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At least 379 records · Page 21

EGS Collab Experiment 1: 3D Seismic Velocity Model and Updated Microseismic Catalog Using Transfer-Learning Aided Double-Difference Tomography

This package contains a 3D Seismic velocity model and an updated microseismic catalog associated with a proceedings paper (Chai et al., 2020) published in the 45th Workshop on Geothermal Reservoir Engineering. The 3D_seismic_velocity_model text file contains x (m), y(m), z(m), P-wave velocity (km/s), P-wave velocity quality indicator (1 for well-constrained; 0 for poorly constrained), S-wave velocity (km/s), and S-wave velocity quality indicator (1 for well-constrained; 0 for poorly constrained). The Updated_MEQ_catalog text file contains event origin time, x(m), y(m), z(m), error in x (m), error in y (m), error in z (m), and RMS misfit (millisecond). The 3D_seismic_P-wave_velocity_model animation file shows slices of the 3D P-wave velocity model. The 3D_seismic_S-wave_velocity_model animation file shows slices of the 3D S-wave velocity model. The Interactive_MEQ_locations API file is an interactive visualization of the updated microseismic event locations. The visualization allows users to view the event locations by dragging, rotating, and zooming in. References: Chai, C., Maceira, M., Santos-Villalobos, H. J., Venkatakrishnan, S. V., Schoenball, M., and EGS Collab Team, 2020, Automatic Seismic Phase Picking Using Deep Learning for the EGS Collab Project, in PROCEEDINGS, 45th Workshop on Geothermal Reservoir Engineering, edited, Stanford University, Stanford, California, 45, 1266-1276.

15 GEOTHERMAL ENERGY↗

Integrative visualization of the molecular structure of a cellular microdomain

Abstract An integrative approach to visualization is used to create a visual snapshot of the structural biology of the polar microdomain of Caulobacter crescentus . The visualization is based on the current state of molecular and cellular knowledge of the microdomain and its cellular context. The collaborative process of researching and executing the visualization has identified aspects that are well determined and areas that require further study. The visualization is useful for dissemination, education, and outreach, and the study lays the groundwork for future 3D modeling and simulation of this well‐studied example of a cellular condensate.

59 BASIC BIOLOGICAL SCIENCES↗

Demonstration of 3D Shower Reconstruction on MicroBooNE Data

Utilizing a sample of $\nu_µ$ inclusive charged current events we select four events which visually contain π 0 decays associated with a neutrino interaction vertex. This sample of charged current induced π 0 s provides us with data-driven photon showers to vet our reconstruction. The π 0 provides us with a standard candle to study how our shower reconstruction performs. The vertex of the interaction is determined by the start point of the long muon track in the event and the π 0 production point. We utilize two different methods to cluster the charge coming from these showers and reconstruct the 3D properties of the showers.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Development and validation of an automatic method to detect the latest contracting viable left ventricular segments to assist guide CRT therapy from gated SPECT myocardial perfusion imaging

Objectives: The purpose of this study is to use ECG-gated SPECT MPI to detect the latest contracting viable left ventricular (LV) segments to help guide the LV probe placement used in CRT therapy and to validate segment selection against the visual integration method by experts. Methods: For each patient, the resting ECG-gated SPECT MPI short-axis images were sampled in 3D to generate a polar map of the perfusion distribution used to determine LV myocardial viability, and to measure LV synchronicity using our phase analysis tool. In the visual integration method, two experts visually interpreted the LV viability and mechanical dyssynchrony from the short-axis images and polar maps of viability and phase, to determine the latest contracting viable segments using the 17-segment model. In the automatic method, the apical segments, septal segments, and segments with more than 50% scar were excluded as these are not candidates for CRT LV probe placement. Amongst the remaining viable segments, the segments, whose phase angles were within 10° of the latest phase angle (the most delayed contracting segment), were identified for potential CRT LV probe placement and ranked based on the phase angles of the segments. Both methods were tested in 36 pre-CRT patients who underwent ECG-gated SPECT MPI. The accuracy was determined as the percent agreement between the visual integration and automatic methods. The automatic method was performed by a second independent operator to evaluate the inter-operator processing reproducibility. Results: In all the 36 patients, the LV lead positions of the 1st choices recommended by the automatic and visual integration methods were in the same segments in 35 patients, which achieved an agreement rate of 97.2%. In the inter-operator reproducibility test, the LV lead positions of the 1st choices recommended by the two operators were in the same segments in 25 patients, and were in the adjacent segments in 7 patients, which achieved an overall agreement of 88.8%. Conclusions: An automatic method has been developed to detect the latest contracting viable LV segments to help guide the LV probe placement used in CRT therapy. The retrospective clinical study with 36 patients suggests that this method has high agreement against the visual integration method by experts and good inter-operator reproducibility. Consequently, this method is promising to be a clinical tool to recommend the CRT LV lead positions.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Quantitative Nanoscale 3D Imaging of Intergranular Corrosion of 304 Stainless Steel Using Hard X-Ray Nanoprobe

