Science.gov

Sample records for 3d density maps

  1. Hot deformation characterization of duplex low-density steel through 3D processing map development

    SciTech Connect

    Mohamadizadeh, A.; Zarei-Hanzaki, A.; Abedi, H.R.; Mehtonen, S.; Porter, D.

    2015-09-15

    The high temperature deformation behavior of duplex low-density Fe–18Mn–8Al–0.8C steel was investigated at temperatures in the range of 600–1000 °C. The primary constitutive analysis indicated that the Zener–Hollomon parameter, which represents the coupled effects of temperature and strain rate, significantly varies with the amount of deformation. Accordingly, the 3D processing maps were developed considering the effect of strain and were used to determine the safe and unsafe deformation conditions in association with the microstructural evolution. The deformation at efficiency domain I (900–1100 °C\\10{sup −} {sup 2}–10{sup −} {sup 3} s{sup −} {sup 1}) was found to be safe at different strains due to the occurrence of dynamic recrystallization in austenite. The safe efficiency domain II (700–900 °C\\1–10{sup −} {sup 1} s{sup −} {sup 1}), which appeared at logarithmic strain of 0.4, was characterized by deformation induced ferrite formation. Scanning electron microscopy revealed that the microband formation and crack initiation at ferrite\\austenite interphases were the main causes of deformation instability at 600–800 °C\\10{sup −} {sup 2}–10{sup −} {sup 3} s{sup −} {sup 1}. The degree of instability was found to decrease by increasing the strain due to the uniformity of microbanded structure obtained at higher strains. The shear band formation at 900–1100 °C\\1–10{sup −} {sup 1} s{sup −} {sup 1} was verified by electron backscattered diffraction. The local dynamic recrystallization of austenite and the deformation induced ferrite formation were observed within shear-banded regions as the results of flow localization. - Graphical abstract: Display Omitted - Highlights: • The 3D processing map is developed for duplex low-density Fe–Mn–Al–C steel. • The efficiency domains shrink, expand or appear with increasing strain. • The occurrence of DRX and DIFF increases the power efficiency. • Crack initiation

  2. RHOCUBE: 3D density distributions modeling code

    NASA Astrophysics Data System (ADS)

    Nikutta, Robert; Agliozzo, Claudia

    2016-11-01

    RHOCUBE models 3D density distributions on a discrete Cartesian grid and their integrated 2D maps. It can be used for a range of applications, including modeling the electron number density in LBV shells and computing the emission measure. The RHOCUBE Python package provides several 3D density distributions, including a powerlaw shell, truncated Gaussian shell, constant-density torus, dual cones, and spiralling helical tubes, and can accept additional distributions. RHOCUBE provides convenient methods for shifts and rotations in 3D, and if necessary, an arbitrary number of density distributions can be combined into the same model cube and the integration ∫ dz performed through the joint density field.

  3. [3D emulation of epicardium dynamic mapping].

    PubMed

    Lu, Jun; Yang, Cui-Wei; Fang, Zu-Xiang

    2005-03-01

    In order to realize epicardium dynamic mapping of the whole atria, 3-D graphics are drawn with OpenGL. Some source codes are introduced in the paper to explain how to produce, read, and manipulate 3-D model data.

  4. Positional Awareness Map 3D (PAM3D)

    NASA Technical Reports Server (NTRS)

    Hoffman, Monica; Allen, Earl L.; Yount, John W.; Norcross, April Louise

    2012-01-01

    The Western Aeronautical Test Range of the National Aeronautics and Space Administration s Dryden Flight Research Center needed to address the aging software and hardware of its current situational awareness display application, the Global Real-Time Interactive Map (GRIM). GRIM was initially developed in the late 1980s and executes on older PC architectures using a Linux operating system that is no longer supported. Additionally, the software is difficult to maintain due to its complexity and loss of developer knowledge. It was decided that a replacement application must be developed or acquired in the near future. The replacement must provide the functionality of the original system, the ability to monitor test flight vehicles in real-time, and add improvements such as high resolution imagery and true 3-dimensional capability. This paper will discuss the process of determining the best approach to replace GRIM, and the functionality and capabilities of the first release of the Positional Awareness Map 3D.

  5. A 3D Geostatistical Mapping Tool

    SciTech Connect

    Weiss, W. W.; Stevenson, Graig; Patel, Ketan; Wang, Jun

    1999-02-09

    This software provides accurate 3D reservoir modeling tools and high quality 3D graphics for PC platforms enabling engineers and geologists to better comprehend reservoirs and consequently improve their decisions. The mapping algorithms are fractals, kriging, sequential guassian simulation, and three nearest neighbor methods.

  6. 3D-HIM: A 3D High-density Interleaved Memory for Bipolar RRAM Design

    DTIC Science & Technology

    2013-05-01

    JOURNAL ARTICLE (Post Print ) 3. DATES COVERED (From - To) DEC 2010 – NOV 2012 4. TITLE AND SUBTITLE 3D -HIM: A 3D HIGH-DENSITY INTERLEAVED MEMORY...emerged as one of the promising candidates for large data storage in computing systems. Moreover, building up RRAM in a three dimensional ( 3D ) stacking...brings in the potential reliability issue. To alleviate the situation, we introduce two novel 3D stacking structures built upon bipolar RRAM

  7. 3D Regression Heat Map Analysis of Population Study Data.

    PubMed

    Klemm, Paul; Lawonn, Kai; Glaßer, Sylvia; Niemann, Uli; Hegenscheid, Katrin; Völzke, Henry; Preim, Bernhard

    2016-01-01

    Epidemiological studies comprise heterogeneous data about a subject group to define disease-specific risk factors. These data contain information (features) about a subject's lifestyle, medical status as well as medical image data. Statistical regression analysis is used to evaluate these features and to identify feature combinations indicating a disease (the target feature). We propose an analysis approach of epidemiological data sets by incorporating all features in an exhaustive regression-based analysis. This approach combines all independent features w.r.t. a target feature. It provides a visualization that reveals insights into the data by highlighting relationships. The 3D Regression Heat Map, a novel 3D visual encoding, acts as an overview of the whole data set. It shows all combinations of two to three independent features with a specific target disease. Slicing through the 3D Regression Heat Map allows for the detailed analysis of the underlying relationships. Expert knowledge about disease-specific hypotheses can be included into the analysis by adjusting the regression model formulas. Furthermore, the influences of features can be assessed using a difference view comparing different calculation results. We applied our 3D Regression Heat Map method to a hepatic steatosis data set to reproduce results from a data mining-driven analysis. A qualitative analysis was conducted on a breast density data set. We were able to derive new hypotheses about relations between breast density and breast lesions with breast cancer. With the 3D Regression Heat Map, we present a visual overview of epidemiological data that allows for the first time an interactive regression-based analysis of large feature sets with respect to a disease.

  8. 3-D capacitance density imaging system

    DOEpatents

    Fasching, G.E.

    1988-03-18

    A three-dimensional capacitance density imaging of a gasified bed or the like in a containment vessel is achieved using a plurality of electrodes provided circumferentially about the bed in levels and along the bed in channels. The electrodes are individually and selectively excited electrically at each level to produce a plurality of current flux field patterns generated in the bed at each level. The current flux field patterns are suitably sensed and a density pattern of the bed at each level determined. By combining the determined density patterns at each level, a three-dimensional density image of the bed is achieved. 7 figs.

  9. MAP3D: a media processor approach for high-end 3D graphics

    NASA Astrophysics Data System (ADS)

    Darsa, Lucia; Stadnicki, Steven; Basoglu, Chris

    1999-12-01

    Equator Technologies, Inc. has used a software-first approach to produce several programmable and advanced VLIW processor architectures that have the flexibility to run both traditional systems tasks and an array of media-rich applications. For example, Equator's MAP1000A is the world's fastest single-chip programmable signal and image processor targeted for digital consumer and office automation markets. The Equator MAP3D is a proposal for the architecture of the next generation of the Equator MAP family. The MAP3D is designed to achieve high-end 3D performance and a variety of customizable special effects by combining special graphics features with high performance floating-point and media processor architecture. As a programmable media processor, it offers the advantages of a completely configurable 3D pipeline--allowing developers to experiment with different algorithms and to tailor their pipeline to achieve the highest performance for a particular application. With the support of Equator's advanced C compiler and toolkit, MAP3D programs can be written in a high-level language. This allows the compiler to successfully find and exploit any parallelism in a programmer's code, thus decreasing the time to market of a given applications. The ability to run an operating system makes it possible to run concurrent applications in the MAP3D chip, such as video decoding while executing the 3D pipelines, so that integration of applications is easily achieved--using real-time decoded imagery for texturing 3D objects, for instance. This novel architecture enables an affordable, integrated solution for high performance 3D graphics.

  10. From Surface Data to 3D Geologic Maps

    NASA Astrophysics Data System (ADS)

    Dhont, D.; Luxey, P.; Longuesserre, V.; Monod, B.; Guillaume, B.

    2008-12-01

    New trends in earth sciences are mostly related to technologies allowing graphical representations of the geology in 3D. However, the concept of 3D geologic map is commonly misused. For instance, displays of geologic maps draped onto DEM in rotating perspective views have been misleadingly called 3D geologic maps, but this still cannot provide any volumetric underground information as a true 3D geologic map should. Here, we present a way to produce mathematically and geometrically correct 3D geologic maps constituted by the volume and shape of all geologic features of a given area. The originality of the method is that it is based on the integration of surface data only consisting of (1) geologic maps, (2) satellite images, (3) DEM and (4) bedding dips and strikes. To generate 3D geologic maps, we used a 3D geologic modeler that combines and extrapolates the surface information into a coherent 3D data set. The significance of geometrically correct 3D geologic maps is demonstrated for various geologic settings and applications. 3D models are of primarily importance for educational purposes because they reveal features that standard 2D geologic maps by themselves could not show. The 3D visualization helps in the understanding of the geometrical relationship between the different geologic features and, in turn, for the quantification of the geology at the regional scale. Furthermore, given the logistical challenges associated with modern oil and mineral exploration in remote and rugged terrain, these volume-based models can provide geological and commercial insight prior to seismic evaluation.

  11. Interactive mapping on 3-D terrain models

    NASA Astrophysics Data System (ADS)

    Bernardin, T.; Cowgill, E.; Gold, R.; Hamann, B.; Kreylos, O.; Schmitt, A.

    2006-10-01

    We present an interactive, real-time mapping system for use with digital elevation models and remotely sensed multispectral imagery that aids geoscientists in the creation and interpretation of geologic/neotectonic maps at length scales of 10 m to 1000 km. Our system provides a terrain visualization of the surface of the Earth or other terrestrial planets by displaying a virtual terrain model generated from a digital elevation model overlain by a color texture generated from orthophotos or satellite imagery. We use a quadtree-based, multiresolution display method to render in real time high-resolution virtual terrain models that span large spatial regions. The system allows users to measure the orientations of geologic surfaces and record their observations by drawing lines directly on the virtual terrain model. In addition, interpretive surfaces can be generated from these drawings and displayed to facilitate understanding of the three-dimensional geometry of geologic surfaces. The main strength of our system is the combination of real-time rendering and interactive mapping performed directly on the virtual terrain model with the ability to navigate the scene while changing viewpoints arbitrarily during mapping. User studies and comparisons with commercially available mapping software show that our system improves mapping accuracy and efficiency and also yields observations that cannot be made with existing systems.

  12. Geological mapping goes 3-D in response to societal needs

    USGS Publications Warehouse

    Thorleifson, H.; Berg, R.C.; Russell, H.A.J.

    2010-01-01

    The transition to 3-D mapping has been made possible by technological advances in digital cartography, GIS, data storage, analysis, and visualization. Despite various challenges, technological advancements facilitated a gradual transition from 2-D maps to 2.5-D draped maps to 3-D geological mapping, supported by digital spatial and relational databases that can be interrogated horizontally or vertically and viewed interactively. Challenges associated with data collection, human resources, and information management are daunting due to their resource and training requirements. The exchange of strategies at the workshops has highlighted the use of basin analysis to develop a process-based predictive knowledge framework that facilitates data integration. Three-dimensional geological information meets a public demand that fills in the blanks left by conventional 2-D mapping. Two-dimensional mapping will, however, remain the standard method for extensive areas of complex geology, particularly where deformed igneous and metamorphic rocks defy attempts at 3-D depiction.

  13. Sodium 3D COncentration MApping (COMA 3D) using 23Na and proton MRI

    NASA Astrophysics Data System (ADS)

    Truong, Milton L.; Harrington, Michael G.; Schepkin, Victor D.; Chekmenev, Eduard Y.

    2014-10-01

    Functional changes of sodium 3D MRI signals were converted into millimolar concentration changes using an open-source fully automated MATLAB toolbox. These concentration changes are visualized via 3D sodium concentration maps, and they are overlaid over conventional 3D proton images to provide high-resolution co-registration for easy correlation of functional changes to anatomical regions. Nearly 5000/h concentration maps were generated on a personal computer (ca. 2012) using 21.1 T 3D sodium MRI brain images of live rats with spatial resolution of 0.8 × 0.8 × 0.8 mm3 and imaging matrices of 60 × 60 × 60. The produced concentration maps allowed for non-invasive quantitative measurement of in vivo sodium concentration in the normal rat brain as a functional response to migraine-like conditions. The presented work can also be applied to sodium-associated changes in migraine, cancer, and other metabolic abnormalities that can be sensed by molecular imaging. The MATLAB toolbox allows for automated image analysis of the 3D images acquired on the Bruker platform and can be extended to other imaging platforms. The resulting images are presented in a form of series of 2D slices in all three dimensions in native MATLAB and PDF formats. The following is provided: (a) MATLAB source code for image processing, (b) the detailed processing procedures, (c) description of the code and all sub-routines, (d) example data sets of initial and processed data. The toolbox can be downloaded at: http://www.vuiis.vanderbilt.edu/~truongm/COMA3D/.

  14. Sodium 3D COncentration MApping (COMA 3D) Using 23Na and Proton MRI

    PubMed Central

    Truong, Milton L.; Harrington, Michael G.; Schepkin, Victor D.; Chekmenev, Eduard Y.

    2014-01-01

    Functional changes of sodium 3D MRI signals were converted into millimolar concentration changes using an open-source fully automated MATLAB toolbox. These concentration changes are visualized via 3D sodium concentration maps, and they are overlaid over conventional 3D proton images to provide high-resolution co-registration for easy correlation of functional changes to anatomical regions. Nearly 5000/hour concentration maps were generated on a personal computer (ca. 2012) using 21.1 T 3D sodium MRI brain images of live rats with spatial resolution of 0.8×0.8×0.8 mm3 and imaging matrices of 60×60×60. The produced concentration maps allowed for non-invasive quantitative measurement of in vivo sodium concentration in the normal rat brain as a functional response to migraine-like conditions. The presented work can also be applied to sodium-associated changes in migraine, cancer, and other metabolic abnormalities that can be sensed by molecular imaging. The MATLAB toolbox allows for automated image analysis of the 3D images acquired on the Bruker platform and can be extended to other imaging platforms. The resulting images are presented in a form of series of 2D slices in all three dimensions in native MATLAB and PDF formats. The following is provided: (a) MATLAB source code for image processing, (b) the detailed processing procedures, (c) description of the code and all sub-routines, (d) example data sets of initial and processed data. The toolbox can be downloaded at: http://www.vuiis.vanderbilt.edu/~truongm/COMA3D/ PMID:25261742

  15. MSV3d: database of human MisSense Variants mapped to 3D protein structure.

    PubMed

    Luu, Tien-Dao; Rusu, Alin-Mihai; Walter, Vincent; Ripp, Raymond; Moulinier, Luc; Muller, Jean; Toursel, Thierry; Thompson, Julie D; Poch, Olivier; Nguyen, Hoan

    2012-01-01

    The elucidation of the complex relationships linking genotypic and phenotypic variations to protein structure is a major challenge in the post-genomic era. We present MSV3d (Database of human MisSense Variants mapped to 3D protein structure), a new database that contains detailed annotation of missense variants of all human proteins (20 199 proteins). The multi-level characterization includes details of the physico-chemical changes induced by amino acid modification, as well as information related to the conservation of the mutated residue and its position relative to functional features in the available or predicted 3D model. Major releases of the database are automatically generated and updated regularly in line with the dbSNP (database of Single Nucleotide Polymorphism) and SwissVar releases, by exploiting the extensive Décrypthon computational grid resources. The database (http://decrypthon.igbmc.fr/msv3d) is easily accessible through a simple web interface coupled to a powerful query engine and a standard web service. The content is completely or partially downloadable in XML or flat file formats. Database URL: http://decrypthon.igbmc.fr/msv3d.

  16. Lithologic identification & mapping test based on 3D inversion of magnetic and gravity

    NASA Astrophysics Data System (ADS)

    Yan, Jiayong; Lv, Qingtian; Qi, Guang; Zhao, Jinhua; Zhang, Yongqian

    2016-04-01

    Though lithologic identification & mapping to achieve ore concentration district transparent within 5km depth is the main way to realize deep fine structures study, to explore deep mineral resources and to reveal metallogenic regularity of large-scale ore district . Owing to the wide covered area, high sampling density and mature three-dimensional inversion algorithm of gravity and magnetic data, so gravity and magnetic inversion become the most likely way to achieve three-dimensional lithologic mapping at the present stage. In this paper, we take Lu-zong(Lujiang county to Zongyang county in Anhui province ,east China) ore district as a case, we proposed lithologic mapping flow based 3D inversion of gravity magnetic and then carry out the lithologic mapping test. Lithologic identification & mapping flow is as follows: 1. Analysis relations between lithology and density and magnetic susceptibility by cross plot. 2.Extracting appropriate residual anomalies from high-precision Bourger gravity and aeromagnetic. 3.Use same mesh, do 3D magnetic and gravity inversion respectively under prior information constrained, and then invert susceptibility and density 3D model. 4. According setp1, construct logical topology operations between density 3D model and susceptibility. 5.Use the logical operations, identify lithogies cell by cell in 3D mesh, and then get 3D lithological model. According this flow, we obtained three-dimensional distribution of five main type lithologies in the Lu-Zong ore district within 5km depth. The result of lithologic mapping not only showed that the shallow characteristics and surface geological mapping are basically Coincide,more importantly ,it reveals the deeper lithologic changes.The lithlogical model make up the insufficient of surface geological mapping. The lithologic mapping test results in Lu-Zong ore concentration district showed that lithological mapping using 3D inversion of gravity and magnetic is a effective method to reveal the

  17. Automatic Texture Mapping of Architectural and Archaeological 3d Models

    NASA Astrophysics Data System (ADS)

    Kersten, T. P.; Stallmann, D.

    2012-07-01

    Today, detailed, complete and exact 3D models with photo-realistic textures are increasingly demanded for numerous applications in architecture and archaeology. Manual texture mapping of 3D models by digital photographs with software packages, such as Maxon Cinema 4D, Autodesk 3Ds Max or Maya, still requires a complex and time-consuming workflow. So, procedures for automatic texture mapping of 3D models are in demand. In this paper two automatic procedures are presented. The first procedure generates 3D surface models with textures by web services, while the second procedure textures already existing 3D models with the software tmapper. The program tmapper is based on the Multi Layer 3D image (ML3DImage) algorithm and developed in the programming language C++. The studies showing that the visibility analysis using the ML3DImage algorithm is not sufficient to obtain acceptable results of automatic texture mapping. To overcome the visibility problem the Point Cloud Painter algorithm in combination with the Z-buffer-procedure will be applied in the future.

  18. 3D Imaging of Density Gradients Using Plenoptic BOS

    NASA Astrophysics Data System (ADS)

    Klemkowsky, Jenna; Clifford, Chris; Fahringer, Timothy; Thurow, Brian

    2016-11-01

    The combination of background oriented schlieren (BOS) and a plenoptic camera, termed Plenoptic BOS, is explored through two proof-of-concept experiments. The motivation of this work is to provide a 3D technique capable of observing density disturbances. BOS uses the relationship between density and refractive index gradients to observe an apparent shift in a patterned background through image comparison. Conventional BOS systems acquire a single line-of-sight measurement, and require complex configurations to obtain 3D measurements, which are not always conducive to experimental facilities. Plenoptic BOS exploits the plenoptic camera's ability to generate multiple perspective views and refocused images from a single raw plenoptic image during post processing. Using such capabilities, with regards to BOS, provides multiple line-of-sight measurements of density disturbances, which can be collectively used to generate refocused BOS images. Such refocused images allow the position of density disturbances to be qualitatively and quantitatively determined. The image that provides the sharpest density gradient signature corresponds to a specific depth. These results offer motivation to advance Plenoptic BOS with an ultimate goal of reconstructing a 3D density field.

  19. A 3D digital map of rat brain.

    PubMed

    Toga, A W; Santori, E M; Hazani, R; Ambach, K

    1995-01-01

    A three dimensional (3D) computerized map of rat brain anatomy created with digital imaging techniques is described. Six male Sprague-Dawley rats, weighing 270-320 g, were used in the generation of this atlas. Their heads were frozen, and closely spaced cryosectional images were digitally captured. Each serial data set was organized into a digital volume, reoriented into a flat skull position, and brought into register with each other. A volume representative of the group following registration was chosen based on its anatomic correspondence with the other specimens as measured by image correlation coefficients and landmark matching. Mean positions of lambda, bregma, and the interaural plane of the group within the common coordinate system were used to transform the representative volume into a 3D map of rat neuroanatomy. images reconstructed from this 3D map are available to the public via Internet with an anonymous file transfer protocol (FTP) and World Wide Web. A complete description of the digital map is provided in a comprehensive set of sagittal planes (up to 0.031 mm spacing) containing stereotaxic reference grids. Sets of coronal and horizontal planes, resampled at the same increment, also are included. Specific anatomic features are identified in a second collection of images. Stylized anatomic boundaries and structural labels were incorporated into selected orthogonal planes. Electronic sharing and interactive use are benefits afforded by a digital format, but the foremost advantage of this 3D map is its whole brain integrated representation of rat in situ neuroanatomy.

