensors is demonstrated using 532 nm laser excitation for acquiring Raman measurements of solid (sulfur) and liquid (cyclohexane) Raman standards as well as real-world, plastic-bonded explosives (PBX) comprising 1,3,5- triamino- 2,4,6- trinitrobenzene (TATB) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) energetic materials. The SHRS is a fixed grating-based dispersive interferometer equipped with an array detector. Each Raman spectrum was extracted from its corresponding fringe image (i.e., interferogram) using a Fourier transform method. Raman measurements were acquired with the SHRS Littrow wavelength set at the laser excitation wavelength over a spectral range of ∼1750 cm −1 with a spectral resolution of ∼8 cm −1 for sapphire and ∼10 cm −1 for silica fiber probes. The large aperture of the SHRS allows much larger fiber diameters to be used without degrading spectral resolution as demonstrated with the larger sapphire collection fiber diameter (330 μm) compared to the silica fiber (100 μm). Unlike the dual silica fiber Raman probe, the dual sapphire fiber Raman probe did not include filtering at the fiber probe tip nearest the sample. Even so, SC sapphire fiber probe measurements produced less background than silica fibers allowing Raman measurements as close as ∼85 cm −1 to the excitation laser. Despite the short lengths of sapphire fiber used to construct the sapphire probe, well-defined, sharp sapphire Raman bands at 420, 580, and 750 cm −1 were observed in the SHRS spectra of cyclohexane and the highly fluorescent HMX-based PBX. SHRS measurements of the latter produced low background interference in the extracted Raman spectrum because the broad band fluorescence (i.e., a direct current, or DC, component) does not contribute to the interferogram intensity (i.e., the alternating current, or AC, component). SHRS spectral resolution, throughput, and signal-to-noise ratio are also discussed along with the merits of using sapphire Raman bands as internal performance references and as internal wavelength calibration standards in Raman measurements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Improving the Concrete Crack Detection Process via a Hybrid Visual Transformer Algorithm

Inspections of concrete bridges across the United States represent a significant commitment of resources, given their biannual mandate for many structures. With a notable number of aging bridges, there is an imperative need to enhance the efficiency of these inspections. This study harnessed the power of computer vision to streamline the inspection process. Our experiment examined the efficacy of a state-of-the-art Visual Transformer (ViT) model combined with distinct image enhancement detector algorithms. We benchmarked against a deep learning Convolutional Neural Network (CNN) model. These models were applied to over 20,000 high-quality images from the Concrete Images for Classification dataset. Traditional crack detection methods often fall short due to their heavy reliance on time and resources. This research pioneers bridge inspection by integrating ViT with diverse image enhancement detectors, significantly improving concrete crack detection accuracy. Notably, a custom-built CNN achieves over 99% accuracy with substantially lower training time than ViT, making it an efficient solution for enhancing safety and resource conservation in infrastructure management. These advancements enhance safety by enabling reliable detection and timely maintenance, but they also align with Industry 4.0 objectives, automating manual inspections, reducing costs, and advancing technological integration in public infrastructure management.

42 ENGINEERING↗

BM3DORNL

BM3DORNL is a high-performance, open-source library for removing streak and ring artifacts from computed-tomography (CT) data, developed for neutron imaging at Oak Ridge National Laboratory's Spallation Neutron Source (VENUS beamline) and applicable to X-ray CT as well. Ring artifacts — concentric rings in reconstructed slices caused by detector pixel-to-pixel response non-uniformities — appear as vertical streaks in the sinogram and degrade both image quality and quantitative analysis. BM3DORNL operates in the sinogram domain using an adaptation of the BM3D (block-matching and 3D collaborative filtering) algorithm (Dabov et al., 2007). It provides a dedicated streak-removal mode, a true multi-scale BM3D variant (after Mäkinen et al., 2021) that suppresses wide streaks single-scale methods miss, and an alternative Fourier–SVD method (~2.6× faster) combining FFT-based energy detection with rank-1 SVD. The computationally intensive core is implemented in Rust with parallel (Rayon) block matching, integral-image pre-screening, and optimized transforms, and is exposed through a simple Python API (with an optional GUI) so it integrates directly into existing tomography reconstruction pipelines. It processes both 2D sinograms and 3D sinogram stacks, is pip-installable for Linux and macOS, and is documented at https://bm3dornl.readthedocs.io.

Zhang, Chen [Oak Ridge National Laboratory (ORNL),↗

Principal components technique analysis for vegetation and land use discrimination

Automatic pre-processing technique called Principal Components (PRINCO) in analyzing LANDSAT digitized data, for land use and vegetation cover, on the Brazilian cerrados was evaluated. The chosen pilot area, 223/67 of MSS/LANDSAT 3, was classified on a GE Image-100 System, through a maximum-likehood algorithm (MAXVER). The same procedure was applied to the PRINCO treated image. PRINCO consists of a linear transformation performed on the original bands, in order to eliminate the information redundancy of the LANDSAT channels. After PRINCO only two channels were used thus reducing computer effort. The original channels and the PRINCO channels grey levels for the five identified classes (grassland, "cerrado", burned areas, anthropic areas, and gallery forest) were obtained through the MAXVER algorithm. This algorithm also presented the average performance for both cases. In order to evaluate the results, the Jeffreys-Matusita distance (JM-distance) between classes was computed. The classification matrix, obtained through MAXVER, after a PRINCO pre-processing, showed approximately the same average performance in the classes separability.