Multi-modal imaging, which visualizes changes in the structure and chemistry of the same region of interest in materials by combining various techniques, is becoming attractive to material scientists. Here, we describe a multi-modal approach to investigate intergranular (IG) corrosion of sensitized stainless steels using synchrotron-based nanoscale X-ray imaging with sensitivity to microstructure and chemical composition. Three-dimensional tomography of 304 stainless steel samples deteriorated by IG corrosion, was carried out using X-ray fluorescence and differential phase contrast imaging. These findings were further supported with surface imaging and chemical analysis using scanning electron microscopy and energy dispersive X-ray spectroscopy. The combined quantitative structural and chemical analysis indicates that chromium segregates along grain boundaries, cracking is due to IG corrosion, and Cr-enrichment occurs on the cracked surfaces. Such quantitative 3D imaging of Cr 23 C 6 nucleation at grain boundaries and Cr enriched oxides at cracked surfaces is a powerful tool to correlate IG corrosion mechanisms at nanoscale with buried grain boundary structure and alloy composition. Such understanding of IG corrosion mechanisms is critical for both the development of predictive multiscale corrosion models, and the engineering of corrosion resistant materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

TU-F-17A-04: Respiratory Phase-Resolved 3D MRI with Isotropic High Spatial Resolution: Determination of the Average Breathing Motion Pattern for Abdominal Radiotherapy Planning

Purpose: To develop a retrospective 4D-MRI technique (respiratory phase-resolved 3D-MRI) for providing an accurate assessment of tumor motion secondary to respiration. Methods: A 3D projection reconstruction (PR) sequence with self-gating (SG) was developed for 4D-MRI on a 3.0T MRI scanner. The respiration-induced shift of the imaging target was recorded by SG signals acquired in the superior-inferior direction every 15 radial projections (i.e. temporal resolution 98 ms). A total of 73000 radial projections obtained in 8-min were retrospectively sorted into 10 time-domain evenly distributed respiratory phases based on the SG information. Ten 3D image sets were then reconstructed offline. The technique was validated on a motion phantom (gadolinium-doped water-filled box, frequency of 10 and 18 cycles/min) and humans (4 healthy and 2 patients with liver tumors). Imaging protocol included 8-min 4D-MRI followed by 1-min 2D-realtime (498 ms/frame) MRI as a reference. Results: The multiphase 3D image sets with isotropic high spatial resolution (1.56 mm) permits flexible image reformatting and visualization. No intra-phase motion-induced blurring was observed. Comparing to 2D-realtime, 4D-MRI yielded similar motion range (phantom: 10.46 vs. 11.27 mm; healthy subject: 25.20 vs. 17.9 mm; patient: 11.38 vs. 9.30 mm), reasonable displacement difference averaged over the 10 phases (0.74mm; 3.63mm; 1.65mm), and excellent cross-correlation (0.98; 0.96; 0.94) between the two displacement series. Conclusion: Our preliminary study has demonstrated that the 4D-MRI technique can provide high-quality respiratory phase-resolved 3D images that feature: a) isotropic high spatial resolution, b) a fixed scan time of 8 minutes, c) an accurate estimate of average motion pattern, and d) minimal intra-phase motion artifact. This approach has the potential to become a viable alternative solution to assess the impact of breathing on tumor motion and determine appropriate treatment margins. Comparison with 4D-CT in a clinical setting is warranted to assess the value of 4D-MRI in radiotherapy planning. This work supported in part by grant 1R03CA173273-01.