  20. High density 3D printed microfluidic valves, pumps, and multiplexers.

    PubMed

    Gong, Hua; Woolley, Adam T; Nordin, Gregory P

    2016-07-07

    In this paper we demonstrate that 3D printing with a digital light processor stereolithographic (DLP-SLA) 3D printer can be used to create high density microfluidic devices with active components such as valves and pumps. Leveraging our previous work on optical formulation of inexpensive resins (RSC Adv., 2015, 5, 106621), we demonstrate valves with only 10% of the volume of our original 3D printed valves (Biomicrofluidics, 2015, 9, 016501), which were already the smallest that have been reported. Moreover, we show that incorporation of a thermal initiator in the resin formulation along with a post-print bake can dramatically improve the durability of 3D printed valves up to 1 million actuations. Using two valves and a valve-like displacement chamber (DC), we also create compact 3D printed pumps. With 5-phase actuation and a 15 ms phase interval, we obtain pump flow rates as high as 40 μL min(-1). We also characterize maximum pump back pressure (i.e., maximum pressure the pump can work against), maximum flow rate (flow rate when there is zero back pressure), and flow rate as a function of the height of the pump outlet. We further demonstrate combining 5 valves and one DC to create a 3-to-2 multiplexer with integrated pump. In addition to serial multiplexing, we also show that the device can operate as a mixer. Importantly, we illustrate the rapid fabrication and test cycles that 3D printing makes possible by implementing a new multiplexer design to improve mixing, and fabricate and test it within one day.

  1. 3-D MAPPING TECHNOLOGIES FOR HIGH LEVEL WASTE TANKS

    SciTech Connect

    Marzolf, A.; Folsom, M.

    2010-08-31

    This research investigated four techniques that could be applicable for mapping of solids remaining in radioactive waste tanks at the Savannah River Site: stereo vision, LIDAR, flash LIDAR, and Structure from Motion (SfM). Stereo vision is the least appropriate technique for the solids mapping application. Although the equipment cost is low and repackaging would be fairly simple, the algorithms to create a 3D image from stereo vision would require significant further development and may not even be applicable since stereo vision works by finding disparity in feature point locations from the images taken by the cameras. When minimal variation in visual texture exists for an area of interest, it becomes difficult for the software to detect correspondences for that object. SfM appears to be appropriate for solids mapping in waste tanks. However, equipment development would be required for positioning and movement of the camera in the tank space to enable capturing a sequence of images of the scene. Since SfM requires the identification of distinctive features and associates those features to their corresponding instantiations in the other image frames, mockup testing would be required to determine the applicability of SfM technology for mapping of waste in tanks. There may be too few features to track between image frame sequences to employ the SfM technology since uniform appearance may exist when viewing the remaining solids in the interior of the waste tanks. Although scanning LIDAR appears to be an adequate solution, the expense of the equipment ($80,000-$120,000) and the need for further development to allow tank deployment may prohibit utilizing this technology. The development would include repackaging of equipment to permit deployment through the 4-inch access ports and to keep the equipment relatively uncontaminated to allow use in additional tanks. 3D flash LIDAR has a number of advantages over stereo vision, scanning LIDAR, and SfM, including full frame

  2. 3-D Mapping of the Galactic Nuclear Region

    NASA Astrophysics Data System (ADS)

    Wang, Q. Daniel

    The Galactic center of our Galaxy provides an excellent laboratory to study the star formation mode and history as well as the structure and dynamics of stars and gas under an extreme galactic nuclear environment. We propose a comprehensive data analysis program to investigate the 3-D properties of the region enclosed by the Central Molecular Zone of the Galaxy. We will capitalize on an extensive data set now available from Planck, Herschel, Spitzer, and Hubble Space Telescopes, as well as the Large Millimeter Telescope and other ground-based facilities. This data set provides sensitive high-resolution probes of the region over the millimeter to nearIR wavelength range. The data set, together with dedicated state-of-art analysis tools that we have been developing, will enable us to obtain (1) the first full-spacing millimeter dust emission image of the region at a resolution better than 10 arcseconds (FWHM), (2) the column density, temperature, and opacity spectral index distributions of dusty gas; (3) the mapping of dust extinction toward individual stars; (4) the line-of-sight locations of individual dense clouds, (5) the global spatial distribution and formation history of stars, and (6) the characterization of environment effects on stellar and gas dynamics in the region. The combined analysis of the dust emission and extinction will represent a major step forward in determining the properties of the dusty gas as well as its effect on the stellar light observations of the region. This body of work will likely have strong implications for our understanding the stellar and gas properties in other galactic nuclei and their role in regulating the evolution of galaxies as whole.

  3. Lidar on small UAV for 3D mapping

    NASA Astrophysics Data System (ADS)

    Tulldahl, H. Michael; Larsson, Hâkan

    2014-10-01

    Small UAV:s (Unmanned Aerial Vehicles) are currently in an explosive technical development phase. The performance of UAV-system components such as inertial navigation sensors, propulsion, control processors and algorithms are gradually improving. Simultaneously, lidar technologies are continuously developing in terms of reliability, accuracy, as well as speed of data collection, storage and processing. The lidar development towards miniature systems with high data rates has, together with recent UAV development, a great potential for new three dimensional (3D) mapping capabilities. Compared to lidar mapping from manned full-size aircraft a small unmanned aircraft can be cost efficient over small areas and more flexible for deployment. An advantage with high resolution lidar compared to 3D mapping from passive (multi angle) photogrammetry is the ability to penetrate through vegetation and detect partially obscured targets. Another advantage is the ability to obtain 3D data over the whole survey area, without the limited performance of passive photogrammetry in low contrast areas. The purpose of our work is to demonstrate 3D lidar mapping capability from a small multirotor UAV. We present the first experimental results and the mechanical and electrical integration of the Velodyne HDL-32E lidar on a six-rotor aircraft with a total weight of 7 kg. The rotating lidar is mounted at an angle of 20 degrees from the horizontal plane giving a vertical field-of-view of 10-50 degrees below the horizon in the aircraft forward directions. For absolute positioning of the 3D data, accurate positioning and orientation of the lidar sensor is of high importance. We evaluate the lidar data position accuracy both based on inertial navigation system (INS) data, and on INS data combined with lidar data. The INS sensors consist of accelerometers, gyroscopes, GPS, magnetometers, and a pressure sensor for altimetry. The lidar range resolution and accuracy is documented as well as the

  4. Probability Density Function at the 3D Anderson Transition

    NASA Astrophysics Data System (ADS)

    Rodriguez, Alberto; Vasquez, Louella J.; Roemer, Rudolf

    2009-03-01

    The probability density function (PDF) for the wavefunction amplitudes is studied at the metal-insulator transition of the 3D Anderson model, for very large systems up to L^3=240^3. The implications of the multifractal nature of the state upon the PDF are presented in detail. A formal expression between the PDF and the singularity spectrum f(α) is given. The PDF can be easily used to carry out a numerical multifractal analysis and it appears as a valid alternative to the more usual approach based on the scaling law of the general inverse participation rations.

  5. Sensing and 3D Mapping of Soil Compaction

    PubMed Central

    Tekin, Yücel; Kul, Basri; Okursoy, Rasim

    2008-01-01

    Soil compaction is an important physical limiting factor for the root growth and plant emergence and is one of the major causes for reduced crop yield worldwide. The objective of this study was to generate 2D/3D soil compaction maps for different depth layers of the soil. To do so, a soil penetrometer was designed, which was mounted on the three-point hitch of an agricultural tractor, consisting of a mechanical system, data acquisition system (DAS), and 2D/3D imaging and analysis software. The system was successfully tested in field conditions, measuring soil penetration resistances as a function of depth from 0 to 40 cm at 1 cm intervals. The software allows user to either tabulate the measured quantities or generate maps as soon as data collection has been terminated. The system may also incorporate GPS data to create geo-referenced soil maps. The software enables the user to graph penetration resistances at a specified coordinate. Alternately, soil compaction maps could be generated using data collected from multiple coordinates. The data could be automatically stratified to determine soil compaction distribution at different layers of 5, 10,.…, 40 cm depths. It was concluded that the system tested in this study could be used to assess the soil compaction at topsoil and the randomly distributed hardpan formations just below the common tillage depths, enabling visualization of spatial variability through the imaging software. PMID:27879888

  6. 3D map of the human corneal endothelial cell

    PubMed Central

    He, Zhiguo; Forest, Fabien; Gain, Philippe; Rageade, Damien; Bernard, Aurélien; Acquart, Sophie; Peoc’h, Michel; Defoe, Dennis M.; Thuret, Gilles

    2016-01-01

    Corneal endothelial cells (CECs) are terminally differentiated cells, specialized in regulating corneal hydration and transparency. They are highly polarized flat cells that separate the cornea from the aqueous humor. Their apical surface, in contact with aqueous humor is hexagonal, whereas their basal surface is irregular. We characterized the structure of human CECs in 3D using confocal microscopy of immunostained whole corneas in which cells and their interrelationships remain intact. Hexagonality of the apical surface was maintained by the interaction between tight junctions and a submembraneous network of actomyosin, braced like a drum. Lateral membranes, which support enzymatic pumps, presented complex expansions resembling interdigitated foot processes at the basal surface. Using computer-aided design and drafting software, we obtained a first simplified 3D model of CECs. By comparing their expression with those in epithelial, stromal and trabecular corneal cells, we selected 9 structural or functional proteins for which 3D patterns were specific to CECs. This first 3D map aids our understanding of the morphologic and functional specificity of CECs and could be used as a reference for characterizing future cell therapy products destined to treat endothelial dysfunctions. PMID:27381832

  7. Computational methods for constructing protein structure models from 3D electron microscopy maps.

    PubMed

    Esquivel-Rodríguez, Juan; Kihara, Daisuke

    2013-10-01

    Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. Resolutions of EM maps have been improving as evidenced by recently reported structures that are solved at high resolutions close to 3Å. Computational methods play a key role in interpreting EM data. Among many computational procedures applied to an EM map to obtain protein structure information, in this article we focus on reviewing computational methods that model protein three-dimensional (3D) structures from a 3D EM density map that is constructed from two-dimensional (2D) maps. The computational methods we discuss range from de novo methods, which identify structural elements in an EM map, to structure fitting methods, where known high resolution structures are fit into a low-resolution EM map. A list of available computational tools is also provided.

  8. Joint Impact Proposal: A complete velocity resolved 3-D [CII] map of the M51 grand-design spiral galaxy: Unraveling the impact of spiral density waves on the evolution of the ISM and star formation.

    NASA Astrophysics Data System (ADS)

    Stutzki, Juergen

    2015-10-01

    We propose to obtain the first complete, velocity resolved [CII] 158um image of the M51 grand-design spiral galaxy with the upGREAT and FIFI-LS instruments on SOFIA. Spiral density waves play a fundamental role on the conversion of atomic to molecular gas, leading to gravitational contraction and thus to star formation. Understanding the impact of spiral density waves on the lifecycle of the interstellar medium and on star formation in galaxies is thus critical for our understanding of galaxy evolution. The [CII] line (in combination with the low-J CO lines and HI 21 cm) is an important tool to diagnose the physical state of the ISM. It can reveal the distribution of the gas that is making a transition between atomic and molecular phases, including the CO-dark H2 gas (hydrogen molecular but carbon ionized, and thus not traced by either HI or CO) in the spiral arms and interarm regions of M51. We will use the high spectral resolution of the upGREAT instrument to resolve spiral arms in velocity, allowing us to study the flow of gas through spiral arms and measure line widths and determine the dynamical state of prominent interarm clouds. The significantly more sensitive FIFI-LS will be used to detect extended faint [CII] emission in the interarm regions and outskirts of the galaxy, including the gas connection to the companion galaxy. The 3-D data cube of velocity-resolved [CII] in this nearby galaxy, combined with the wealth of ancillary data, can be used for a large set of investigations by the broader astronomical community. It will provide for the first time the link between the detailed physical processes in the star-forming ISM in the Milky Way and the average properties of distant external galaxies. This complete map will be also an excellent showcase of SOFIA's capabilities for years to come.

  9. Joint Impact Proposal: A complete velocity resolved 3-D [CII] map of the M51 grand-design spiral galaxy: Unraveling the impact of spiral density waves on the evolution of the ISM and star formation.

    NASA Astrophysics Data System (ADS)

    Pineda, Jorge

    2015-10-01

    We propose to obtain the first complete, velocity resolved [CII] 158um image of the M51 grand-design spiral galaxy with the upGREAT and FIFI-LS instruments on SOFIA. Spiral density waves play a fundamental role on the conversion of atomic to molecular gas, leading to gravitational contraction and thus to star formation. Understanding the impact of spiral density waves on the lifecycle of the interstellar medium and on star formation in galaxies is thus critical for our understanding of galaxy evolution. The [CII] line (in combination with the low-J CO lines and HI 21 cm) is an important tool to diagnose the physical state of the ISM. It can reveal the distribution of the gas that is making a transition between atomic and molecular phases, including the CO-dark H2 gas (hydrogen molecular but carbon ionized, and thus not traced by either HI or CO) in the spiral arms and interarm regions of M51. We will use the high spectral resolution of the upGREAT instrument to resolve spiral arms in velocity, allowing us to study the flow of gas through spiral arms and measure line widths and determine the dynamical state of prominent interarm clouds. The significantly more sensitive FIFI-LS will be used to detect extended faint [CII] emission in the interarm regions and outskirts of the galaxy, including the gas connection to the companion galaxy. The 3-D data cube of velocity--resolved [CII] in this nearby galaxy, combined with the wealth of ancillary data, can be used for a large set of investigations by the broader astronomical community. It will provide for the first time the link between the detailed physical processes in the star-forming ISM in the Milky Way and the average properties of distant external galaxies. This complete map will be also an excellent showcase of SOFIA's capabilities for years to come.

  10. Density-tapered spiral arrays for ultrasound 3-D imaging.

    PubMed

    Ramalli, Alessandro; Boni, Enrico; Savoia, Alessandro Stuart; Tortoli, Piero

    2015-08-01

    The current high interest in 3-D ultrasound imaging is pushing the development of 2-D probes with a challenging number of active elements. The most popular approach to limit this number is the sparse array technique, which designs the array layout by means of complex optimization algorithms. These algorithms are typically constrained by a few steering conditions, and, as such, cannot guarantee uniform side-lobe performance at all angles. The performance may be improved by the ungridded extensions of the sparse array technique, but this result is achieved at the expense of a further complication of the optimization process. In this paper, a method to design the layout of large circular arrays with a limited number of elements according to Fermat's spiral seeds and spatial density modulation is proposed and shown to be suitable for application to 3-D ultrasound imaging. This deterministic, aperiodic, and balanced positioning procedure attempts to guarantee uniform performance over a wide range of steering angles. The capabilities of the method are demonstrated by simulating and comparing the performance of spiral and dense arrays. A good trade-off for small vessel imaging is found, e.g., in the 60λ spiral array with 1.0λ elements and Blackman density tapering window. Here, the grating lobe level is -16 dB, the lateral resolution is lower than 6λ the depth of field is 120λ and, the average contrast is 10.3 dB, while the sensitivity remains in a 5 dB range for a wide selection of steering angles. The simulation results may represent a reference guide to the design of spiral sparse array probes for different application fields.

  11. Geomorphological maps and 3d models in cave research

    NASA Astrophysics Data System (ADS)

    Ballesteros, Daniel; Jiménez-Sánchez, Montserrat; José Domínguez-Cuesta, María

    2013-04-01

    Cave geomorphological processes and features can be studied by geomorphological maps although topographic maps, aerial photos and GPS are not available. Methods in cave geomorphological mapping are conditioned by cave environment configuration, the need of using speleological techniques, and limitations arising from the projection of the 3D data from the cave to a 2D plan. Some of our previous works in the Cantabrian Mountains and Cantabrian Coast (NW Spain) established the approach of the design of cave geomorphological maps and its legend. Today we are improving the display of cave process combining geomorphological maps and 3d models based on the experience obtained from the research of one cave from the Cantabrian Coast and four caves in the Picos de Europa National Park (funded by GEOCAVE project, Spanish National Parks Agency). The five caves are developed in Carboniferous limestone affected by faults and thrusts. The method of work includes: 1) the elaboration of the cave survey at 1:50 to 1:500 scale; 2) the check of the cave survey of three caves by closed loops; 3) the mapping of cave features based on the performed survey; 4) the 3d modeling of the caves approximating each survey shoot by an octagonal prism; and 5) the implementation and management of the survey and geomorphological map in a Geographic Information System. Based on the survey, the cavities are small caves to deep alpine shafts with 281 to 4,438 m length and up to 738 m deep. The precision of the cave maps only could be estimated in two caves at a cavity scale, displaying both of them a 2.49 % error. The prisms of the 3d model was classified into four groups according to the morphology of the cave passage: 1) canyons, 2) phreatic and epiphreatic tubes, 3) soutirage conduits, 4) mixed forms composed by phreatic and epiphreatic tubes modified by fluvial incision, 5) pitches and 6) irregular passages enlarged strongly by gravity process. According to our previous works geomorphological

  12. 3D Gel Map of Arabidopsis Complex I

    PubMed Central

    Peters, Katrin; Belt, Katharina; Braun, Hans-Peter

    2013-01-01

    Complex I has a unique structure in plants and includes extra subunits. Here, we present a novel study to define its protein constituents. Mitochondria were isolated from Arabidopsis thaliana cell cultures, leaves, and roots. Subunits of complex I were resolved by 3D blue-native (BN)/SDS/SDS-PAGE and identified by mass spectrometry. Overall, 55 distinct proteins were found, seven of which occur in pairs of isoforms. We present evidence that Arabidopsis complex I consists of 49 distinct types of subunits, 40 of which represent homologs of bovine complex I. The nine other subunits represent special proteins absent in the animal linage of eukaryotes, most prominently a group of subunits related to bacterial gamma-type carbonic anhydrases. A GelMap http://www.gelmap.de/arabidopsis-3d-complex-i/ is presented for promoting future complex I research in Arabidopsis thaliana. PMID:23761796

  13. Real time 3-D electron density reconstruction over Europe by using TaD profiler

    NASA Astrophysics Data System (ADS)

    Kutiev, I.; Marinov, P.; Belehaki, A.

    2016-07-01

    The TaD (Topside Sounder Model (TSM)-assisted Digisonde) profiler, developed on the basis of the Topside Sounder Model (TSM), provides vertical electron density profiles (EDP) over Digisondes from the bottomside ionosphere up to Global Navigation Satellite Systems (GNSS) orbit heights. TaD EDP uses the Digisonde bottomside profile and extends it above the F2 layer peak, representing O+ distribution by α-Chapman formula and H+ distribution by a single exponent. Topside scale height HT and transition height hT are taken from TSM, while the plasmasphere scale height Hp is defined as a function of HT. All profile parameters are adjusted to the current conditions comparing the profile integral with the GNSS vertical total electron content (TEC) retrieved from the European Reference Frame (EUREF) maps. To expand to three dimensions (3-D), European maps of foF2 and hmF2 are produced, based on Digisonde data, with spatial resolution 1°×1° in latitude and longitude, and TaD profiles are calculated at each grid node. Electron density (ED) at any point of the 3-D space is obtained by linear interpolation of TaD parameters between neighbor nodes. Samples of two dimensional (2-D) electron density distribution (EDD) at different cross sections of the 3-D space between 200 km and 1150 km over the mapping area are presented, along with distributions of the electron density along various raypaths of GNSS signals. The modeled 3-D EDD is compared with vertical (vTEC) and slant (sTEC) TEC parameters calculated from individual GNSS receivers. The model error (relative deviation of model from the data), based on 6780 data values, is 10% for sTEC and 6% for vTEC.

  14. Georeferenced LiDAR 3D Vine Plantation Map Generation

    PubMed Central

    Llorens, Jordi; Gil, Emilio; Llop, Jordi; Queraltó, Meritxell

    2011-01-01

    The use of electronic devices for canopy characterization has recently been widely discussed. Among such devices, LiDAR sensors appear to be the most accurate and precise. Information obtained with LiDAR sensors during reading while driving a tractor along a crop row can be managed and transformed into canopy density maps by evaluating the frequency of LiDAR returns. This paper describes a proposed methodology to obtain a georeferenced canopy map by combining the information obtained with LiDAR with that generated using a GPS receiver installed on top of a tractor. Data regarding the velocity of LiDAR measurements and UTM coordinates of each measured point on the canopy were obtained by applying the proposed transformation process. The process allows overlap of the canopy density map generated with the image of the intended measured area using Google Earth®, providing accurate information about the canopy distribution and/or location of damage along the rows. This methodology was applied and tested on different vine varieties and crop stages in two important vine production areas in Spain. The results indicate that the georeferenced information obtained with LiDAR sensors appears to be an interesting tool with the potential to improve crop management processes. PMID:22163952

  15. Georeferenced LiDAR 3D vine plantation map generation.

    PubMed

    Llorens, Jordi; Gil, Emilio; Llop, Jordi; Queraltó, Meritxell

    2011-01-01

    The use of electronic devices for canopy characterization has recently been widely discussed. Among such devices, LiDAR sensors appear to be the most accurate and precise. Information obtained with LiDAR sensors during reading while driving a tractor along a crop row can be managed and transformed into canopy density maps by evaluating the frequency of LiDAR returns. This paper describes a proposed methodology to obtain a georeferenced canopy map by combining the information obtained with LiDAR with that generated using a GPS receiver installed on top of a tractor. Data regarding the velocity of LiDAR measurements and UTM coordinates of each measured point on the canopy were obtained by applying the proposed transformation process. The process allows overlap of the canopy density map generated with the image of the intended measured area using Google Earth(®), providing accurate information about the canopy distribution and/or location of damage along the rows. This methodology was applied and tested on different vine varieties and crop stages in two important vine production areas in Spain. The results indicate that the georeferenced information obtained with LiDAR sensors appears to be an interesting tool with the potential to improve crop management processes.

