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At least 973 records · Page 54
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

A New Workflow of X-ray CT Image Processing and Data Analysis of Structural Features in Rock Using Open-Source Software

X-ray computed tomography (CT) images of rock specimens often contain artifacts which must be corrected before scientific analyses are performed. Here, we present a new workflow of automated image processing to utilize poor-quality X-ray CT scan images. The workflow runs on the open-source image analysis software and efficiently separates desired features from low-contrast scanned images. The new workflow is a two-step technique using contrast enhancement and automated feature segmentation to generate noise-free binary images. The results of binary images using the proposed workflow and using a conventional thresholding technique are analyzed to show the quality of the proposed method. The paper also presents a workflow of estimating the structural geometries of features in two and three dimensions. The results of the structural feature analyses and computational time were compared between the open-source (ImageJ) and commercial image analysis software (Bruker Computed Tomography Analyzer). The commercial software was more computationally efficient, but the task-specific macros in open-source software enabled the user-desired automation in image processing and data extraction of desired structural features of comparable quality.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Historic Context, Character-Defining Elements, And Photographic Record For A 26.45-Mile Segment Of The 138-Kilovolt Power Transmission System, Areas 3, 5, 6, And 23, Nevada National Security Site, Nye County, Nevada

The subject of this report is the 138-kilovolt (kV) power transmission line on the Nevada National Security Site (NNSS) (see Figure 1). The NNSS, formerly the Nevada Test Site (NTS), was the main continental nuclear test site for the United States between 1951 and 1992. Known as the battleground of the Cold War, the NNSS hosted a total of 928 nuclear tests during that period. It also served as the location of numerous scientific advancements in the fields of rocketry, big-hole drilling, nuclear waste management, and defense. From its construction in the 1960s through the present day, the 138 kV line has provided electrical power to the numerous buildings, facilities, experiments, and tests on the NNSS. The Department of Energy (DOE), in consultation with the Nevada State Historic Preservation Officer (SHPO), has determined that it may contribute to the character and significance of the Mercury Historic District (MHD) on the NNSS, as well as other historic districts that have not been recorded or evaluated yet. The purpose of this report is to fulfill two of the stipulations in the Memorandum of Agreement DEGM58-22NA25553 between the U.S. Department of Energy and the Nevada State Historic Preservation Officer Regarding Installation of a 138-kilovolt Transmission Line from the Mercury Switching Station to the U1a Facility and the Removal of the Historic 138-kilovolt Transmission Line from the Mercury Switching Station to the U1a Facility in Areas 1, 3, 5, 6, and 23 of the Nevada National Security Site (MOA). The MOA was executed as part of the DOE’s obligations under Section 106 of the National Historic Preservation Act (NHPA) to mitigate the adverse effects of two undertakings on historic properties. In particular, this report fulfills MOA Stipulations III.C.1-3, which state that the Department of Energy (DOE) will prepare the following: A historic context for the 138 kV transmission line and identification of the line’s characterdefining elements; High-quality digital images of the 26.45-mile segment of the 138 kV transmission line that is subject to the two undertakings for which the MOA was executed; and Photograph catalogs and map keys showing photograph viewpoints and directions.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1979

USDA analyst review of the LACIE IMAGE-100 hybrid system test

Fifty operational segments from the U.S.S.R., 40 test segments from Canada, and 24 test segments from the United States were used to provide a wide range of geographic conditions for USDA analysts during a test to determine the effectiveness of labeling single pixel training fields (dots) using Procedure 1 on the 1-100 hybrid system, and clustering and classifying on the Earth Resources Interactive Processing System. The analysts had additional on-line capabilities such as interactive dot labeling, class or cluster map overlay flickers, and flashing of all dots of equal spectral value. Results on the 1-100 hybrid system are described and analyst problems and recommendations are discussed.

