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At least 361 records · Page 20

Direct Visualization of Magnetic Correlations in Frustrated Spinel ZnFe 2 O 4

Magnetic materials with the spinel structure (A 2+ B 3+ 2 O 4 ) form the core of numerous magnetic devices, and ZnFe 2 O 4 constitutes a peculiar example where the nature of the magnetism is still unresolved. Susceptibility measurements revealed a cusp around T c = 13 K resembling an antiferromagnetic transition, despite the positive Curie–Weiss temperature determined to be Θ CW = 102.8(1) K. Bifurcation of field-cooled and zero-field-cooled data below T c in conjunction with a frequency dependence of the peak position and a non-zero imaginary component below T c shows it is in fact associated with a spin-glass transition. Highly structured magnetic diffuse neutron scattering from single crystals develops between 50 K and 25 K revealing the presence of magnetic disorder which is correlated in nature. Here, the 3D-mΔPDF method is used to visualize the local magnetic ordering preferences, and ferromagnetic nearest-neighbor and antiferromagnetic third nearest-neighbor correlations are shown to be dominant. Their temperature dependence is extraordinary with some flipping in sign and a strongly varying correlation length. The correlations can be explained by orbital interaction mechanisms for the magnetic pathways and a preferred spin cluster. This study demonstrates the power of the 3D-mΔPDF method in visualizing complex quantum phenomena thereby providing a way to obtain an atomic-scale understanding of magnetic frustration.

36 MATERIALS SCIENCE↗

3D Feature Extraction for Unstructured Grids

Visualization techniques provide tools that help scientists identify observed phenomena in scientific simulation. To be useful, these tools must allow the user to extract regions, classify and visualize them, abstract them for simplified representations, and track their evolution. Object Segmentation provides a technique to extract and quantify regions of interest within these massive datasets. This article explores basic algorithms to extract coherent amorphous regions from two-dimensional and three-dimensional scalar unstructured grids. The techniques are applied to datasets from Computational Fluid Dynamics and those from Finite Element Analysis.

Silver, Deborah↗

BioSig3D: High Content Screening of Three-Dimensional Cell Culture Models

BioSig3D is a computational platform for high-content screening of three-dimensional (3D) cell culture models that are imaged in full 3D volume. It provides an end-to-end solution for designing high content screening assays, based on colony organization that is derived from segmentation of nuclei in each colony. BioSig3D also enables visualization of raw and processed 3D volumetric data for quality control, and integrates advanced bioinformatics analysis. The system consists of multiple computational and annotation modules that are coupled together with a strong use of controlled vocabularies to reduce ambiguities between different users. It is a web-based system that allows users to: design an experiment by defining experimental variables, upload a large set of volumetric images into the system, analyze and visualize the dataset, and either display computed indices as a heatmap, or phenotypic subtypes for heterogeneity analysis, or download computed indices for statistical analysis or integrative biology. BioSig3D has been used to profile baseline colony formations with two experiments: (i) morphogenesis of a panel of human mammary epithelial cell lines (HMEC), and (ii) heterogeneity in colony formation using an immortalized non-transformed cell line. These experiments reveal intrinsic growth properties of well-characterized cell lines that are routinely used for biological studies. BioSig3D is being released with seed datasets and video-based documentation.

Science & Technology - Other Topics↗

Visualizing the Internal Nanocrystallinity of Calcite Due to Nonclassical Crystallization by 3D Coherent X–Ray Diffraction Imaging

The internal crystallinity of calcite is investigated for samples synthesized using two approaches: precipitation from solution and the ammonium carbonate diffusion method. Scanning electron microscopy (SEM) analyses reveal that the calcite products precipitated using both approaches have a well–defined rhombohedron shape, consistent with the euhedral crystal habit of the mineral. The internal structure of these calcite crystals is characterized using Bragg coherent diffraction imaging (BCDI) to determine the 3D electron density and the atomic displacement field. BCDI reconstructions for crystals synthesized using the ammonium carbonate diffusion approach have the expected euhedral shape, with internal strain fields and few internal defects. In contrast, the crystals synthesized by precipitation from solution have very complex external shapes and defective internal structures, presenting null electron density regions and pronounced displacement field distributions. These heterogeneities are interpreted as multiple crystalline domains, created by a nonclassical crystallization mechanism, where smaller nanoparticles coalescence into the final euhedral particles. The combined use of SEM, X–ray diffraction (XRD), and BCDI allows for structurally differentiating calcite crystals grown with different approaches, opening new opportunities to understand how grain boundaries and internal defects alter calcite reactivity.