  16. 3D-Digital soil property mapping by geoadditive models

    NASA Astrophysics Data System (ADS)

    Papritz, Andreas

    2016-04-01

    In many digital soil mapping (DSM) applications, soil properties must be predicted not only for a single but for multiple soil depth intervals. In the GlobalSoilMap project, as an example, predictions are computed for the 0-5 cm, 5-15 cm, 15-30 cm, 30-60 cm, 60-100 cm, 100-200 cm depth intervals (Arrouays et al., 2014). Legacy soil data are often used for DSM. It is common for such datasets that soil properties were measured for soil horizons or for layers at varying soil depth and with non-constant thickness (support). This poses problems for DSM: One strategy is to harmonize the soil data to common depth prior to the analyses (e.g. Bishop et al., 1999) and conduct the statistical analyses for each depth interval independently. The disadvantage of this approach is that the predictions for different depths are computed independently from each other so that the predicted depth profiles may be unrealistic. Furthermore, the error induced by the harmonization to common depth is ignored in this approach (Orton et al. 2016). A better strategy is therefore to process all soil data jointly without prior harmonization by a 3D-analysis that takes soil depth and geographical position explicitly into account. Usually, the non-constant support of the data is then ignored, but Orton et al. (2016) presented recently a geostatistical approach that accounts for non-constant support of soil data and relies on restricted maximum likelihood estimation (REML) of a linear geostatistical model with a separable, heteroscedastic, zonal anisotropic auto-covariance function and area-to-point kriging (Kyriakidis, 2004.) Although this model is theoretically coherent and elegant, estimating its many parameters by REML and selecting covariates for the spatial mean function is a formidable task. A simpler approach might be to use geoadditive models (Kammann and Wand, 2003; Wand, 2003) for 3D-analyses of soil data. geoAM extend the scope of the linear model with spatially correlated errors to

  17. Disaster Prevention Coastal Map Production by MMS & C3D

    NASA Astrophysics Data System (ADS)

    Hatake, Shuhei; Kohori, Yuki; Watanabe, Yasushi

    2016-06-01

    In March 2011, Eastern Japan suffered serious damage of Tsunami caused by a massive earthquake. In 2012, Ministry of Land, Infrastructure and Transport published "Guideline of setting assumed areas of inundation by Tsunami" to establish the conditions of topography data used for simulation of Tsunami. In this guideline, the elevation data prepared by Geographical Survey Institute of Japan and 2m/5m/10m mesh data of NSDI are adopted for land area, while 500m mesh data of Hydrographic and Oceanographic Department of Japan Coast Guard and sea charts are adopted for water area. These data, however, do not have continuity between land area and water area. Therefore, in order to study the possibility of providing information for coastal disaster prevention, we have developed an efficient method to acquire continuous topography over land and water including tidal zone. Land area data are collected by Mobile Mapping System (MMS) and water area depth data are collected by interferometry echo sounder (C3D), and both data are simultaneously acquired on a same boat. Elaborate point cloud data of 1m or smaller are expected to be used for realistic simulation of Tsunami waves going upstream around shoreline. Tests were made in Tokyo Bay (in 2014) and Osaka Bay (in 2015). The purpose the test in Osaka Bay is to make coastal map for disaster prevention as a countermeasure for predicted Nankai massive earthquake. In addition to Tsunami simulation, the continuous data covering land and marine areas are expected to be used effectively for maintenance and repair of aged port and river facilities, maintenance and investigation of dykes, and ecosystem preservation.

  18. 3D mapping and simulation of Geneva Lake environmental data

    NASA Astrophysics Data System (ADS)

    Villard, Roch; Maignan, Michel; Kanevski, Mikhail; Rapin, Francois; Klein, Audrey

    2010-05-01

    The Geneva Lake is the biggest alpine and subalpine lake in central Europe. The depth of this lake is 309 meters and its total volume of water is 89 billions m3. It takes, on average, around twelve years so that waters of the lake are completely brewed. Furthermore the Geneva lake waters are rich in dissolved substances as carbonate, sulfate. The quantity of particles in suspension in the lake, which mainly arrived from the Rhône, is nowadays around height million of tones. The International Commission for the Leman Lake (CIPEL) works about the improvement of the quality of this lake since 1962. In the present study three dimensional environmental data (temperature, oxygen and nitrate) which cover the period from 1954 to 2008, for a total of 27'500 cases are investigated. We are interested to study the evolution of the temperature of the lake because there is an impact on the reproduction of fishes and also because the winter brewing of the water makes the re-oxygenation of deep-water. In order that biological balance is maintained in a lake, there must be enough oxygen in the water. Moreover, we work on nitrate distribution and evolution because contributions in fertilizers cause eutrophication of lake. The data are very numerous when we consider the time series, some of them with more than 300 occurrences, but there are between 2 and 15 data available for spatial cartography. The basic methodology used for the analysis, mapping and simulations of 3D patterns of environmental data is based on geostatistical predictions (family of kriging models) and conditional stochastic simulations. Spatial and temporal variability, 3D monitoring networks changing over time, make this study challenging. An important problem is also to make interpolation/simulations over a long period of time, like ten years. One way used to overcome this problem, consists in using a weighted average of ten variograms during this period. 3D mapping was carried out using environment data for

  19. 3D Color Digital Elevation Map of AFM Sample

    NASA Technical Reports Server (NTRS)

    2008-01-01

    This color image is a three dimensional (3D) view of a digital elevation map of a sample collected by NASA's Phoenix Mars Lander's Atomic Force Microscope (AFM).

    The image shows four round pits, only 5 microns in depth, that were micromachined into the silicon substrate, which is the background plane shown in red. This image has been processed to reflect the levelness of the substrate.

    A Martian particle only one micrometer, or one millionth of a meter, across is held in the upper left pit.

    The rounded particle shown at the highest magnification ever seen from another world is a particle of the dust that cloaks Mars. Such dust particles color the Martian sky pink, feed storms that regularly envelop the planet and produce Mars' distinctive red soil.

    The particle was part of a sample informally called 'Sorceress' delivered to the AFM on the 38th Martian day, or sol, of the mission (July 2, 2008). The AFM is part of Phoenix's microscopic station called MECA, or the Microscopy, Electrochemistry, and Conductivity Analyzer.

    The AFM was developed by a Swiss-led consortium, with Imperial College London producing the silicon substrate that holds sampled particles.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  20. 3-D capacitance density imaging of fluidized bed

    DOEpatents

    Fasching, George E.

    1990-01-01

    A three-dimensional capacitance density imaging of a gasified bed or the like in a containment vessel is achieved using a plurality of electrodes provided circumferentially about the bed in levels and along the bed in channels. The electrodes are individually and selectively excited electrically at each level to produce a plurality of current flux field patterns generated in the bed at each level. The current flux field patterns are suitably sensed and a density pattern of the bed at each level determined. By combining the determined density patterns at each level, a three-dimensional density image of the bed is achieved.

  1. Sector mapping method for 3D detached retina visualization.

    PubMed

    Zhai, Yi-Ran; Zhao, Yong; Zhong, Jie; Li, Ke; Lu, Cui-Xin; Zhang, Bing

    2016-10-01

    A new sphere-mapping algorithm called sector mapping is introduced to map sector images to the sphere of an eyeball. The proposed sector-mapping algorithm is evaluated and compared with the plane-mapping algorithm adopted in previous work. A simulation that maps an image of concentric circles to the sphere of the eyeball and an analysis of the difference in distance between neighboring points in a plane and sector were used to compare the two mapping algorithms. A three-dimensional model of a whole retina with clear retinal detachment was generated using the Visualization Toolkit software. A comparison of the mapping results shows that the central part of the retina near the optic disc is stretched and its edges are compressed when the plane-mapping algorithm is used. A better mapping result is obtained by the sector-mapping algorithm than by the plane-mapping algorithm in both the simulation results and real clinical retinal detachment three-dimensional reconstruction.

  2. Low Cost and Efficient 3d Indoor Mapping Using Multiple Consumer Rgb-D Cameras

    NASA Astrophysics Data System (ADS)

    Chen, C.; Yang, B. S.; Song, S.

    2016-06-01

    Driven by the miniaturization, lightweight of positioning and remote sensing sensors as well as the urgent needs for fusing indoor and outdoor maps for next generation navigation, 3D indoor mapping from mobile scanning is a hot research and application topic. The point clouds with auxiliary data such as colour, infrared images derived from 3D indoor mobile mapping suite can be used in a variety of novel applications, including indoor scene visualization, automated floorplan generation, gaming, reverse engineering, navigation, simulation and etc. State-of-the-art 3D indoor mapping systems equipped with multiple laser scanners product accurate point clouds of building interiors containing billions of points. However, these laser scanner based systems are mostly expensive and not portable. Low cost consumer RGB-D Cameras provides an alternative way to solve the core challenge of indoor mapping that is capturing detailed underlying geometry of the building interiors. Nevertheless, RGB-D Cameras have a very limited field of view resulting in low efficiency in the data collecting stage and incomplete dataset that missing major building structures (e.g. ceilings, walls). Endeavour to collect a complete scene without data blanks using single RGB-D Camera is not technic sound because of the large amount of human labour and position parameters need to be solved. To find an efficient and low cost way to solve the 3D indoor mapping, in this paper, we present an indoor mapping suite prototype that is built upon a novel calibration method which calibrates internal parameters and external parameters of multiple RGB-D Cameras. Three Kinect sensors are mounted on a rig with different view direction to form a large field of view. The calibration procedure is three folds: 1, the internal parameters of the colour and infrared camera inside each Kinect are calibrated using a chess board pattern, respectively; 2, the external parameters between the colour and infrared camera inside each

  3. B1-insensitive T2 mapping of healthy thigh muscles using a T2-prepared 3D TSE sequence

    PubMed Central

    Klupp, Elisabeth; Weidlich, Dominik; Schlaeger, Sarah; Baum, Thomas; Cervantes, Barbara; Deschauer, Marcus; Kooijman, Hendrik; Rummeny, Ernst J.; Zimmer, Claus; Kirschke, Jan S.; Karampinos, Dimitrios C.

    2017-01-01

    Purpose To propose a T2-prepared 3D turbo spin echo (T2prep 3D TSE) sequence for B1-insensitive skeletal muscle T2 mapping and compare its performance with 2D and 3D multi-echo spin echo (MESE) for T2 mapping in thigh muscles of healthy subjects. Methods The performance of 2D MESE, 3D MESE and the proposed T2prep 3D TSE in the presence of transmit B1 and B0 inhomogeneities was first simulated. The thigh muscles of ten young and healthy subjects were then scanned on a 3 T system and T2 mapping was performed using the three sequences. Transmit B1-maps and proton density fat fraction (PDFF) maps were also acquired. The subjects were scanned three times to assess reproducibility. T2 values were compared among sequences and their sensitivity to B1 inhomogeneities was compared to simulation results. Correlations were also determined between T2 values, PDFF and B1. Results The left rectus femoris muscle showed the largest B1 deviations from the nominal value (from 54.2% to 92.9%). Significant negative correlations between T2 values and B1 values were found in the left rectus femoris muscle for 3D MESE (r = -0.72, p<0.001) and 2D MESE (r = -0.71, p<0.001), but not for T2prep 3D TSE (r = -0.32, p = 0.09). Reproducibility of T2 expressed by root mean square coefficients of variation (RMSCVs) were equal to 3.5% in T2prep 3D TSE, 2.6% in 3D MESE and 2.4% in 2D MESE. Significant differences between T2 values of 3D sequences (T2prep 3D TSE and 3D MESE) and 2D MESE were found in all muscles with the highest values for 2D MESE (p<0.05). No significant correlations were found between PDFF and T2 values. Conclusion A strong influence of an inhomogeneous B1 field on the T2 values of 3D MESE and 2D MESE was shown, whereas the proposed T2prep 3D TSE gives B1-insensitive and reproducible thigh muscle T2 mapping. PMID:28196133

  4. The 3D Stacking Bipolar RRAM for High Density

    DTIC Science & Technology

    2011-06-01

    ICF International, Fairfax, Virginia, USA. (email: robinson.pino@icfi.com) Copyright (c) 2012 IEEE. Personal use of this material is permitted. However...density as D = 1/(A · T ), where, A and T represent a single memory cell area and memory layer thickness, respectively. Accordingly, we have D3D−conv...SM in the worst-case condition. -- 4x4 8x8 16x16 32x32 64x64 0 20 40 60 80 100 R on =5 kΩ R on =10 kΩ R on =5 kΩ R on =10 kΩ Array size P o rt io

  5. Towards High Density 3-D Memory in Diamond

    NASA Astrophysics Data System (ADS)

    Henshaw, Jacob; Dhomkar, Siddharth; Meriles, Carlos; Jayakumar, Harishankar

    The nitrogen-vacancy (NV) center in diamond is presently the focus of widespread attention for applications ranging from quantum information processing to nanoscale metrology. Of great utility is the ability to optically initialize the NV charge state, which has an immediate impact on the center's light emission properties. Here, we use two-color microscopy in NV-rich, type-1b diamond to demonstrate fluorescence-encoded long-term storage of classical information. As a proof of principle, we write, reset, and rewrite various patterns with 2-D binary bit density comparable to present DVD-ROM technology. The strong fluorescence signal originating from the diffraction-limited bit volume allows us to transition from binary to multi-valued encoding, which translates into a significant storage capacity boost. Finally, we show that our technique preserves information written on different planes of the diamond crystal and thus serves as a platform for three-dimensional storage. Substantial enhancement in the bit density could be achieved with the aid of super resolution microscopy techniques already employed to discriminate between NVs with sub-diffraction, nanometer accuracy, a regime where the storage capacity could exceed 1017 bytes/cm3 We acknowledge support from the National Science Foundation through Grant NSF-1314205.

  6. Impact of Building Heights on 3d Urban Density Estimation from Spaceborne Stereo Imagery

    NASA Astrophysics Data System (ADS)

    Peng, Feifei; Gong, Jianya; Wang, Le; Wu, Huayi; Yang, Jiansi

    2016-06-01

    In urban planning and design applications, visualization of built up areas in three dimensions (3D) is critical for understanding building density, but the accurate building heights required for 3D density calculation are not always available. To solve this problem, spaceborne stereo imagery is often used to estimate building heights; however estimated building heights might include errors. These errors vary between local areas within a study area and related to the heights of the building themselves, distorting 3D density estimation. The impact of building height accuracy on 3D density estimation must be determined across and within a study area. In our research, accurate planar information from city authorities is used during 3D density estimation as reference data, to avoid the errors inherent to planar information extracted from remotely sensed imagery. Our experimental results show that underestimation of building heights is correlated to underestimation of the Floor Area Ratio (FAR). In local areas, experimental results show that land use blocks with low FAR values often have small errors due to small building height errors for low buildings in the blocks; and blocks with high FAR values often have large errors due to large building height errors for high buildings in the blocks. Our study reveals that the accuracy of 3D density estimated from spaceborne stereo imagery is correlated to heights of buildings in a scene; therefore building heights must be considered when spaceborne stereo imagery is used to estimate 3D density to improve precision.

  7. Mapping 3-D functional capillary geometry in rat skeletal muscle in vivo

    PubMed Central

    Milkovich, Stephanie; Goldman, Daniel; Ellis, Christopher G.

    2012-01-01

    We have developed a novel mapping software package to reconstruct microvascular networks in three dimensions (3-D) from in vivo video images for use in blood flow and O2 transport modeling. An intravital optical imaging system was used to collect video sequences of blood flow in microvessels at different depths in the tissue. Functional images of vessels were produced from the video sequences and were processed using automated edge tracking software to yield location and geometry data for construction of the 3-D network. The same video sequences were analyzed for hemodynamic and O2 saturation data from individual capillaries in the network. Simple user-driven commands allowed the connection of vessel segments at bifurcations, and semiautomated registration enabled the tracking of vessels across multiple focal planes and fields of view. The reconstructed networks can be rotated and manipulated in 3-D to verify vessel connections and continuity. Hemodynamic and O2 saturation measurements made in vivo can be indexed to corresponding vessels and visualized using colorized maps of the vascular geometry. Vessels in each reconstruction are saved as text-based files that can be easily imported into flow or O2 transport models with complete geometry, hemodynamic, and O2 transport conditions. The results of digital morphometric analysis of seven microvascular networks showed mean capillary diameters and overall capillary density consistent with previous findings using histology and corrosion cast techniques. The described mapping software is a valuable tool for the quantification of in vivo microvascular geometry, hemodynamics, and oxygenation, thus providing rich data sets for experiment-based computational models. PMID:22140042

  8. New algorithms to map asymmetries of 3D surfaces.

    PubMed

    Combès, Benoît; Prima, Sylvain

    2008-01-01

    In this paper, we propose a set of new generic automated processing tools to characterise the local asymmetries of anatomical structures (represented by surfaces) at an individual level, and within/between populations. The building bricks of this toolbox are: (1) a new algorithm for robust, accurate, and fast estimation of the symmetry plane of grossly symmetrical surfaces, and (2) a new algorithm for the fast, dense, nonlinear matching of surfaces. This last algorithm is used both to compute dense individual asymmetry maps on surfaces, and to register these maps to a common template for population studies. We show these two algorithms to be mathematically well-grounded, and provide some validation experiments. Then we propose a pipeline for the statistical evaluation of local asymmetries within and between populations. Finally we present some results on real data.

  9. Mapping 3D Large-Scale Structure at z ˜2 with Lyman-α Forest Tomographic Mapping

    NASA Astrophysics Data System (ADS)

    Lee, Khee-Gan; Hennawi, J. F.; White, M.; Croft, R. A.; Prochaska, J. X.; Schlegel, D. J.; Suzuki, N.; Kneib, J.; Bailey, S. J.; Spergel, D. N.; Rix, H.; Strauss, M. A.

    2014-01-01

    The Lyman-α (Lyα) forest absorption at z>2 traces the underlying dark-matter distribution, and with a sufficient density of background sightlines can be used to create 3D tomographic maps of large-scale structure. Since the useful Lyα forest in each sightline spans ˜400-500 h-1Mpc, Lyα forest tomography can efficiently map out large-scale structure at z˜2. The Cosmic Lyman-Alpha Program for the Tomographic Reconstruction of Absorption Probes (CLAPTRAP) will be the first survey to attempt this technique. We aim to obtain spectra for a background grid of faint quasars and bright LBGs at 23D map with similar 3 h-1Mpc resolution to be reconstructed from the data. In a recent paper, we have found that spectra with S/N ˜ 4 per Å are sufficient to make excellent-quality tomographic maps that clearly trace the underlying dark-matter distribution at overdensities of order unity. This requires integrations of several hours on moderate-resolution spectrographs mounted on existing 8-10m telescopes, such as LRIS on the Keck-I telescope and VIMOS on the Very Large Telescopes. We aim to observe ˜1500-2000 background sources over 1 sq deg of the COSMOS field with Lyα forest coverage over 2.0map out a total comoving volume of ˜106h-3Mpc3, equivalent to the zCOSMOS and DEEP2 galaxy redshift maps out to z˜1. The total time requirement is 16 nights on either VLT-VIMOS or Keck-LRIS. The resulting tomographic maps will be the first 3D maps of large-scale structure at z>1. In conjunction with the rich multi-wavelength data from the COSMOS survey, these maps will facilitate the study of galaxies in the context of the large-scale environment, reveal the topology of large-scale structure at high-redshifts, and allow the direct detection of galaxy protoclusters at the intersections of the cosmic web. The

  10. Representativeness of 2D models to simulate 3D unstable variable density flow in porous media

    NASA Astrophysics Data System (ADS)

    Knorr, Bastian; Xie, Yueqing; Stumpp, Christine; Maloszewski, Piotr; Simmons, Craig T.

    2016-11-01

    Variable density flow in porous media has been studied primarily using numerical models because it is a semi-chaotic and transient process. Most of these studies have been 2D, owing to the computational restrictions on 3D simulations, and the ability to observe variable density flow in 2D experimentation. However, it is recognised that variable density flow is a three-dimensional process. A 3D system may cause weaker variable density flow than a 2D system due to stronger dispersion, but may also result in bigger fingers and hence stronger variable density flow because of more space for fingers to coalesce. This study aimed to determine the representativeness of 2D modelling to simulate 3D variable density flow. 3D homogeneous sand column experiments were conducted at three different water flow velocities with three different bromide tracer solutions mixed with methanol resulting in different density ratios. Both 2D axisymmetric and 3D numerical simulations were performed to reproduce experimental data. Experimental results showed that the magnitude of variable density flow increases with decreasing flow rates and decreasing density ratios. The shapes of the observed breakthrough curves differed significantly from those produced by 2D axisymmetric and 3D simulations. Compared to 2D simulations, the onset of instabilities was delayed but the growth was more pronounced in 3D simulations. Despite this difference, both 2D axisymmetric and 3D models successfully simulated mass recovery with high efficiency (between 77% and 99%). This study indicates that 2D simulations are sufficient to understand integrated features of variable density flow in homogeneous sand column experiments.

  11. Acquisition of 3-D Map Structures for Mobile Robots

    DTIC Science & Technology

    2007-11-02

    god of metalsmiths). In 1495, Leonardo da Vinci had created plans for a mechanical man [12]. However, it was not until the 1950s and 1960s (when...and return to the sensor a moment later. Since these sensors determine distance by the time of flight of the ping (or beam), the delay makes the sensor...obtained. To complicate matters even more, the density of the air (since that affects the sonar wave’s time of flight ) and the reflectiveness of the

  12. 3D current source density imaging based on acoustoelectric effect: a simulation study using unipolar pulses

    PubMed Central

    Yang, Renhuan; Li, Xu; Liu, Jun; He, Bin

    2011-01-01

    It is of importance to image electrical activity and properties of biological tissues. Recently hybrid imaging modality combing ultrasound scanning and source imaging through the acousto-electric (AE) effect has generated considerable interest. Such modality has the potential to provide high spatial resolution current density imaging by utilizing the pressure induced AE resistivity change confined at the ultrasound focus. In this study, we investigate a novel 3-dimensional (3D) ultrasound current source density imaging (UCSDI) approach using unipolar ultrasound pulses. Utilizing specially designed unipolar ultrasound pulses and by combining AE signals associated to the local resistivity changes at the focusing point, we are able to reconstruct the 3D current density distribution with the boundary voltage measurements obtained while performing a 3D ultrasound scan. We have shown in computer simulation that using the present method, it is feasible to image with high spatial resolution an arbitrary 3D current density distribution in an inhomogeneous conductive media. PMID:21628774

  13. Face recognition using 3D facial shape and color map information: comparison and combination

    NASA Astrophysics Data System (ADS)

    Godil, Afzal; Ressler, Sandy; Grother, Patrick

    2004-08-01

    In this paper, we investigate the use of 3D surface geometry for face recognition and compare it to one based on color map information. The 3D surface and color map data are from the CAESAR anthropometric database. We find that the recognition performance is not very different between 3D surface and color map information using a principal component analysis algorithm. We also discuss the different techniques for the combination of the 3D surface and color map information for multi-modal recognition by using different fusion approaches and show that there is significant improvement in results. The effectiveness of various techniques is compared and evaluated on a dataset with 200 subjects in two different positions.

