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DOE OSTI2025

Weighted FFT estimators for 1D and 3D correlations of the Lyman- α forest

Correlations in the Lyman-α (Lyα) forest, both as a function of line of sight separation (1D) and 3D separation, provide a unique window to the distribution of matter at redshifts not accessible by current galaxy surveys. While optimal quadratic estimators have been used to measure 1D correlations, they are computationally expensive and difficult to extend to 3D analyses. On the other hand, estimators based on the Fast Fourier Transform (FFT) are significantly faster, but are affected by missing data in the spectra (masked pixels) and so far have not used pixel weights to reduce the uncertainties in the measurement. In this publication we describe how to compute the window matrix that enables forward-modelling the impact of masked pixels and weights on the FFT-based estimators. Here, we use Gaussian and hydrodynamical simulations with artificially masked pixels to validate the method on the measurement of 1D correlations. Finally, we show that the formalism can be extended to model the impact on 3D correlations, in particular on the cross-spectrum, the correlation of 1D Fourier modes as a function of transverse separation. This work will enable more precise clustering measurements with the Lyα forest dataset recently collected by the Dark Energy Spectroscopic Instrument (DESI).

Lokken, Martine [Univ. Autonoma de Barcelona (Spai↗

DOE OSTI2022

Application of recoil-imaging time projection chambers to directional neutron background measurements in the SuperKEKB accelerator tunnel

Gaseous time projection chambers (TPCs) with high readout segmentation are capable of reconstructing detailed 3D ionization distributions of nuclear recoils resulting from elastic neutron scattering. Here, using a system of six compact TPCs with pixel ASIC readout, filled with a 70:30 mixture of He:CO 2 gas, we analyze the first directional measurements of beam-induced neutron backgrounds in the tunnel regions surrounding the Belle II detector at the SuperKEKB e + e – collider. With the use of 3D recoil tracking, we show that these TPCs are capable of maintaining nearly 100% nuclear recoil purity to reconstructed ionization energies (E reco ) as low as 5 keV ee . Using a large sample of Monte-Carlo (MC)-simulated 4 He, 12 C, and 16 O recoil tracks, we find consistency between predicted and measured recoil energy spectra in five of the six TPCs, providing useful validation of the neutron production mechanisms modeled in simulation. Restricting this sample to 4 He recoil tracks with E reco > 40 keV ee , we further demonstrate axial angular resolutions within 8° and we introduce a procedure that under suitable conditions, correctly assigns the vector direction to 91% of these simulated 4 He recoils. Applying this procedure to assign vector directions to measured 4 He recoil tracks, we observe consistency between the angular distributions of observed and simulated recoils, providing first experimental evidence of localized neutron “hotspots” in the accelerator tunnel. Observed rates of nuclear recoils in these TPCs suggest that simulation overestimates the neutron flux from these hotspots. Despite this, we estimate these hotspots to produce the majority of neutron backgrounds in the accelerator tunnel at SuperKEKB’s target luminosity of 6.3 x 10 35 cm –2 s –1 , making them important regions to continue to monitor.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

Induced Current Detector Simulation

We describe simulations of a detector concept with small, low capacitance, pixels with pitch/thickness ratio on the order of 10. The simulation utilizes 2D and 3D TCAD simulations followed by a generic SPICE front-end model including noise and Landau fluctuations. We also investigate the properties of weighting fields of various geometries. We investigate whether the transient induced current signals can be used to improve pattern recognition and establish track angle.