Ashburn, P.↗
DOE OSTI2014

Structural analysis of cortical porosity applied to HR-pQCT data

Purpose: The investigation of cortical porosity is an important aspect of understanding biological, pathoetiological, and biomechanical processes occurring within the skeleton. With the emergence of HR-pQCT as a noninvasive tool suitable for clinical use, cortical porosity at appendicular sites can be directly visualizedin vivo. The aim of this study was to introduce a novel topological analysis of the cortical pore network for HR-pQCT data and determine the influence of resolution on measures of cortical pore network microstructure and topology. Methods: Cadaveric radii were scanned using HR-pQCT at two different voxel sizes (41 and 82μm) and also using μCT at a voxel size of 18 μm. HR-pQCT and μCT image sets were spatially coregistered. Segmentation and quantification of cortical porosity (Ct.Po) and mean pore diameter (Ct.Po.Dm) were achieved using an established extended cortical analysis technique. Topological classification of individual pores was performed using topology-preserving skeletonization and multicolor dilation algorithms. Based on the pore skeleton topological classification, the following parameters were quantified: total number of planar surface-skeleton canals (N.Slabs), tubular curve-skeleton canals (N.Tubes), and junction elements (N.Junctions), mean slab volume (Slab.Vol), mean tube volume (Tube.Vol), mean slab orientation (Slab.θ), mean tube orientation (Tube.θ), N.Slabs/N.Tubes, and integral (total) slab volume/integral tube volume (iSlab.Vol/iTube.Vol). An in vivo reproducibility study was also conducted to assess short-term precision of the topology parameters. Precision error was characterized using root mean square coefficient of variation (RMSCV%). Results: Correlations toμCT values for Ct.Po were significant for both the 41 and 82 μm HR-pQCT data (41: r{sup 2} = 0.82, p < 0.001, 82: r{sup 2} = 0.75, p < 0.001). For Ct.Po.Dm, only the 41 μm data were significantly predictive of μCT values (r{sup 2} = 0.72, p < 0.01) Data at both HR-pQCT voxel sizes were strongly predictive of the μCT values for N.Slabs (41: r{sup 2} = 0.93, p < 0.001; 82: r{sup 2} = 0.84, p < 0.001), N.Tubes (41: r{sup 2} = 0.94, p < 0.001; 82: r{sup 2} = 0.84, p < 0.001), and N.Junctions (41: r{sup 2} = 0.93, p < 0.001; 82: r{sup 2} = 0.78, p < 0.001), though proportional bias was evident in these correlations. Weak correlations were seen for iSlab.Vol/iTube.Vol at both voxel sizes (41: r{sup 2} = 0.52, p < 0.01; 82: r{sup 2} = 0.39, p < 0.05). Slab.Vol was significantly correlated to μCT data at 41 μm (r{sup 2} = 0.60, p < 0.01) but not at 82 μm, while Tube.Vol was significantly correlated at both voxel sizes (41: r{sup 2} = 0.79, p < 0.001; 82: r{sup 2} = 0.68, p < 0.01). In vivo precision error for these parameters ranged from 2.31 to 9.68 RMSCV%. Conclusions: Strong correlations betweenμCT- and HR-pQCT-derived measurements were found, particularly in HR-pQCT images obtained at 41 μm. These data are in agreement with our previous study investigating the effect of voxel size on standard HR-pQCT metrics of trabecular and cortical microstructure, and extend our previous findings to include topological descriptors of the cortical pore network.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2026

Automated Bacterial Identification and Morphological Feature Analysis in Low‐Dose Cryo‐EM Using YOLOv11

Bacteria rapidly adapt to environmental cues through morphological and ultrastructural changes that correlate with physiology and behavior. Cryogenic transmission electron microscopy (cryo‐TEM) can capture these phenotypic changes in near‐native, vitrified states, but manual analysis of low‐dose micrographs is labor intensive and limits throughput. Here, we present an end‐to‐end workflow that combines low‐dose cryo‐TEM imaging with a YOLOv11‐based instance‐segmentation model to automatically identify bacteria and quantify key structural features directly from the micrographs. This workflow enables (i) robust bacterial localization and counting from low‐magnification atlas/montage images, (ii) automated measurements of cell‐envelope (outer–inner membrane) thickness and anisotropy from higher‐magnification views, and (iii) detection and quantification of bacteria–flagella interactions, including overlap length and curvature metrics for interacting versus noninteracting flagella. Using Pantoea sp. YR343 grown under distinct media conditions, we show that the automated measurements agree with manual annotations while substantially reducing analysis time. Together, these tools provide a practical framework for scalable bacterial identification and quantitative phenotyping in low‐dose cryo‐TEM datasets and establish a foundation for extending cryo‐TEM image analysis toward higher‐throughput studies of microbial heterogeneity and biointerfaces.