36 MATERIALS SCIENCE↗

RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB

Abstract Motivation Membrane proteins are encoded by approximately one fifth of human genes but account for more than half of all US FDA approved drug targets. Thanks to new technological advances, the number of membrane proteins archived in the PDB is growing rapidly. However, automatic identification of membrane proteins or inference of membrane location is not a trivial task. Results We present recent improvements to the RCSB Protein Data Bank web portal (RCSB PDB, rcsb.org) that provide a wealth of new membrane protein annotations integrated from four external resources: OPM, PDBTM, MemProtMD and mpstruc. We have substantially enhanced the presentation of data on membrane proteins. The number of membrane proteins with annotations available on rcsb.org was increased by ∼80%. Users can search for these annotations, explore corresponding tree hierarchies, display membrane segments at the 1D amino acid sequence level, and visualize the predicted location of the membrane layer in 3D. Availability and implementation Annotations, search, tree data and visualization are available at our rcsb.org web portal. Membrane visualization is supported by the open-source Mol* viewer (molstar.org and github.com/molstar/molstar). Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Vegetation and vantage point influence visibility across diverse ecosystems: Implications for animal ecology

Visual information can influence animal behavior and habitat use in diverse ways. Visibility is the property that relates 3D habitat structure to accessibility of visual information. Despite the importance of visibility in animal ecology, this property remains largely unstudied. Our objective was to assess how habitat structure from diverse environments and animal position within that structure can influence visibility. We gathered terrestrial lidar data (1 cm at 10 m) in four ecosystems (forest, shrub-steppe, prairie, and desert) to characterize viewsheds (i.e., estimates of visibility based on spatially explicit sightlines) from multiple vantage points. Both ecosystem-specific structure and animal position influenced potential viewsheds. Generally, as height of the vantage point above the ground increased, viewshed extent also increased, but the relationships were not linear. In low-structure ecosystems (prairie, shrub-steppe, and desert), variability in viewsheds decreased as vantage points increased to heights above the vegetation canopy. In the forest, however, variation in viewsheds was highest at intermediate heights, and markedly lower at the lowest and highest vantage points. These patterns are likely linked to the amount, heterogeneity, and distribution of vegetation structure occluding sightlines. Our work is the first to apply a new method that can be used to estimate viewshed properties relevant to animals (i.e., viewshed extent and variability). We demonstrate that these properties differ across terrestrial landscapes in complex ways that likely influence many facets of animal ecology and behavior.

Rachel Stein↗

Retrieving spin textures on curved magnetic thin films with full-field soft X-ray microscopies

X-ray tomography is a well-established technique to characterize 3D structures in material sciences and biology; its magnetic analogue—magnetic X-ray tomography—is yet to be developed. We demonstrate the visualization and reconstruction of magnetic domain structures in a 3D curved magnetic thin films with tubular shape by means of full-field soft X-ray microscopies. In the 3D arrangement of the magnetization is retrieved from a set of 2D projections by analysing the evolution of the magnetic contrast with varying projection angle. By using reconstruction algorithms to analyse the angular evolution of 2D projections provides quantitative information about domain patterns and magnetic coupling phenomena between windings of azimuthally and radially magnetized tubular objects. In conclusion, the present approach represents a first milestone towards visualizing magnetization textures of 3D curved thin films with virtually arbitrary shape.