43 PARTICLE ACCELERATORS↗

DOE OSTI2023

Holographic Fabrication of 3D Moiré Photonic Crystals Using Circularly Polarized Laser Beams and a Spatial Light Modulator

A moiré photonic crystal is an optical analog of twisted graphene. A 3D moiré photonic crystal is a new nano-/microstructure that is distinguished from bilayer twisted photonic crystals. Holographic fabrication of a 3D moiré photonic crystal is very difficult due to the coexistence of the bright and dark regions, where the exposure threshold is suitable for one region but not for the other. In this paper, we study the holographic fabrication of 3D moiré photonic crystals using an integrated system of a single reflective optical element (ROE) and a spatial light modulator (SLM) where nine beams (four inner beams + four outer beams + central beam) are overlapped. By modifying the phase and amplitude of the interfering beams, the interference patterns of 3D moiré photonic crystals are systemically simulated and compared with the holographic structures to gain a comprehensive understanding of SLM-based holographic fabrication. We report the holographic fabrication of phase and beam intensity ratio-dependent 3D moiré photonic crystals and their structural characterization. Superlattices modulated in the z-direction of 3D moiré photonic crystals have been discovered. This comprehensive study provides guidance for future pixel-by-pixel phase engineering in SLM for complex holographic structures.

42 ENGINEERING↗

DOE OSTI2024

3D Chiplet-Based Readout for Detectors

Heterogeneous vertical integration of chiplets provides a promising way to meet the challenging requirements of pixel detectors operating in extreme environments.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

Image Collection Simulation Using High-Resolution Atmospheric Modeling

A new method is described for simulating the passive remote sensing image collection of ground targets that includes effects from atmospheric physics and dynamics at fine spatial and temporal scales. The innovation in this research is the process of combining a high-resolution weather model with image collection simulation to attempt to account for heterogeneous and high-resolution atmospheric effects on image products. The atmosphere was modeled on a 3D voxel grid by a Large-Eddy Simulation (LES) driven by forcing data constrained by local ground-based and air-based observations. The spatial scale of the atmospheric model (10–100 m) came closer than conventional weather forecast scales (10–100 km) to approaching the scale of typical commercial multispectral imagery (2 m). This approach was demonstrated through a ground truth experiment conducted at the Department of Energy Atmospheric Radiation Measurement Southern Great Plains site. In this experiment, calibrated targets (colored spectral tarps) were placed on the ground, and the scene was imaged with WorldView-3 multispectral imagery at a resolution enabling the tarps to be visible in at least 9–12 image pixels. The image collection was simulated with Digital Imaging and Remote Sensing Image Generation (DIRSIG) software, using the 3D atmosphere from the LES model to generate a high-resolution cloud mask. The high-resolution atmospheric model-predicted cloud coverage was usually within 23% of the measured cloud cover. The simulated image products were comparable to the WorldView-3 satellite imagery in terms of the variations of cloud distributions and spectral properties of the ground targets in clear-sky regions, suggesting the potential utility of the proposed modeling framework in improving simulation capabilities, as well as testing and improving the operation of image collection processes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Evaluation of Electron Tomography Capabilities for Shale Imaging

Despite the advantageous resolution of electron tomography (ET), reconstruction of three-dimensional (3D) images from multiple two-dimensional (2D) projections presents several challenges, including small signal-to-noise ratios, and a limited projection range. This study evaluates the capabilities of ET for thin sections of shale, a complex nanoporous medium. A numerical phantom with 1.24 nm pixel size is constructed based on the tomographic reconstruction of a Barnett shale. A dataset of 2D projection images is numerically generated from the 3D phantom and studied over a range of conditions. First, common reconstruction techniques are used to reconstruct the shale structure. The reconstruction uncertainty is quantified by comparing overall values of storage and transport metrics, as well as the misclassification of pore voxels compared to the phantom. We then select the most robust reconstruction technique and we vary the acquisition conditions to quantify the effect of artifacts. We find a strong agreement for large pores over the different acquisition workflows, while a wider variability exists for nanometer-scale features. Furthermore, the limited projection range and reconstruction are identified as the main experimental bottlenecks, thereby suggesting that sample thinning, advanced holders, and advanced reconstruction algorithms offer opportunities for improvement.

