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At least 217 records · Page 12

Improving Scientific Data Analysis Through Multi-touch Enabled Interactive Data Visualization with Applications to Neutron Science

Scientific data analysis is an inherently exploratory process that requires flexible human interaction with data visualization and anal- ysis tools. In this paper, we describe challenges in neutron scattering data analysis and present our approach for allowing more effective human interaction. In addition to multi-touch enabled data visualiza- tion techniques, we describe color scale enhancements, layouts, and visual analytics approaches for 3D volume slicing. Since challenges in neutron science are echoed in most scientific fields, we generalize the project objective and present a case for bridging the gap between the latest advances in interactive data visualization and practical scientific scenarios where new critical knowledge is buried in large volumes of complex data.

Steed, Chad↗

SU-E-T-154: Establishment and Implement of 3D Image Guided Brachytherapy Planning System

Purpose: Cannot observe the dose intuitionally is a limitation of the existing 2D pre-implantation dose planning. Meanwhile, a navigation module is essential to improve the accuracy and efficiency of the implantation. Hence a 3D Image Guided Brachytherapy Planning System conducting dose planning and intra-operative navigation based on 3D multi-organs reconstruction is developed. Methods: Multi-organs including the tumor are reconstructed in one sweep of all the segmented images using the multiorgans reconstruction method. The reconstructed organs group establishs a three-dimensional visualized operative environment. The 3D dose maps of the three-dimentional conformal localized dose planning are calculated with Monte Carlo method while the corresponding isodose lines and isodose surfaces are displayed in a stereo view. The real-time intra-operative navigation is based on an electromagnetic tracking system (ETS) and the fusion between MRI and ultrasound images. Applying Least Square Method, the coordinate registration between 3D models and patient is realized by the ETS which is calibrated by a laser tracker. The system is validated by working on eight patients with prostate cancer. The navigation has passed the precision measurement in the laboratory. Results: The traditional marching cubes (MC) method reconstructs one organ at one time and assembles them together. Compared to MC, presented multi-organs reconstruction method has superiorities in reserving the integrality and connectivity of reconstructed organs. The 3D conformal localized dose planning, realizing the 'exfoliation display' of different isodose surfaces, helps make sure the dose distribution has encompassed the nidus and avoid the injury of healthy tissues. During the navigation, surgeons could observe the coordinate of instruments real-timely employing the ETS. After the calibration, accuracy error of the needle position is less than 2.5mm according to the experiments. Conclusion: The speed and quality of 3D reconstruction, the efficiency in dose planning and accuracy in navigation all can be improved simultaneously.

60 APPLIED LIFE SCIENCES↗

Quasi 3D ECE imaging system for study of MHD instabilities in KSTAR

A second electron cyclotron emission imaging (ECEI) system has been installed on the KSTAR tokamak, toroidally separated by 1/16th of the torus from the first ECEI system. For the first time, the dynamical evolutions of MHD instabilities from the plasma core to the edge have been visualized in quasi-3D for a wide range of the KSTAR operation (B{sub 0} = 1.7∼3.5 T). This flexible diagnostic capability has been realized by substantial improvements in large-aperture quasi-optical microwave components including the development of broad-band polarization rotators for imaging of the fundamental ordinary ECE as well as the usual 2nd harmonic extraordinary ECE.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Portable interactive visualization of large-scale simulations in geotechnical engineering using Unity3D

Development in large-scale geotechnical engineering simulation places tremendous demand for efficient visualization of such simulation data. This study presents a lightweight software tool, i.e. Geotechnical Interactive Visualization (GIV), as a solution to this challenge, which achieves efficient interactive visualization of large-scale simulations data in geotechnical engineering. Visualization data flow and algorithms specifically optimized for common geotechnical engineering applications are implemented in GIV. GIV can visualize geotechnical structure models with time-varying attributes attached to mesh with fixed topology, and also models with time-varying mesh topologies but no attributes attached, the two most common visualization tasks in geotechnical engineering. Furthermore, challenges for large-scale simulation data visualization, including parallel simulation data redundancy, massive data size, dynamic user interaction, and portability are overcome via specifically designed algorithms for simulation data preprocessing and optimized visualization modules using the powerful 3D rendering and interactive game engine Unity3D. Comparison of GIV with several widely used visualization tools for the visualization of large-scale idealized datasets and realistic geotechnical simulations highlights the visualization efficiency, smooth interactivity, and lightweight features of GIV.

