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DOE OSTI2024

Live cell imaging of cellular dynamics in poplar wood using computational cannula microscopy

This study presents significant advancements in computational cannula microscopy for live imaging of cellular dynamics in poplar wood tissues. Leveraging machine-learning models such as pix2pix for image reconstruction, we achieved high-resolution imaging with a field of view of 55µm using a 50µm-core diameter probe. Our method allows for real-time image reconstruction at 0.29 s per frame with a mean absolute error of 0.07. We successfully captured cellular-level dynamics in vivo , demonstrating morphological changes at resolutions as small as 3µm. We implemented two types of probabilistic neural network models to quantify confidence levels in the reconstructed images. This approach facilitates context-aware, human-in-the-loop analysis, which is crucial for in vivo imaging where ground-truth data is unavailable. Using this approach we demonstrated deep in vivo computational imaging of living plant tissue with high confidence (disagreement score ⪅0.2). This work addresses the challenges of imaging live plant tissues, offering a practical and minimally invasive tool for plant biologists.

Ingold, Alexander (ORCID:0009000752380016)↗

DOE OSTI2025

Improved field assessments of chemicals and explosives using high-resolution gamma-ray spectroscopy with a tagged neutron interrogation system

A fi eld-portable tagged neutron interrogation system is being developed for detection of explosives and chemical warfare agents by prompt gamma-ray neutron activation analysis. The system combines an associated particle imaging deuterium-tritium neutron generator with a high-purity germanium gamma-ray detector. Fine spatial resolution neutron and alpha detectors enable precise mapping of characteristic gamma-ray emission distributions onto high-clarity neutron radiographic images. A narrow coincidence gate associated with each tagged neutron ensures a large signal-to-background ratio, thus signifi cantly improving sensitivity to the chemical compositions of the items being assessed. Recent experimental results recorded from test objects involving mock explosives and other chemicals are presented.

46 - INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AN↗

DOE OSTI2025

Improved field assessments of chemicals and explosives using high-resolution gamma-ray spectroscopy with a tagged neutron interrogation system

46 - INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AN↗

DOE OSTI2020

A Digital Imaging Method for Evaluating the Kinetics of Vapochromic Response

This work describes the use of a cell phone camera and the L*a*b method (color space specified by the International Commission on Illumination) to characterize the color change in different vapochromic systems. In this study we have developed a semi-automatic color change analysis software that digitally analyzes images (e.g., video frames) collected while a vapochromic material is absorbing vapor. The advantages of using this method, as compared to reflectance spectroscopy or transmission spectroscopy through a thin film, include low cost, convenience, portability, ease of sample preparation, the absence of need for specialized equipment, and the ease of simultaneously collecting data on different samples under identical conditions. In addition, this method arguably provides direct insight into what a human would observe when monitoring these color changes by eye. Limitations of the method also are discussed in this paper.

cell phone camera, colorimetric sensing, vapor det↗

DOE OSTI2023

A Joint Roman Space Telescope and Rubin Observatory Synthetic Wide-Field Imaging Survey

We present and validate 20 deg(2) of overlapping synthetic imaging surveys representing the full depth of the Nancy Grace Roman Space Telescope High-Latitude Imaging Survey (HLIS) and 5 yr of observations of the Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST). The two synthetic surveys are summarized, with reference to the existing 300 deg(2) of LSST simulated imaging produced as part of Dark Energy Science Collaboration (DESC) Data Challenge 2 (DC2). Both synthetic surveys observe the same simulated DESC DC2 universe. For the synthetic Roman survey, we simulate for the first time fully chromatic images along with the detailed physics of the Sensor Chip Assemblies derived from lab measurements using the flight detectors. The simulated imaging and resulting pixel-level measurements of photometric properties of objects span a wavelength range of similar to 0.3-2.0 mu m. We also describe updates to the Roman simulation pipeline, changes in how astrophysical objects are simulated relative to the original DC2 simulations, and the resulting simulated Roman data products. We use these simulations to explore the relative fraction of unrecognized blends in LSST images, finding that 20-30 per cent of objects identified in LSST images with i-band magnitudes brighter than 25 can be identified as multiple objects in Roman images. These simulations provide a unique testing ground for the development and validation of joint pixel-level analysis techniques of ground- and space-based imaging data sets in the second half of the 2020s - in particular the case of joint Roman-LSST analyses.