YOLOv11↗
DOE OSTI2013

Evaluation of a semiautomated lung mass calculation technique for internal dosimetry applications

Purpose: The authors sought to evaluate a simple, semiautomated lung mass estimation method using computed tomography (CT) scans obtained using a variety of acquisition techniques and reconstruction parameters for mass correction of medical internal radiation dose-based internal radionuclide radiation absorbed dose estimates.Methods: CT scans of 27 patients with lung cancer undergoing stereotactic body radiation therapy treatment planning with PET/CT were analyzed retrospectively. For each patient, free-breathing (FB) and respiratory-gated 4DCT scans were acquired. The 4DCT scans were sorted into ten respiratory phases, representing one complete respiratory cycle. An average CT reconstruction was derived from the ten-phase reconstructions. Mid expiration breath-hold CT scans were acquired in the same session for many patients. Deep inspiration breath-hold diagnostic CT scans of many of the patients were obtained from different scanning sessions at similar time points to evaluate the effect of contrast administration and maximum inspiration breath-hold. Lung mass estimates were obtained using all CT scan types, and intercomparisons made to assess lung mass variation according to scan type. Lung mass estimates using the FB CT scans from PET/CT examinations of another group of ten male and ten female patients who were 21–30 years old and did not have lung disease were calculated and compared with reference lung mass values. To evaluate the effect of varying CT acquisition and reconstruction parameters on lung mass estimation, an anthropomorphic chest phantom was scanned and reconstructed with different CT parameters. CT images of the lungs were segmented using the OsiriX MD software program with a seed point of about −850 HU and an interval of 1000. Lung volume, and mean lung, tissue, and air HUs were recorded for each scan. Lung mass was calculated by assuming each voxel was a linear combination of only air and tissue. The specific gravity of lung volume was calculated using the formula (lung HU − air HU)/(tissue HU − air HU), and mass = specific gravity × total volume × 1.04 g/cm{sup 3}.Results: The range of calculated lung masses was 0.51–1.29 kg. The average male and female lung masses during FB CT were 0.80 and 0.71 kg, respectively. The calculated lung mass varied across the respiratory cycle but changed to a lesser degree than did lung volume measurements (7.3% versus 15.4%). Lung masses calculated using deep inspiration breath-hold and average CT were significantly larger (p < 0.05) than were some masses calculated using respiratory-phase and FB CT. Increased voxel size and smooth reconstruction kernels led to high lung mass estimates owing to partial volume effects.Conclusions: Organ mass correction is an important component of patient-specific internal radionuclide dosimetry. Lung mass calculation necessitates scan-based density correction to account for volume changes owing to respiration. The range of lung masses in the authors’ patient population represents lung doses for the same absorbed energy differing from 25% below to 64% above the dose found using reference phantom organ masses. With proper management of acquisition parameters and selection of FB or midexpiration breath hold scans, lung mass estimates with about 10% population precision may be achieved.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
NASA NTRS2008

Computer-implemented system and method for automated and highly accurate plaque analysis, reporting, and visualization

A computer-implemented system and method of intra-oral analysis for measuring plaque removal is disclosed. The system includes hardware for real-time image acquisition and software to store the acquired images on a patient-by-patient basis. The system implements algorithms to segment teeth of interest from surrounding gum, and uses a real-time image-based morphing procedure to automatically overlay a grid onto each segmented tooth. Pattern recognition methods are used to classify plaque from surrounding gum and enamel, while ignoring glare effects due to the reflection of camera light and ambient light from enamel regions. The system integrates these components into a single software suite with an easy-to-use graphical user interface (GUI) that allows users to do an end-to-end run of a patient record, including tooth segmentation of all teeth, grid morphing of each segmented tooth, and plaque classification of each tooth image.

Kemp, James Herbert↗
DOE OSTI2023

Multimodal Few-Shot Segmentation of Electron Micrographs

Scanning transmission electron microscopy (STEM) is one of the most used methods of analyzing the chemistry and composition of materials. By analyzing microstructures, these microscopes can help scientists better understand the molecular underpinnings of microelectronics, batteries, and more. However, STEM data can be difficult to interpret, so recent developments have been made in applications of machine learning to analyze these images. The PNNL-developed pyCHIP Classifier has achieved results in segmenting STEM these images via few-shot learning, a method which requires little data and human input, perfect for quickly analysis. In my internship I (Eli Meyers) investigated a multimodal improvement of this classifier by incorporating energy dispersive x-ray spectroscopy (EDS) data into the classification process for a more accurate segmentation. Furthermore, I encoded the spectral data by training a mass spectrometry encoder on the EDS data to extract a more meaningful representation of the data.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Quantitative wood–adhesive penetration with X-ray computed tomography