  14. Identifying the third dimension in 2D fluoroscopy to create 3D cardiac maps.

    PubMed

    Sra, Jasbir; Krum, David; Choudhuri, Indrajit; Belanger, Barry; Palma, Mark; Brodnick, Donald; Rowe, Daniel B

    2016-12-22

    Three-dimensional cardiac mapping is important for optimal visualization of the heart during cardiac ablation for the treatment of certain arrhythmias. However, many hospitals and clinics worldwide cannot afford the high cost of the current mapping systems. We set out to determine if, using predefined algorithms, comparable 3D cardiac maps could be created by a new device that relies on data generated from single-plane fluoroscopy and patient recording and monitoring systems, without the need for costly equipment, infrastructure changes, or specialized catheters. The study included phantom and animal experiments to compare the prototype test device, Navik 3D, with the existing CARTO 3 System. The primary endpoint directly compared: (a) the 3D distance between the Navik 3D-simulated ablation location and the back-projected ground truth location of the pacing and mapping catheter electrode, and (b) the same distance for CARTO. The study's primary objective was considered met if the 95% confidence lower limit was greater than 0.75% for the Navik 3D-CARTO difference between the 2 distances, or less than or equal to 2 mm. Study results showed that the Navik 3D performance was equivalent to the CARTO system, and that accurate 3D cardiac maps can be created using data from equipment that already exists in all electrophysiology labs.

  15. gEMfitter: a highly parallel FFT-based 3D density fitting tool with GPU texture memory acceleration.

    PubMed

    Hoang, Thai V; Cavin, Xavier; Ritchie, David W

    2013-11-01

    Fitting high resolution protein structures into low resolution cryo-electron microscopy (cryo-EM) density maps is an important technique for modeling the atomic structures of very large macromolecular assemblies. This article presents "gEMfitter", a highly parallel fast Fourier transform (FFT) EM density fitting program which can exploit the special hardware properties of modern graphics processor units (GPUs) to accelerate both the translational and rotational parts of the correlation search. In particular, by using the GPU's special texture memory hardware to rotate 3D voxel grids, the cost of rotating large 3D density maps is almost completely eliminated. Compared to performing 3D correlations on one core of a contemporary central processor unit (CPU), running gEMfitter on a modern GPU gives up to 26-fold speed-up. Furthermore, using our parallel processing framework, this speed-up increases linearly with the number of CPUs or GPUs used. Thus, it is now possible to use routinely more robust but more expensive 3D correlation techniques. When tested on low resolution experimental cryo-EM data for the GroEL-GroES complex, we demonstrate the satisfactory fitting results that may be achieved by using a locally normalised cross-correlation with a Laplacian pre-filter, while still being up to three orders of magnitude faster than the well-known COLORES program.

  16. Fast Semantic Segmentation of 3d Point Clouds with Strongly Varying Density

    NASA Astrophysics Data System (ADS)

    Hackel, Timo; Wegner, Jan D.; Schindler, Konrad

    2016-06-01

    We describe an effective and efficient method for point-wise semantic classification of 3D point clouds. The method can handle unstructured and inhomogeneous point clouds such as those derived from static terrestrial LiDAR or photogammetric reconstruction; and it is computationally efficient, making it possible to process point clouds with many millions of points in a matter of minutes. The key issue, both to cope with strong variations in point density and to bring down computation time, turns out to be careful handling of neighborhood relations. By choosing appropriate definitions of a point's (multi-scale) neighborhood, we obtain a feature set that is both expressive and fast to compute. We evaluate our classification method both on benchmark data from a mobile mapping platform and on a variety of large, terrestrial laser scans with greatly varying point density. The proposed feature set outperforms the state of the art with respect to per-point classification accuracy, while at the same time being much faster to compute.

  17. Density functional theory optimized basis sets for gradient corrected functionals: 3d transition metal systems.

    PubMed

    Calaminici, Patrizia; Janetzko, Florian; Köster, Andreas M; Mejia-Olvera, Roberto; Zuniga-Gutierrez, Bernardo

    2007-01-28

    Density functional theory optimized basis sets for gradient corrected functionals for 3d transition metal atoms are presented. Double zeta valence polarization and triple zeta valence polarization basis sets are optimized with the PW86 functional. The performance of the newly optimized basis sets is tested in atomic and molecular calculations. Excitation energies of 3d transition metal atoms, as well as electronic configurations, structural parameters, dissociation energies, and harmonic vibrational frequencies of a large number of molecules containing 3d transition metal elements, are presented. The obtained results are compared with available experimental data as well as with other theoretical data from the literature.

  18. The effect of volumetric (3D) tactile symbols within inclusive tactile maps.

    PubMed

    Gual, Jaume; Puyuelo, Marina; Lloveras, Joaquim

    2015-05-01

    Point, linear and areal elements, which are two-dimensional and of a graphic nature, are the morphological elements employed when designing tactile maps and symbols for visually impaired users. However, beyond the two-dimensional domain, there is a fourth group of elements - volumetric elements - which mapmakers do not take sufficiently into account when it comes to designing tactile maps and symbols. This study analyses the effect of including volumetric, or 3D, symbols within a tactile map. In order to do so, the researchers compared two tactile maps. One of them uses only two-dimensional elements and is produced using thermoforming, one of the most popular systems in this field, while the other includes volumetric symbols, thus highlighting the possibilities opened up by 3D printing, a new area of production. The results of the study show that including 3D symbols improves the efficiency and autonomous use of these products.

  19. Velocity and Density Models Incorporating the Cascadia Subduction Zone for 3D Earthquake Ground Motion Simulations

    USGS Publications Warehouse

    Stephenson, William J.

    2007-01-01

    INTRODUCTION In support of earthquake hazards and ground motion studies in the Pacific Northwest, three-dimensional P- and S-wave velocity (3D Vp and Vs) and density (3D rho) models incorporating the Cascadia subduction zone have been developed for the region encompassed from about 40.2?N to 50?N latitude, and from about -122?W to -129?W longitude. The model volume includes elevations from 0 km to 60 km (elevation is opposite of depth in model coordinates). Stephenson and Frankel (2003) presented preliminary ground motion simulations valid up to 0.1 Hz using an earlier version of these models. The version of the model volume described here includes more structural and geophysical detail, particularly in the Puget Lowland as required for scenario earthquake simulations in the development of the Seattle Urban Hazards Maps (Frankel and others, 2007). Olsen and others (in press) used the model volume discussed here to perform a Cascadia simulation up to 0.5 Hz using a Sumatra-Andaman Islands rupture history. As research from the EarthScope Program (http://www.earthscope.org) is published, a wealth of important detail can be added to these model volumes, particularly to depths of the upper-mantle. However, at the time of development for this model version, no EarthScope-specific results were incorporated. This report is intended to be a reference for colleagues and associates who have used or are planning to use this preliminary model in their research. To this end, it is intended that these models will be considered a beginning template for a community velocity model of the Cascadia region as more data and results become available.

  20. Identifying the third dimension in 2D fluoroscopy to create 3D cardiac maps

    PubMed Central

    Krum, David; Choudhuri, Indrajit; Belanger, Barry; Palma, Mark; Brodnick, Donald; Rowe, Daniel B.

    2016-01-01

    Three-dimensional cardiac mapping is important for optimal visualization of the heart during cardiac ablation for the treatment of certain arrhythmias. However, many hospitals and clinics worldwide cannot afford the high cost of the current mapping systems. We set out to determine if, using predefined algorithms, comparable 3D cardiac maps could be created by a new device that relies on data generated from single-plane fluoroscopy and patient recording and monitoring systems, without the need for costly equipment, infrastructure changes, or specialized catheters. The study included phantom and animal experiments to compare the prototype test device, Navik 3D, with the existing CARTO 3 System. The primary endpoint directly compared: (a) the 3D distance between the Navik 3D–simulated ablation location and the back-projected ground truth location of the pacing and mapping catheter electrode, and (b) the same distance for CARTO. The study’s primary objective was considered met if the 95% confidence lower limit was greater than 0.75% for the Navik 3D–CARTO difference between the 2 distances, or less than or equal to 2 mm. Study results showed that the Navik 3D performance was equivalent to the CARTO system, and that accurate 3D cardiac maps can be created using data from equipment that already exists in all electrophysiology labs. PMID:28018976

  1. An image encryption algorithm based on 3D cellular automata and chaotic maps

    NASA Astrophysics Data System (ADS)

    Del Rey, A. Martín; Sánchez, G. Rodríguez

    2015-05-01

    A novel encryption algorithm to cipher digital images is presented in this work. The digital image is rendering into a three-dimensional (3D) lattice and the protocol consists of two phases: the confusion phase where 24 chaotic Cat maps are applied and the diffusion phase where a 3D cellular automata is evolved. The encryption method is shown to be secure against the most important cryptanalytic attacks.

  2. Real-time volume rendering of 4D image using 3D texture mapping

    NASA Astrophysics Data System (ADS)

    Hwang, Jinwoo; Kim, June-Sic; Kim, Jae Seok; Kim, In Young; Kim, Sun Il

    2001-05-01

    Four dimensional image is 3D volume data that varies with time. It is used to express deforming or moving object in virtual surgery of 4D ultrasound. It is difficult to render 4D image by conventional ray-casting or shear-warp factorization methods because of their time-consuming rendering time or pre-processing stage whenever the volume data are changed. Even 3D texture mapping is used, repeated volume loading is also time-consuming in 4D image rendering. In this study, we propose a method to reduce data loading time using coherence between currently loaded volume and previously loaded volume in order to achieve real time rendering based on 3D texture mapping. Volume data are divided into small bricks and each brick being loaded is tested for similarity to one which was already loaded in memory. If the brick passed the test, it is defined as 3D texture by OpenGL functions. Later, the texture slices of the brick are mapped into polygons and blended by OpenGL blending functions. All bricks undergo this test. Continuously deforming fifty volumes are rendered in interactive time with SGI ONYX. Real-time volume rendering based on 3D texture mapping is currently available on PC.

  3. Added Value of 3D Proton-Density Weighted Images in Diagnosis of Intracranial Arterial Dissection

    PubMed Central

    Kim, Jin Woo; Kim, Young Dae; Lee, Seung-Koo; Lim, Soo Mee; Oh, Se Won

    2016-01-01

    Background An early and reliable diagnosis of intracranial arterial dissection is important to reduce the risk of neurological complication. The purpose of this study was to assess the clinical usefulness of three-dimensional high-resolution MRI (3D-HR-MRI) including pre- and post-contrast T1-weighted volumetric isotropic turbo spin echo acquisition with improved motion-sensitized driven equilibrium preparation (3D-iMSDE-T1) and proton-density weighted image (3D-PD) in detecting dissection and to evaluate the added value of 3D-PD in diagnosing intracranial arterial dissection. Methods We retrospectively recruited patients who underwent 3D-HR-MRI with clinical suspicion of arterial dissection. Among them, we selected patients who were diagnosed with definite dissection according to the Spontaneous Cervicocephalic Arterial Dissections Study criteria. For each patient, the presence of intimal flap, intramural hematoma, and vessel dilatation were evaluated independently by two neuroradiologists on each sequence. Interobserver agreement was assessed. Results Seventeen patients (mean age: 41 ± 10 [SD] years; 13 men) were diagnosed with definite dissection. The intimal flaps were more frequently detected on 3D-PD (88.2%, 15/17) than on 3D-iMSDE-T1 (29.4%, 5/17), and post-contrast 3D-iMSDE-T1 (35.3%, 6/17; P = 0.006 and P = 0.004, respectively). No significant difference was found in the detection rate of intramural hematomas (59–71%) and vascular dilatations (47%) on each sequence. Interobserver agreement for detection of dissection findings showed almost perfect agreement (k = 0.84–1.00), except for detection of intimal flaps on pre-contrast 3D-iMSDE-T1 (k = 0.62). After addition of 3D-PD to pre- and post-contrast 3D-iMSDE-T1, more patients were diagnosed with definite dissection with the initial MRI (88.2% vs. 47.1%; P = 0.039). Conclusions The intimal flap might be better visualized on the 3D-PD sequence than the 3D-iMSDE-T1 sequences, allowing diagnosis of

  4. The application of iterative closest point (ICP) registration to improve 3D terrain mapping estimates using the flash 3D ladar system

    NASA Astrophysics Data System (ADS)

    Woods, Jack; Armstrong, Ernest E.; Armbruster, Walter; Richmond, Richard

    2010-04-01

    The primary purpose of this research was to develop an effective means of creating a 3D terrain map image (point-cloud) in GPS denied regions from a sequence of co-bore sighted visible and 3D LIDAR images. Both the visible and 3D LADAR cameras were hard mounted to a vehicle. The vehicle was then driven around the streets of an abandoned village used as a training facility by the German Army and imagery was collected. The visible and 3D LADAR images were then fused and 3D registration performed using a variation of the Iterative Closest Point (ICP) algorithm. The ICP algorithm is widely used for various spatial and geometric alignment of 3D imagery producing a set of rotation and translation transformations between two 3D images. ICP rotation and translation information obtain from registering the fused visible and 3D LADAR imagery was then used to calculate the x-y plane, range and intensity (xyzi) coordinates of various structures (building, vehicles, trees etc.) along the driven path. The xyzi coordinates information was then combined to create a 3D terrain map (point-cloud). In this paper, we describe the development and application of 3D imaging techniques (most specifically the ICP algorithm) used to improve spatial, range and intensity estimates of imagery collected during urban terrain mapping using a co-bore sighted, commercially available digital video camera with focal plan of 640×480 pixels and a 3D FLASH LADAR. Various representations of the reconstructed point-clouds for the drive through data will also be presented.

  5. Reconstruction of the ionospheric 3D electron density distribution by assimilation of ionosonde measurements and operational TEC estimations

    NASA Astrophysics Data System (ADS)

    Gerzen, Tatjana; Wilken, Volker; Jakowski, Norbert; Hoque, Mainul M.

    2013-04-01

    New methods to generate maps of the F2 layer peak electron density of the ionosphere (NmF2) and to reconstruct the ionospheric 3D electron density distribution will be presented. For validation, reconstructed NmF2 maps will be compared with peak electron density measurements from independent ionosonde stations. The ionosphere is the ionized part of the upper Earth's atmosphere lying between about 50 km and 1000 km above the Earth's surface. From the applications perspective the electron density, Ne, is certainly one of the most important parameters of the ionosphere because of its strong impact on radio signal propagation. Especially the critical frequency, foF2, which is related to the F2 layer peak electron density, NmF2, according to the equation NmF2-m3 = 1.24 ? 1010(foF2-MHz)2 and builds the lower limit for the maximum usable frequency MUF, is of particular interest with regard to the HF radio communication applications. In a first order approximation the ionospheric delay of transionospheric radio waves of frequency f is proportional to 1-f2 and to the integral of the electron density (total electron content - TEC) along the ray path. Thus, the information about the total electron content along the receiver-to-satellite ray path can be obtained from the dual frequency measurements permanently transmitted by GNSS satellites. As data base for our reconstruction approaches we use the vertical sounding measurements of the ionosonde stations providing foF2 and routinely generated TEC maps in SWACI (http://swaciweb.dlr.de) at DLR Neustrelitz. The basic concept of our approach is the following one: To reconstruct NmF2 maps we assimilate the ionosonde data into the global Neustrelitz F2 layer Peak electron Density Model (NPDM) by means of a successive corrections method. The TEC maps are produced by assimilating actual ground based GPS measurements providing TEC into an operational version of Neustrelitz TEC Model (NTCM). Finally, the derived NmF2 and TEC maps in

  6. Vulnerability mapping of groundwater contamination based on 3D lithostratigraphical models of porous aquifers.

    PubMed

    Ducci, Daniela; Sellerino, Mariangela

    2013-03-01

    The aim of this paper is to apply a methodology in order to reconstruct a lithostratigraphic 3D model of an aquifer so as to define some parameters involved in the evaluation of the aquifer vulnerability to contamination of porous aquifers. The DRASTIC, SINTACS and AVI methods have been applied to an alluvial coastal aquifer of southern Italy. The stratigraphic reconstruction has been obtained by interpolating stratigraphic data from more than one borehole per 2 km. The lithostratigraphic reconstruction of a 3D model has been applied and used for three-dimensional or two-dimensional representations. In the first two methods, the layers of the vadose zone and the aquifer media have been evaluated not only by the interpolation of the single boreholes and piezometers, but also by the 3D model, assigning the scores of the parameters of each layer of the 3D model. The comparison between the maps constructed from the weighted values in each borehole and the maps deriving from the attribution of the values of each layer of the 3D model, highlights that the second representation avoids or minimizes the "bullseye" effect linked to the presence of boreholes with higher or lower values. The study has demonstrated that it is possible to integrate a 3D lithostratigraphic model of an aquifer in the assessment of the parameters involved in the evaluation of the aquifer vulnerability to contamination by Point Count System methods.

  7. 3D mapping of airway wall thickening in asthma with MSCT: a level set approach

    NASA Astrophysics Data System (ADS)

    Fetita, Catalin; Brillet, Pierre-Yves; Hartley, Ruth; Grenier, Philippe A.; Brightling, Christopher

    2014-03-01

    Assessing the airway wall thickness in multi slice computed tomography (MSCT) as image marker for airway disease phenotyping such asthma and COPD is a current trend and challenge for the scientific community working in lung imaging. This paper addresses the same problem from a different point of view: considering the expected wall thickness-to-lumen-radius ratio for a normal subject as known and constant throughout the whole airway tree, the aim is to build up a 3D map of airway wall regions of larger thickness and to define an overall score able to highlight a pathological status. In this respect, the local dimension (caliber) of the previously segmented airway lumen is obtained on each point by exploiting the granulometry morphological operator. A level set function is defined based on this caliber information and on the expected wall thickness ratio, which allows obtaining a good estimate of the airway wall throughout all segmented lumen generations. Next, the vascular (or mediastinal dense tissue) contact regions are automatically detected and excluded from analysis. For the remaining airway wall border points, the real wall thickness is estimated based on the tissue density analysis in the airway radial direction; thick wall points are highlighted on a 3D representation of the airways and several quantification scores are defined. The proposed approach is fully automatic and was evaluated (proof of concept) on a patient selection coming from different databases including mild, severe asthmatics and normal cases. This preliminary evaluation confirms the discriminative power of the proposed approach regarding different phenotypes and is currently extending to larger cohorts.

  8. 3-D ultrafast Doppler imaging applied to the noninvasive mapping of blood vessels in vivo.

    PubMed

    Provost, Jean; Papadacci, Clement; Demene, Charlie; Gennisson, Jean-Luc; Tanter, Mickael; Pernot, Mathieu

    2015-08-01

    Ultrafast Doppler imaging was introduced as a technique to quantify blood flow in an entire 2-D field of view, expanding the field of application of ultrasound imaging to the highly sensitive anatomical and functional mapping of blood vessels. We have recently developed 3-D ultrafast ultrasound imaging, a technique that can produce thousands of ultrasound volumes per second, based on a 3-D plane and diverging wave emissions, and demonstrated its clinical feasibility in human subjects in vivo. In this study, we show that noninvasive 3-D ultrafast power Doppler, pulsed Doppler, and color Doppler imaging can be used to perform imaging of blood vessels in humans when using coherent compounding of 3-D tilted plane waves. A customized, programmable, 1024-channel ultrasound system was designed to perform 3-D ultrafast imaging. Using a 32 × 32, 3-MHz matrix phased array (Vermon, Tours, France), volumes were beamformed by coherently compounding successive tilted plane wave emissions. Doppler processing was then applied in a voxel-wise fashion. The proof of principle of 3-D ultrafast power Doppler imaging was first performed by imaging Tygon tubes of various diameters, and in vivo feasibility was demonstrated by imaging small vessels in the human thyroid. Simultaneous 3-D color and pulsed Doppler imaging using compounded emissions were also applied in the carotid artery and the jugular vein in one healthy volunteer.

  9. Design of 3D scanner for surface contour mapping by ultrasonic sensor

    NASA Astrophysics Data System (ADS)

    Munir, Muhammad Miftahul; Billah, Mohammad Aziz; Surachman, Arif; Budiman, Maman; Khairurrijal

    2015-04-01

    Surface mapping systems have attracted great attention due to their potential applications in many areas. In this paper, a simple 3D scanner based on ultrasonic sensor was designed for mapping a contour of object surface. The scanner using an SRF02 ultrasonic sensor, a microcontroller and radio frequency (RF) module to collect coordinates of object surface (point cloud), and sent data to computer. The point cloud collection process was performed by moving two ultrasonic sensors in y and x directions. Both sensors measure a distance from an object surface to a reference point of each sensor. The measurement results represent the point cloud of object surface and the data will be sent to computer via RF module. The point cloud then converted to 3D model using MATLAB. It was found that the object contours can be reconstructed very well by the developed 3D scanner system.

  10. The Use of Uas for Rapid 3d Mapping in Geomatics Education

    NASA Astrophysics Data System (ADS)

    Teo, Tee-Ann; Tian-Yuan Shih, Peter; Yu, Sz-Cheng; Tsai, Fuan

    2016-06-01

    With the development of technology, UAS is an advance technology to support rapid mapping for disaster response. The aim of this study is to develop educational modules for UAS data processing in rapid 3D mapping. The designed modules for this study are focused on UAV data processing from available freeware or trial software for education purpose. The key modules include orientation modelling, 3D point clouds generation, image georeferencing and visualization. The orientation modelling modules adopts VisualSFM to determine the projection matrix for each image station. Besides, the approximate ground control points are measured from OpenStreetMap for absolute orientation. The second module uses SURE and the orientation files from previous module for 3D point clouds generation. Then, the ground point selection and digital terrain model generation can be archived by LAStools. The third module stitches individual rectified images into a mosaic image using Microsoft ICE (Image Composite Editor). The last module visualizes and measures the generated dense point clouds in CloudCompare. These comprehensive UAS processing modules allow the students to gain the skills to process and deliver UAS photogrammetric products in rapid 3D mapping. Moreover, they can also apply the photogrammetric products for analysis in practice.

  11. Stratified shear flow in an inclined duct: near-instantaneous 3D velocity and density measurements

    NASA Astrophysics Data System (ADS)

    Partridge, Jamie; Lefauve, Adrien; Dalziel, Stuart; Linden, Paul

    2016-11-01

    We present results from a new experimental setup to study the exchange flow in an inclined square duct between two reservoirs containing fluids of different densities. This system can exhibit stratified shear wave motions, and has a distinct parameter threshold above which turbulence is triggered and progressively fills a larger fraction of the duct. To probe these intrinsically 3D flows, we introduce a new setup in which a traversing laser sheet allows us to obtain near-instantaneous 3D velocity and density fields. Three components of velocity are measured on successive 2D planes using stereo particle image velocimetry (PIV) with density information obtained simultaneously using laser induced fluorescence (LIF). Supported by EPSRC Programme Grant EP/K034529/1 entitled "Mathematical Underpinnings of Stratified Turbulence".