gravitational lensing↗

DOE OSTI2022

3013 Inner Container Closure Weld Region (ICCWR) Characterization by Wide Area 3D Measurement System (WAMS) Analysis (FY21 Progress Report)

As part of the 3013 Surveillance Program, through-wall penetration from stress corrosion cracking (SCC) of the 3013 inner containers has been identified as the most credible condition for failure withing the 50- years lifetime. Chlorides contained in Pu-bearing material, together with intra-canister humidity levels, metallurgical conditions, and internal stresses have been found to produce corrosion in the Inner Container Closure Weld Region (ICCWR) of the 3013 canister system. A Laser Confocal Microscope (LCM) is used as part of the 3013 Surveillance Program protocol to identify the prevalence of corrosion and corrosionrelated cracking in the ICCWR2. With the LCM, a close visual examination is made of the ICCWR surface along with measurements of corrosion-related features. LCM inspections produce immense amounts of image data that is time intensive to analyze. There is also a 9-year backlog of images, with approximately 49 canisters that must be evaluated. To expedite data analysis and reduce the amount of generated data, a Wide Area 3D Measurement System (WAMS) microscope has been added to the examination protocol. Although WAMS is a lower resolution microscope, small features of interest can be still identified. The advantage of collecting data for the full circumference using the WAMS is that it can take about 1/16 of the time needed with the LCM. Both systems offer capabilities that combined can be utilized to expedite the examination of the ICCWR. The WAMS is an efficient system for screening and identification of corrosion features while the LCM can be utilized to obtain higher resolution images areas identified by the WAMS. This report explains and justifies the data collection methods used with the WAMS. It includes a summary of the data generated by WAMS in FY21. The goals set for data collection in FY21 were met. A total of twenty-two DE’s were imaged, and analysis was carried out on eleven samples. The analyzed samples showed large numbers of potential cracks and pits distributed throughout the surfaces. Lastly, to explain the advantages of the WAMS, its capabilities were compared to those of a simpler microscope. Micrographs of the samples imaged in FY21 and those analyzed are included in the appendices.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2025

Block segmentation in feature space for realtime object detection in high granularity images

Computer vision has applications in object detection, image recognition and classification, and object tracking. One of the challenges of computer vision is the presence of useful information at multiple distance scales. Filtering techniques may sacrifice details at small scales in order to prioritize the analysis of large-scale features of the image. We present a strategy for coarse-graining multidimensional data while maintaining fine-grained detail for subsequent analysis. The algorithm is based on fixed-size block segmentation in the feature space. We apply this strategy to solve the long-standing challenge of detecting particle trajectories at the Large Hadron Collider in real time.

Computer vision↗

DOE OSTI2023

Peri-Net-Pro: the neural processes with quantified uncertainty for crack patterns

Abstract This paper develops a deep learning tool based on neural processes (NPs) called the Peri-Net-Pro, to predict the crack patterns in a moving disk and classifies them according to the classification modes with quantified uncertainties. In particular, image classification and regression studies are conducted by means of convolutional neural networks (CNNs) and NPs. First, the amount and quality of the data are enhanced by using peridynamics to theoretically compensate for the problems of the finite element method (FEM) in generating crack pattern images. Second, case studies are conducted with the prototype microelastic brittle (PMB), linear peridynamic solid (LPS), and viscoelastic solid (VES) models obtained by using the peridynamic theory. The case studies are performed to classify the images by using CNNs and determine the suitability of the PMB, LBS, and VES models. Finally, a regression analysis is performed on the crack pattern images with NPs to predict the crack patterns. The regression analysis results confirm that the variance decreases when the number of epochs increases by using the NPs. The training results gradually improve, and the variance ranges decrease to less than 0.035. The main finding of this study is that the NPs enable accurate predictions, even with missing or insufficient training data. The results demonstrate that if the context points are set to the 10th, 100th, 300th, and 784th, the training information is deliberately omitted for the context points of the 10th, 100th, and 300th, and the predictions are different when the context points are significantly lower. However, the comparison of the results of the 100th and 784th context points shows that the predicted results are similar because of the Gaussian processes in the NPs. Therefore, if the NPs are employed for training, the missing information of the training data can be supplemented to predict the results.