36 MATERIALS SCIENCE↗

TU-F-BRF-04: Registration of 3D Transesophageal Echocardiography and X-Ray Fluoroscopy Using An Inverse Geometry X-Ray System

Purpose: To develop a method for the fusion of 3D echocardiography and Scanning-Beam Digital X-ray (SBDX) fluoroscopy to assist with catheter device and soft tissue visualization during interventional procedures. Methods: SBDX is a technology for low-dose inverse geometry x-ray fluoroscopy that performs digital tomosynthesis at multiple planes in real time. In this study, transesophageal echocardiography (TEE) images were fused with SBDX images by estimating the 3D position and orientation (the “pose”) of the TEE probe within the x-ray coordinate system and then spatially transforming the TEE image data to match this pose. An initial pose estimate was obtained through tomosynthesis-based 3D localization of points along the probe perimeter. Position and angle estimates were then iteratively refined by comparing simulated projections of a 3D probe model against SBDX x-ray images. Algorithm performance was quantified by imaging a TEE probe in different known orientations and locations within the x-ray field (0-30 degree tilt angle, up to 50 mm translation). Fused 3D TEE/SBDX imaging was demonstrated by imaging a tissue-mimicking polyvinyl alcohol cylindrical cavity as a catheter was navigated along the cavity axis. Results: Detected changes in probe tilt angle agreed with the known changes to within 1.2 degrees. For a 50 mm translation along the source-detector axis, the detected translation was 50.3 mm. Errors for in-plane translations ranged from 0.1 to 0.9 mm. In a fused 3D TEE/SBDX display, the catheter device was well visualized and coincident with the device shadow in the TEE images. The TEE images portrayed phantom boundaries that were not evident under x-ray. Conclusion: Registration of soft tissue anatomy derived from TEE imaging and device imaging from SBDX x-ray fluoroscopy is feasible. The simultaneous 3D visualization of these two modalities may be useful in interventional procedures involving the navigation of devices to soft tissue anatomy.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Bringing Planetary Science Mission Outreach to the Deaf and Blind Communities

Introduction: Technology for enhancing outreach, like 3D printing, and science communication products, such as videos and podcasts, can be utilized within the planetary science community, especially for the engagement and excitement of current or upcoming planetary exploration missions. However, these communication products can also be further enhanced for the benefit of the blind and deaf communities. While such products may already be readily available, such projects are not easily accessible to blind and/or deaf certified educators, which often rely on making their own resources or do not have the funds to provide such resources (e.g., cost of 3D printers or cost of braille books). The planetary science community can have better practices to reach these broader audiences. Best practices can include transcripts from podcasts, transcripts in videos, and large-font captions. Images on websites and social media accounts should also include alt-text descriptive captions. 3D printing can also enhance planetary science for the blind community, through tactile posters, maps, and pamphlets. Planetary data can also be augmented by providing different tactile geological maps (e.g., topography or various datasets), and audio-visual videos freely available for educators. Visual Engagement: Visual engagement consists of several avenues to consider, the three main themes includes: 1) swag; 2) videos; 3) interactive exploration. Swag can include the fun visual take-home materials, such as stickers, posters, bookmarks, etc. Videos can include educational-specific videos (available freely via YouTube or by other educational-specific streaming avenues, such as Nebula or Curiosity Stream), provided they have Closed Captioning (CC). The use of QR codes to such videos or websites can also benefit to being added on swag. Interactive exploration can also be sub-divided by different types of engagement. A popular and still fairly new technology for public engagement is the use of virtual reality (VR). While this has been mainly for martian and lunar surface exploration [1], the deaf communities can benefit from VR through a more extensive look at our solar system and beyond (for example, a VR experience of the flight path, or visual map of the heliosphere/dynamics of our Sun). Audio Engagement: Audio tools can also be a useful avenue of communication, especially for the blind communities. Audio archiving can certainly be transcripts from the video engagements, but also the use of podcasts can also be a benefit. Podcasting can take on two forms: 1) interview engagement; and 2) update engagement. For interviews, scientists can communicate with STEM-specific podcast platforms to make other listener-bases aware of what is going on with a specific mission. For update-type communication, missions may opt to have an archived podcast of news, updates, and the teams involved. The most important aspect of such podcasts would be for the need of complimentary transcripts (including descriptive transcripts if sounds are included), and the limited use of jargon. Research Engagement: There have been several examples of involving the blind and low-vision communities in citizen science, such as through the NASA Heliophysics division. Examples include the NASA PUNCH (Polarimeter to Unify the Corona and Heliosphere) mission led by the Southwest Research Institute [2], which include blind and visually-impaired citizens to assist in the Sun’s coronal rhythms.” Another example is the Eclipse Soundscapes: Citizen Science Project (ES:CSP), which documents observations of acoustical changes of nature and ecosystems during solar eclipse events [3]. Inclusivity: A major theme that is necessary for public engagement is inclusivity and the awareness of reaching broader audiences. Outreach to include hearing/seeing impaired communities are still lacking in the sciences. There are several opportunities that the planetary sciences could take. Other projects that have emerged from the space sciences include adding transcripts to visual engagement [4], and the use of 3D printing for the visually-impaired [5]. References: [1] Olgin, J. (2020) 51st LPSC, Abstract 2137. [2] https://scitechdaily.com/outreach-for-nasa-punch-mission-embraces-ancient-and-modern-sun-watching-theme/ [3] https://science.nasa.gov/science-activation-team/eclipse-soundscapes [4] NASA International Observe the Moon Night (Blind and Deaf Accessible), Youtube Video ( https://www.youtube.com/watch?v=neHCfg0S3-Q) [5] Richardson, J., et al. (2018) AGU Fall Meeting, Abstract ED23F-0963.