  12. 3D printed elastic honeycombs with graded density for tailorable energy absorption

    NASA Astrophysics Data System (ADS)

    Bates, Simon R. G.; Farrow, Ian R.; Trask, Richard S.

    2016-04-01

    This work describes the development and experimental analysis of hyperelastic honeycombs with graded densities, for the purpose of energy absorption. Hexagonal arrays are manufactured from thermoplastic polyurethane (TPU) via fused filament fabrication (FFF) 3D printing and the density graded by varying cell wall thickness though the structures. Manufactured samples are subject to static compression tests and their energy absorbing potential analysed via the formation of energy absorption diagrams. It is shown that by grading the density through the structure, the energy absorption profile of these structures can be manipulated such that a wide range of compression energies can be efficiently absorbed.

  13. Perceived density of road maps.

    PubMed

    Schwartz-Chassidim, Hadas; Meyer, Joachim; Parmet, Yisrael; Rogatka, Efrat; Amzaleg, Ohad

    2014-11-01

    Maps should be designed so that users can comprehend and use the information. Display decisions, such as choosing the scale at which an area is shown, depend on properties of the displayed information such as the perceived density (PD) of the information. Taking a psychophysical approach we suggest that the PD of information in a road map is related to the scale and properties of the mapped area. 54 participants rated the PD of 60 maps from different regions. We provide a simple model that predicts the PD of electronic road map displays, using the logarithm of the number of roads, the logarithm of the number of junctions and the length of the shown roads. The PD model was cross-validated using a different set of 60 maps (n = 44). The model can be used for automatically adjusting display scales and for evaluating map designs, considering the required PD to perform a map-related task.

  14. From digital mapping to GIS-based 3D visualization of geological maps: example from the Western Alps geological units

    NASA Astrophysics Data System (ADS)

    Balestro, Gianni; Cassulo, Roberto; Festa, Andrea; Fioraso, Gianfranco; Nicolò, Gabriele; Perotti, Luigi

    2015-04-01

    Collection of field geological data and sharing of geological maps are nowadays greatly enhanced by using digital tools and IT (Information Technology) applications. Portable hardware allows accurate GPS localization of data and homogeneous storing of information in field databases, whereas GIS (Geographic Information Systems) applications enable generalization of field data and realization of geological map databases. A further step in the digital processing of geological map information consists of building virtual visualization by means of GIS-based 3D viewers, that allow projection and draping of significant geological features over photo-realistic terrain models. Digital fieldwork activities carried out by the Authors in the Western Alps, together with building of geological map databases and related 3D visualizations, are an example of application of the above described digital technologies. Digital geological mapping was performed by means of a GIS mobile software loaded on a rugged handheld device, and lithological, structural and geomorphological features with their attributes were stored in different layers that form the field database. The latter was then generalized through usual map processing steps such as outcrops interpolation, characterization of geological boundaries and selection of meaningful punctual observations. This map databases was used for building virtual visualizations through a GIS-based 3D-viewer that loaded detailed DTM (resolution of 5 meters) and aerial images. 3D visualizations were focused on projection and draping of significant stratigraphic contacts (e.g. contacts that separate different Quaternary deposits) and tectonic contacts (i.e. exhumation-related contacts that dismembered original ophiolite sequences). In our experience digital geological mapping and related databases ensured homogeneous data storing and effective sharing of information, and allowed subsequent building of 3D GIS-based visualizations. The latters gave

  15. Protein contact maps: A binary depiction of protein 3D structures

    NASA Astrophysics Data System (ADS)

    Emerson, Isaac Arnold; Amala, Arumugam

    2017-01-01

    In recent years, there has been a considerable interest in examining the structure and dynamics of complex networks. Proteins in 3D space may also be considered as complex systems emerged through the interactions of their constituent amino acids. This representation provides a powerful framework to uncover the general organized principle of protein contact network. Here we reviewed protein contact map in terms of protein structure prediction and analyses. In addition, we had also discussed the various computational techniques for the prediction of protein contact maps and the tools to visualize contact maps.

  16. Measuring distances and reddenings for a billion stars: Toward a 3D dust map from Pan-STARRS 1

    SciTech Connect

    Green, Gregory Maurice; Finkbeiner, Douglas P.; Schlafly, Edward F.; Rix, Hans-Walter; Jurić, Mario; Burgett, Will; Chambers, Kenneth C.; Flewelling, Heather; Kudritzki, Rolf Peter; Magnier, Eugene; Tonry, John; Wainscoat, Richard; Waters, Christopher; Draper, Peter W.; Metcalfe, Nigel; Martin, Nicolas

    2014-03-10

    We present a method to infer reddenings and distances to stars based only on their broad-band photometry, and show how this method can be used to produce a three-dimensional (3D) dust map of the Galaxy. Our method samples from the full probability density function of distance, reddening, and stellar type for individual stars, as well as the full uncertainty in reddening as a function of distance in the 3D dust map. We incorporate prior knowledge of the distribution of stars in the Galaxy and the detection limits of the survey. For stars in the Pan-STARRS 1 (PS1) 3π survey, we demonstrate that our reddening estimates are unbiased and accurate to ∼0.13 mag in E(B – V) for the typical star. Based on comparisons with mock catalogs, we expect distances for main-sequence stars to be constrained to within ∼20%-60%, although this range can vary, depending on the reddening of the star, the precise stellar type, and its position on the sky. A later paper will present a 3D map of dust over the three quarters of the sky surveyed by PS1. Both the individual stellar inferences and the 3D dust map will enable a wealth of Galactic science in the plane. The method we present is not limited to the passbands of the PS1 survey but may be extended to incorporate photometry from other surveys, such as the Two Micron All Sky Survey, the Sloan Digital Sky Survey (where available), and in the future, LSST and Gaia.

  17. 3D Geological Mapping - uncovering the subsurface to increase environmental understanding

    NASA Astrophysics Data System (ADS)

    Kessler, H.; Mathers, S.; Peach, D.

    2012-12-01

    Geological understanding is required for many disciplines studying natural processes from hydrology to landscape evolution. The subsurface structure of rocks and soils and their properties occupies three-dimensional (3D) space and geological processes operate in time. Traditionally geologists have captured their spatial and temporal knowledge in 2 dimensional maps and cross-sections and through narrative, because paper maps and later two dimensional geographical information systems (GIS) were the only tools available to them. Another major constraint on using more explicit and numerical systems to express geological knowledge is the fact that a geologist only ever observes and measures a fraction of the system they study. Only on rare occasions does the geologist have access to enough real data to generate meaningful predictions of the subsurface without the input of conceptual understanding developed from and knowledge of the geological processes responsible for the deposition, emplacement and diagenesis of the rocks. This in turn has led to geology becoming an increasingly marginalised science as other disciplines have embraced the digital world and have increasingly turned to implicit numerical modelling to understand environmental processes and interactions. Recent developments in geoscience methodology and technology have gone some way to overcoming these barriers and geologists across the world are beginning to routinely capture their knowledge and combine it with all available subsurface data (of often highly varying spatial distribution and quality) to create regional and national geological three dimensional geological maps. This is re-defining the way geologists interact with other science disciplines, as their concepts and knowledge are now expressed in an explicit form that can be used downstream to design process models structure. For example, groundwater modellers can refine their understanding of groundwater flow in three dimensions or even directly

  18. 3D mapping of the dense interstellar gas around the Local Bubble

    NASA Astrophysics Data System (ADS)

    Lallement, R.; Welsh, B. Y.; Vergely, J. L.; Crifo, F.; Sfeir, D.

    2003-12-01

    We present intermediate results from a long-term program of mapping the neutral absorption characteristics of the local interstellar medium, motivated by the availability of accurate and consistent parallaxes from the Hipparcos satellite. Equivalent widths of the interstellar NaI D-line doublet at 5890 Å are presented for the lines-of-sight towards some 311 new target stars lying within ~ 350 pc of the Sun. Using these data, together with NaI absorption measurements towards a further ~ 240 nearby targets published in the literature (for many of them, in the directions of molecular clouds), and the ~ 450 lines-of-sight already presented by (Sfeir et al. \\cite{sfeir99}), we show 3D absorption maps of the local distribution of neutral gas towards 1005 sight-lines with Hipparcos distances as viewed from a variety of different galactic projections. The data are synthesized by means of two complementary methods, (i) by mapping of iso-equivalent width contours, and (ii) by density distribution calculation from the inversion of column-densities, a method devised by Vergely et al. (\\cite{vergely01}). Our present data confirms the view that the local cavity is deficient in cold and neutral interstellar gas. The closest dense and cold gas ``wall'', in the first quadrant, is at ~ 55-60 pc. There are a few isolated clouds at closer distance, if the detected absorption is not produced by circumstellar material. The maps reveal narrow or wide ``interstellar tunnels'' which connect the Local Bubble to surrounding cavities, as predicted by the model of Cox & Smith (1974). In particular, one of these tunnels, defined by stars at 300 to 600 pc from the Sun showing negligible sodium absorption, connects the well known CMa void (Gry et al. \\cite{gry85}), which is part of the Local Bubble, with the supershell GSH 238+00+09 (Heiles \\cite{heiles98}). High latitude lines-of-sight with the smallest absorption are found in two ``chimneys'', whose directions are perpendicular to the

  19. RESEARCH NOTE: Empirical 3-D basis for the internal density of a planet

    NASA Astrophysics Data System (ADS)

    Chambat, Frédéric; Ricard, Yanick

    2005-07-01

    Various papers have discussed the forward relationships between internal density anomalies of a planet and its external gravity field. The inverse modelling, i.e. finding the internal density anomalies from the external potential is known to be highly non-unique. In this research note, we explain how a 3-D basis can be built to represent the internal density variations that includes a subset that explicitly spans the kernel of the forward gravity operator. This representation clarifies the origin of the non-uniqueness of the gravity sources and implies the existence of a natural minimal norm inverse for the internal density. We illustrate these ideas by comparing a tomographic model of the mantle to the minimal norm density.

  20. Breast density measurement: 3D cone beam computed tomography (CBCT) images versus 2D digital mammograms

    NASA Astrophysics Data System (ADS)

    Han, Tao; Lai, Chao-Jen; Chen, Lingyun; Liu, Xinming; Shen, Youtao; Zhong, Yuncheng; Ge, Shuaiping; Yi, Ying; Wang, Tianpeng; Yang, Wei T.; Shaw, Chris C.

    2009-02-01

    Breast density has been recognized as one of the major risk factors for breast cancer. However, breast density is currently estimated using mammograms which are intrinsically 2D in nature and cannot accurately represent the real breast anatomy. In this study, a novel technique for measuring breast density based on the segmentation of 3D cone beam CT (CBCT) images was developed and the results were compared to those obtained from 2D digital mammograms. 16 mastectomy breast specimens were imaged with a bench top flat-panel based CBCT system. The reconstructed 3D CT images were corrected for the cupping artifacts and then filtered to reduce the noise level, followed by using threshold-based segmentation to separate the dense tissue from the adipose tissue. For each breast specimen, volumes of the dense tissue structures and the entire breast were computed and used to calculate the volumetric breast density. BI-RADS categories were derived from the measured breast densities and compared with those estimated from conventional digital mammograms. The results show that in 10 of 16 cases the BI-RADS categories derived from the CBCT images were lower than those derived from the mammograms by one category. Thus, breasts considered as dense in mammographic examinations may not be considered as dense with the CBCT images. This result indicates that the relation between breast cancer risk and true (volumetric) breast density needs to be further investigated.

  1. 3D volume MR temperature mapping for HIFU heating trajectory comparisons

    NASA Astrophysics Data System (ADS)

    Todd, Nick; Vyas, Urvi; de Bever, Josh; Payne, Allison; Parker, Dennis L.

    2012-10-01

    Many areas of MR-guided thermal therapy research would benefit from temperature maps with high spatial and temporal resolution that cover a large 3-D volume. This paper describes an approach to achieve these goals that is suitable for research applications where retrospective reconstruction of the temperature maps is acceptable. The method acquires undersampled data from a modified 3-D segmented EPI sequence and creates images using a temporally constrained reconstruction algorithm. The 3-D images can be zero-filled to arbitrarily small voxel spacing in all directions and then converted into temperature maps using the standard proton resonance frequency (PRF) shift technique. During HIFU heating experiments, the proposed method was used to obtain temperature maps with 1.5×1.5×3.0 mm resolution, 288×162×78 mm field of view, and 1.7 second temporal resolution. The approach is validated to demonstrate that it can accurately capture the spatial characteristics and time dynamics of rapidly changing HIFU-induced temperature distributions. An example application is presented where the method is used to analyze and compare different HIFU volumetric heating trajectories.

  2. Boosting Power Density of Microbial Fuel Cells with 3D Nitrogen-Doped Graphene Aerogel Electrode.

    PubMed

    Yang, Yang; Liu, Tianyu; Zhu, Xun; Zhang, Feng; Ye, Dingding; Liao, Qiang; Li, Yat

    2016-08-01

    A 3D nitrogen-doped graphene aerogel (N-GA) as an anode material for microbial fuel cells (MFCs) is reported. Electron microscopy images reveal that the N-GA possesses hierarchical porous structure that allows efficient diffusion of both bacterial cells and electron mediators in the interior space of 3D electrode, and thus, the colonization of bacterial communities. Electrochemical impedance spectroscopic measurements further show that nitrogen doping considerably reduces the charge transfer resistance and internal resistance of GA, which helps to enhance the MFC power density. Importantly, the dual-chamber milliliter-scale MFC with N-GA anode yields an outstanding volumetric power density of 225 ± 12 W m(-3) normalized to the total volume of the anodic chamber (750 ± 40 W m(-3) normalized to the volume of the anode). These power densities are the highest values report for milliliter-scale MFCs with similar chamber size (25 mL) under the similar measurement conditions. The 3D N-GA electrode shows great promise for improving the power generation of MFC devices.

  3. Boosting Power Density of Microbial Fuel Cells with 3D Nitrogen‐Doped Graphene Aerogel Electrode

    PubMed Central

    Yang, Yang; Liu, Tianyu; Zhang, Feng; Ye, Dingding; Liao, Qiang

    2016-01-01

    A 3D nitrogen‐doped graphene aerogel (N‐GA) as an anode material for microbial fuel cells (MFCs) is reported. Electron microscopy images reveal that the N‐GA possesses hierarchical porous structure that allows efficient diffusion of both bacterial cells and electron mediators in the interior space of 3D electrode, and thus, the colonization of bacterial communities. Electrochemical impedance spectroscopic measurements further show that nitrogen doping considerably reduces the charge transfer resistance and internal resistance of GA, which helps to enhance the MFC power density. Importantly, the dual‐chamber milliliter‐scale MFC with N‐GA anode yields an outstanding volumetric power density of 225 ± 12 W m−3 normalized to the total volume of the anodic chamber (750 ± 40 W m−3 normalized to the volume of the anode). These power densities are the highest values report for milliliter‐scale MFCs with similar chamber size (25 mL) under the similar measurement conditions. The 3D N‐GA electrode shows great promise for improving the power generation of MFC devices. PMID:27818911

  4. Mapping 3D fiber orientation in tissue using dual-angle optical polarization tractography

    PubMed Central

    Wang, Y.; Ravanfar, M.; Zhang, K.; Duan, D.; Yao, G.

    2016-01-01

    Optical polarization tractography (OPT) has recently been applied to map fiber organization in the heart, skeletal muscle, and arterial vessel wall with high resolution. The fiber orientation measured in OPT represents the 2D projected fiber angle in a plane that is perpendicular to the incident light. We report here a dual-angle extension of the OPT technology to measure the actual 3D fiber orientation in tissue. This method was first verified by imaging the murine extensor digitorum muscle placed at various known orientations in space. The accuracy of the method was further studied by analyzing the 3D fiber orientation of the mouse tibialis anterior muscle. Finally we showed that dual-angle OPT successfully revealed the unique 3D “arcade” fiber structure in the bovine articular cartilage. PMID:27867698

  5. Mapping 3D fiber orientation in tissue using dual-angle optical polarization tractography.

    PubMed

    Wang, Y; Ravanfar, M; Zhang, K; Duan, D; Yao, G

    2016-10-01

    Optical polarization tractography (OPT) has recently been applied to map fiber organization in the heart, skeletal muscle, and arterial vessel wall with high resolution. The fiber orientation measured in OPT represents the 2D projected fiber angle in a plane that is perpendicular to the incident light. We report here a dual-angle extension of the OPT technology to measure the actual 3D fiber orientation in tissue. This method was first verified by imaging the murine extensor digitorum muscle placed at various known orientations in space. The accuracy of the method was further studied by analyzing the 3D fiber orientation of the mouse tibialis anterior muscle. Finally we showed that dual-angle OPT successfully revealed the unique 3D "arcade" fiber structure in the bovine articular cartilage.

  6. Choroidal Thickness in Patients With Reticular Pseudodrusen Using 3D 1060-nm OCT Maps

    PubMed Central

    Haas, Paulina; Esmaeelpour, Marieh; Ansari-Shahrezaei, Siamak; Drexler, Wolfgang; Binder, Susanne

    2014-01-01

    Purpose. To map and analyze choroidal thickness (ChT) in AMD patients with reticular pseudodrusen (RPD) using three-dimensional (3D) 1060-nm optical coherence tomography (OCT). Methods. Fifty eyes from 25 patients with RPD were grouped according to the severity of AMD and the presence of RPD. All patients were imaged by high-speed (60,000 A-scans/s) 3D 1060-nm OCT over a 36 × 36° field of view. Choroidal thickness maps were automatically generated and compared with RPD areas visualized by fundus autofluorescence and infrared imaging. Retinal thickness maps, ChT maps, Haller's and Sattler's layer thickness were statistically analyzed between groups. Results. The mean ± SD (micrometers) subfoveal ChT was 201 ± 88 μm, 145 ± 48 μm, and 271 ± 130 μm for dry AMD with RPD, wet AMD with RPD, and eyes with wet AMD and no RPD, respectively. Choroidal thickness maps demonstrated the most significant choroidal thinning within eyes with wet AMD and RPD. Sattler's and Haller's layer thickness differed across the Early Treatment Diabetic Retinopathy Study grid when compared between eyes with and without RPD. Within eyes with RPD, ChT maps visualized that ChT was thicker below RDP areas than non-RPD areas. Conclusions. The 3D 1060-nm OCT choroidal maps over a large field of view offer noninvasive visualization for demonstrating local thickening correlation with RPD within each eye and overall thinning owing to AMD severity and RPD. This choroidal thinning was most striking in Sattler's layer, suggesting a choroidopathy of this vascular layer. PMID:24651554

  7. Comparison of interferometric and stereo-radargrammetric 3D metrics in mapping of forest resources

    NASA Astrophysics Data System (ADS)

    Karila, K.; Karjalainen, M.; Yu, X.; Vastaranta, M.; Holopainen, M.; Hyyppa, J.

    2015-04-01

    Accurate forest resources maps are needed in diverse applications ranging from the local forest management to the global climate change research. In particular, it is important to have tools to map changes in forest resources, which helps us to understand the significance of the forest biomass changes in the global carbon cycle. In the task of mapping changes in forest resources for wide areas, Earth Observing satellites could play the key role. In 2013, an EU/FP7-Space funded project "Advanced_SAR" was started with the main objective to develop novel forest resources mapping methods based on the fusion of satellite based 3D measurements and in-situ field measurements of forests. During the summer 2014, an extensive field surveying campaign was carried out in the Evo test site, Southern Finland. Forest inventory attributes of mean tree height, basal area, mean stem diameter, stem volume, and biomass, were determined for 91 test plots having the size of 32 by 32 meters (1024 m2). Simultaneously, a comprehensive set of satellite and airborne data was collected. Satellite data also included a set of TanDEM-X (TDX) and TerraSAR-X (TSX) X-band synthetic aperture radar (SAR) images, suitable for interferometric and stereo-radargrammetric processing to extract 3D elevation data representing the forest canopy. In the present study, we compared the accuracy of TDX InSAR and TSX stereo-radargrammetric derived 3D metrics in forest inventory attribute prediction. First, 3D data were extracted from TDX and TSX images. Then, 3D data were processed as elevations above the ground surface (forest canopy height values) using an accurate Digital Terrain Model (DTM) based on airborne laser scanning survey. Finally, 3D metrics were calculated from the canopy height values for each test plot and the 3D metrics were compared with the field reference data. The Random Forest method was used in the forest inventory attributes prediction. Based on the results InSAR showed slightly better

  8. Depth map coding using residual segmentation for 3D video system

    NASA Astrophysics Data System (ADS)

    Lee, Cheon; Ho, Yo-Sung

    2013-06-01

    Advanced 3D video systems employ multi-view video-plus-depth data to support the free-viewpoint navigation and comfortable 3D viewing; thus efficient depth map coding becomes an important issue. Unlike the color image, the depth map has a property that depth values of the inner part of an object are monotonic, but those of object boundaries change abruptly. Therefore, residual data generated by prediction errors around object boundaries consume many bits in depth map coding. Representing them with segment data can be better than the use of the conventional transformation around the boundary regions. In this paper, we propose an efficient depth map coding method using a residual segmentation instead of using transformation. The proposed residual segmentation divides residual data into two regions with a segment map and two mean values. If the encoder selects the proposed method in terms of rates, two quantized mean values and an index of the segment map are transmitted. Simulation results show significant gains of up to 10 dB compared to the state-of-the-art coders, such as JPEG2000 and H.264/AVC. [Figure not available: see fulltext.

  9. SU-F-BRF-08: Conformal Mapping-Based 3D Surface Matching and Registration

    SciTech Connect

    Song, Y; Zeng, W; Gu, X; Liu, C

    2014-06-15

    Purpose: Recently, non-rigid 3D surface matching and registration has been used extensively in engineering and medicine. However, matching 3D surfaces undergoing non-rigid deformation accurately is still a challenging mathematical problem. In this study, we present a novel algorithm to address this issue by introducing intrinsic symmetry to the registration Methods: Our computational algorithm for symmetric conformal mapping is divided into three major steps: 1) Finding the symmetric plane; 2) Finding feature points; and 3) Performing cross registration. The key strategy is to preserve the symmetry during the conformal mapping, such that the image on the parameter domain is symmetric and the area distortion factor on the parameter image is also symmetric. Several novel algorithms were developed using different conformal geometric tools. One was based on solving Riemann-Cauchy equation and the other one employed curvature flow Results: Our algorithm was implemented using generic C++ on Windows XP and used conjugate gradient search optimization for acceleration. The human face 3D surface images were acquired using a high speed 3D scanner based on the phase-shifting method. The scanning speed was 30 frames/sec. The image resolution for each frame was 640 × 480. For 3D human face surfaces with different expressions, postures, and boundaries, our algorithms were able to produce consistent result on the texture pattern on the overlapping region Conclusion: We proposed a novel algorithm to improve the robustness of conformal geometric methods by incorporating the symmetric information into the mapping process. To objectively evaluate its performance, we compared it with most existing techniques. Experimental results indicated that our method outperformed all the others in terms of robustness. The technique has a great potential in real-time patient monitoring and tracking in image-guided radiation therapy.