60 APPLIED LIFE SCIENCES↗

OPEN-Augmented Reality GUI for Bioenergy Crop Phenotyping and Precision Agriculture (Donald Danforth Plant Science Center Final Scientific Technical Report)

The project led by the Donald Danforth Plant Science Center, in collaboration with Arizona State University, George Washington University, and Saint Louis University, has made significant strides in advancing the phenotypic analysis of bioenergy crops through the development of an innovative AI processing pipeline. This initiative was primarily funded by ARPA-E, with additional cost-sharing provided by the participating institutions. The project successfully utilized a variety of sensors—3D scanners, thermal, RGB, and hyperspectral—to refine algorithms for data-driven trait signature identification and improve the classification and visualization of plant traits. The developed AI processing pipeline is capable of handling the complex, multidimensional data characteristic of dynamic agricultural environments. 1) Contributions to understanding: The research has advanced the field of plant phenomics by showcasing the synergistic use of various sensor data to enhance the precision of trait analysis in bioenergy crops. Through the integration of 3D scanners, thermal, RGB, and hyperspectral sensors, the project has developed robust data-driven trait signature algorithms and visualization techniques. These innovations have facilitated detailed monitoring and management of plant traits, providing vital insights into plant growth dynamics and stress responses. Further, the project has broadened our understanding of how machine learning can be effectively applied in multi-sensor environments to refine trait analysis. By leveraging diverse datasets, the research has not only improved the accuracy of phenotypic assessments but also established a versatile methodological framework that can be extended beyond agriculture to other fields requiring detailed phenotypic analysis. 2) Technical effectiveness and economic feasibility: The AI processing pipeline developed in this project demonstrated significant technical effectiveness, achieving high throughput analysis of extensive phenotypic data and meeting targeted accuracies. This system exemplified the capability of advanced machine learning technologies to efficiently manage and analyze large, complex datasets. Economically, the implementation of the project-developed pipelines may offer substantial cost savings across multiple sectors. It enhances data analysis processes and significantly reduces the need for manual data interpretation, thereby decreasing both the time and resources required. 3) Public benefit: The project has significantly broadened the scope of agricultural methodologies to enhance phenotypic analysis, with potential applications in various sectors beyond agriculture. Additionally, the initiative fostered an enriching educational and collaborative environment, significantly enhancing the technical skills of participants. It also made substantial contributions to the scientific community by providing open-access data sets and tools, encouraging ongoing research and development across various disciplines. Overall, the project not only met its scientific goals but also showcased the extensive utility of integrating advanced machine learning and sensor data analysis technologies. These advancements have proven instrumental in driving forward both theoretical research and practical applications, setting a strong foundation for future explorations and innovations in data-driven science.

60 APPLIED LIFE SCIENCES↗

TU-F-17A-01: BEST IN PHYSICS (JOINT IMAGING-THERAPY) - An Automatic Toolkit for Efficient and Robust Analysis of 4D Respiratory Motion

Purpose: To provide an automatic image analysis toolkit to process thoracic 4-dimensional computed tomography (4DCT) and extract patient-specific motion information to facilitate investigational or clinical use of 4DCT. Methods: We developed an automatic toolkit in MATLAB to overcome the extra workload from the time dimension in 4DCT. This toolkit employs image/signal processing, computer vision, and machine learning methods to visualize, segment, register, and characterize lung 4DCT automatically or interactively. A fully-automated 3D lung segmentation algorithm was designed and 4D lung segmentation was achieved in batch mode. Voxel counting was used to calculate volume variations of the torso, lung and its air component, and local volume changes at the diaphragm and chest wall to characterize breathing pattern. Segmented lung volumes in 12 patients are compared with those from a treatment planning system (TPS). Voxel conversion was introduced from CT# to other physical parameters, such as gravity-induced pressure, to create a secondary 4D image. A demon algorithm was applied in deformable image registration and motion trajectories were extracted automatically. Calculated motion parameters were plotted with various templates. Machine learning algorithms, such as Naive Bayes and random forests, were implemented to study respiratory motion. This toolkit is complementary to and will be integrated with the Computational Environment for Radiotherapy Research (CERR). Results: The automatic 4D image/data processing toolkit provides a platform for analysis of 4D images and datasets. It processes 4D data automatically in batch mode and provides interactive visual verification for manual adjustments. The discrepancy in lung volume calculation between this and the TPS is <±2% and the time saving is by 1–2 orders of magnitude. Conclusion: A framework of 4D toolkit has been developed to analyze thoracic 4DCT automatically or interactively, facilitating both investigational and clinical use. More software tools are under development for automatic analysis of other 4D imaging modalities. This research is in part supported by NIH (U54CA137788/132378) and City Seed FY13(Grant No. 93348-14 01). AY would like to thank MSKCC summer medical student research program supported by National Cancer Institute and hosted by Department of Medical Physics at MSKCC.