C J Ahrens↗

3D camera assisted fully automated calibration of scanning laser Doppler vibrometers

Scanning laser Doppler vibrometers (LDV) are used to measure full-field vibration shapes of products and structures. In most commercially available scanning laser Doppler vibrometer systems the user manually draws a grid of measurement locations on a 2D camera image of the product. The determination of the correct physical measurement locations can be a time consuming and diffcult task. In this paper we present a new methodology for product testing and quality control that integrates 3D imaging techniques with vibration measurements. This procedure allows to test prototypes in a shorter period because physical measurements locations will be located automatically. The proposed methodology uses a 3D time-of-flight camera to measure the location and orientation of the test-object. The 3D image of the time-of-flight camera is then matched with the 3D-CAD model of the object in which measurement locations are pre-defined. A time of flight camera operates strictly in the near infrared spectrum. To improve the signal to noise ratio in the time-of-flight measurement, a time-of-flight camera uses a band filter. As a result of this filter, the laser spot of most laser vibrometers is invisible in the time-of-flight image. Therefore a 2D RGB-camera is used to find the laser-spot of the vibrometer. The laser spot is matched to the 3D image obtained by the time-of-flight camera. Next an automatic calibration procedure is used to aim the laser at the (pre)defined locations. Another benefit from this methodology is that it incorporates automatic mapping between a CAD model and the vibration measurements. This mapping can be used to visualize measurements directly on a 3D CAD model. Secondly the orientation of the CAD model is known with respect to the laser beam. This information can be used to find the direction of the measured vibration relatively to the surface of the object. With this direction, the vibration measurements can be compared more precisely with numerical experiments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

From 2D to 4D: a containerized workflow and browser to explore dynamic chromatin architecture

Background Characterizing the physical organization of the genome is essential for understanding long-range gene regulation, chromatin compartmentalization, and epigenetic accessibility. Hi-C experiments generate two-dimensional (2D) genome-wide contact maps of chromatin interactions by capturing the spatial proximity between genomic loci, which reveal interaction frequencies but lack the spatial resolution needed to interpret the three-dimensional (3D) genome structure(s). Emerging evidence suggests that epigenetic regulation is closely linked to 3D genome architecture, and that structural changes over time (4D) drive key biological processes in development, disease, and environmental response. Thus, integrating 3D structure with functional data is critical for a more complete understanding of genome regulation. Previous work, most notably the 4DHiC chromosome modeling framework, has shown that physical multi-dimensional modeling approaches rooted in polymer physics and molecular dynamics can resolve these structures at biologically meaningful resolutions by integrating temporal Hi-C data with physical constraints to uncover dynamic chromosome reorganization. Thus, molecular dynamics simulations, constrained by Hi-C contact matrices, can resolve fine-scale structural changes and reveal functionally significant transitions in chromatin conformation. Results Herein, we present the 4D Genome Browser Workflow (4DGBWorkflow) and the 4D Genome Browser (4DGB). The algorithm is based on the 4DHiC method, and the containerized tool is an end-to-end workflow that can transform, filter, and view 4D epigenomics and chromatin datasets, allowing non-specialists to apply three-dimensional modeling principles to diverse datasets and experimental conditions. The software executes on a laptop running macOS, Linux or Windows. From input Hi-C files (.hic), the 4DGBWorkflow produces 3D reconstructions of chromosomes, integrates the reconstruction with track data (e.g., epigenetic marks, transcriptome profiles), and provides comparative visualization of the results in a single workflow. Conclusions The 4DGBWorkflow and 4D Genome Browser are open-source tools for comparative analysis and visualization of 4D chromosome datasets, including chromatin architecture and epigenomic signals. Automatic integration of Hi-C data with molecular dynamics democratizes the construction of time resolved 3D genome structures, simplifying complex simulations and data integration schemes.