  10. Generation of 3-D surface maps in waste storage silos using a structured light source

    NASA Technical Reports Server (NTRS)

    Burks, B. L.; Rowe, J. C.; Dinkins, M. A.; Christensen, B.; Selleck, C.; Jacoboski, D.; Markus, R.

    1992-01-01

    Surface contours inside the large waste storage tanks typical of the Department of Energy (DOE) complex are, in general, highly irregular. In addition to pipes and other pieces of equipment in the tanks, the surfaces may have features such as mounds, fissures, crystalline structures, and mixed solid and liquid forms. Prior to remediation activities, it will be necessary to characterize the waste to determine the most effective remediation approaches. Surface contour data will be required both prior to and during remediation. The use is described of a structured light source to generate 3-D surface contour maps of the interior of waste storage silos at the Feed Materials Production Center at Fernald, OH. The landscape inside these large waste storage tanks bears a strong resemblance to some of the landscapes that might be encountered during lunar or planetary exploration. Hence, these terrestrial 3-D mapping techniques may be directly applicable to extraterrestrial exploration. In further development, it will be demonstrated that these 3-D data can be used for robotic task planning just as 3-D surface contour data of a satellite could be used to plan maintenance tasks for a space-based servicing robot.

  11. VizieR Online Data Catalog: 3D interstellar extinct. map within nearest kpc (Gontcharov, 2012)

    NASA Astrophysics Data System (ADS)

    Gontcharov, G. A.

    2016-07-01

    The product of the previously constructed 3D maps of stellar reddening (2010AstL...36..584G) and Rv variations (2012AstL...38...12G) has allowed us to produce a 3D interstellar extinction map within the nearest kiloparsec from the Sun with a spatial resolution of 100pc and an accuracy of 0.2m. This map is compared with the 2D reddening map by Schlegel et al. (1998ApJ...500..525S), the 3D extinction map at high latitudes by Jones et al. (2011AJ....142...44J), and the analytical 3D extinction models by Arenou et al. (1992A&A...258..104A) and Gontcharov (2009AstL...35..780G). In all cases, we have found good agreement and show that there are no systematic errors in the new map everywhere except the direction toward the Galactic center. We have found that the map by Schlegel et al. (1998ApJ...500..525S) reaches saturation near the Galactic equator at E(B-V)>0.8m, has a zero-point error and systematic errors gradually increasing with reddening, and among the analytical models those that take into account the extinction in the Gould Belt are more accurate. Our extinction map shows that it is determined by reddening variations at low latitudes and Rv variations at high ones. This naturally explains the contradictory data on the correlation or anticorrelation between reddening and Rv available in the literature. There is a correlation in a thin layer near the Galactic equator, because both reddening and Rv here increase toward the Galactic center. There is an anticorrelation outside this layer, because higher values of Rv correspond to lower reddening at high and middle latitudes. Systematic differences in sizes and other properties of the dust grains in different parts of the Galaxy manifest themselves in this way. The largest structures within the nearest kiloparsec, including the Local Bubble, the Gould Belt, the Great Tunnel, the Scorpius, Perseus, Orion, and other complexes, have manifested themselves in the constructed map. (1 data file).

  12. Web GIS in practice VII: stereoscopic 3-D solutions for online maps and virtual globes

    PubMed Central

    Boulos, Maged N Kamel; Robinson, Larry R

    2009-01-01

    Because our pupils are about 6.5 cm apart, each eye views a scene from a different angle and sends a unique image to the visual cortex, which then merges the images from both eyes into a single picture. The slight difference between the right and left images allows the brain to properly perceive the 'third dimension' or depth in a scene (stereopsis). However, when a person views a conventional 2-D (two-dimensional) image representation of a 3-D (three-dimensional) scene on a conventional computer screen, each eye receives essentially the same information. Depth in such cases can only be approximately inferred from visual clues in the image, such as perspective, as only one image is offered to both eyes. The goal of stereoscopic 3-D displays is to project a slightly different image into each eye to achieve a much truer and realistic perception of depth, of different scene planes, and of object relief. This paper presents a brief review of a number of stereoscopic 3-D hardware and software solutions for creating and displaying online maps and virtual globes (such as Google Earth) in "true 3D", with costs ranging from almost free to multi-thousand pounds sterling. A practical account is also given of the experience of the USGS BRD UMESC (United States Geological Survey's Biological Resources Division, Upper Midwest Environmental Sciences Center) in setting up a low-cost, full-colour stereoscopic 3-D system. PMID:19849837

  13. 3D mapping of elastic modulus using shear wave optical micro-elastography

    NASA Astrophysics Data System (ADS)

    Zhu, Jiang; Qi, Li; Miao, Yusi; Ma, Teng; Dai, Cuixia; Qu, Yueqiao; He, Youmin; Gao, Yiwei; Zhou, Qifa; Chen, Zhongping

    2016-10-01

    Elastography provides a powerful tool for histopathological identification and clinical diagnosis based on information from tissue stiffness. Benefiting from high resolution, three-dimensional (3D), and noninvasive optical coherence tomography (OCT), optical micro-elastography has the ability to determine elastic properties with a resolution of ~10 μm in a 3D specimen. The shear wave velocity measurement can be used to quantify the elastic modulus. However, in current methods, shear waves are measured near the surface with an interference of surface waves. In this study, we developed acoustic radiation force (ARF) orthogonal excitation optical coherence elastography (ARFOE-OCE) to visualize shear waves in 3D. This method uses acoustic force perpendicular to the OCT beam to excite shear waves in internal specimens and uses Doppler variance method to visualize shear wave propagation in 3D. The measured propagation of shear waves agrees well with the simulation results obtained from finite element analysis (FEA). Orthogonal acoustic excitation allows this method to measure the shear modulus in a deeper specimen which extends the elasticity measurement range beyond the OCT imaging depth. The results show that the ARFOE-OCE system has the ability to noninvasively determine the 3D elastic map.

  14. 3D mapping of elastic modulus using shear wave optical micro-elastography

    PubMed Central

    Zhu, Jiang; Qi, Li; Miao, Yusi; Ma, Teng; Dai, Cuixia; Qu, Yueqiao; He, Youmin; Gao, Yiwei; Zhou, Qifa; Chen, Zhongping

    2016-01-01

    Elastography provides a powerful tool for histopathological identification and clinical diagnosis based on information from tissue stiffness. Benefiting from high resolution, three-dimensional (3D), and noninvasive optical coherence tomography (OCT), optical micro-elastography has the ability to determine elastic properties with a resolution of ~10 μm in a 3D specimen. The shear wave velocity measurement can be used to quantify the elastic modulus. However, in current methods, shear waves are measured near the surface with an interference of surface waves. In this study, we developed acoustic radiation force (ARF) orthogonal excitation optical coherence elastography (ARFOE-OCE) to visualize shear waves in 3D. This method uses acoustic force perpendicular to the OCT beam to excite shear waves in internal specimens and uses Doppler variance method to visualize shear wave propagation in 3D. The measured propagation of shear waves agrees well with the simulation results obtained from finite element analysis (FEA). Orthogonal acoustic excitation allows this method to measure the shear modulus in a deeper specimen which extends the elasticity measurement range beyond the OCT imaging depth. The results show that the ARFOE-OCE system has the ability to noninvasively determine the 3D elastic map. PMID:27762276

  15. 3D Magnetic Induction Maps of Nanoscale Materials Revealed by Electron Holographic Tomography

    PubMed Central

    2015-01-01

    The investigation of three-dimensional (3D) ferromagnetic nanoscale materials constitutes one of the key research areas of the current magnetism roadmap and carries great potential to impact areas such as data storage, sensing, and biomagnetism. The properties of such nanostructures are closely connected with their 3D magnetic nanostructure, making their determination highly valuable. Up to now, quantitative 3D maps providing both the internal magnetic and electric configuration of the same specimen with high spatial resolution are missing. Here, we demonstrate the quantitative 3D reconstruction of the dominant axial component of the magnetic induction and electrostatic potential within a cobalt nanowire (NW) of 100 nm in diameter with spatial resolution below 10 nm by applying electron holographic tomography. The tomogram was obtained using a dedicated TEM sample holder for acquisition, in combination with advanced alignment and tomographic reconstruction routines. The powerful approach presented here is widely applicable to a broad range of 3D magnetic nanostructures and may trigger the progress of novel spintronic nonplanar nanodevices. PMID:27182110

  16. Web GIS in practice VII: stereoscopic 3-D solutions for online maps and virtual globes

    USGS Publications Warehouse

    Boulos, Maged N.K.; Robinson, Larry R.

    2009-01-01

    Because our pupils are about 6.5 cm apart, each eye views a scene from a different angle and sends a unique image to the visual cortex, which then merges the images from both eyes into a single picture. The slight difference between the right and left images allows the brain to properly perceive the 'third dimension' or depth in a scene (stereopsis). However, when a person views a conventional 2-D (two-dimensional) image representation of a 3-D (three-dimensional) scene on a conventional computer screen, each eye receives essentially the same information. Depth in such cases can only be approximately inferred from visual clues in the image, such as perspective, as only one image is offered to both eyes. The goal of stereoscopic 3-D displays is to project a slightly different image into each eye to achieve a much truer and realistic perception of depth, of different scene planes, and of object relief. This paper presents a brief review of a number of stereoscopic 3-D hardware and software solutions for creating and displaying online maps and virtual globes (such as Google Earth) in "true 3D", with costs ranging from almost free to multi-thousand pounds sterling. A practical account is also given of the experience of the USGS BRD UMESC (United States Geological Survey's Biological Resources Division, Upper Midwest Environmental Sciences Center) in setting up a low-cost, full-colour stereoscopic 3-D system.

  17. Web GIS in practice VII: stereoscopic 3-D solutions for online maps and virtual globes.

    PubMed

    Boulos, Maged N Kamel; Robinson, Larry R

    2009-10-22

    Because our pupils are about 6.5 cm apart, each eye views a scene from a different angle and sends a unique image to the visual cortex, which then merges the images from both eyes into a single picture. The slight difference between the right and left images allows the brain to properly perceive the 'third dimension' or depth in a scene (stereopsis). However, when a person views a conventional 2-D (two-dimensional) image representation of a 3-D (three-dimensional) scene on a conventional computer screen, each eye receives essentially the same information. Depth in such cases can only be approximately inferred from visual clues in the image, such as perspective, as only one image is offered to both eyes. The goal of stereoscopic 3-D displays is to project a slightly different image into each eye to achieve a much truer and realistic perception of depth, of different scene planes, and of object relief. This paper presents a brief review of a number of stereoscopic 3-D hardware and software solutions for creating and displaying online maps and virtual globes (such as Google Earth) in "true 3D", with costs ranging from almost free to multi-thousand pounds sterling. A practical account is also given of the experience of the USGS BRD UMESC (United States Geological Survey's Biological Resources Division, Upper Midwest Environmental Sciences Center) in setting up a low-cost, full-colour stereoscopic 3-D system.

  18. 3-D density imaging with muon flux measurements from underground galleries

    NASA Astrophysics Data System (ADS)

    Lesparre, N.; Cabrera, J.; Marteau, J.

    2017-03-01

    Atmospheric muon flux measurements provide information on subsurface density distribution. In this study, muon flux was measured underground, in the Tournemire experimental platform (France). The objective was to image the medium between the galleries and the surface and evaluate the feasibility to detect the presence of discontinuities, for example, produced by secondary subvertical faults or by karstic networks. Measurements were performed from three different sites with a partial overlap of muon trajectories, offering the possibility to seek density variations at different depths. The conversion of the measured muon flux to average density values showed global variations further analysed through a 3-D nonlinear inversion procedure. Main results are the presence of a very low density region at the level of the upper aquifer, compatible with the presence of a karstic network hosting local cavities, and the absence of secondary faults. We discuss the validity of the present results and propose different strategies to improve the accuracy of such measurements and analysis.

  19. 3D Mapping of Glacially-Sculpted Bedrock in Central Park

    NASA Astrophysics Data System (ADS)

    Laderman, L.; Stark, C. P.; Creyts, T. T.

    2014-12-01

    The movement of glaciers and ice sheets through sliding over bedrock depends on the configuration of the subglacial hydrological system. Over time, the glacier erodes the bedrock, which in turn changes water drainage pathways, the overall interaction with the ice, and potentially sliding rates. Drainage can take many forms. At the largest scale, subglacial lakes tens of kilometers in length store water, but the individual pathways are often on the order of meters or smaller. Studies at such a fine scale are only possible by looking at deglaciated beds to infer water drainage. 3D mapping can resolve centimeter scale features and inform studies of the processes that created them. In this survey, Agisoft Photoscan's structure from motion algorithm is used to create a map of Umpire Rock in New York's Central Park from digital photographs. Over 3300 photographs are taken at a separation of roughly half a meter to cover the 1000 square meter survey area. The surface is imaged in separate sections and the resulting point clouds are each aligned with a central section using Photoscan's Align Chunks tool. This process allows additional areas to easily be added to the 3D map. The scale of the final model is accurate to 1mm across the survey area and 3D meshes with a surface resolution of up to 5mm can be created. The distribution of striation directions and sizes on surfaces across the outcrop gives the overall flow direction of the ice and, more locally, illustrates how ice deforms around bedrock features. In addition to striations, we identify cavities and subtle drainage features that are oblique to ice flow. This study demonstrates the relative ease of 3D mapping bedrock outcrops from digital photographs, and indicates the utility of applying this process to more recently deglaciated areas.

  20. 3D Density Structure and LOS Observations of a Model CME

    NASA Astrophysics Data System (ADS)

    Manchester, W. B.; Lugaz, N.; Gombosi, T.; de Zeeuw, D.; Sokolov, I.; Toth, G.

    2004-12-01

    We present synthetic Thomson-scattered white-light images of a simulated coronal mass ejection (CME). The simulations are based on a 3-D MHD model of a CME propagating through a bimodal solar wind characteristic of solar minimum. The CME is driven by a 3-D Gibson-Low flux rope inserted in the helmet streamer of the steady-state corona. Synthetic coronograph images are produced that follow the evolution of the CME to 1 AU from several points of view. The white light images provide a basis for comparison with wide angle coronographs, like those of SMEI or STEREO. We find that a large amount of plasma is swept up from the solar wind by the CME-driven shock wave, which dominates the density structure far from the Sun. We also find that the shape of this compressed plasma is highly distorted by the variation in speed of the ambient solar wind. Comparisons of 2-D integrated images to the 3-D density structure show that the viewing angle severely effects the line-of-sight appearance of the CME, as well as the estimated mass of the CME from such 2D images.

  1. Large-scale Inference Problems in Astronomy: Building a 3D Galactic Dust Map

    NASA Astrophysics Data System (ADS)

    Finkbeiner, Douglas

    2016-03-01

    The term ''Big Data'' has become trite, as modern technology has made data sets of terabytes or even petabytes easy to store. Such data sets provide a sandbox in which to develop new statistical inference techniques that can extract interesting results from increasingly rich (and large) databases. I will give an example from my work on mapping the interstellar dust of the Milky Way. 2D emission-based maps have been used for decades to estimate the reddening and emission from interstellar dust, with applications from CMB foregrounds to surveys of large-scale structure. For studies within the Milky Way, however, the third dimension is required. I will present our work on a 3D dust map based on Pan-STARRS1 and 2MASS over 3/4 of the sky (http://arxiv.org/abs/1507.01005), assess its usefulness relative to other dust maps, and discuss future work. Supported by the NSF.

  2. Digital mono- and 3D stereo-photogrammetry for geological and geomorphological mapping

    NASA Astrophysics Data System (ADS)

    Scapozza, Cristian; Schenker, Filippo Luca; Castelletti, Claudio; Bozzini, Claudio; Ambrosi, Christian

    2016-04-01

    The generalization of application of digital tools for managing, mapping and updating geological data have become widely accepted in the last decennia. Despite the increasing quality and availability of digital topographical maps, orthorectified aerial photographs (orthophotos) and high resolution (5 up to 0.5 m) Digital Elevation Models (DEMs), a correct recognition of the kind, the nature and the boundaries of geological formations and geomophological landforms, unconsolidated sedimentary deposits or slope instabilities is often very difficult on conventional two-dimensional (2D) products, in particular in steep zones (rock walls and talus slopes), under the forest cover, for a very complex topography and in deeply urbanised zones. In many cases, photo-interpretative maps drawn only by 2D data sets must be improved by field verifications or, at least, by field oblique photographs. This is logical, because our natural perception of the real world is three-dimensional (3D), which is partially disabled by the application of 2D visualization techniques. Here we present some examples of application of digital mapping based on a 3D visualization (for aerial and satellite images photo-interpretation) or on a terrestrial perception by digital mono-photogrammetry (for oblique photographs). The 3D digital mapping was performed thanks to an extension of the software ESRI® ArcGIS™ called ArcGDS™. This methodology was also applied on historical aerial photographs (normally analysed by optical stereo-photogrammetry), which were digitized by scanning and then oriented and aero-triangulated thanks to the ArcGDS™ software, allowing the 3D visualisation and the mapping in a GIS environment (Ambrosi and Scapozza, 2015). The mono-photogrammetry (or monoplotting) is the technique of photogrammetrical georeferentiation of single oblique unrectified photographs, which are related to a DEM. In other words, the monoplotting allows relating each pixel of the photograph to the

  3. Processing of noised residual stress phase maps by using a 3D phase unwrapping algorithm

    NASA Astrophysics Data System (ADS)

    Viotti, Matias R.; Fantin, Analucia V.; Albertazzi, Armando; Willemann, Daniel P.

    2013-07-01

    The measurement of residual stress by using digital speckle pattern interferometry (DSPI) combined with the hole drilling technique is a valuable and fast tool for integrity evaluation of civil structures and mechanical parts. However, in some cases, measured phase maps are badly corrupted by noise which makes phase unwrapping a difficult and unsuccessful task. By following recommendations given by the ASTM E837 standard, 20 consecutive hole steps should be performed for the measurement of non-uniform stresses. As a consequence, 20 difference phase maps along the hole depth will be available for the DSPI technique. An adaptive phase unwrapping algorithm could be used in order to unwrap images following paths localized along well modulated pixels and performing two dimensional phase unwrapping (following paths inside a difference phase map corresponding to a hole step) or 3D phase unwrapping (similar to a temporal phase unwrapping following paths located at well-modulated pixels in a previous or a subsequent hole image). Non-corrupted and corrupted hole-drilling tests were processed with a traditional phase unwrapping algorithm as well as with the proposed 3D approach. Comparisons between unwrapped phase maps and simulated ones have shown that the proposed method gave results with best accordance than 2D results.

  4. An Assimilative 3-D Model of Coronal Density from Multi-Spacecraft Observations

    NASA Astrophysics Data System (ADS)

    Kamalabadi, F.; Hewett, R.; Butala, M.; Frazin, R. A.

    2009-12-01

    White-light coronagraph images observed at different solar rotation angles and from multiple perspectives can be combined to produce quantitative three-dimensional (3-D) reconstructions of persistent, large-scale coronal density. In this work, we present a computationally feasible data assimilation framework for the reconstruction of the time-dependent, 3-D electron density in the solar corona. We present quantitative reconstructions computed from simultaneous dual spacecraft measurements from the Solar Terrestrial Relations Observatory (STEREO) and compare the new time-dependent reconstructions of coronal density to a sequence of static reconstructions. We find that our new dynamic reconstructions are more robust at capturing transient features of the corona and are less prone to computational artifacts that result from the static assumption. The assimilation of STEREO COR1 coronagraph measurements poses some new challenges to conventional solar tomography algorithms. The STEREO data have higher spatial resolution and are measured at higher cadence, with new images available from each spacecraft every 5 to 10 minutes. We comment on the scalability of the data assimilation framework and note its suitability for the STEREO data volume and for the much greater data volume soon to be offered by the Solar Dynamics Observatory.

  5. 3D mapping of somatotopic reorganization with small animal functional MRI

    PubMed Central

    Yu, Xin; Wang, Shumin; Chen, Der-Yow; Dodd, Stephen; Goloshevsky, Artem; Koretsky, Alan P.