60 APPLIED LIFE SCIENCES↗

The application of cinematic rendering to CT evaluation of upper tract urothelial tumors: principles and practice

Upper tract urothelial carcinoma (UTUC) is a relatively uncommon but aggressive genitourinary malignancy for which multi-phase contrast-enhanced computed tomography (CT) plays an important role in evaluation and staging. 3D imaging with maximum intensity projection (MIP) and volume-rendered (VR) images has been described as a useful means of evaluating UTUC. In this study, we describe the technique of a novel 3D methodology known as cinematic rendering (CR) and provide clinical examples of UTUC visualized with CR. CR utilizes a complex universal lighting model in order to create photorealistic images with improved detail and depth in comparison to MIP or VR images. In the case of UTUC, CR can be used in different contrast phases to show abnormally thickened and enhancing urothelium or filling defects in the renal collecting system or ureters in the excretory phase. CR images can also be manipulated in order to generate translucent views of the upper urinary tract in order to add conspicuity to intraluminal findings.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Identification of optimal landforms to reduce impacts on the landscape using LiDAR for hosting a new highway

Highlights: •New territorial indicators were designed to quantify landscape impacts. •Reduction of visual impacts caused by new roads from planning and design stages. •LIDAR and 3D realistic views were considered to locate observer's views. •Bands of less cumulative impact were obtained as guides for highway tracing. •Preventive and corrective measures for impact mitigation were located.

54 ENVIRONMENTAL SCIENCES↗

The effects of neutral gas heating on H mode transition and maintenance currents in a 13.56 MHz planar coil inductively coupled plasma reactor

The H mode transition and maintenance currents in a 13.56 MHz laboratory 6 turn planar coil inductively coupled plasma (ICP) reactor are simulated for low pressure argon discharge range of 0.02-0.3 mbar with neutral gas heating and at ambient temperature. An experimentally fitted 3D power evolution plot for 0.02 mbar argon pressure is also shown to visualize the effects of hysteresis in the system. Comparisons between simulation and experimental measurements show good agreement in the pressure range of 0.02-0.3 mbar for transition currents and 0.02-0.1 mbar for maintenance currents only when neutral gas heating is considered. This suggests that neutral gas heating plays a non-negligible role in determining the mode transition points of a rf ICP system.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

An Update on Improvements to NiCE Support for RELAP-7

The Multiphysics Object-Oriented Simulation Environment (MOOSE) is a framework that facilitates the development of applications that rely on finite-element analysis to solve a coupled, nonlinear system of partial differential equations. RELAP-7 represents an update to the venerable RELAP-5 simulator that is built upon this framework and attempts to model the balance-of-plant concerns in a full nuclear plant. This report details the continued support and integration of RELAP-7 and the NEAMS Integrated Computational Environment (NiCE). RELAP-7 is fully supported by the NiCE due to on-going work to tightly integrate NiCE with the MOOSE framework, and subsequently the applications built upon it. NiCE development throughout the first quarter of FY15 has focused on improvements, bug fixes, and feature additions to existing MOOSE-based application support. Specifically, this report will focus on improvements to the NiCE MOOSE Model Builder, the MOOSE application job launcher, and the 3D Nuclear Plant Viewer. This report also includes a comprehensive tutorial that guides RELAP-7 users through the basic NiCE workflow: from input generation and 3D Plant modeling, to massively parallel job launch and post-simulation data visualization.

