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DOE OSTI2011

Virtual monochromatic imaging in dual-source dual-energy CT: Radiation dose and image quality

Purpose: To evaluate the image quality of virtual monochromatic images synthesized from dual-source dual-energy computed tomography (CT) in comparison with conventional polychromatic single-energy CT for the same radiation dose. Methods: In dual-energy CT, besides the material-specific information, one may also synthesize monochromatic images at different energies, which can be used for routine diagnosis similar to conventional polychromatic single-energy images. In this work, the authors assessed whether virtual monochromatic images generated from dual-source CT scanners had an image quality similar to that of polychromatic single-energy images for the same radiation dose. First, the authors provided a theoretical analysis of the optimal monochromatic energy for either the minimum noise level or the highest iodine contrast to noise ratio (CNR) for a given patient size and dose partitioning between the low- and high-energy scans. Second, the authors performed an experimental study on a dual-source CT scanner to evaluate the noise and iodine CNR in monochromatic images. A thoracic phantom with three sizes of attenuating rings was used to represent four adult sizes. For each phantom size, three dose partitionings between the low-energy (80 kV) and the high-energy (140 kV) scans were used in the dual-energy scan. Monochromatic images at eight energies (40 to 110 keV) were generated for each scan. Phantoms were also scanned at each of the four polychromatic single energy (80, 100, 120, and 140 kV) with the same radiation dose. Results: The optimal virtual monochromatic energy depends on several factors: phantom size, partitioning of the radiation dose between low- and high-energy scans, and the image quality metrics to be optimized. With the increase of phantom size, the optimal monochromatic energy increased. With the increased percentage of radiation dose on the low energy scan, the optimal monochromatic energy decreased. When maximizing the iodine CNR in monochromatic images, the optimal energy was lower than that when minimizing noise level. When the total radiation dose was equally distributed between low and high energy in dual-energy scans, for minimum noise, the optimal energies were 68, 71, 74, and 77 keV for small, medium, large, and extra-large (xlarge) phantoms, respectively; for maximum iodine CNR, the optimal energies were 66, 68, 70, 72 keV. With the optimal monochromatic energy, the noise level was similar to and the CNR was better than that in a single-energy scan at 120 kV for the same radiation dose. Compared to an 80 kV scan, however, the iodine CNR in monochromatic images was lower for the small, medium, and large phantoms. Conclusions: In dual-source dual-energy CT, optimal virtual monochromatic energy depends on patient size, dose partitioning, and the image quality metric optimized. With the optimal monochromatic energy, the noise level was similar to and the iodine CNR was better than that in 120 kV images for the same radiation dose. Compared to single-energy 80 kV images, the iodine CNR in virtual monochromatic images was lower for small to large phantom sizes.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2013

A virtual trial framework for quantifying the detectability of masses in breast tomosynthesis projection data

Purpose: Digital breast tomosynthesis (DBT) is a promising breast cancer screening tool that has already begun making inroads into clinical practice. However, there is ongoing debate over how to quantitatively evaluate and optimize these systems, because different definitions of image quality can lead to different optimal design strategies. Powerful and accurate tools are desired to extend our understanding of DBT system optimization and validate published design principles. Methods: The authors developed a virtual trial framework for task-specific DBT assessment that uses digital phantoms, open-source x-ray transport codes, and a projection-space, spatial-domain observer model for quantitative system evaluation. The authors considered evaluation of reconstruction algorithms as a separate problem and focused on the information content in the raw, unfiltered projection images. Specifically, the authors investigated the effects of scan angle and number of angular projections on detectability of a small (3 mm diameter) signal embedded in randomly-varying anatomical backgrounds. Detectability was measured by the area under the receiver-operating characteristic curve (AUC). Experiments were repeated for three test cases where the detectability-limiting factor was anatomical variability, quantum noise, or electronic noise. The authors also juxtaposed the virtual trial framework with other published studies to illustrate its advantages and disadvantages. Results: The large number of variables in a virtual DBT study make it difficult to directly compare different authors' results, so each result must be interpreted within the context of the specific virtual trial framework. The following results apply to 25% density phantoms with 5.15 cm compressed thickness and 500 {mu}m{sup 3} voxels (larger 500 {mu}m{sup 2} detector pixels were used to avoid voxel-edge artifacts): 1. For raw, unfiltered projection images in the anatomical-variability-limited regime, AUC appeared to remain constant or increase slightly with scan angle. 2. In the same regime, when the authors fixed the scan angle, AUC increased asymptotically with the number of projections. The threshold number of projections for asymptotic AUC performance depended on the scan angle. In the quantum- and electronic-noise dominant regimes, AUC behaviors as a function of scan angle and number of projections sometimes differed from the anatomy-limited regime. For example, with a fixed scan angle, AUC generally decreased with the number of projections in the electronic-noise dominant regime. These results are intended to demonstrate the capabilities of the virtual trial framework, not to be used as optimization rules for DBT. Conclusions: The authors have demonstrated a novel simulation framework and tools for evaluating DBT systems in an objective, task-specific manner. This framework facilitates further investigation of image quality tradeoffs in DBT.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