3D scanning transmission electron microscopy↗

DOE OSTI2024

Three-Dimensional Ultrastructure of Arabidopsis Cotyledons Infected with Colletotrichum higginsianum

We used serial block-face scanning electron microscopy (SBF-SEM) to study the host–pathogen interface between Arabidopsis cotyledons and the hemibiotrophic fungus Colletotrichum higginsianum. By combining high-pressure freezing and freeze-substitution with SBF-SEM, followed by segmentation and reconstruction of the imaging volume using the freely accessible software IMOD, we created 3D models of the series of cytological events that occur during the Colletotrichum–Arabidopsis susceptible interaction. We found that the host cell membranes underwent massive expansion to accommodate the rapidly growing intracellular hypha. As the fungal infection proceeded from the biotrophic to the necrotrophic stage, the host cell membranes went through increasing levels of disintegration culminating in host cell death. Intriguingly, we documented autophagosomes in proximity to biotrophic hyphae using transmission electron microscopy (TEM) and a concurrent increase in autophagic flux between early to mid/late biotrophic phase of the infection process. Occasionally, we observed osmiophilic bodies in the vicinity of biotrophic hyphae using TEM only and near necrotrophic hyphae under both TEM and SBF-SEM. Overall, we established a method for obtaining serial SBF-SEM images, each with a lateral ( x-y) pixel resolution of 10 nm and an axial ( z) resolution of 40 nm, that can be reconstructed into interactive 3D models using the IMOD. Application of this method to the Colletotrichum–Arabidopsis pathosystem allowed us to more fully understand the spatial arrangement and morphological architecture of the fungal hyphae after they penetrate epidermal cells of Arabidopsis cotyledons and the cytological changes the host cell undergoes as the infection progresses toward necrotrophy. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

Biochemistry & Molecular Biology↗

DOE OSTI2024

Chiral Kirigami for Bend‐Tolerant Reconfigurable Hologram with Continuously Variable Chirality Measures

Abstract Despite the commonality of static holograms, the holography with multiple information layers and reconfigurable grey‐scale images at communication frequencies remain a confluence of scientific challenges. One well‐known difficulty is the simultaneous modulation of phase and amplitude of electromagnetic wavefronts with a high modulation depth. A less appreciated challenge is scrambling of the information and images with hologram bending. Here, this work shows that chirality‐guided pixelation of plasmonic kirigami sheets enables tunable multiplexed holography at terahertz (THz) frequencies. The convex and concave structures with slanted Au strips exhibit gradual variations in geometries facilitating modulation of light ellipticity reaching 40 deg. Real‐time switching of 3D images of the letter “ M ” and the Mona Lisa demonstrates the possibility of complex grey‐scale information content and importance of continuously variable mirror asymmetry. Microscale chirality measures of each pixel experiences little change with bending while retaining controllable reconfigurability upon stretching, which translates to remarkable resilience of chiral holograms to bending. Simplicity of their design with local chirality measures opens the door to information technologies with fault‐tolerant THz encryption, wearable holographic devices, and new communication technologies.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Pxl

The code consists of several scripts. The image is fetched from a predefined URL, downloaded, and is displayed in the virtual environment at a predefined location. The image is also dynamically scaled to fit in the virtual environment depending on its size. The image is sent to have each pixel's value written to a CSV file. While the CSV is being written, a dictionary is populated with values that map each pixel to a temperature reading. The image's height, width, position and references to its corners are sent to make a button that is the same size as the image and placed right behind the image in the virtual scene. The button defines behavior that should be triggered when the user pushes the image. Unity provides visual cues that alert the user when they are about to touch something in the virtual environment. The code holds references to the cues for the left and right hands. The button queries the cue tracker and receives the position of the active cue in the form of a 3D vector. The 3D vector is compared to the bottom left corner of the image to transform the world space coordinates of the cue to the pixel space of the image. The specific pixel is approximated relative to how far left and up the user touched from the bottom left corner of the image. The approximated pixel value, which is represented as a coordinate in 2D space, is used to retrieve the temperature value associated with the approximated pixel. A window of text is then updated to display the temperature reading.