    2009-01-01

    There are few in vivo noninvasive methods to study neuroplasticity in animal brains. Functional MRI (fMRI) has been developed for animal brain mapping, but few fMRI studies have analyzed functional alteration due to plasticity in animal models. One major limitation is that fMRI maps are characterized by statistical parametric mapping making the apparent boundary dependent on the statistical threshold used. Here, we developed a method to characterize the location of center-of-mass in fMRI maps that is shown not to be sensitive to statistical threshold. Utilizing centers-of-mass as anchor points to fit the spatial distribution of the BOLD response enabled quantitative group analysis of altered boundaries of functional somatosensory maps. This approach was used to study cortical reorganization in the rat primary somatosensory cortex (S1) after sensory deprivation to the barrel cortex by follicle ablation (F.A.). FMRI demonstrated an enlarged nose S1 representation in the 3D somatotopic functional maps. This result clearly demonstrates that fMRI enables the spatial mapping of functional changes that can characterize multiple regions of S1 cortex and still be sensitive to changes due to plasticity. PMID:19770051

  6. Enhanced Rgb-D Mapping Method for Detailed 3d Modeling of Large Indoor Environments

    NASA Astrophysics Data System (ADS)

    Tang, Shengjun; Zhu, Qing; Chen, Wu; Darwish, Walid; Wu, Bo; Hu, Han; Chen, Min

    2016-06-01

    RGB-D sensors are novel sensing systems that capture RGB images along with pixel-wise depth information. Although they are widely used in various applications, RGB-D sensors have significant drawbacks with respect to 3D dense mapping of indoor environments. First, they only allow a measurement range with a limited distance (e.g., within 3 m) and a limited field of view. Second, the error of the depth measurement increases with increasing distance to the sensor. In this paper, we propose an enhanced RGB-D mapping method for detailed 3D modeling of large indoor environments by combining RGB image-based modeling and depth-based modeling. The scale ambiguity problem during the pose estimation with RGB image sequences can be resolved by integrating the information from the depth and visual information provided by the proposed system. A robust rigid-transformation recovery method is developed to register the RGB image-based and depth-based 3D models together. The proposed method is examined with two datasets collected in indoor environments for which the experimental results demonstrate the feasibility and robustness of the proposed method

  7. Development of Mobile Mapping System for 3D Road Asset Inventory

    PubMed Central

    Sairam, Nivedita; Nagarajan, Sudhagar; Ornitz, Scott

    2016-01-01

    Asset Management is an important component of an infrastructure project. A significant cost is involved in maintaining and updating the asset information. Data collection is the most time-consuming task in the development of an asset management system. In order to reduce the time and cost involved in data collection, this paper proposes a low cost Mobile Mapping System using an equipped laser scanner and cameras. First, the feasibility of low cost sensors for 3D asset inventory is discussed by deriving appropriate sensor models. Then, through calibration procedures, respective alignments of the laser scanner, cameras, Inertial Measurement Unit and GPS (Global Positioning System) antenna are determined. The efficiency of this Mobile Mapping System is experimented by mounting it on a truck and golf cart. By using derived sensor models, geo-referenced images and 3D point clouds are derived. After validating the quality of the derived data, the paper provides a framework to extract road assets both automatically and manually using techniques implementing RANSAC plane fitting and edge extraction algorithms. Then the scope of such extraction techniques along with a sample GIS (Geographic Information System) database structure for unified 3D asset inventory are discussed. PMID:26985897

  8. Development of Mobile Mapping System for 3D Road Asset Inventory.

    PubMed

    Sairam, Nivedita; Nagarajan, Sudhagar; Ornitz, Scott

    2016-03-12

    Asset Management is an important component of an infrastructure project. A significant cost is involved in maintaining and updating the asset information. Data collection is the most time-consuming task in the development of an asset management system. In order to reduce the time and cost involved in data collection, this paper proposes a low cost Mobile Mapping System using an equipped laser scanner and cameras. First, the feasibility of low cost sensors for 3D asset inventory is discussed by deriving appropriate sensor models. Then, through calibration procedures, respective alignments of the laser scanner, cameras, Inertial Measurement Unit and GPS (Global Positioning System) antenna are determined. The efficiency of this Mobile Mapping System is experimented by mounting it on a truck and golf cart. By using derived sensor models, geo-referenced images and 3D point clouds are derived. After validating the quality of the derived data, the paper provides a framework to extract road assets both automatically and manually using techniques implementing RANSAC plane fitting and edge extraction algorithms. Then the scope of such extraction techniques along with a sample GIS (Geographic Information System) database structure for unified 3D asset inventory are discussed.

  9. Representation and coding of large-scale 3D dynamic maps

    NASA Astrophysics Data System (ADS)

    Cohen, Robert A.; Tian, Dong; Krivokuća, Maja; Sugimoto, Kazuo; Vetro, Anthony; Wakimoto, Koji; Sekiguchi, Shunichi

    2016-09-01

    combined with depth and color measurements of the surrounding environment. Localization could be achieved with GPS, inertial measurement units (IMU), cameras, or combinations of these and other devices, while the depth measurements could be achieved with time-of-flight, radar or laser scanning systems. The resulting 3D maps, which are composed of 3D point clouds with various attributes, could be used for a variety of applications, including finding your way around indoor spaces, navigating vehicles around a city, space planning, topographical surveying or public surveying of infrastructure and roads, augmented reality, immersive online experiences, and much more. This paper discusses application requirements related to the representation and coding of large-scale 3D dynamic maps. In particular, we address requirements related to different types of acquisition environments, scalability in terms of progressive transmission and efficiently rendering different levels of details, as well as key attributes to be included in the representation. Additionally, an overview of recently developed coding techniques is presented, including an assessment of current performance. Finally, technical challenges and needs for future standardization are discussed.

  10. Multislice diffusion mapping for 3-D evolution of cerebral ischemia in a rat stroke model.

    PubMed

    Reith, W; Hasegawa, Y; Latour, L L; Dardzinski, B J; Sotak, C H; Fisher, M

    1995-01-01

    Diffusion-weighted magnetic resonance imaging (DWI) can quantitatively demonstrate cerebral ischemia within minutes after the onset of ischemia. The use of a DWI echo-planar multislice technique in this study and the mapping of the apparent diffusion coefficient (ADC) of water, a reliable indicator of ischemic regions, allow for the detection of the three-dimensional (3-D) evolution of ischemia in a rat stroke model. We evaluated 13 time points from 5 to 180 minutes after occlusion of the middle cerebral artery (MCA) and monitored the 3-D spread of ischemia. Within 5 minutes after the onset of ischemia, regions with reduced ADC values occurred. The core of the lesion, with the lowest absolute ADC values, first appeared in the lateral caudoputamen and frontoparietal cortex, then spread to adjacent areas. The volume of ischemic tissue was 224 +/- 48.5 mm3 (mean +/- SEM) after 180 minutes, ranging from 92 to 320 mm3, and this correlated well with the corrected infarct volume at postmortem (194 +/- 23.1 mm3, r = 0.72, p < 0.05). This experiment demonstrated that 3-D multislice diffusion mapping can detect ischemic regions noninvasively 5 minutes after MCA occlusion and follow the development of ischemia. The distribution of changes in absolute ADC values within the ischemic region can be followed over time, giving important information about the evolution of focal ischemia.

  11. Efficient 3D movement-based kernel density estimator and application to wildlife ecology

    USGS Publications Warehouse

    Tracey-PR, Jeff; Sheppard, James K.; Lockwood, Glenn K.; Chourasia, Amit; Tatineni, Mahidhar; Fisher, Robert N.; Sinkovits, Robert S.

    2014-01-01

    We describe an efficient implementation of a 3D movement-based kernel density estimator for determining animal space use from discrete GPS measurements. This new method provides more accurate results, particularly for species that make large excursions in the vertical dimension. The downside of this approach is that it is much more computationally expensive than simpler, lower-dimensional models. Through a combination of code restructuring, parallelization and performance optimization, we were able to reduce the time to solution by up to a factor of 1000x, thereby greatly improving the applicability of the method.

  12. The BGY3dM model for the approximation of solvent densities.

    PubMed

    Griebel, Michael; Jager, Lukas

    2008-11-07

    We present a new approach for the approximation of solvent densities around solutes of arbitrary shape. Our model represents a three-dimensional (3d) Born-Green-Yvon (BGY) equation for an arbitrary solute immersed into a molecular (M) solvent, the BGY3dM model. It comprises the famous Kirkwood approximation as closure relation. The molecules of the solvent are modeled as rigid bodies by taking the limit of an infinite restoring force for the intramolecular interactions. Furthermore, short-range potentials as well as the long-range Coulomb interaction are taken into account. The resulting integro-differential equations are efficiently solved by a Picard iteration and a solution of the linearized equations using Fourier transformations. We compare the results obtained from the presented BGY3dM method with results obtained by extensive molecular dynamics simulations for a HCl-like model solvent. Furthermore, we apply the method to carbon disulfide as solvent. The overall performance of the method is promising.

  13. High-Resolution Variable-Density 3D Cones Coronary MRA

    PubMed Central

    Addy, Nii Okai; Ingle, R. Reeve; Wu, Holden H.; Hu, Bob S.; Nishimura, Dwight G.

    2015-01-01

    Purpose To improve the spatial/temporal resolution of whole-heart coronary MR angiography (CMRA) by developing a variable-density (VD) 3D cones acquisition suitable for image reconstruction with parallel imaging and compressed sensing techniques. Methods A VD 3D cones trajectory design incorporates both radial and spiral trajectory undersampling techniques to achieve higher resolution. This design is used to generate a VD cones trajectory with 0.8 mm/66 ms isotropic spatial/temporal resolution, using a similar number of readouts as our previous fully sampled cones trajectory (1.2 mm/100 ms). Scans of volunteers and patients are performed to evaluate the performance of the VD trajectory, using non-Cartesian L1-ESPIRiT for high-resolution image reconstruction. Results With gridding reconstruction, the high-resolution scans experience an expected drop in signal-to-noise and contrast-to-noise ratios, but with L1-ESPIRiT, the apparent noise is substantially reduced. Compared to 1.2 mm images, in each volunteer, the L1-ESPIRiT 0.8 mm images exhibit higher vessel sharpness values in the right and left anterior descending arteries. Conclusion CMRA with isotropic sub-millimeter spatial resolution and high temporal resolution can be performed with VD 3D cones to improve the depiction of coronary arteries. PMID:26172829

  14. Texture mapping 3D models of indoor environments with noisy camera poses

    NASA Astrophysics Data System (ADS)

    Cheng, Peter; Anderson, Michael; He, Stewart; Zakhor, Avideh

    2013-03-01

    Automated 3D modeling of building interiors is used in applications such as virtual reality and environment mapping. Texturing these models allows for photo-realistic visualizations of the data collected by such modeling systems. While data acquisition times for mobile mapping systems are considerably shorter than for static ones, their recovered camera poses often suffer from inaccuracies, resulting in visible discontinuities when successive images are projected onto a surface for texturing. We present a method for texture mapping models of indoor environments that starts by selecting images whose camera poses are well-aligned in two dimensions. We then align images to geometry as well as to each other, producing visually consistent textures even in the presence of inaccurate surface geometry and noisy camera poses. Images are then composited into a final texture mosaic and projected onto surface geometry for visualization. The effectiveness of the proposed method is demonstrated on a number of different indoor environments.

  15. Virtual 3D tumor marking-exact intraoperative coordinate mapping improve post-operative radiotherapy

    PubMed Central

    2011-01-01

    The quality of the interdisciplinary interface in oncological treatment between surgery, pathology and radiotherapy is mainly dependent on reliable anatomical three-dimensional (3D) allocation of specimen and their context sensitive interpretation which defines further treatment protocols. Computer-assisted preoperative planning (CAPP) allows for outlining macroscopical tumor size and margins. A new technique facilitates the 3D virtual marking and mapping of frozen sections and resection margins or important surgical intraoperative information. These data could be stored in DICOM format (Digital Imaging and Communication in Medicine) in terms of augmented reality and transferred to communicate patient's specific tumor information (invasion to vessels and nerves, non-resectable tumor) to oncologists, radiotherapists and pathologists. PMID:22087558

  16. 3D mapping of neuronal migration in the embryonic mouse brain with magnetic resonance microimaging.

    PubMed

    Deans, Abby E; Wadghiri, Youssef Zaim; Aristizábal, Orlando; Turnbull, Daniel H

    2015-07-01

    A prominent feature of the developing mammalian brain is the widespread migration of neural progenitor (NP) cells during embryogenesis. A striking example is provided by NP cells born in the ventral forebrain of mid-gestation stage mice, which subsequently migrate long distances to their final positions in the cortex and olfactory bulb. Previous studies have used two-dimensional histological methods, making it difficult to analyze three-dimensional (3D) migration patterns. Unlike histology, magnetic resonance microimaging (micro-MRI) is a non-destructive, quantitative and inherently 3D imaging method for analyzing mouse embryos. To allow mapping of migrating NP cells with micro-MRI, cells were labeled in situ in the medial (MGE) and lateral (LGE) ganglionic eminences, using targeted in utero ultrasound-guided injection of micron-sized particles of iron-oxide (MPIO). Ex vivo micro-MRI and histology were then performed 5-6days after injection, demonstrating that the MPIO had magnetically labeled the migrating NP populations, which enabled 3D visualization and automated segmentation of the labeled cells. This approach was used to analyze the distinct patterns of migration from the MGE and LGE, and to construct rostral-caudal migration maps from each progenitor region. Furthermore, abnormal migratory phenotypes were observed in Nkx2.1(-/-) embryos, most notably a significant increase in cortical neurons derived from the Nkx2.1(-/-) LGE. Taken together, these results demonstrate that MPIO labeling and micro-MRI provide an efficient and powerful approach for analyzing 3D cell migration patterns in the normal and mutant mouse embryonic brain.

  17. High power density microbial fuel cell with flexible 3D graphene-nickel foam as anode.

    PubMed

    Wang, Hanyu; Wang, Gongming; Ling, Yichuan; Qian, Fang; Song, Yang; Lu, Xihong; Chen, Shaowei; Tong, Yexiang; Li, Yat

    2013-11-07

    The structure and electrical conductivity of anode play a significant role in the power generation of microbial fuel cells (MFCs). In this study, we developed a three-dimensional (3D) reduced graphene oxide-nickel (denoted as rGO-Ni) foam as an anode for MFC through controlled deposition of rGO sheets onto the nickel foam substrate. The loading amount of rGO sheets and electrode surface area can be controlled by the number of rGO loading cycles. 3D rGO-Ni foam anode provides not only a large accessible surface area for microbial colonization and electron mediators, but also a uniform macro-porous scaffold for effective mass diffusion of the culture medium. Significantly, at a steady state of the power generation, the MFC device with flexible rGO-Ni electrodes produced an optimal volumetric power density of 661 W m(-3) calculated based on the volume of anode material, or 27 W m(-3) based on the volume of the anode chamber. These values are substantially higher than that of plain nickel foam, and other conventional carbon based electrodes (e.g., carbon cloth, carbon felt, and carbon paper) measured in the same conditions. To our knowledge, this is the highest volumetric power density reported for mL-scale MFC device with a pure strain of Shewanella oneidensis MR-1. We also demonstrated that the MFC device can be operated effectively in a batch-mode at least for a week. These new 3D rGO-Ni electrodes show great promise for improving the power generation of MFC devices.

  18. Development and application of a ray-tracing code integrating with 3D equilibrium mapping in LHD ECH experiments

    NASA Astrophysics Data System (ADS)

    Tsujimura, T., Ii; Kubo, S.; Takahashi, H.; Makino, R.; Seki, R.; Yoshimura, Y.; Igami, H.; Shimozuma, T.; Ida, K.; Suzuki, C.; Emoto, M.; Yokoyama, M.; Kobayashi, T.; Moon, C.; Nagaoka, K.; Osakabe, M.; Kobayashi, S.; Ito, S.; Mizuno, Y.; Okada, K.; Ejiri, A.; Mutoh, T.

    2015-11-01

    The central electron temperature has successfully reached up to 7.5 keV in large helical device (LHD) plasmas with a central high-ion temperature of 5 keV and a central electron density of 1.3× {{10}19} m-3. This result was obtained by heating with a newly-installed 154 GHz gyrotron and also the optimisation of injection geometry in electron cyclotron heating (ECH). The optimisation was carried out by using the ray-tracing code ‘LHDGauss’, which was upgraded to include the rapid post-processing three-dimensional (3D) equilibrium mapping obtained from experiments. For ray-tracing calculations, LHDGauss can automatically read the relevant data registered in the LHD database after a discharge, such as ECH injection settings (e.g. Gaussian beam parameters, target positions, polarisation and ECH power) and Thomson scattering diagnostic data along with the 3D equilibrium mapping data. The equilibrium map of the electron density and temperature profiles are then extrapolated into the region outside the last closed flux surface. Mode purity, or the ratio between the ordinary mode and the extraordinary mode, is obtained by calculating the 1D full-wave equation along the direction of the rays from the antenna to the absorption target point. Using the virtual magnetic flux surfaces, the effects of the modelled density profiles and the magnetic shear at the peripheral region with a given polarisation are taken into account. Power deposition profiles calculated for each Thomson scattering measurement timing are registered in the LHD database. The adjustment of the injection settings for the desired deposition profile from the feedback provided on a shot-by-shot basis resulted in an effective experimental procedure.

  19. Mapping cardiac fiber orientations from high-resolution DTI to high-frequency 3D ultrasound

    NASA Astrophysics Data System (ADS)

    Qin, Xulei; Wang, Silun; Shen, Ming; Zhang, Xiaodong; Wagner, Mary B.; Fei, Baowei

    2014-03-01

    The orientation of cardiac fibers affects the anatomical, mechanical, and electrophysiological properties of the heart. Although echocardiography is the most common imaging modality in clinical cardiac examination, it can only provide the cardiac geometry or motion information without cardiac fiber orientations. If the patient's cardiac fiber orientations can be mapped to his/her echocardiography images in clinical examinations, it may provide quantitative measures for diagnosis, personalized modeling, and image-guided cardiac therapies. Therefore, this project addresses the feasibility of mapping personalized cardiac fiber orientations to three-dimensional (3D) ultrasound image volumes. First, the geometry of the heart extracted from the MRI is translated to 3D ultrasound by rigid and deformable registration. Deformation fields between both geometries from MRI and ultrasound are obtained after registration. Three different deformable registration methods were utilized for the MRI-ultrasound registration. Finally, the cardiac fiber orientations imaged by DTI are mapped to ultrasound volumes based on the extracted deformation fields. Moreover, this study also demonstrated the ability to simulate electricity activations during the cardiac resynchronization therapy (CRT) process. The proposed method has been validated in two rat hearts and three canine hearts. After MRI/ultrasound image registration, the Dice similarity scores were more than 90% and the corresponding target errors were less than 0.25 mm. This proposed approach can provide cardiac fiber orientations to ultrasound images and can have a variety of potential applications in cardiac imaging.

  20. Breast Density Analysis with Automated Whole-Breast Ultrasound: Comparison with 3-D Magnetic Resonance Imaging.

    PubMed

    Chen, Jeon-Hor; Lee, Yan-Wei; Chan, Si-Wa; Yeh, Dah-Cherng; Chang, Ruey-Feng

    2016-05-01

    In this study, a semi-automatic breast segmentation method was proposed on the basis of the rib shadow to extract breast regions from 3-D automated whole-breast ultrasound (ABUS) images. The density results were correlated with breast density values acquired with 3-D magnetic resonance imaging (MRI). MRI images of 46 breasts were collected from 23 women without a history of breast disease. Each subject also underwent ABUS. We used Otsu's thresholding method on ABUS images to obtain local rib shadow information, which was combined with the global rib shadow information (extracted from all slice projections) and integrated with the anatomy's breast tissue structure to determine the chest wall line. The fuzzy C-means classifier was used to extract the fibroglandular tissues from the acquired images. Whole-breast volume (WBV) and breast percentage density (BPD) were calculated in both modalities. Linear regression was used to compute the correlation of density results between the two modalities. The consistency of density measurement was also analyzed on the basis of intra- and inter-operator variation. There was a high correlation of density results between MRI and ABUS (R(2) = 0.798 for WBV, R(2) = 0.825 for PBD). The mean WBV from ABUS images was slightly smaller than the mean WBV from MR images (MRI: 342.24 ± 128.08 cm(3), ABUS: 325.47 ± 136.16 cm(3), p < 0.05). In addition, the BPD calculated from MR images was smaller than the BPD from ABUS images (MRI: 24.71 ± 15.16%, ABUS: 28.90 ± 17.73%, p < 0.05). The intra-operator and inter-operator variant analysis results indicated that there was no statistically significant difference in breast density measurement variation between the two modalities. Our results revealed a high correlation in WBV and BPD between MRI and ABUS. Our study suggests that ABUS provides breast density information useful in the assessment of breast health.

  1. Amoeboid migration mode adaption in quasi-3D spatial density gradients of varying lattice geometry

    NASA Astrophysics Data System (ADS)

    Gorelashvili, Mari; Emmert, Martin; Hodeck, Kai F.; Heinrich, Doris

    2014-07-01

    Cell migration processes are controlled by sensitive interaction with external cues such as topographic structures of the cell’s environment. Here, we present systematically controlled assays to investigate the specific effects of spatial density and local geometry of topographic structure on amoeboid migration of Dictyostelium discoideum cells. This is realized by well-controlled fabrication of quasi-3D pillar fields exhibiting a systematic variation of inter-pillar distance and pillar lattice geometry. By time-resolved local mean-squared displacement analysis of amoeboid migration, we can extract motility parameters in order to elucidate the details of amoeboid migration mechanisms and consolidate them in a two-state contact-controlled motility model, distinguishing directed and random phases. Specifically, we find that directed pillar-to-pillar runs are found preferably in high pillar density regions, and cells in directed motion states sense pillars as attractive topographic stimuli. In contrast, cell motion in random probing states is inhibited by high pillar density, where pillars act as obstacles for cell motion. In a gradient spatial density, these mechanisms lead to topographic guidance of cells, with a general trend towards a regime of inter-pillar spacing close to the cell diameter. In locally anisotropic pillar environments, cell migration is often found to be damped due to competing attraction by different pillars in close proximity and due to lack of other potential stimuli in the vicinity of the cell. Further, we demonstrate topographic cell guidance reflecting the lattice geometry of the quasi-3D environment by distinct preferences in migration direction. Our findings allow to specifically control amoeboid cell migration by purely topographic effects and thus, to induce active cell guidance. These tools hold prospects for medical applications like improved wound treatment, or invasion assays for immune cells.

  2. Dose distribution and mapping with 3D imaging presentation in intraoral and panoramic examinations

    NASA Astrophysics Data System (ADS)

    Chen, Hsiu-Ling; Huang, Yung-Hui; Wu, Tung-Hsin; Wang, Shih-Yuan; Lee, Jason J. S.

    2011-10-01

    In current medical imaging applications, high quality images not only provide more diagnostic value for anatomic delineation but also offer functional information for treatment direction. However, this approach would potentially subscribe higher radiation dose in dental radiographies, which has been putatively associated with low-birth-weight during pregnancy, which affects the hypothalamus-pituitary-thyroid axis or thereby directly affects the reproductive organs. The aim of this study was to apply the high resolution 3-D image mapping technique to evaluate radiation doses from the following aspects: (1) verifying operating parameters of dental X-ray units, (2) measuring the leakage radiations and (3) mapping dose with 3-D radiographic imaging to evaluate dose distribution in head and neck regions. From the study results, we found that (1) leakage radiation from X-ray units was about 21.31±15.24 mR/h (<100 mR/h), (2) error of actual tube voltage for 60 kVp setting was from 0.2% to 6.5%, with an average of 2.5% (<7%) and (3) the error of exposure time for a 0.5-1.5 s setting was within 0.7-8.5%, with an average of 7.3% (<10%) error as well. Our 3-D dose mapping demonstrated that dose values were relatively lower in soft tissues and higher in bone surfaces compared with other investigations. Multiple causes could contribute to these variations, including irradiation geometry, image equipment and type of technique applied, etc. From the results, we also observed that larger accumulated doses were presented in certain critical organs, such as salivary gland, thyroid gland and bone marrow. Potential biological affects associated with these findings warrant further investigation.