3D Genome Browser↗

Visualization of Jet Impingement and Ignition in a Piston-Cylinder Chamber

The transportation sector accounts for almost a third of the United States' energy consumption. We are developing predictive simulations of the complex in-cylinder processes of internal combustion engines to improve performance and decrease pollutant emissions. We provide a first look at the jet impingement and ignition inside a piston-cylinder chamber using volume rendering. Through the visualization, we constructed a complete 3D picture of the jet impingement on the piston-bowl walls leading to the formation of pockets of auto-ignition of the fuel-air mixture. These auto-ignition pockets subsequently lead to flame stabilization, releasing the chemical energy for conversion to useful work. A detailed physical picture of flame stabilization, as provided by the visualization techniques presented in this study, help in the design of next-generation internal combustion engines.

91 SC - Advanced Scientific Computing Reseach (ASC↗

Falcon: Visual analysis of large, irregularly sampled, and multivariate time series data in additive manufacturing

Flexible visual analysis of long, high-resolution, and irregularly sampled time series data from multiple sensor streams is a challenge in several domains. In the field of additive manufacturing, this capability is critical for realizing the full potential of large-scale 3D printers. Here, we propose a visual analytics approach that helps additive manufacturing researchers acquire a deep understanding of patterns in log and imagery data collected by 3D printers. Our specific goals include discovering patterns related to defects and system performance issues, optimizing build configurations to avoid defects, and increasing production efficiency. We introduce Falcon, a new visual analytics system that allows users to interactively explore large, time-oriented data sets from multiple linked perspectives. Falcon provides overviews, detailed views, and unique segmented time series visualizations, all with adjustable scale options. To illustrate the effectiveness of Falcon at providing thorough and efficient knowledge discovery, we present a practical case study involving experts in additive manufacturing and data from a large-scale 3D printer. The techniques described are applicable to the analysis of any quantitative time series, though the focus of this paper is on additive manufacturing.

97 MATHEMATICS AND COMPUTING↗

3D Localization of Defects in Facility Inspection

Wind tunnels are crucial facilities that support the aerospace industry. However, these facilities are large, complex, and pose unique maintenance and inspection requirements. Manual inspections to identify defects such as cracks, missing fasteners, leaks, and foreign objects are important but labor and schedule intensive. Our goal is to utilize small Unmanned Aircraft Systems (sUAS) and computer vision-based analysis to automate the inspection of the interior and exterior of NASA’s critical wind tunnel facilities. We detect missing fasteners as our defect class, and detect existing fasteners to provide potential future missing fastener sites for preventative maintenance. These detections are done on both 2D raw images and in 3D space to provide a visual reference and real world location to facilitate repairs. A dataset was created consisting of images taken along a grid-like pattern of an interior tunnel section in the AEDC National Full-Scale Aerodynamics Complex (NFAC) at NASA Ames Research Center. Our method uses object detection to create image level bounding boxes of the fasteners and missing fasteners, then uses photogrammetry to create a mapping from 2D image locations to 3D real world locations. The image level bounding boxes and the 2D to 3D mapping are then combined to determine the 3D location of the defects. We describe the data collection, photogrammetry, and computer vision techniques used for object detection as well as a quantitative analysis of the method.