42 ENGINEERING↗

Multiscale microstructural characterization of Sn-rich alloys by three dimensional (3D) X-ray synchrotron tomography and focused ion beam (FIB) tomography

Sn-rich (Pb-free) alloys serve as electrical and mechanical interconnects in electronic packaging. It is critical to quantify the microstructures of Sn-rich alloys to obtain a fundamental understanding of their properties. In this work, the intermetallic precipitates in Sn-3.5Ag and Sn-0.7Cu, and globular lamellae in Sn-37Pb solder joints were visualized and quantified using 3D X-ray synchrotron tomography and focused ion beam (FIB) tomography. 3D reconstructions were analyzed to extract statistics on particle size and spatial distribution. In the Sn-Pb alloy the interconnectivity of Sn-rich and Pb-rich constituents was quantified. It will be shown that multiscale characterization using 3D X-ray and FIB tomography enabled the characterization of the complex morphology, distribution, and statistics of precipitates and contiguous phases over a range of length scales. - Highlights: Black-Right-Pointing-Pointer Multiscale characterization by X-ray synchrotron and focused ion beam tomography. Black-Right-Pointing-Pointer Characterized microstructural features in several Sn-based alloys. Black-Right-Pointing-Pointer Quantified size, fraction, and clustering of microstructural features.

36 MATERIALS SCIENCE↗

Evaluation of camera-based freehand SPECT in preoperative sentinel lymph node mapping for melanoma patients

Assessment of lymphatic status via sentinel lymph node (SLN) biopsy is an integral and crucial part of melanoma surgical oncology. The most common technique for sentinel node mapping is preoperative planar scintigraphy of an injected gamma-emitting lymphatic tracer followed by intraoperative node localization using a non-imaging gamma probe with auditory feedback. In recent years, intraoperative visualization of SLNs in 3D has become possible by coupling the probe to an external system capable of tracking its location and orientation as it is read out, thereby enabling computation of the 3D distribution of the tracer (freehand SPECT). In this project, the non-imaging probe of the fhSPECT system was replaced by a unique handheld gamma camera containing an array of sodium iodide crystals optically coupled to an array of silicon photomultipliers (SiPMs). A feasibility study was performed in which preoperative SLN mapping was performed using camera fhSPECT and the number of detected nodes was compared to that visualized by lymphoscintigraphy, probe fhSPECT, and to the number ultimately excised under non-imaging probe guidance. Among five subjects, SLNs were detected in nine lymphatic basins, with one to five SLNs detected per basin. A basin-by-basin comparison showed that the number of SLNs detected using camera fhSPECT exceeded that using lymphoscintigraphy and probe fhSPECT in seven of nine basins and five of five basins, respectively. (Probe fhSPECT scans were not performed for four basins.) It exceeded the number excised under non-imaging probe guidance for seven of nine basins and equaled the number excised for the other two basins. Freehand SPECT using a prototype SiPM-based gamma camera demonstrates high sensitivity for detection of SLNs in a preoperative setting. Camera fhSPECT is a potential means for efficiently obtaining real-time 3D activity distribution maps in applications such as image-guided percutaneous biopsy, and surgical SLN biopsy or radioguided tumor excision.

60 APPLIED LIFE SCIENCES↗

Aggregating in vitro-grown adipocytes to produce macroscale cell-cultured fat tissue with tunable lipid compositions for food applications

We present a method of producing bulk cell-cultured fat tissue for food applications. Mass transport limitations (nutrients, oxygen, waste diffusion) of macroscale 3D tissue culture are circumvented by initially culturing murine or porcine adipocytes in 2D, after which bulk fat tissue is produced by mechanically harvesting and aggregating the lipid-filled adipocytes into 3D constructs using alginate or transglutaminase binders. The 3D fat tissues were visually similar to fat tissue harvested from animals, with matching textures based on uniaxial compression tests. The mechanical properties of cultured fat tissues were based on binder choice and concentration, and changes in the fatty acid compositions of cellular triacylglyceride and phospholipids were observed after lipid supplementation (soybean oil) during in vitro culture. This approach of aggregating individual adipocytes into a bulk 3D tissue provides a scalable and versatile strategy to produce cultured fat tissue for food-related applications, thereby addressing a key obstacle in cultivated meat production.