97 MATHEMATICS AND COMPUTING↗

Quant-CT: Segmenting and Quantifying Computed Tomography

Quant-CT is currently a plugin to ImageJ, designed as a Java-class that provides control mechanism for the user to choose volumes of interest within porous material, followed by the selection of image subsamples for automated tuning of parameters for filters and classifiers, and finally measurement of material geometry, porosity, and visualization. Denoising is mandatory before any image interpretation, and we implemented a new 3D java code that performs bilateral filtering of data. Segmentation of the dense material is essential before any quantifications about geological sample structure, and we invented new schemes to deal with over segmentation when using statistical region merging algorithm to pull out grains that compose imaged material. It make uses of ImageJ API and other standard and thirty-party APIs. Quant-CT conception started in 2011 under Scidac-e sponsor, and details of the first prototype were documented in publications below. While it is used right now for microtomography images, it can potentially be used by anybody with 3D image data obtained by experiment or produced by simulation.

Daniela Ushizima, Wes Bethel↗

3D Motion of DNA-Au Nanoconjugates in Graphene Liquid Cell Electron Microscopy

Liquid-phase transmission electron microscopy (TEM) can probe and visualize dynamic events with structural or functional details at the nanoscale in a liquid medium. Prior efforts have focused on the growth and transformation kinetics of hard material systems, relying on their stability under electron beam. Our recently developed graphene liquid cell technique pushed the spatial resolution of such imaging to the atomic scale but still focused on growth trajectories of metallic nanocrystals. Here, we adopt this technique to imaging three-dimensional (3D) dynamics of soft materials instead, double strand (dsDNA) connecting Au nanocrystals as one example, at nanometer resolution. We show first that a graphene liquid cell can seal an aqueous sample solution of a lower vapor pressure than previously investigated well against the high vacuum in TEM. Then, from quantitative analysis of real time nanocrystal trajectories, we show that the status and configuration of dsDNA dictate the motions of linked nanocrystals throughout the imaging time of minutes. This sustained connecting ability of dsDNA enables this unprecedented continuous imaging of its dynamics via TEM. Moreover, the inert graphene surface minimizes sample-substrate interaction and allows the whole nanostructure to rotate freely in the liquid environment; we thus develop and implement the reconstruction of 3D configuration and motions of the nanostructure from the series of 2D projected TEM images captured while it rotates. In addition to further proving the nanoconjugate structural stability, this reconstruction demonstrates 3D dynamic imaging by TEM beyond its conventional use in seeing a flattened and dry sample. Altogether, we foresee the new and exciting use of graphene liquid cell TEM in imaging 3D biomolecular transformations or interaction dynamics at nanometer resolution.

3D motion↗

Structural response of 3D-printed rubber lattice structures under compressive fatigue

In this work, a new direct UV curing, polyurethane-like, highly stretchable rubber, Elastic ToughRubber 90™ (ETR 90), is demonstrated for 3D printing via photocuring with Texas Instruments DLP® optical systems. An array of test specimens, comprising a sandwich structure with a body-centered cubic lattice core, are 3D printed from ETR 90. The compressive behavior of these specimens is characterized up to 10 k and up to 100 k fatigue-loading cycles. The internal, visually obstructed, structures under loads are visualized using in situ X-ray tomography. All lattice structures remain intact and full recovery is observed, indicating the cyclic durability of the 3D-printed rubber.

36 MATERIALS SCIENCE↗

Dispersion curve regression – assisted wideband local wavenumber analysis for characterizing three-dimensional (3D) profile of hidden corrosion damage