Micro X-ray computed tomography (XCT) was used to analyze the 3D adhesive penetration behavior of different wood–adhesive bondlines. Three adhesives, a phenol formaldehyde (PF), a polymeric diphenylmethane diisocyanate (pMDI), and a hybrid polyvinyl acetate (PVA), all tagged with iodine for enhanced X-ray attenuation, were used to prepare single-bondline laminates in two softwoods, Douglas-fir and loblolly pine, and one hardwood, a hybrid polar. Adhesive penetration depth was measured with two separate calculations, and results were compared with 2D fluorescent micrographs. A total of 54 XCT scans were collected, representing six replicates of each treatment type; each replicate, however, consisted of approximately 1500 individual, cross-section slices stacked along the specimen length. As these adhesives were highly modified, the presented results do not indicate typical behavior for their broader adhesive classes. Still, clear penetration differences were observed between each adhesive type, and between wood species bonded with both the PF and pMDI adhesives. Furthermore, penetration results depended on the calculation method used. Two adhesive types with noticeably different resin distributions in the cured bondline, showed relatively similar penetration depths when calculated with a traditional effective penetration equation. However, when the same data was calculated with a weighted penetration calculation, which accounts for both adhesive area and depth, the results appeared to better represent the different distributions depicted in the photomicrographs and tomograms. Additionally, individual replicate comparisons showed variation due to specimen anatomy, not easily observed or interpreted from 2D images. Finally, 3D views of segmented 3D adhesive phases offered unique, in-situ views of the cured adhesive structures. In particular, voids formed by CO 2 bubbles generated during pMDI cure were clearly visible in penetrated columns of the solidified adhesive.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2017

Characterization of fission gas bubbles in irradiated U-10Mo fuel

Irradiated U-10Mo fuel samples were prepared with traditional mechanical potting and polishing methods with in a hot cell. They were then removed and imaged with an SEM located outside of a hot cell. The images were then processed with basic imaging techniques from 3 separate software packages. The results were compared and a baseline method for characterization of fission gas bubbles in the samples is proposed. It is hoped that through adoption of or comparison to this baseline method that sample characterization can be somewhat standardized across the field of post irradiated examination of metal fuels.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses

Complex morphological traits are the product of many genes with transient or lasting developmental effects that interact in anatomical context. Mouse models are a key resource for disentangling such effects, because they offer myriad tools for manipulating the genome in a controlled environment. Unfortunately, phenotypic data are often obtained using laboratory-specific protocols, resulting in self-contained datasets that are difficult to relate to one another for larger scale analyses. To enable meta-analyses of morphological variation, particularly in the craniofacial complex and brain, we created MusMorph, a database of standardized mouse morphology data spanning numerous genotypes and developmental stages, including E10.5, E11.5, E14.5, E15.5, E18.5, and adulthood. To standardize data collection, we implemented an atlas-based phenotyping pipeline that combines techniques from image registration, deep learning, and morphometrics. Alongside stage-specific atlases, we provide aligned micro-computed tomography images, dense anatomical landmarks, and segmentations (if available) for each specimen (N = 10,056). Our workflow is open-source to encourage transparency and reproducible data collection.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2016

SU-F-T-516: Effects of Inter-Fraction Organ Displacement/deformation On the Delivered Doses to the Heart, Esophagus, and Lungs in Patients Receiving Thoracic Radiotherapy

Purpose: To quantitatively assess the effects of inter-fraction changes in organ shape and location on the delivered dose distribution to the organs at risk (OAR) in lung cancer patients. Methods: This study analyzes treatment data of 10 patients, who were treated to 60Gy in 30 fractions. In each fraction a cone beam CT (CBCT) was acquired. Each CBCT was registered with the planning CT using deformable registration tools within MIM Software. The daily setup shifts were used to translate the planned dose distribution on the deformed planning CT. The structures of lungs, esophagus and heart were re-delineated by a physician on each CBCT. The doses delivered to each OAR, reflecting changes in the position and shape variations, were recomputed. Resultant daily dose volume histograms (DVHs) for OARs were computed and compared to those from the planning CT. Results: Based on the findings of two patients and 24 CBCTs analyzed so far, higher doses are delivered to the lungs and esophagus compared to the treatment plan. The dose differences per fraction between the delivered doses and those in the treatment plan are: for patient 1, lung mean dose = 5.3±1.3cGy and esophagus mean dose = 3.4±3.5cGy. For patient 2, lung mean dose = 12.0±3.9cGy and esophagus mean dose = 34.2±7.5cGy. Regarding the maximum dose to heart, the results varied (−18.9±22.0cGy for patient1 and 53.0±62.2cGy for patient2). Conclusion: The dosimetric effects of inter-fractional anatomical variations could be estimated using deformable image registration and manual organ segmentation for each CBCT. A considerable dose distribution variation between fractions was observed for the OARs. These changes are currently not taken into account while treating the patients and these may explain cases with severe side effects even when the treatment plan looks satisfactory. These results suggest the need for automated daily dose tracking and accumulation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