Yuen Jr, John Se Kit (ORCID:0000000198541654)↗

Influence of Entrainment on Centimeter-Scale Cloud Microphysics in Marine Stratocumulus Clouds Observed during CSET

Abstract Cloud microphysical relationships observed during the Cloud System Evolution in the Trades (CSET) campaign held between Northern California and Hawaii were analyzed to study the effects of entrainment and subsequent mixing of free-tropospheric and cloudy air on cloud microphysical properties of marine stratocumulus clouds. The data measured by Holographic Detector for Clouds (HOLODEC) were extensively used because they could provide the 3D positions and sizes of droplets within sample volume on the centimeter scale, making it possible to explore the 3D spatial distribution of droplets, which has not been possible for conventional cloud probes. This study focused on analyzing the 3D spatial distribution of droplets and visual traits of inhomogeneous mixing and on quantifying the relationship between 3D spatial distributions and traits of inhomogeneous mixing. Two types of spatial distributions are compared. The first is measured droplet spatial distribution and the second type is generated randomly distributed droplets using the Monte Carlo approach, that is, to analyze whether or not clustering is strong enough to classify as a clustered distribution for a hologram. The difference between the two types of spatial distributions depends on whether they are affected by entrainment and mixing. The holograms observed near the cloud top, where the effects of entrainment and mixing would be immediate, showed relatively high confidence in the significance test for spatially clustered populations of droplets. Moreover, spatially clustered holograms appeared to exhibit stronger visual traits of inhomogeneous mixing than perfectly randomly distributed holograms only when observed near the cloud top. On the other hand, these characteristics did not appear for holograms observed deeper into the cloud where the effects of entrainment and mixing would be reduced. Such 3D structural characteristics of droplet distributions seem to be consistent with vertical circulation mixing.

Meteorology & Atmospheric Sciences↗

Leaf microscopy applications in photosynthesis research: identifying the gaps

Abstract Leaf imaging via microscopy has provided critical insights into research on photosynthesis at multiple junctures, from the early understanding of the role of stomata, through elucidating C4 photosynthesis via Kranz anatomy and chloroplast arrangement in single cells, to detailed explorations of diffusion pathways and light utilization gradients within leaves. In recent decades, the original two-dimensional (2D) explorations have begun to be visualized in three-dimensional (3D) space, revising our understanding of structure–function relationships between internal leaf anatomy and photosynthesis. In particular, advancing new technologies and analyses are providing fresh insight into the relationship between leaf cellular components and improving the ability to model net carbon fixation, water use efficiency, and metabolite turnover rate in leaves. While ground-breaking developments in imaging tools and techniques have expanded our knowledge of leaf 3D structure via high-resolution 3D and time-series images, there is a growing need for more in vivo imaging as well as metabolite imaging. However, these advances necessitate further improvement in microscopy sciences to overcome the unique challenges a green leaf poses. In this review, we discuss the available tools, techniques, challenges, and gaps for efficient in vivo leaf 3D imaging, as well as innovations to overcome these difficulties.

Plant Sciences↗

Volumetric Density-Equalizing Reference Map with Applications

The density-equalizing map, a technique developed for cartogram creation, has been widely applied to data visualization but only for 2D applications. Here, we propose a novel method called the volumetric density-equalizing reference map (VDERM) for computing density-equalizing map for volumetric domains. Given a prescribed density distribution in a volumetric domain in $\mathbb{R}^3$, the proposed method continuously deforms the domain, with different volume elements enlarged or shrunk according to the density distribution. With the aid of the proposed method, medical and sociological data can be visualized via deformations of 3D objects. The method can also be applied to adaptive remeshing and shape modeling. Furthermore, by exploiting the time-dependent nature of the proposed method, applications to shape morphing can be easily achieved. Experimental results are presented to demonstrate the effectiveness of the proposed method.

97 MATHEMATICS AND COMPUTING↗

From Voxels to Knowledge: A Practical Guide to the Segmentation of Complex Electron Microscopy 3D-Data

Modern 3D electron microscopy approaches have recently allowed unprecedented insight into the 3D ultrastructural organization of cells and tissues, enabling the visualization of large macromolecular machines, such as adhesion complexes, as well as higher-order structures, such as the cytoskeleton and cellular organelles in their respective cell and tissue context. Given the inherent complexity of cellular volumes, it is essential to first extract the features of interest in order to allow visualization, quantification, and therefore comprehension of their 3D organization. Each data set is defined by distinct characteristics, e.g., signal-to-noise ratio, crispness (sharpness) of the data, heterogeneity of its features, crowdedness of features, presence or absence of characteristic shapes that allow for easy identification, and the percentage of the entire volume that a specific region of interest occupies. All these characteristics need to be considered when deciding on which approach to take for segmentation. The six different 3D ultrastructural data sets presented were obtained by three different imaging approaches: resin embedded stained electron tomography, focused ion beam- and serial block face- scanning electron microscopy (FIB-SEM, SBF-SEM) of mildly stained and heavily stained samples, respectively. For these data sets, four different segmentation approaches have been applied: (1) fully manual model building followed solely by visualization of the model, (2) manual tracing segmentation of the data followed by surface rendering, (3) semi-automated approaches followed by surface rendering, or (4) automated custom-designed segmentation algorithms followed by surface rendering and quantitative analysis. Depending on the combination of data set characteristics, it was found that typically one of these four categorical approaches outperforms the others, but depending on the exact sequence of criteria, more than one approach may be successful. Based on these data, we propose a triage scheme that categorizes both objective data set characteristics and subjective personal criteria for the analysis of the different data sets.