Mathematics↗

DOE OSTI2021

Image-Based Methods to Score Fungal Pathogen Symptom Progression and Severity in Excised Arabidopsis Leaves

Image-based symptom scoring of plant diseases is a powerful tool for associating disease resistance with plant genotypes. Advancements in technology have enabled new imaging and image processing strategies for statistical analysis of time-course experiments. There are several tools available for analyzing symptoms on leaves and fruits of crop plants, but only a few are available for the model plant Arabidopsis thaliana (Arabidopsis). Arabidopsis and the model fungus Botrytis cinerea (Botrytis) comprise a potent model pathosystem for the identification of signaling pathways conferring immunity against this broad host-range necrotrophic fungus. Here, we present two strategies to assess severity and symptom progression of Botrytis infection over time in Arabidopsis leaves. Thus, a pixel classification strategy using color hue values from red-green-blue (RGB) images and a random forest algorithm was used to establish necrotic, chlorotic, and healthy leaf areas. Secondly, using chlorophyll fluorescence (ChlFl) imaging, the maximum quantum yield of photosystem II (Fv/Fm) was determined to define diseased areas and their proportion per total leaf area. Both RGB and ChlFl imaging strategies were employed to track disease progression over time. This has provided a robust and sensitive method for detecting sensitive or resistant genetic backgrounds. A full methodological workflow, from plant culture to data analysis, is described.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Multiscale Characterization of Additive Manufacturing Components with Computed Tomography, 3D X-ray Microscopy, and Deep Learning

Additive manufacturing (AM) facilitates the creation of complex-geometry parts, driving advancements in lightweight aerospace components, high-efficiency engine cooling channels, and customized medical implants. However, ensuring the quality and reliability of AM parts remains challenging due to internal defects, surface irregularities, porosity, and residual trapped powder, which are often inaccessible to traditional inspection methods. Recent developments in X-ray computed tomography (XCT) and 3D X-ray microscopy (XRM), particularly systems equipped with resolution-at-a-distance (RaaD™) capabilities, enable high-resolution, non-destructive evaluation of AM components across multiple scales, from sub-micrometer to macroscopic levels. This paper explores modern XCT and XRM techniques for multiscale characterization of AM parts, focusing on their ability to detect and analyze defects such as porosity, cracks, inclusions, and surface roughness, while offering insights into defect formation mechanisms, material properties, and process-induced variations. The integration of deep learning (DL) frameworks, including Simurgh, DeepRecon, and DeepScout, enhances XCT/XRM workflows by reducing scan times, improving resolution recovery, and enabling accurate defect detection even with limited projection data. These DL-based methods overcome limitations of traditional reconstruction techniques, enabling faster, more reliable characterization of dense materials like Inconel 718 and novel alloys such as AlCe. Applications include process parameter optimization, high-throughput quality control, and multistage AM process evaluation, with DL-enhanced workflows accelerating analysis times from weeks to days. Correlative imaging approaches further validate XCT and XRM data against scanning electron microscopy (SEM) images of physically sectioned samples, confirming the accuracy of DL-based reconstructions and enabling comprehensive defect analysis. While challenges remain in generalizing DL models to diverse materials and imaging conditions, improvements in resolution, noise reduction, and defect detection highlight the transformative potential of these methods. This multiscale and correlative approach enables precise identification and correlation of microstructural features with the overall performance of AM components. By integrating advanced XCT, XRM, and DL techniques, this paper demonstrates a significant leap forward in AM characterization, offering valuable insights into the relationships between processing parameters, microstructure, and part performance, and driving innovations that enhance the quality and reliability of AM products for demanding industrial applications.

Additive manufacturing↗

DOE OSTI2020

Slycat Enables Synchronized 3D Comparison of Surface Mesh Ensembles [Brief]

In support of analyst requests for Mobile Guardian Transport studies, researchers at Sandia National Laboratories have expanded data types for the Slycat ensemble-analysis and visualization tool to include 3D surface meshes. This new capability represents a significant advance in our ability to perform detailed comparative analysis of simulation results. Analyzing mesh data rather than images provides greater flexibility for post-processing exploratory analysis.