. Otis, KrystianeS [Idaho National Laboratory (INL↗

DOE OSTI2024

Predicting Missing Regions in Charged Particle Tracks Using a Sparse 3D Convolutional Neural Network

The 2x2 Demonstrator is a prototype of ND-LAr, the liquid argon time-projection chamber of the Deep Underground Neutrino Experiment’s Near Detector complex. Both the 2x2 Demonstrator and ND-LAr are modular detectors that will have pixelated charge readouts and inactive regions wherein there is no sensitivity to charge deposition and light signals that arise from charged particle interactions with liquid argon. In the 2x2, these inactive regions are located in between the active detector modules, which introduces the challenge of inferring what charge signals ought to look like in these regions. This study explores the use of a Sparse 3D Convolutional Neural Network (ConvNet) to infer missing regions in charged particle tracks. Hits corresponding to energy depositions are voxelized into a three-dimensional grid for each track. Voxels that fall into predefined inactive regions are removed to simulate the lack of detector output. The model is trained to infer the topology of the missing track voxels, with the ultimate goal of inferring the missing charge or energy values in these voxels as well. Results indicate that this approach shows promise in prediction of missing track regions with some accuracy.

Utaegbulam, Hilary↗

DOE OSTI2026

Pixelated plastic scintillator array manufacturing using fast-, photo-curable resin

Pixelated plastic scintillator arrays can serve as high efficiency and high resolution neutron imaging detectors. Manufacturing these arrays is intensive in both time and labor. This article presents a fabrication method based on additive manufacturing for two-dimensional plastic organic scintillator arrays using a custom-built automated assembly machine and a custom photocurable resin that has significant non-aromatic acrylate oligomer content. The process involves two main stages: fully autonomous production of one-dimensional layered arrays, followed by semi-autonomous cutting and stacking to form two-dimensional pixel arrays. One-dimensional arrays were manufactured at a rate of around 4 layers per hour with minimal defects and tight dimensional tolerances, while two-dimensional arrays up to 7 x 7 pixels and 70 mm in length were completed in approximately 3.5 hours. Final arrays exhibited dimensional deviations of less than 0.5 mm. Two-dimensional arrays read out by a multi-anode photomultiplier tube demonstrated per-pixel position resolution and pulse-shape discrimination, enabling gamma–neutron interaction separation in mixed radiation environments.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Efficient reconstruction and validation of heterogeneous microstructures for energy applications

The digital reconstruction of microstructures is necessary for simulations in fields ranging from geology to electrochemistry, but the state-of-the-art digital reconstruction techniques often compromise between resolution and field of view. It is challenging to retain detailed microstructure information in large-scale reconstructions. Here, this study investigates different aspects of the Yeong-Torquato algorithm based on correlation functions to make it more efficient. We achieve this goal by reducing the computational complexity of the chord-length distribution function and the two-point correlation function, applying the random sphere-packing method as the initial condition, and restricting potential voxel swaps to interfaces. In addition, a novel superposition parallel scheme is introduced to aid in searching for potential voxel swaps. The algorithm proposed is validated by comparing the pore-size distributions of reconstructed 3D custom battery electrodes from a sample dataset obtained from transmission X-ray microscopy. From a sample image with 200 x 200 pixels, the code can reconstruct a 300 x 300 x 300 structure in under 22 h and reconstruct a 400 x 400 x 400 structure in 43 h with eight cores.

42 ENGINEERING↗

DOE OSTI2021

High resolution x-ray emission spectrometer for multiple hard x-ray emission lines: Demonstration for Cu Kα and Kβ emissions

In this work, we present a compact 3D printed x-ray emission spectrometer based on the von Hamos geometry that represents a significant upgrade to the existing von Hamos geometry-based miniature x-ray emission spectrometer (miniXES). The upgrades include the incorporation of a higher pixel density 500K detector for improved energy resolution and an enlarged sample area to accommodate a wider range of sample formats. The versatile spectrometer houses removable crystal holders that can be easily exchanged, as well as movable alignment eyelets that give flexibility in Bragg angle selection. Designed for ease of manufacture, all the components, except for the apertures, can be 3D printed and readily assembled. We describe its implementation in measurements of resonant and non-resonant Cu Kα and Kβ x-ray emission and report the theoretical and measured energy resolution and collected solid angle of the emission.