SU-E-J-94: Geometric and Dosimetric Evaluation of Deformation Image Registration Algorithms Using Virtual Phantoms Generated From Patients with Lung Cancer

Purpose: To generate virtual phantoms with clinically relevant deformation and use them to objectively evaluate geometric and dosimetric uncertainties of deformable image registration (DIR) algorithms. Methods: Ten lung cancer patients undergoing adaptive 3DCRT planning were selected. For each patient, a pair of planning CT (pCT) and replanning CT (rCT) were used as the basis for virtual phantom generation. Manually adjusted meshes were created for selected ROIs (e.g. PTV, lungs, spinal cord, esophagus, and heart) on pCT and rCT. The mesh vertices were input into a thin-plate spline algorithm to generate a reference displacement vector field (DVF). The reference DVF was used to deform pCT to generate a simulated replanning CT (srCT) that was closely matched to rCT. Three DIR algorithms (Demons, B-Spline, and intensity-based) were applied to these ten virtual phantoms. The images, ROIs, and doses were mapped from pCT to srCT using the DVFs computed by these three DIRs and compared to those mapped using the reference DVF. Results: The average Dice coefficients for selected ROIs were from 0.85 to 0.96 for Demons, from 0.86 to 0.97 for intensity-based, and from 0.76 to 0.95 for B-Spline. The average Hausdorff distances for selected ROIs were from 2.2 to 5.4 mm for Demons, from 2.3 to 6.8 mm for intensity-based, and from 2.4 to 11.4 mm for B-Spline. The average absolute dose errors for selected ROIs were from 0.2 to 0.6 Gy for Demons, from 0.1 to 0.5 Gy for intensity-based, and from 0.5 to 1.5 Gy for B-Spline. Conclusion: Virtual phantoms were modeled after patients with lung cancer and were clinically relevant for adaptive radiotherapy treatment replanning. Virtual phantoms with known DVFs serve as references and can provide a fair comparison when evaluating different DIRs. Demons and intensity-based DIRs were shown to have smaller geometric and dosimetric uncertainties than B-Spline. Z Shen: None; K Bzdusek: an employee of Philips Healthcare; J Greskovich: None; P Xia: received research grants from Philips Healthcare and Siemens Healthcare.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