Small Unmanned Aircraft Systems (sUAS)↗

3D microstructure reconstruction of casting aluminum alloy based on serial block-face scanning electron microscopy

In this work, the inner microstructure of aluminum-silicon casting alloy was experimentally investigated to reveal the spatial morphology and phase distribution. Its industrial use is as a light-weight structural material. As a powerful three-dimensional (3D) imaging tool at the nano-scale, the serial block-face scanning electron microscopy (SBFSEM) was employed to investigate the specimens. After being 3D reconstructed, the images were visualized to identify preference for several specific intermetallics by quantitative analysis. It was found that these phases have certain relationships in spatial distribution and differences in spatial shapes. In conclusion, the spatial distribution of cracks was studied to understand their propagation and growth.

3D microstructure reconstruction↗

SynopFrame: Multiscale time-dependent visual abstraction framework for analyzing DNA nanotechnology simulations

We present an open-source framework, SynopFrame, that allows DNA nanotechnology (DNA-nano) experts to analyze and understand molecular dynamics simulation trajectories of their designs. We use a multiscale multi-dimensional abstraction space, connect the representations to a projected conformational space plot of the structure’s temporal sequence, and thus enable experts to analyze the dynamics of their structural designs and, specifically, failure cases of the assembly. In addition, our time-dependent abstraction representation allows the biologists, for the first time in a smooth and structurally clear way, to identify and observe temporal transitions of a DNA-nano design from one configuration to another, and to highlight important periods of the simulation for further analysis. We realize SynopFrame as a dashboard of the different synchronized 3D spatial and 2D schematic visual representations, with a color overlay to show essential properties such as the status of hydrogen bonds. The linking of the spatial, schematic, and abstract views ensures that users can effectively analyze the high-frequency motion. We also categorize the status of the hydrogen bonds into a new format to allow us to color-encode it and overlay it on the representations. To demonstrate the utility of SynopFrame, we describe example usage scenarios and report user feedback.

Abstraction space↗

3D Imaging of Microbial Biofilms: Integration of Synchrotron Imaging and an Interactive Visualization Interface

Understanding the interactions of structured communities known as “biofilms” and other complex matrixes is possible through the X-ray micro tomography imaging of the biofilms. Feature detection and image processing for this type of data focuses on efficiently identifying and segmenting biofilms and bacteria in the datasets. The datasets are very large and often require manual interventions due to low contrast between objects and high noise levels. Thus new software is required for the effectual interpretation and analysis of the data. This work specifies the evolution and application of the ability to analyze and visualize high resolution X-ray micro tomography datasets.

Biofilm Viewer↗

Skeletides: A Modular, Simplified Physical Model of Protein Secondary Structure

Three-dimensional (3D) models are essential for visualization and conceptual understanding of complex architectures such as protein structure. Although there is a plethora of software platforms that allow digital depictions of protein structure at an atomic level in silico, physical models are needed to convey an intuitive understanding of biomolecular architecture. However, it is a challenge to represent all the relevant features of proteins in a single physical model due to their sheer structural complexity. Here, we describe a modular protein model that focuses only on representation of the secondary structure—the underlying structural skeleton. The simplified model consists of amino acid units, which can be linked together to reproduce the two most fundamental structural features of protein secondary structure: the relative positions of the amino acid alpha carbon atoms, and the intra-main chain hydrogen bonding pattern. We use 3D printing and magnets to create a set of three modular amino acid building blocks, which when linked together into a chain, can faithfully represent alpha helices, beta sheets, and turns. These simple to make models can be used to quickly assemble the alpha carbon trace of an entire protein domain, which conveys a tactile experience of the complexity of protein skeletal architecture. These models highlight the modularity of protein structure: where a single structural unit, the amino acid, can be linked together to form a larger, regular secondary structure. These models also have a propensity to spontaneously organize into alpha helices and beta sheets, as demonstrated by their ability to autonomously assemble when placed in a circulating water tank. These models provide a missing educational tool to expand knowledge of protein structure, foster deeper insight into protein folding, and inspire greater interest in biomacromolecular architecture.

36 MATERIALS SCIENCE↗