3D printing↗

DOE OSTI2023

Universal Polarization Transformations: Spatial Programming of Polarization Scattering Matrices Using a Deep Learning‐Designed Diffractive Polarization Transformer

Abstract Controlled synthesis of optical fields having nonuniform polarization distributions presents a challenging task. Here, a universal polarization transformer is demonstrated that can synthesize a large set of arbitrarily‐selected, complex‐valued polarization scattering matrices between the polarization states at different positions within its input and output field‐of‐views (FOVs). This framework comprises 2D arrays of linear polarizers positioned between isotropic diffractive layers, each containing tens of thousands of diffractive features with optimizable transmission coefficients. After its deep learning‐based training, this diffractive polarization transformer can successfully implement N i N o = 10 000 different spatially‐encoded polarization scattering matrices with negligible error, where N i and N o represent the number of pixels in the input and output FOVs, respectively. This universal polarization transformation framework is experimentally validated in the terahertz spectrum by fabricating wire‐grid polarizers and integrating them with 3D‐printed diffractive layers to form a physical polarization transformer. Through this set‐up, an all‐optical polarization permutation operation of spatially‐varying polarization fields is demonstrated, and distinct spatially‐encoded polarization scattering matrices are simultaneously implemented between the input and output FOVs of a compact diffractive processor. This framework opens up new avenues for developing novel devices for universal polarization control and may find applications in, e.g., remote sensing, medical imaging, security, material inspection, and machine vision.

Optical neural networks↗

DOE OSTI2023

Video-rate Raman-based metabolic imaging by Airy light-sheet illumination and photon-sparse detection

Despite its massive potential, Raman imaging represents just a modest fraction of all research and clinical microscopy to date. This is due to the ultralow Raman scattering cross-sections of most biomolecules that impose low-light or photon-sparse conditions. Bioimaging under such conditions is suboptimal, as it either results in ultralow frame rates or requires increased levels of irradiance. Here, we overcome this tradeoff by introducing Raman imaging that operates at both video rates and 1,000-fold lower irradiance than state-of-the-art methods. To accomplish this, we deployed a judicially designed Airy light-sheet microscope to efficiently image large specimen regions. Further, we implemented subphoton per pixel image acquisition and reconstruction to confront issues arising from photon sparsity at just millisecond integrations. We demonstrate the versatility of our approach by imaging a variety of samples, including the three-dimensional (3D) metabolic activity of single microbial cells and the underlying cell-to-cell variability. To image such small-scale targets, we again harnessed photon sparsity to increase magnification without a field-of-view penalty, thus, overcoming another key limitation in modern light-sheet microscopy.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Extremized nonlinear and linearized responses in soft metamaterials enabled by gradient-based design and grayscale digital light processing

In this study, we develop a gradient-based design approach that exploits grayscale digital light processing (DLP) 3D printing for extremizing the nonlinear and linearized response of soft metamaterials — materials that harness engineered geometric instabilities to undergo large and programmable changes in configuration. Grayscale DLP approaches modulate local mechanical properties at the pixel scale by tuning the light intensity within a single grayscale image, unlocking an exceptionally large design space. To effectively navigate this space, we develop smooth mappings between local light intensity values and global quantities of interest that characterize the behavior of soft metamaterials. Enabling these smooth mappings are robust and differentiable nonlinear finite element simulations powered by a trust region solver. A PDE-constrained optimization problem is then solved to invert these mappings and produce light intensity distributions that endow the printed part with varying stiffness and flexibility in distinctive regions. It is shown that optimizing the distribution of soft and stiff phases throughout a metamaterial structure results in markedly different buckling and self-contact configurations to drive extremized nonlinear compression and linearized vibration responses. Optimized light intensity distributions are translated to grayscale images and directly used to print soft metamaterial samples, showing remarkable agreement between the buckling and self-contact response in simulated and measured deformed configurations.

Additive manufacturing↗

DOE OSTI2026

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),↗