WE-AB-BRA-12: Virtual Endoscope Tracking for Endoscopy-CT Image Registration

Purpose: The use of endoscopy in radiotherapy will remain limited until we can register endoscopic video to CT using standard clinical equipment. In this phantom study we tested a registration method using virtual endoscopy to measure CT-space positions from endoscopic video. Methods: Our phantom is a contorted clay cylinder with 2-mm-diameter markers in the luminal surface. These markers are visible on both CT and endoscopic video. Virtual endoscope images were rendered from a polygonal mesh created by segmenting the phantom’s luminal surface on CT. We tested registration accuracy by tracking the endoscope’s 6-degree-of-freedom coordinates frame-to-frame in a video recorded as it moved through the phantom, and using these coordinates to measure CT-space positions of markers visible in the final frame. To track the endoscope we used the Nelder-Mead method to search for coordinates that render the virtual frame most similar to the next recorded frame. We measured the endoscope’s initial-frame coordinates using a set of visible markers, and for image similarity we used a combination of mutual information and gradient alignment. CT-space marker positions were measured by projecting their final-frame pixel addresses through the virtual endoscope to intersect with the mesh. Registration error was quantified as the distance between this intersection and the marker’s manually-selected CT-space position. Results: Tracking succeeded for 6 of 8 videos, for which the mean registration error was 4.8±3.5mm (24 measurements total). The mean error in the axial direction (3.1±3.3mm) was larger than in the sagittal or coronal directions (2.0±2.3mm, 1.7±1.6mm). In the other 2 videos, the virtual endoscope got stuck in a false minimum. Conclusion: Our method can successfully track the position and orientation of an endoscope, and it provides accurate spatial mapping from endoscopic video to CT. This method will serve as a foundation for an endoscopy-CT registration framework that is clinically valuable and requires no specialized equipment.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

Virtual machine-based simulation platform for mobile ad-hoc network-based cyber infrastructure

In modeling and simulating complex systems such as mobile ad-hoc networks (MANETs) in de-fense communications, it is a major challenge to reconcile multiple important considerations: the rapidity of unavoidable changes to the software (network layers and applications), the difficulty of modeling the critical, implementation-dependent behavioral effects, the need to sustain larger scale scenarios, and the desire for faster simulations. Here we present our approach in success-fully reconciling them using a virtual time-synchronized virtual machine(VM)-based parallel ex-ecution framework that accurately lifts both the devices as well as the network communications to a virtual time plane while retaining full fidelity. At the core of our framework is a scheduling engine that operates at the level of a hypervisor scheduler, offering a unique ability to execute multi-core guest nodes over multi-core host nodes in an accurate, virtual time-synchronized manner. In contrast to other related approaches that suffer from either speed or accuracy issues, our framework provides MANET node-wise scalability, high fidelity of software behaviors, and time-ordering accuracy. The design and development of this framework is presented, and an ac-tual implementation based on the widely used Xen hypervisor system is described. Benchmarks with synthetic and actual applications are used to identify the benefits of our approach. The time inaccuracy of traditional emulation methods is demonstrated, in comparison with the accurate execution of our framework verified by theoretically correct results expected from analytical models of the same scenarios. In the largest high fidelity tests, we are able to perform virtual time-synchronized simulation of 64-node VM-based full-stack, actual software behaviors of MANETs containing a mix of static and mobile (unmanned airborne vehicle) nodes, hosted on a 32-core host, with full fidelity of unmodified ad-hoc routing protocols, unmodified application executables, and user-controllable physical layer effects including inter-device wireless signal strength, reachability, and connectivity.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2012

Virtual tool mark generation for efficient striation analysis in forensic science