Parada, N. D. J.↗

Radar image registration and rectification

Two techniques for radar image registration and rectification are presented. In the registration method, a general 2-D polynomial transform is defined to accomplish the geometric mapping from one image into the other. The degree and coefficients of the polynomial are obtained using an a priori found tiepoint data set. In the second part of the paper, a rectification procedure is developed that models the distortion present in the radar image in terms of the radar sensor's platform parameters and the topographic variations of the imaged scene. This model, the ephemeris data and the digital topographic data are then used in rectifying the radar image. The two techniques are then used in registering and rectifying two examples of radar imagery. Each method is discussed as to its benefits, shortcomings and registration accuracy.

Naraghi, M.↗

Correcting for Nonlinearity in a Photodetector

Simple positive-feedback circuit varies bias voltage as necessary. Ideal detector biased with constant voltage, detector current proportional to photon flux plus constant offset. Detector connected between inverting input and ground, and feedback from operational amplifier through feedback resistor Rf make voltage at inverting input equal to noninverting input. Bias voltage held constant. Principle applied to linearizing mercury cadmium telluride infrared detectors in Fourier-transform spectrometers and other spectral and imaging instruments.

Schindler, R. A.↗

An interactive environment for the analysis of large Earth observation and model data sets

We propose to develop an interactive environment for the analysis of large Earth science observation and model data sets. We will use a standard scientific data storage format and a large capacity (greater than 20 GB) optical disk system for data management; develop libraries for coordinate transformation and regridding of data sets; modify the NCSA X Image and X Data Slice software for typical Earth observation data sets by including map transformations and missing data handling; develop analysis tools for common mathematical and statistical operations; integrate the components described above into a system for the analysis and comparison of observations and model results; and distribute software and documentation to the scientific community.

Bowman, Kenneth P.↗

Measuring Low-Order Aberrations in a Segmented Telescope

The in-focus PSF optimizer (IPO) is an algorithm for use in monitoring and controlling the alignment of the segments of a segmented-mirror astronomical telescope. IPO is so named because it computes wave-front aberrations of the telescope from digitized pointspread functions (PSFs) measured in infocus images. Inasmuch as distant astronomical objects that behave optically as point sources can typically be seen in almost any astronomical image, the main benefit afforded by IPO may be to enable maintenance of mirror-segment alignments without detracting from valuable scientific-observation time. IPO evolved from prescription-retrieval type algorithms. Prescription retrieval uses in-focus and out-of-focus PSFs to infer the state of an imaging optical system. The state, in this context, refers to the positions, orientations, and low-order figure errors of the optical elements in the system. Both prescription- retrieval and IPO use an iterative, nonlinear, least-squares optimizer to compute the optimal state parameters such that a digital computer-generated model image matches the digitized image acquired from the real system. The difference between IPO and prescription- retrieval algorithms is that IPO is specifically designed to utilize infocus images only. Although the restriction to in-focus images limits IPO to calculating only the lowest-order wave front aberrations, it also causes the resulting computation to take much less time because fewer degrees of freedom are included in the optimization process. In the prescription retrieval software developed at JPL, the model images are generated using the ray-trace/physical optics program, MACOS. IPO, on the other hand, uses a linear sensitivity matrix to compute the exit-pupil wave front from the system parameters; the wave front is then converted into a complex pupil field, which is then propagated to the image plane via a fast Fourier transform. This approach is computationally faster and requires less computer memory than is needed for prescription retrieval.

Ohara, Catherine↗

The Primordial Inflation Explorer (PIXIE)

The Primordial Inflation Explorer is an Explorer-class mission to measure the gravity-wave signature of primordial inflation through its distinctive imprint on the linear polarization of the cosmic microwave background. PIXIE uses an innovative optical design to achieve background-limited sensitivity in 400 spectral channels spanning 2.5 decades in frequency from 30 GHz to 6 THz (1 cm to 50 micron wavelength). Multi-moded non-imaging optics feed a polarizing Fourier Transform Spectrometer to produce a set of interference fringes, proportional to the difference spectrum between orthogonal linear polarizations from the two input beams. The differential design and multiple signal modulations spanning 11 orders of magnitude in time combine to reduce the instrumental signature and confusion from unpolarized sources to negligible levels. PIXIE will map the full sky in Stokes I, Q, and U parameters with angular resolution 2.6 deg and sensitivity 0.2 uK per 1 deg square pixel. The principal science goal is the detection and characterization of linear polarization from an inflationary epoch in the early universe, with tensor-to-scalar ratio r <10(exp -3) at 5 standard deviations. In addition, the rich PIXIE data will constrain physical processes ranging from Big Bang cosmology to the nature of the first stars to the physical conditions within the interstellar medium of the Galaxy. We describe the PIXIE instrument and mission architecture needed to detect the signature of an inflationary epoch in the early universe using only 4 semiconductor bolometers.