3D electron microscopy↗

Simultaneous 3D–2D image registration and C-arm calibration: Application to endovascular image-guided interventions

Purpose: Three-dimensional to two-dimensional (3D–2D) image registration is a key to fusion and simultaneous visualization of valuable information contained in 3D pre-interventional and 2D intra-interventional images with the final goal of image guidance of a procedure. In this paper, the authors focus on 3D–2D image registration within the context of intracranial endovascular image-guided interventions (EIGIs), where the 3D and 2D images are generally acquired with the same C-arm system. The accuracy and robustness of any 3D–2D registration method, to be used in a clinical setting, is influenced by (1) the method itself, (2) uncertainty of initial pose of the 3D image from which registration starts, (3) uncertainty of C-arm’s geometry and pose, and (4) the number of 2D intra-interventional images used for registration, which is generally one and at most two. The study of these influences requires rigorous and objective validation of any 3D–2D registration method against a highly accurate reference or “gold standard” registration, performed on clinical image datasets acquired in the context of the intervention. Methods: The registration process is split into two sequential, i.e., initial and final, registration stages. The initial stage is either machine-based or template matching. The latter aims to reduce possibly large in-plane translation errors by matching a projection of the 3D vessel model and 2D image. In the final registration stage, four state-of-the-art intrinsic image-based 3D–2D registration methods, which involve simultaneous refinement of rigid-body and C-arm parameters, are evaluated. For objective validation, the authors acquired an image database of 15 patients undergoing cerebral EIGI, for which accurate gold standard registrations were established by fiducial marker coregistration. Results: Based on target registration error, the obtained success rates of 3D to a single 2D image registration after initial machine-based and template matching and final registration involving C-arm calibration were 36%, 73%, and 93%, respectively, while registration accuracy of 0.59 mm was the best after final registration. By compensating in-plane translation errors by initial template matching, the success rates achieved after the final stage improved consistently for all methods, especially if C-arm calibration was performed simultaneously with the 3D–2D image registration. Conclusions: Because the tested methods perform simultaneous C-arm calibration and 3D–2D registration based solely on anatomical information, they have a high potential for automation and thus for an immediate integration into current interventional workflow. One of the authors’ main contributions is also comprehensive and representative validation performed under realistic conditions as encountered during cerebral EIGI.

60 APPLIED LIFE SCIENCES↗

Performance Evaluation of Augmented Teleoperation of Contact Manipulation Tasks

At Argonne National Laboratory, an enhanced telerobotic concept has been suggested by providing augmented virtual fixtures for precise and dexterous manipulation. The proposed technology incorporated a human-robot interface that can assist personnel on the processes of Deactivation and Decommissioning in sites of high radiation. It has been implemented on a dual-arm robot system, known as Baxter, by integrating the Robotic Operating System (ROS) with 3D sensors and visual-haptic operator interface. However, what remained before its practical utilization is the capability for precisely placing the virtual fixtures. To this end, the objectives involved camera calibration, which required hardware fabrication and setup, as well as modification and implementation of ROS. The goal of this Research and Development is to develop an augmented-reality- based operator interface for human-inclusive, intelligent, and autonomous robotic system for the Deactivation and Decommissioning (D and D) of radioactive sites. The objectives are to develop: Collaborative Robot; Multi-modal Mixed-Reality Human-Robot Interface; Intelligent and Autonomous Behaviors. In order to achieve this, Baxter's Head-Kinect camera and Left-Hand camera need to be calibrated to overlap the real environment with the simulated environment. Camera calibration, which is crucial for precisely placing the virtual fixtures, was successful after running the simulations. The real and simulated environments overlapped, permitting the utilization of augmented teleoperation and the dexterous manipulation of Baxter for D and D applications in nuclear sites. Future steps: Performance evaluation of augmented teleoperation of contact manipulation tasks: Multiple-Camera 3D Reconstruction and Automation. Oculus Interface: Augmented reality and machine learning for enhanced telerobotic operation (Augmented Tele-autonomy): Machine-learning techniques for complex and flexible autonomous robotic behaviors. Interactive remote operation of robotic systems. Mesh cutting with simulation and real robot.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Resolving three-dimensional nanoscale heterogeneities in lithium metal batteries with cryoelectron tomography