In 2009, a National Academy of Sciences report called for investigation into the scienti c basis behind tool mark comparisons (National Academy of Sciences, 2009). Answering this call, Chumbley et al. (2010) attempted to prove or disprove the hypothesis that tool marks are unique to a single tool. They developed a statistical algorithm that could, in most cases, discern matching and non-matching tool marks made at di erent angles by sequentially numbered screwdriver tips. Moreover, in the cases where the algorithm misinterpreted a pair of marks, an experienced forensics examiner could discern the correct outcome. While this research served to con rm the basic assumptions behind tool mark analysis, it also suggested that statistical analysis software could help to reduce the examiner's workload. This led to a new tool mark analysis approach, introduced in this thesis, that relies on 3D scans of screwdriver tip and marked plate surfaces at the micrometer scale from an optical microscope. These scans are carefully cleaned to remove noise from the data acquisition process and assigned a coordinate system that mathematically de nes angles and twists in a natural way. The marking process is then simulated by using a 3D graphics software package to impart rotations to the tip and take the projection of the tip's geometry in the direction of tool travel. The edge of this projection, retrieved from the 3D graphics software, becomes a virtual tool mark. Using this method, virtual marks are made at increments of 5 and compared to a scan of the evidence mark. The previously developed statistical package from Chumbley et al. (2010) performs the comparison, comparing the similarity of the geometry of both marks to the similarity that would occur due to random chance. The resulting statistical measure of the likelihood of the match informs the examiner of the angle of the best matching virtual mark, allowing the examiner to focus his/her mark analysis on a smaller range of angles. Preliminary results are quite promising. In a study with both sides of 6 screwdriver tips and 34 corresponding marks, the method distinguished known matches from known non-matches with zero false positive matches and only two matches mistaken for non-matches. For matches, it could predict the correct marking angle within 5-10 . Moreover, on a standard desktop computer, the virtual marking software is capable of cleaning 3D tip and plate scans in minutes and producing a virtual mark and comparing it to a real mark in seconds. These results support several of the professional conclusions of the tool mark analysis com- munity, including the idea that marks produced by the same tool only match if they are made at similar angles. The method also displays the potential to automate part of the comparison process, freeing the examiner to focus on other tasks, which is important in busy, backlogged crime labs. Finally, the method o ers the unique chance to directly link an evidence mark to the tool that produced it while reducing potential damage to the evidence.

42 ENGINEERING↗

DOE OSTI2017

Enabling Diverse Software Stacks on Supercomputers using High Performance Virtual Clusters.

While large-scale simulations have been the hallmark of the High Performance Computing (HPC) community for decades, Large Scale Data Analytics (LSDA) workloads are gaining attention within the scientific community not only as a processing component to large HPC simulations, but also as standalone scientific tools for knowledge discovery. With the path towards Exascale, new HPC runtime systems are also emerging in a way that differs from classical distributed com- puting models. However, system software for such capabilities on the latest extreme-scale DOE supercomputing needs to be enhanced to more appropriately support these types of emerging soft- ware ecosystems. In this paper, we propose the use of Virtual Clusters on advanced supercomputing resources to enable systems to support not only HPC workloads, but also emerging big data stacks. Specifi- cally, we have deployed the KVM hypervisor within Cray's Compute Node Linux on a XC-series supercomputer testbed. We also use libvirt and QEMU to manage and provision VMs directly on compute nodes, leveraging Ethernet-over-Aries network emulation. To our knowledge, this is the first known use of KVM on a true MPP supercomputer. We investigate the overhead our solution using HPC benchmarks, both evaluating single-node performance as well as weak scaling of a 32-node virtual cluster. Overall, we find single node performance of our solution using KVM on a Cray is very efficient with near-native performance. However overhead increases by up to 20% as virtual cluster size increases, due to limitations of the Ethernet-over-Aries bridged network. Furthermore, we deploy Apache Spark with large data analysis workloads in a Virtual Cluster, ef- fectively demonstrating how diverse software ecosystems can be supported by High Performance Virtual Clusters.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Methods and systems relating to an augmented virtuality environment

Systems and methods relating to an augmented virtuality system are disclosed. A method of operating an augmented virtuality system may comprise displaying imagery of a real-world environment in an operating picture. The method may further include displaying a plurality of virtual icons in the operating picture representing at least some assets of a plurality of assets positioned in the real-world environment. Additionally, the method may include displaying at least one virtual item in the operating picture representing data sensed by one or more of the assets of the plurality of assets and remotely controlling at least one asset of the plurality of assets by interacting with a virtual icon associated with the at least one asset.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

An Integrated FDD System for HVAC&R Based on Virtual Sensors

According to the U.S Department of Energy, space heating, ventilation and air conditioning system account for 40% of residential primary energy use and for 30% of primary energy use in commercial buildings. A study released by the Energy Information Administration indicated that packaged air conditioners are widely used in 46% of all commercial buildings in the U.S. This study indicates that the annual cooling energy consumption related to the packaged air conditioner is about 160 trillion Btus. Therefore, an automated FDD system that can automatically detect and diagnose faults and evaluate fault impacts has the potential for improving energy efficiency along with reducing service costs and comfort complaints. The primary bottlenecks to diagnostic implementation in the field are the high initial costs of additional sensors. To prevent those limitations, virtual sensors with low cost measurements and simple models are developed to estimate quantities that would be expensive and or difficult to measure directly. The use of virtual sensors can reduce costs compared to the use of real sensors and provide additional information for economic assessment. The virtual sensor can be embedded in a permanently installed control or monitoring system and continuous monitoring potentially leads to early detection of faults. The virtual sensors of individual equipment components can be integrated to estimate overall diagnostic information using the output of each virtual sensor.