Corrosion as common damage in civil, petrochemical, nuclear, and aerospace structures affects the integrity and safety of the structures and may lead to catastrophic failures. This paper presents dispersion curve regression-assisted local wavenumber analysis method, which can analyze the time–space wavefield containing wideband information of wave-damage interaction and further extract the structural information carried by such wavefield for characterizing hidden corrosion damage in an isotropic plate. To acquire the time–space wavefield, a noncontact scanning laser Doppler vibrometer is used. In our analysis method, the acquired time–space wavefield is firstly processed to generate a local wavenumber function. The derived wavenumber function is further analyzed with a dispersion curve regression step, which searches in a set of theoretical frequency-wavenumber dispersion curves for different plate thicknesses and identifies the optimal plate thickness whose theoretical curve best matches the frequency-wavenumber relation contained in the local wavenumber function. By this means, a 3D profile including both in plane and thickness dimensions of the structure can be constructed for corrosion visualization and quantification. The experimental study demonstrates that our method can quantify the profile of hidden uniform corrosion in metal plates in terms of its in-plane shape and size as well as its out-of-plane depth in the subwavelength scale. Moreover, compared to previous Lamb wave-based corrosion inspection methods, our technique allows for noncontact 3D characterization of hidden corrosion from a far distance to the structure. Finally, we believe this work will inspire new 3D damage quantification methods that are based on wavefield analysis as well as enable potential applications for the quantification of hidden corrosion in civil, petrochemical, nuclear, and aerospace structures.

42 ENGINEERING↗

A VR-based volumetric medical image segmentation and visualization system with natural human interaction

Volume rendering produces informative two-dimensional (2D) images from a 3-dimensional (3D) volume. It highlights the region of interest and facilitates a good comprehension of the entire data set. However, volume rendering faces a few challenges. First, a high-dimensional transfer function is usually required to differentiate the target from its neighboring objects with subtle variance. Unfortunately, designing such a transfer function is a strenuously trial-and-error process. Second, manipulating/visualizing a 3D volume with a traditional 2D input/output device suffers dimensional limitations. To address all the challenges, we design NUI-VR 2 , a natural user interface-enabled volume rendering system in the virtual reality space. NUI-VR 2 marries volume rendering and interactive image segmentation. It transforms the original volume into a probability map with image segmentation. A simple linear transfer function will highlight the target well in the probability map. More importantly, we set the entire image segmentation and volume rendering pipeline in an immersive virtual reality environment with a natural user interface. NUI-VR 2 eliminates the dimensional limitations in manipulating and perceiving 3D volumes and dramatically improves the user experience.

42 ENGINEERING↗

MO-G-17A-03: MR-Based Cortical Bone Segmentation for PET Attenuation Correction with a Non-UTE 3D Fast GRE Sequence

Purpose: To determine the feasibility of identifying cortical bone on MR images with a short-TE 3D fast-GRE sequence for attenuation correction of PET data in PET/MR. Methods: A water-fat-bone phantom was constructed with two pieces of beef shank. MR scans were performed on a 3T MR scanner (GE Discovery™ MR750). A 3D GRE sequence was first employed to measure the level of residual signal in cortical bone (TE{sub 1}/TE{sub 2}/TE{sub 3}=2.2/4.4/6.6ms, TR=20ms, flip angle=25°). For cortical bone segmentation, a 3D fast-GRE sequence (TE/TR=0.7/1.9ms, acquisition voxel size=2.5×2.5×3mm{sup 3}) was implemented along with a 3D Dixon sequence (TE{sub 1}/TE{sub 2}/TR=1.2/2.3/4.0ms, acquisition voxel size=1.25×1.25×3mm{sup 3}) for water/fat imaging. Flip angle (10°), acquisition bandwidth (250kHz), FOV (480×480×144mm{sup 3}) and reconstructed voxel size (0.94×0.94×1.5mm{sup 3}) were kept the same for both sequences. Soft tissue and fat tissue were first segmented on the reconstructed water/fat image. A tissue mask was created by combining the segmented water/fat masks, which was then applied on the fast-GRE image (MRFGRE). A second mask was created to remove the Gibbs artifacts present in regions in close vicinity to the phantom. MRFGRE data was smoothed with a 3D anisotropic diffusion filter for noise reduction, after which cortical bone and air was separated using a threshold determined from the histogram. Results: There is signal in the cortical bone region in the 3D GRE images, indicating the possibility of separating cortical bone and air based on signal intensity from short-TE MR image. The acquisition time for the 3D fast-GRE sequence was 17s, which can be reduced to less than 10s with parallel imaging. The attenuation image created from water-fat-bone segmentation is visually similar compared to reference CT. Conclusion: Cortical bone and air can be separated based on intensity in MR image with a short-TE 3D fast-GRE sequence. Further research is required to optimize the strategy to reduce Gibbs artifacts.

60 APPLIED LIFE SCIENCES↗