Current direct observation of sensitive battery materials and interfaces primarily relies on two-dimensional (2D) imaging, leaving out their three-dimensional (3D) relationship. Here, in this study, we used cryoelectron tomography (cryo-ET) to visualize the lithium metal anode in 3D at nanometer resolution and cryoelectron microscopy (cryo-EM) to reveal atomic details in local regions. We imaged both freshly prepared and calendar-aged Li metal anodes to reveal the development of LiH in Li dendrites and the Li-LiH interface, as well as the development of the solid-electrolyte interphase (SEI). Using a convolutional neural network-based technique, the 3D arrangement of Li metal, along with nanoscale LiH and Cu heterogeneities in dendrites, was visualized and annotated. In longer-term calendar aging, we observed more substantial LiH growth accompanied by extended SEI growth. Our results show that the growth of LiH and the extended SEI during battery calendar aging are temporally and spatially separate processes.

LiH↗

Evaluation of pore structures and cracking in cement paste exposed to elevated temperatures by X-ray computed tomography

When cement-based materials are exposed to the high temperatures induced by fire, which can rapidly cause temperatures of over 1000 °C, the changes in pore structure and density prevail. In the present study, mortar specimens were subjected to a series of increasing temperatures to explore the temperature-dependent evolution of internal pore structure. High-performance X-ray computed tomography (CT) was used to observe the evolution of temperature-induced discontinuities at the sub-millimeter level. X-ray diffraction (XRD) and scanning electron microscopy (SEM) were employed to investigate the cause of physical changes in the heated mortar specimens. Results exhibit the changes in pore structure caused by elevated temperatures, and thermally induced fractures. We discuss the progressive formation of thermally induced fracture networks, which is a prerequisite for spalling failure of cement-based materials by fire, based on visual observations of the 3D internal structures revealed by X-ray CT.

36 MATERIALS SCIENCE↗

Jas4pp — A data-analysis framework for physics and detector studies

This paper describes the Jas4pp framework for exploring physics cases and for detector-performance studies of future particle collision experiments. Jas4pp is a multi-platform Java program for numeric calculations, scientific visualization in 2D and 3D, storing data in various file formats and displaying collision events and detector geometries. It also includes complex data-analysis algorithms for function minimization, regression analysis, event reconstruction (such as jet reconstruction), limit settings and other libraries widely used in particle physics. The framework can be used with several scripting languages, such as Python/Jython, Groovy and JShell. Several benchmark tests discussed in the paper illustrate significant improvements in the performance of the Groovy and JShell scripting languages compared to the standard Python implementation in C. Furthermore, the improvements for numeric computations in Java are attributed to recent enhancements in the Java Virtual Machine.

97 MATHEMATICS AND COMPUTING↗

Poster — Thur Eve — 10: Partial kV CBCT, complete kV CBCT and EPID in breast treatment: a dose comparison study for skin, breasts, heart and lungs

The advantages of kilovoltage cone beam CT (kV CBCT) imaging over electronic portal imaging device (EPID) such as accurate 3D anatomy, soft tissue visualization, fast rigid registration and enhanced precision on patient positioning has lead to its increasing use in clinics. The benefits of this imaging technique are at the cost of increasing the dose to healthy surrounding organs. Our center has moved toward the use of daily partial rotation kV CBCT to restrict the dose to healthy tissues. This study aims to better quantify radiation doses from different image-guidance techniques such as tangential EPID, complete and partial kV CBCT for breast treatments. Cross-calibrated ionization chambers and kV calibrated Gafchromic films were used to measure the dose to the heart, lungs, breasts and skin. It was found that performing partial kV CBCT decreases the heart dose by about 36%, the lungs dose by 31%, the contralateral breast dose by 41% and the ipsilateral breast dose by 43% when compared to a full rotation CBCT. The skin dose measured for a full rotation CBCT was about 0.8 cGy for the contralateral breast and about 0.3 cGy for the ipsilateral breast. The study is still ongoing and results on skin doses for partial rotation kV CBCT as well as for tangential EPID images are upcoming.

60 APPLIED LIFE SCIENCES↗

PNNL-Predictive-Phenomics/ProCaliper

ProCaliper is a Python library that curates, organizes, and computes protein structure features in a way that easily interfaces with user-provided experimental data. It extracts or computes protein binding site, active site, charge, pLDDT (order/disorder), acid dissociation, protonation, solvent accessible surface area, disulfide bond distance, and protein secondary structure data using precomputed protein structures and publicly available databases. It provides a unified API for integrating additional residue-level data and for visualizing residue features in 3D.

Rozum, Jordan [Pacific Northwest National Lab]↗