Kim, Woohyun↗

DOE OSTI2017

ViRPET--combination of virtual reality and PET brain imaging

Various methods, systems and apparatus are provided for brain imaging during virtual reality stimulation. In one example, among others, a system for virtual ambulatory environment brain imaging includes a mobile brain imager configured to obtain positron emission tomography (PET) scans of a subject in motion, and a virtual reality (VR) system configured to provide one or more stimuli to the subject during the PET scans. In another example, a method for virtual ambulatory environment brain imaging includes providing stimulation to a subject through a virtual reality (VR) system; and obtaining a positron emission tomography (PET) scan of the subject while moving in response to the stimulation from the VR system. The mobile brain imager can be positioned on the subject with an array of imaging photodetector modules distributed about the head of the subject.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

ViRPET—combination of virtual reality and PET brain imaging

Majewski, Stanislaw↗

DOE OSTI2019

Using virtual sensors to accommodate industrial asset control systems during cyber attacks

In some embodiments, an industrial asset may be associated with a plurality of monitoring nodes, each monitoring node generating a series of monitoring node values over time that represent operation of the industrial asset. A threat detection computer may determine that an attacked monitoring node is currently being attacked. Responsive to this determination, a virtual sensor coupled to the plurality of monitoring nodes may estimate a series of virtual node values for the attacked monitoring node(s) based on information received from monitoring nodes that are not currently being attacked. The virtual sensor may then replace the series of monitoring node values from the attacked monitoring node(s) with the virtual node values. Note that in some embodiments, virtual node values may be estimated for a particular node even before it is determined that the node is currently being attacked.

20 FOSSIL-FUELED POWER PLANTS↗

DOE OSTI2020

Using virtual sensors to accommodate industrial asset control systems during cyber attacks

Mestha, Lalit Keshav↗

DOE OSTI2017

Virtualized hardware environments for supporting digital I and C verification - 324

The technology of virtualized hardware testing platforms within the nuclear context in order to provide a framework for evaluating virtualized hardware/software approaches is discussed. To understand the applicability of virtualized hardware approaches, we have developed a virtual hardware model of an actual smart sensor using the Imperas product OVPsim development environment, as is seen in . An evaluation of the modeling effort required to create the digital I and C smart sensor is provided, followed by an analysis and findings on the various tools in the OVPsim environment for supporting testing, evidence collecting, and analysis. The analyzed tools include traditional input/output testing, model-based testing, mutation testing, and fault injection techniques. Finally, the goal of this research effort is to analyze virtual hardware platforms and present findings to the nuclear community on the efficacy and viability of this technology as a complementary means to actual hardware-in-the-loop testing Factory Acceptance Testing for Nuclear Power Plant (NPP) digital I and C systems. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2018

Harnessing Data Movement in Virtual Clusters for In-Situ Execution

As a result of increasing data volume and velocity, Big Data science at exascale has shifted towards the in-situ paradigm, where large scale simulations run concurrently alongside data analytics. With in-situ, data generated from simulations can be processed while still in memory, thereby avoiding the slow storage bottleneck. However, running simulations and analytics together on shared resources will likely result in substantial contention if left unmanaged, as demonstrated in this work, leading to much reduced efficiency of simulations and analytics. Recently, virtualization technologies such as Linux containers have been widely applied to data centers and physical clusters to provide highly efficient and elastic resource provisioning for consolidated workloads including scientific simulations and data analytics. In this paper, we investigate to facilitate network traffic manipulation and reduce mutual interference on the network for in-situ applications in virtual clusters. In order to dynamically allocate the network bandwidth when it is needed, we adopt SARIMA-based techniques to analyze and predict MPI traffic issued from simulations. Although this can be an effective technique, the naïve usage of network virtualization can lead to performance degradation for bursty asynchronous transmissions within an MPI job. Here, we analyze and resolve this performance degradation in virtual clusters.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