36 MATERIALS SCIENCE↗

DOE OSTI2025

H420 Imager Calibration Procedure: Field of View Scan

Gamma-ray imagers with coded apertures have a finite field of view (FOV) within which an image of a source can be generated. A “FOV scan” is a facet of imager calibration procedure that involves collecting specialized data for a range of source locations filling the FOV in order to understand and correct for differences in imager performance. Systematic distortions reveal relative displacements between internal imager components, which can be accounted for in data analysis. The success of this scan requires a stable imager position during the full measurement duration (~hours). This document summarizes the hardware and software tools required to conduct a FOV calibration scan of an H3D H420 Coded Aperture Gamma-Ray Imager.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2022

Sulphur variations in annually layered stalagmites using benchtop micro-XRF

Variation of sulphur in annually laminated stalagmites can be used to infer the impact of past volcanic activities, anthropogenic pollution, and climate change due to increased bushfire activity. The synchrotron radiation micro-X-Ray fluorescence (SR-XRF) microprobe is a powerful tool to analyse and image sulphur recorded in stalagmites with micrometre resolution. However, access to SR-XRF beamlines can be limited, so researchers must select the most promising stalagmites for imaging. Benchtop micro-XRF is an effective tool for trace elemental analysis of speleothem samples and is a candidate for routine laboratory measurement of sulphur along stalagmite laminae and screening for SR-XRF. Here, this study describes a protocol using matrix-matched standards to measure annual variations of sulphur at trace to percent level along the laminae of two Western Australian stalagmites, one of which already having been analysed using SR-XRF. Parameters that affected quantitation include X-ray tube voltage and current, spot size of the X-ray beam and stalagmite surface roughness and porosity. The use of a 20 μm X-ray spot size provides sub-annual spatial resolution that can be completed in an overnight scan. The features in a 1000 point micro-XRF analysis of sulphur along a 20 mm transect show good consistency with SR-XRF microprobe data. Micro-XRF mapping was also performed to produce chemical images on the stalagmite and compared with Raman and X-ray diffraction (XRD) to confirm that the stalagmite is exclusively calcite, with no aragonite, and that the source of sulphur in the samples was gypsum and anhydrite. Regions of very high sulphur in the micro-XRF maps were found to be artefacts due to diffraction of the incident beam but these could be efficiently removed by using a multiple point statistics approach to produce a clean image suitable for analysis of the laminae. This work shows the potential of micro-XRF for routine analysis of sulphur in stalagmites, and to streamline sample characterisation before SR-XRF imaging.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Dark Energy Survey Year 1 Results: Cosmological Constraints from Cluster Abundances, Weak Lensing, and Galaxy Correlations

We present the first joint analysis of cluster abundances and auto or cross-correlations of three cosmic tracer fields: galaxy density, weak gravitational lensing shear, and cluster density split by optical richness. From a joint analysis (4×2pt+N) of cluster abundances, three cluster cross-correlations, and the auto correlations of the galaxy density measured from the first year data of the Dark Energy Survey, we obtain Ωm=0.305-0.038+0.055 and σ8=0.783-0.054+0.064. This result is consistent with constraints from the DES-Y1 galaxy clustering and weak lensing two-point correlation functions for the flat νΛCDM model. Consequently, we combine cluster abundances and all two-point correlations from across all three cosmic tracer fields (6×2pt+N) and find improved constraints on cosmological parameters as well as on the cluster observable-mass scaling relation. This analysis is an important advance in both optical cluster cosmology and multiprobe analyses of upcoming wide imaging surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Spatially resolved absolute quantitation in thin tissue by mass spectrometry

Mass spectrometry (MS) has become the de facto tool for routine quantitative analysis of biomolecules. MS is increasingly being used to reveal the spatial distribution of proteins, metabolites, and pharmaceuticals in tissue and interest in this area has led to a number of novel spatially resolved MS technologies. Most spatially resolved MS measurements are qualitative in nature due to a myriad of potential biases, such as sample heterogeneity, sampling artifacts, and ionization effects. As applications of spatially resolved MS in the pharmacological and clinical fields increase, demand has become high for quantitative MS imaging and profiling data. As a result, several varied technologies now exist that provide differing levels of spatial and quantitative information. Furthermore, this review provides an overview of MS profiling and imaging technologies that have demonstrated quantitative analysis from tissue. Focus is given on the fundamental processes affecting quantitative analysis in an array of MS imaging and profiling technologies and methods to address these biases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Proton deflectometry with in situ x-ray reference for absolute measurement of electromagnetic fields in high-energy-density plasmas