TH-AB-207A-06: The Use of Realistic Phantoms to Predict CT Dose to Pediatric Patients

Purpose: To predict pediatric patient dose from diagnostic CT scans using Monte Carlo simulation of realistic reference phantoms of various ages, weights, and heights. Methods: A series of deformable pediatric reference phantoms using Non-Uniform Rational B-Splines (NURBS) was developed for a large range of ages, percentiles, and reference anatomy. Individual bones were modeled using age-dependent factors, and red marrow was modeled as functions of age and spatial distribution based on Cristy1. Organ and effective doses for the phantom series were calculated using Monte Carlo simulation of chest, abdominopelvic, and chest-abdomen-pelvis CT exams. Non-linear regression was performed to determine the relationship between dose-length-product (DLP)-normalized organ and effective doses and phantom diameter. Patient-specific voxel computational phantoms were also created by manual segmentation of previously acquired CT images for 40 pediatric patients (0.7 to 17 years). Organ and effective doses were determined by Monte Carlo simulation of these patient-specific phantoms. Each patient was matched to the closest pediatric reference phantom based primarily on age and diameter for all major organs within the torso. Results: A total of 80 NURBS phantoms were created ranging from newborn to 15 years with height/weight percentiles from 10 to 90%. Organ and effective dose normalized by DLP correlated strongly with exponentially decreasing average phantom diameter (R{sup 2} > 0.95 for most organs). A similar relationship was determined for the patient-specific voxel phantoms. Differences between patient-phantom matched organ-dose values ranged from 0.37 to 2.39 mGy (2.87% to 22.1%). Conclusion: Dose estimation using NURBS-based pediatric reference phantoms offers the ability to predict patient dose before and after CT examinations, and physicians and scientists can use this information in their analysis of dose prescriptions for particular subjects and study types. This may lead to practices that minimize radiation dose while still achieving high quality images and, ultimately, improved patient care. NIH/NCI 1 R01 CA155400-01A1.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

SkX_NN: Neural Network for skyrmion identification in Lorentz TEM

A neural network for segmenting and processing Lorentz TEM images of skyrmion lattices. This software based on U-Net architecture is capable of identifying skyrmions in out-of-focus Lorentz TEM images based on training data. This isspecifically useful for analyzing large area data from in-situ experiments.

PHATAK, CHARUDATTA↗
DOE OSTI2014

Developing a Massively Parallel Forward Projection Radiography Model for Large-Scale Industrial Applications

This project utilizes Graphics Processing Units (GPUs) to compute radiograph simulations for arbitrary objects. The generation of radiographs, also known as the forward projection imaging model, is computationally intensive and not widely utilized. The goal of this research is to develop a massively parallel algorithm that can compute forward projections for objects with a trillion voxels (3D pixels). To achieve this end, the data are divided into blocks that can each t into GPU memory. The forward projected image is also divided into segments to allow for future parallelization and to avoid needless computations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2026

Advancing SiC clad fuel performance model: bridging micro- and macro-scale models and experimental validation

This report presents a workflow for advancing fuel performance modeling of SiC composite cladding for light-water reactors by linking microscale, experimental data-informed finite element analysis with rod-scale fuel performance codes such as BISON. The workflow uses X-ray computed tomography (XCT) to capture the actual geometry and processing-induced defects of as-fabricated SiC composite tube specimens, particularly porosity and wall-thickness variations, and converts the segmented XCT volumes into image-based finite element meshes for high fidelity structural analysis.

Koyanagi, Takaaki [Oak Ridge National Laboratory (↗
NASA NTRS1979

Robotic vision

Robotic vision, involving the use of a vision system to control a process, is discussed. Design and selection of active sensors employing radiation of radio waves, sound waves, and laser light, respectively, to light up unobservable features in the scene are considered, as are design and selection of passive sensors, which rely on external sources of illumination. The segmentation technique by which an image is separated into different collections of contiguous picture elements having such common characteristics as color, brightness, or texture is examined, with emphasis on the edge detection technique. The IMFEX (image feature extractor) system performing edge detection and thresholding at 30 frames/sec television frame rates is described. The template matching and discrimination approach to recognize objects are noted. Applications of robotic vision in industry for tasks too monotonous or too dangerous for the workers are mentioned.

Williams, D. S.↗