State of the Art of Molecular Visualization in Immersive Virtual Environments

Abstract Visualization plays a crucial role in molecular and structural biology. It has been successfully applied to a variety of tasks, including structural analysis and interactive drug design. While some of the challenges in this area can be overcome with more advanced visualization and interaction techniques, others are challenging primarily due to the limitations of the hardware devices used to interact with the visualized content. Consequently, visualization researchers are increasingly trying to take advantage of new technologies to facilitate the work of domain scientists. Some typical problems associated with classic 2D interfaces, such as regular desktop computers, are a lack of natural spatial understanding and interaction, and a limited field of view. These problems could be solved by immersive virtual environments and corresponding hardware, such as virtual reality head‐mounted displays. Thus, researchers are investigating the potential of immersive virtual environments in the field of molecular visualization. There is already a body of work ranging from educational approaches to protein visualization to applications for collaborative drug design. This review focuses on molecular visualization in immersive virtual environments as a whole, aiming to cover this area comprehensively. We divide the existing papers into different groups based on their application areas, and types of tasks performed. Furthermore, we also include a list of available software tools. We conclude the report with a discussion of potential future research on molecular visualization in immersive environments.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

A $C^1$-Conforming Arbitrary-Order Two-Dimensional Virtual Element Method for the Fourth-Order Phase-Field Equation

We present a two-dimensional conforming virtual element method for the fourth-order phase-field equation. Our proposed numerical approach to the solution of this high-order phase-field (HOPF) equation relies on the design of an arbitrary-order accurate, virtual element space with $C^1$ global regularity. Such regularity is guaranteed by taking the values of the virtual element functions and their full gradient at the mesh vertices as degrees of freedom. Attaining high-order accuracy requires also edge polynomial moments of the trace of the virtual element functions and their normal derivatives. In this work, we detail the scheme construction, and prove its convergence by deriving error estimates in different norms. A set of representative test cases allows us to assess the behavior of the method.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Long-term socioeconomic trends and climate variability as drivers of virtual water scarcity in China

Water scarcity can have far-reaching sectoral impacts beyond its physical location through the propagation of virtual water flows. Socioeconomic and hydroclimatic changes affect local and virtual water scarcity by altering availability and demand. Yet most studies of this phenomenon focus on volumetric footprints, and the few on water scarcity risk have not examined hydroclimatic variability beyond long-term trends. In this study, we ask how gross domestic product (GDP) and population changes, long-term meteorological trends, sea surface temperature (SST) patterns, and interannual meteorological variability affect water scarcity in China, both locally (through the local water scarcity risk index, LWSR) and remotely (through the virtual water scarcity risk index, VWSR). Counterfactual scenarios were compared in a regression-and-simulation framework, with the socioeconomic and meteorological drivers varying over 1923–2019 and the multi-regional input–output structure staying fixed at 2017. Relative to a 5 year baseline centered on 2017, GDP and population changes have induced a cumulative 17%–50% increase in LWSR and 13%–21% increase in VWSR, outweighing the effect of long-term meteorological trends. phase change in one of two examined SST patterns induce 4%–13% differences in LWSR and 1%–4% differences in VWSR. Interannual meteorological variability induces 10%–20% standard deviations in LWSR and 3%–7% in VWSR. The findings highlight the importance of using longer time series to accurately assess local and virtual water scarcity situations. Water scarcity management should prioritize socioeconomic factors when planning at century-long timescales and prioritize hydroclimatic factors at multidecadal or shorter timescales. water managers should consider interannual variabilities in LWSR and VWSR and plan for potential occurrences of extreme conditions.

climate variability↗