In this work, we report a technique of proton deflectometry that uses a grid and an in situ reference x-ray grid image for precise measurements of magnetic fields in high-energy-density plasmas. A D 3 He fusion implosion provides a bright point source of both protons and x-rays, which is split into beamlets by a grid. The protons undergo deflections as they propagate through the plasma region of interest, whereas the x-rays travel along straight lines. The x-ray image, therefore, provides a zero-deflection reference image. The line-integrated magnetic fields are inferred from the shifts of beamlets between the deflected (proton) and reference (x-ray) images. We developed a system for analysis of these data, including automatic algorithms to find beamlet locations and to calculate their deflections from the reference image. The technique is verified in an experiment performed at OMEGA to measure a nonuniform magnetic field in vacuum and then applied to observe the interaction of an expanding plasma plume with the magnetic field.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Evidence for large baryonic feedback at low and intermediate redshifts from kinematic Sunyaev-Zel’dovich observations with ACT and DESI photometric galaxies

Recent advances in cosmological observations have provided an unprecedented opportunity to investigate the distribution of baryons relative to the underlying matter. In this work, we show that the gas is more extended than the dark matter, and the amount of baryonic feedback at $z \lesssim 1$ disfavors low-feedback models such as that of state-of-the-art hydrodynamical simulation IllustrisTNG compared with high-feedback models such as that of the original Illustris simulation. This has important implications for bridging the gap between theory and observations and understanding galaxy formation and evolution. Furthermore, a better grasp of the baryon-dark matter link is critical to future cosmological analyses, which are currently impeded by our limited knowledge of baryonic feedback. Here, we measure the kinematic Sunyaev-Zel'dovich (kSZ) effect from the Atacama Cosmology Telescope (ACT), stacked on the luminous red galaxy (LRG) sample of the Dark Energy Spectroscopic Instrument (DESI) imaging survey. This is the first analysis to use photometric redshifts for reconstructing galaxy velocities. Due to the large number of galaxies comprising the DESI imaging survey, this is the highest signal-to-noise stacked kSZ measurement to date: we detect the signal at 13$σ$, finding strong evidence that the gas is more spread out than the dark matter, as well as a preference for larger feedback compared to some commonly used state-of-the-art hydrodynamical simulations. Here, our work opens up the possibility of recalibrating large hydrodynamical simulations using the kSZ effect. In addition, our findings highlight the importance of properly accounting for baryonic feedback with future surveys such as LSST through direct probes such as the kSZ, and shed light on long-standing enigmas in astrophysics, such as the “missing baryon” problem.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Contactless Position Measurement System for Remote Alignment of Highly Reflective Objects

The Contactless Position Measurement System (CPMS) permits automatic alignment of highly-reflecting components that cannot or should not be touched by human hands, such as those used in SRF cavities. CPMS also has application during maintenance of fusion reactors, when the components in the reactor are radioactive. The length of time for which humans can handle the components in order to carry out maintenance or repairs is limited. We would like to measure the relative positions of such objects so we can bring them into alignment with motorized stages, thus eliminating the need for human contact. The CPMS is a computer vision system that measures the location of highly reflective components to within a fraction of a millimeter by finding the edges of silhouette images. This is done by placing a uniform, infrared backlight behind the components, and viewing each component with two low-aberration, infrared cameras. Each of these stereoscopic cameras are located within a coordinate system we set up with reference platforms, light sources, and survey cameras distributed around the perimeter of the string assembly room, or fusion reactor. We obtain stereoscopic silhouette images of each component, and we use these to determine the position of the component within our string assembly coordinate system. The CPMS combines the silhouette images with knowledge of the dimensions of the objects to obtain the relative positions of components in its field of view. These position measurements then allow us to mechanically maneuver the components into contact. Once we know where they are, we can move the components to where they are supposed to be with motorized stages or other mechanical means, check they are in the right place, and bolt them together. In Phase I, we built a prototype infrared backlights and cameras, tested it, wrote an analysis program to fit the images. At a range of 50 cm, we are able to measure the relative positions of two stainless steel flanges with an accuracy of 150 μm rms. The next steps are to test the analysis program with motorized stages, build a full-size prototype, and implement it in an cleanroom with SRF cavity assembly. This can be done in a cost effective way given the materials with which the system is designed. As Open Source Instruments achieved more in Phase I than anticipated, despite not receiving a Phase II SBIR grant, we hope to move forward with product development and sales with a testing partner.

43 PARTICLE ACCELERATORS↗