Kogut, Alan J.↗

Photogrammetry Toolbox Reference Manual

Specialized photogrammetric and image processing MATLAB functions useful for wind tunnel and other ground-based testing of aerospace structures are described. These functions include single view and multi-view photogrammetric solutions, basic image processing to determine image coordinates, 2D and 3D coordinate transformations and least squares solutions, spatial and radiometric camera calibration, epipolar relations, and various supporting utility functions.

Liu, Tianshu↗

The Primordial Inflation Explorer (PIXIE)

The Primordial Inflation Explorer is an Explorer-class mission to measure the gravity-wave signature of primordial inflation through its distinctive imprint on the linear polarization of the cosmic microwave background. PIXIE uses an innovative optical design to achieve background-limited sensitivity in 400 spectral channels spanning 2.5 decades in frequency from 30 GHz to 6 THz (1 cm to 50 micron wavelength). Multi-moded non-imaging optics feed a polarizing Fourier Transform Spectrometer to produce a set of interference fringes, proportional to the difference spectrum between orthogonal linear polarizations from the two input beams. Multiple levels of symmetry and signal modulation combine to reduce the instrumental signature and confusion from unpolarized sources to negligible levels. PIXIE will map the full sky in Stokes I, Q, and U parameters with angular resolution 2.6 deg and sensitivity 0.2 μK per 1 deg square pixel. The principal science goal is the detection and characterization of linear polarization from an inflationary epoch in the early universe, with tensor-to-scalar ratio r less than 10(exp −3) at 5 standard deviations. In addition, PIXIE will measure the absolute frequency spectrum to constrain physical processes ranging from inflation to the nature of the first stars to the physical conditions within the interstellar medium of the Galaxy. We describe the PIXIE instrument and mission architecture with an emphasis on the expected level of systematic error suppression.

Primordial Inflation Explorer is an Explorer-class↗

The Primordial Inflation Explorer (PIXIE)

The Primordial Inflation Explorer is an Explorer-class mission to open new windows on the early universe through measurements of the polarization and absolute frequency spectrum of the cosmic microwave background. PIXIE will measure the gravitational-wave signature of primordial inflation through its distinctive imprint in linear polarization, and characterize the thermal history of the universe through precision measurements of distortions in the blackbody spectrum. PIXIE uses an innovative optical design to achieve background-limited sensitivity in 400 spectral channels spanning over 7 octaves in frequency from 30 GHz to 6 THz (1 cm to 50 micron wavelength). Multi-moded non-imaging optics feed a polarizing Fourier Transform Spectrometer to produce a set of interference fringes, proportional to the difference spectrum between orthogonal linear polarizations from the two input beams. Multiple levels of symmetry and signal modulation combine to reduce systematic errors to negligible levels. PIXIE will map the full sky in Stokes I, Q, and U parameters with angular resolution 2.6 degrees and sensitivity 70 nK per 1degree square pixel. The principal science goal is the detection and characterization of linear polarization from an inflationary epoch in the early universe, with tensor-to-scalar ratio r < 10(exp. -3) at 5 standard deviations. The PIXIE mission complements anticipated ground-based polarization measurements such as CMBS4, providing a cosmic-variance-limited determination of the large-scale E-mode signal to measure the optical depth, constrain models of reionization, and provide a firm detection of the neutrino mass (the last unknown parameter in the Standard Model of particle physics). In addition, PIXIE will measure the absolute frequency spectrum to characterize deviations from a blackbody with sensitivity 3 orders of magnitude beyond the seminal COBE/FIRAS limits. The sky cannot be black at this level; the expected results will constrain physical processes ranging from inflation to the nature of the first stars and the physical conditions within the interstellar medium of the Galaxy. We describe the PIXIE instrument and mission architecture required to measure the CMB to the limits imposed by astrophysical foregrounds.

Kogut, Alan↗

The SunPy Project: An Interoperable Ecosystem for Solar Data Analysis

The SunPy Project is a community of scientists and software developers creating an ecosystem of Python packages for solar physics. The project includes the sunpy core package as well as a set of affiliated packages. The sunpy core package provides general purpose tools to access data from different providers, read image and time series data, and transform between commonly used coordinate systems. Affiliated packages perform more specialized tasks that do not fall within the more general scope of the sunpy core package. In this article, we give a high-level overview of the SunPy Project, how it is broader than the sunpy core package, and how the project curates and fosters the affiliated package system. We demonstrate how components of the SunPy ecosystem, including sunpy and several affiliated packages, work together to enable multi-instrument data analysis workflows. We also describe members of the SunPy Project and how the project interacts with the wider solar physics and scientific Python communities. Finally, we discuss the future direction and priorities of the SunPy Project.

Solar physics↗