  3. 3D mapping of lithium in battery electrodes using neutron activation

    NASA Astrophysics Data System (ADS)

    He, Yuping; Downing, R. Gregory; Wang, Howard

    2015-08-01

    The neutron depth profiling technique based on the neutron activation reaction, 6Li (n, α) 3H, was applied with two dimensional (2D) pinhole aperture scans to spatially map lithium in 3D. The technique was used to study model LiFePO4 electrodes of rechargeable batteries for spatial heterogeneities of lithium in two cathode films that had undergone different electrochemical cycling histories. The method is useful for better understanding the functioning and failure of batteries using lithium as the active element.

  4. Efficient dense blur map estimation for automatic 2D-to-3D conversion

    NASA Astrophysics Data System (ADS)

    Vosters, L. P. J.; de Haan, G.

    2012-03-01

    Focus is an important depth cue for 2D-to-3D conversion of low depth-of-field images and video. However, focus can be only reliably estimated on edges. Therefore, Bea et al. [1] first proposed an optimization based approach to propagate focus to non-edge image portions, for single image focus editing. While their approach produces accurate dense blur maps, the computational complexity and memory requirements for solving the resulting sparse linear system with standard multigrid or (multilevel) preconditioning techniques, are infeasible within the stringent requirements of the consumer electronics and broadcast industry. In this paper we propose fast, efficient, low latency, line scanning based focus propagation, which mitigates the need for complex multigrid or (multilevel) preconditioning techniques. In addition we propose facial blur compensation to compensate for false shading edges that cause incorrect blur estimates in people's faces. In general shading leads to incorrect focus estimates, which may lead to unnatural 3D and visual discomfort. Since visual attention mostly tends to faces, our solution solves the most distracting errors. A subjective assessment by paired comparison on a set of challenging low-depth-of-field images shows that the proposed approach achieves equal 3D image quality as optimization based approaches, and that facial blur compensation results in a significant improvement.

  5. Pore detection in Computed Tomography (CT) soil 3D images using singularity map analysis

    NASA Astrophysics Data System (ADS)

    Sotoca, Juan J. Martin; Tarquis, Ana M.; Saa Requejo, Antonio; Grau, Juan B.

    2016-04-01

    X-ray Computed Tomography (CT) images have significantly helped the study of the internal soil structure. This technique has two main advantages: 1) it is a non-invasive technique, i.e., it doesńt modify the internal soil structure, and 2) it provides a good resolution. The major disadvantage is that these images are sometimes low-contrast in the solid/pore interface. One of the main problems in analyzing soil structure through CT images is to segment them in solid/pore space. To do so, we have different segmentation techniques at our disposal that are mainly based on thresholding methods in which global or local thresholds are calculated to separate pore space from solid space. The aim of this presentation is to develop the fractal approach to soil structure using "singularity maps" and the "Concentration-Area (CA) method". We will establish an analogy between mineralization processes in ore deposits and morphogenesis processes in soils. Resulting from this analogy a new 3D segmentation method is proposed, the "3D Singularity-CA" method. A comparison with traditional 3D segmentation methods will be performed to show the main differences among them.

  6. A Novel 2D-to-3D Video Conversion Method Using Time-Coherent Depth Maps

    PubMed Central

    Yin, Shouyi; Dong, Hao; Jiang, Guangli; Liu, Leibo; Wei, Shaojun

    2015-01-01

    In this paper, we propose a novel 2D-to-3D video conversion method for 3D entertainment applications. 3D entertainment is getting more and more popular and can be found in many contexts, such as TV and home gaming equipment. 3D image sensors are a new method to produce stereoscopic video content conveniently and at a low cost, and can thus meet the urgent demand for 3D videos in the 3D entertaiment market. Generally, 2D image sensor and 2D-to-3D conversion chip can compose a 3D image sensor. Our study presents a novel 2D-to-3D video conversion algorithm which can be adopted in a 3D image sensor. In our algorithm, a depth map is generated by combining global depth gradient and local depth refinement for each frame of 2D video input. Global depth gradient is computed according to image type while local depth refinement is related to color information. As input 2D video content consists of a number of video shots, the proposed algorithm reuses the global depth gradient of frames within the same video shot to generate time-coherent depth maps. The experimental results prove that this novel method can adapt to different image types, reduce computational complexity and improve the temporal smoothness of generated 3D video. PMID:26131674

  7. BioMEA: a versatile high-density 3D microelectrode array system using integrated electronics.

    PubMed

    Charvet, Guillaume; Rousseau, Lionel; Billoint, Olivier; Gharbi, Sadok; Rostaing, Jean-Pierre; Joucla, Sébastien; Trevisiol, Michel; Bourgerette, Alain; Chauvet, Philippe; Moulin, Céline; Goy, François; Mercier, Bruno; Colin, Mikael; Spirkovitch, Serge; Fanet, Hervé; Meyrand, Pierre; Guillemaud, Régis; Yvert, Blaise

    2010-04-15

    Microelectrode arrays (MEAs) offer a powerful tool to both record activity and deliver electrical microstimulations to neural networks either in vitro or in vivo. Microelectronics microfabrication technologies now allow building high-density MEAs containing several hundreds of microelectrodes. However, dense arrays of 3D micro-needle electrodes, providing closer contact with the neural tissue than planar electrodes, are not achievable using conventional isotropic etching processes. Moreover, increasing the number of electrodes using conventional electronics is difficult to achieve into compact devices addressing all channels independently for simultaneous recording and stimulation. Here, we present a full modular and versatile 256-channel MEA system based on integrated electronics. First, transparent high-density arrays of 3D-shaped microelectrodes were realized by deep reactive ion etching techniques of a silicon substrate reported on glass. This approach allowed achieving high electrode aspect ratios, and different shapes of tip electrodes. Next, we developed a dedicated analog 64-channel Application Specific Integrated Circuit (ASIC) including one amplification stage and one current generator per channel, and analog output multiplexing. A full modular system, called BIOMEA, has been designed, allowing connecting different types of MEAs (64, 128, or 256 electrodes) to different numbers of ASICs for simultaneous recording and/or stimulation on all channels. Finally, this system has been validated experimentally by recording and electrically eliciting low-amplitude spontaneous rhythmic activity (both LFPs and spikes) in the developing mouse CNS. The availability of high-density MEA systems with integrated electronics will offer new possibilities for both in vitro and in vivo studies of large neural networks.

  8. Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps

    NASA Astrophysics Data System (ADS)

    Kumari, Amrita; Dorai, Kavita

    2013-06-01

    NMR chemical shifts are accurate indicators of molecular environment and have been extensively used as aids in protein structure determination. This work focuses on creating empirical 3D correlation maps of backbone chemical shift nuclei for use as identifiers of secondary structure elements in proteins. A correlated database of backbone nuclei chemical shifts was constructed from experimental structural data gathered from entries in the Protein Data Bank (PDB) as well as isotropic chemical shift values from the RefDB database. Rigorous statistical analysis of the maps led to the conclusion that specific correlations between triplets of backbone chemical shifts are best able to differentiate between different secondary structures such as α-helices, β-strands and turns. The method is compared with similar techniques that use NMR chemical shift information as aids in biomolecular structure determination and performs well in tests done on experimental data determined for different types of proteins, including large multi-domain proteins and membrane proteins.

  9. Structured light 3D depth map enhancement and gesture recognition using image content adaptive filtering

    NASA Astrophysics Data System (ADS)

    Ramachandra, Vikas; Nash, James; Atanassov, Kalin; Goma, Sergio

    2013-03-01

    A structured-light system for depth estimation is a type of 3D active sensor that consists of a structured-light projector that projects an illumination pattern on the scene (e.g. mask with vertical stripes) and a camera which captures the illuminated scene. Based on the received patterns, depths of different regions in the scene can be inferred. In this paper, we use side information in the form of image structure to enhance the depth map. This side information is obtained from the received light pattern image reflected by the scene itself. The processing steps run real time. This post-processing stage in the form of depth map enhancement can be used for better hand gesture recognition, as is illustrated in this paper.

  10. Inlining 3d Reconstruction, Multi-Source Texture Mapping and Semantic Analysis Using Oblique Aerial Imagery

    NASA Astrophysics Data System (ADS)

    Frommholz, D.; Linkiewicz, M.; Poznanska, A. M.

    2016-06-01

    This paper proposes an in-line method for the simplified reconstruction of city buildings from nadir and oblique aerial images that at the same time are being used for multi-source texture mapping with minimal resampling. Further, the resulting unrectified texture atlases are analyzed for façade elements like windows to be reintegrated into the original 3D models. Tests on real-world data of Heligoland/ Germany comprising more than 800 buildings exposed a median positional deviation of 0.31 m at the façades compared to the cadastral map, a correctness of 67% for the detected windows and good visual quality when being rendered with GPU-based perspective correction. As part of the process building reconstruction takes the oriented input images and transforms them into dense point clouds by semi-global matching (SGM). The point sets undergo local RANSAC-based regression and topology analysis to detect adjacent planar surfaces and determine their semantics. Based on this information the roof, wall and ground surfaces found get intersected and limited in their extension to form a closed 3D building hull. For texture mapping the hull polygons are projected into each possible input bitmap to find suitable color sources regarding the coverage and resolution. Occlusions are detected by ray-casting a full-scale digital surface model (DSM) of the scene and stored in pixel-precise visibility maps. These maps are used to derive overlap statistics and radiometric adjustment coefficients to be applied when the visible image parts for each building polygon are being copied into a compact texture atlas without resampling whenever possible. The atlas bitmap is passed to a commercial object-based image analysis (OBIA) tool running a custom rule set to identify windows on the contained façade patches. Following multi-resolution segmentation and classification based on brightness and contrast differences potential window objects are evaluated against geometric constraints and

  11. Intra-retinal layer segmentation of 3D optical coherence tomography using coarse grained diffusion map.

    PubMed

    Kafieh, Raheleh; Rabbani, Hossein; Abramoff, Michael D; Sonka, Milan

    2013-12-01

    Optical coherence tomography (OCT) is a powerful and noninvasive method for retinal imaging. In this paper, we introduce a fast segmentation method based on a new variant of spectral graph theory named diffusion maps. The research is performed on spectral domain (SD) OCT images depicting macular and optic nerve head appearance. The presented approach does not require edge-based image information in localizing most of boundaries and relies on regional image texture. Consequently, the proposed method demonstrates robustness in situations of low image contrast or poor layer-to-layer image gradients. Diffusion mapping applied to 2D and 3D OCT datasets is composed of two steps, one for partitioning the data into important and less important sections, and another one for localization of internal layers. In the first step, the pixels/voxels are grouped in rectangular/cubic sets to form a graph node. The weights of the graph are calculated based on geometric distances between pixels/voxels and differences of their mean intensity. The first diffusion map clusters the data into three parts, the second of which is the area of interest. The other two sections are eliminated from the remaining calculations. In the second step, the remaining area is subjected to another diffusion map assessment and the internal layers are localized based on their textural similarities. The proposed method was tested on 23 datasets from two patient groups (glaucoma and normals). The mean unsigned border positioning errors (mean ± SD) was 8.52 ± 3.13 and 7.56 ± 2.95 μm for the 2D and 3D methods, respectively.

  12. Mass Movement Susceptibility in the Western San Juan Mountains, Colorado: A Preliminary 3-D Mapping Approach

    NASA Astrophysics Data System (ADS)

    Kelkar, K. A.; Giardino, J. R.

    2015-12-01

    Mass movement is a major activity that impacts lives of humans and their infrastructure. Human activity in steep, mountainous regions is especially at risk to this potential hazard. Thus, the identification and quantification of risk by mapping and determining mass movement susceptibility are fundamental in protecting lives, resources and ensuring proper land use regulation and planning. Specific mass-movement processes including debris flows, rock falls, snow avalanches and landslides continuously modify the landscape of the San Juan Mountains. Historically, large-magnitude slope failures have repeatedly occurred in the region. Common triggers include intense, long-duration precipitation, freeze-thaw processes, human activity and various volcanic lithologies overlying weaker sedimentary formations. Predicting mass movement is challenging because of its episodic and spatially, discontinuous occurrence. Landslides in mountain terrain are characterized as widespread, highly mobile and have a long duration of activity. We developed a 3-D model for landslide susceptibility using Geographic Information Systems Technology (GIST). The study area encompasses eight USGS quadrangles: Ridgway, Dallas, Mount Sneffels, Ouray, Telluride, Ironton, Ophir and Silverton. Fieldwork consisted of field reconnaissance mapping at 1:5,000 focusing on surficial geomorphology. Field mapping was used to identify potential locations, which then received additional onsite investigation and photographic documentation of features indicative of slope failure. A GIS module was created using seven terrain spatial databases: geology, surficial geomorphology (digitized), slope aspect, slope angle, vegetation, soils and distance to infrastructure to map risk. The GIS database will help determine risk zonation for the study area. Correlations between terrain parameters leading to slope failure were determined through the GIS module. This 3-D model will provide a spatial perspective of the landscape to

  13. Evaluation Model for Pavement Surface Distress on 3d Point Clouds from Mobile Mapping System

    NASA Astrophysics Data System (ADS)

    Aoki, K.; Yamamoto, K.; Shimamura, H.

    2012-07-01

    This paper proposes a methodology to evaluate the pavement surface distress for maintenance planning of road pavement using 3D point clouds from Mobile Mapping System (MMS). The issue on maintenance planning of road pavement requires scheduled rehabilitation activities for damaged pavement sections to keep high level of services. The importance of this performance-based infrastructure asset management on actual inspection data is globally recognized. Inspection methodology of road pavement surface, a semi-automatic measurement system utilizing inspection vehicles for measuring surface deterioration indexes, such as cracking, rutting and IRI, have already been introduced and capable of continuously archiving the pavement performance data. However, any scheduled inspection using automatic measurement vehicle needs much cost according to the instruments' specification or inspection interval. Therefore, implementation of road maintenance work, especially for the local government, is difficult considering costeffectiveness. Based on this background, in this research, the methodologies for a simplified evaluation for pavement surface and assessment of damaged pavement section are proposed using 3D point clouds data to build urban 3D modelling. The simplified evaluation results of road surface were able to provide useful information for road administrator to find out the pavement section for a detailed examination and for an immediate repair work. In particular, the regularity of enumeration of 3D point clouds was evaluated using Chow-test and F-test model by extracting the section where the structural change of a coordinate value was remarkably achieved. Finally, the validity of the current methodology was investigated by conducting a case study dealing with the actual inspection data of the local roads.

  14. A 3D endoscopy reconstruction as a saliency map for analysis of polyp shapes

    NASA Astrophysics Data System (ADS)

    Ruano, Josue; Martínez, Fabio; Gómez, Martín.; Romero, Eduardo

    2015-01-01

    A first diagnosis of colorectal cancer is performed by examination of polyp shape and appearance during an endoscopy routine procedure. However, the video-endoscopy is highly noisy because exacerbated physiological conditions like increased motility or secretion may limit the visual analysis of lesions. In this work a 3D reconstruction of the digestive tract is proposed, facilitating the polyp shape evaluation by highlighting its surface geometry and allowing an analysis from different perspectives. The method starts by a spatio-temporal map, constructed to group the different regions of the tract by their similar dynamic patterns during the sequence. Then, such map was convolved with a second derivative of a Gaussian kernel that emulates the camera distortion and allows to highlight the polyp surface. The position initialization in each frame of the kernel was computed from expert manual delineation and propagated along the sequence based on. Results show reliable reconstructions, with a salient 3D polyp structure that can then be better observed.

  15. Multi-layer 3D imaging using a few viewpoint images and depth map

    NASA Astrophysics Data System (ADS)

    Suginohara, Hidetsugu; Sakamoto, Hirotaka; Yamanaka, Satoshi; Suyama, Shiro; Yamamoto, Hirotsugu

    2015-03-01

    In this paper, we propose a new method that makes multi-layer images from a few viewpoint images to display a 3D image by the autostereoscopic display that has multiple display screens in the depth direction. We iterate simple "Shift and Subtraction" processes to make each layer image alternately. The image made in accordance with depth map like a volume slicing by gradations is used as the initial solution of iteration process. Through the experiments using the prototype stacked two LCDs, we confirmed that it was enough to make multi-layer images from three viewpoint images to display a 3D image. Limiting the number of viewpoint images, the viewing area that allows stereoscopic view becomes narrow. To broaden the viewing area, we track the head motion of the viewer and update screen images in real time so that the viewer can maintain correct stereoscopic view within +/- 20 degrees area. In addition, we render pseudo multiple viewpoint images using depth map, then we can generate motion parallax at the same time.

  16. Mapping gray-scale image to 3D surface scanning data by ray tracing

    NASA Astrophysics Data System (ADS)

    Li, Peng; Jones, Peter R. M.

    1997-03-01

    The extraction and location of feature points from range imaging is an important but difficult task in machine vision based measurement systems. There exist some feature points which are not able to be detected from pure geometric characteristics, particularly in those measurement tasks related to the human body. The Loughborough Anthropometric Shadow Scanner (LASS) is a whole body surface scanner based on structured light technique. Certain applications of LASS require accurate location of anthropometric landmarks from the scanned data. This is sometimes impossible from existing raw data because some landmarks do not appear in the scanned data. Identification of these landmarks has to resort to surface texture of the scanned object. Modifications to LASS were made to allow gray-scale images to be captured before or after the object was scanned. Two-dimensional gray-scale image must be mapped to the scanned data to acquire the 3D coordinates of a landmark. The method to map 2D images to the scanned data is based on the colinearity conditions and ray-tracing method. If the camera center and image coordinates are known, the corresponding object point must lie on a ray starting from the camera center and connecting to the image coordinate. By intersecting the ray with the scanned surface of the object, the 3D coordinates of a point can be solved. Experimentation has demonstrated the feasibility of the method.

  17. New 3D seismicity maps using chromo-stereoscopy with two alternative freewares

    NASA Astrophysics Data System (ADS)

    Okamoto, Y.

    2011-12-01

    Seismicity maps play a key role in an introduction of geosciences studies or outreach programs. Various techniques are used in order to show earthquakes in a three dimensional field. To use "chromo-stereoscopy" is our simple and easier-making solution. The Chroma Depth 3D Glasses are employed for this purpose. The glasses consist of two transparent blazed grating films covered with a paper holder and cost a little (1 US$). Looking through these glasses, the colored chart turns into three dimensional perspective due to the mechanism that the color codes make a depth dimension with dispersion. We use two complementary freewares to make maps, the GMT (Generic Mapping Tools, Wessel and Smith.1988) and the POV-Ray (Persistence of Vision Pty. Ltd. 2004). The two softwares have their own advantages; the GMT is specialized for map making with simple scripts, while the POV-Ray produces realistic 3D rendering images with more complicated scripts. The earthquakes are plotted with the rainbow color codes depending on their depths in a black background as printed or PC images. Therefore, the red colored shallow earthquakes are float in front and blue colored ones sink deeper. This effect is so amazing that the students who first wear these glasses are strongly moved and fascinated with this simple mechanism. The data used here are from JMA seismicity catalogue and USGS (ANSS) catalogue. The POV-Ray version needs coastline data, so we got them from the Coastline Extractor (NGDC) web site. Also, the POR-Ray has no function to draw lines in three dimensions, so we had to make some trials for showing them in relief. The main target of our map is "the Wadati-Beniof zone", in which the sub-ducting oceanic plate surface is fringed by deeper earthquakes colored yellow, green to blue. The active volcanic regions such as the Hawaii islands or the active fault regions such as the San Andreas Fault are also effective targets of our method. However, since their shallow complicated seismic

  18. Re-Dimensional Thinking in Earth Science: From 3-D Virtual Reality Panoramas to 2-D Contour Maps

    ERIC Educational Resources Information Center

    Park, John; Carter, Glenda; Butler, Susan; Slykhuis, David; Reid-Griffin, Angelia

    2008-01-01

    This study examines the relationship of gender and spatial perception on student interactivity with contour maps and non-immersive virtual reality. Eighteen eighth-grade students elected to participate in a six-week activity-based course called "3-D GeoMapping." The course included nine days of activities related to topographic mapping.…

  19. Gravity Field Analysis and 3D Density Modeling of the Lithosphere Along the Dead Sea Transform

    NASA Astrophysics Data System (ADS)

    Goetze, H.; Ebbing, J.; Hese, F.; Kollersberger, T.; Schmidt, S.; Rybakov, M.; Hassouneh, M.; Hrahsha, M.; El Kelani, R.

    2002-12-01

    The gravity field of Dead Sea Rift / Dead Sea Transform was investigated with regard to the isostatic state, the crustal density structure of the orogeny and the rigidity of the lithosphere in the Central Arava Valley. Our multi-national and interdisciplinary gravity group with participants from the Geophysical Institute of Israel, the Natural Resources Authority (Jordan), and the An-Najah National University (Palestine), is aiming to study the crustal density structure, the isostatic state of the lithosphere and mechanical properties of the Dead Sea Rift system under the framework of the international DESERT program which is coordinated by the GeoForschungsZentrum (GFZ, Potsdam, Germany). The study area is located about 100 km away from both the basin of the Dead Sea and the Gulf of Elat/Aqaba basin, respectively. Between March and May 2002 some 800 new gravity observations were recorded at a local (Arava valley) and regional scale (along the DESERT seismic line). Station spacing in the Arava valley was 100 - 300 m and in the nearest neighborhood of the fault 50 m only. The survey of detailed observations covered an area of 10 by 10 km and was completed by a likewise dense survey at the western side of the valley in Israel. All gravity data were tied to the IGSN -71 gravity datum and are terrain-corrected as well. The station complete Bouguer gravity field, Free air anomaly and residual isostatic anomalies (based on both Airy and Vening-Meinesz models) were merged with the existing regional gravity data bases of the region. Constraining information for the 3D density models at regional and local came from recent geophysical field data acquisition and consist of seismic, seismological, electromagnetic, and geologic studies which represent the integrated part of the interdisciplinary research program. Novel methods e.g. curvature techniques, and Euler deconvolution of the gravity fields shed new insight into the structure of upper and lower crust and the causing

  20. The 3D heat flux density distribution on a novel parabolic trough wavy absorber

    NASA Astrophysics Data System (ADS)

    Demagh, Yassine; Kabar, Yassine; Bordja, Lyes; Noui, Samira

    2016-05-01

    The non-uniform concentrated solar flux distribution on the outer surface of the absorber pipe can lead to large circumferential gradient temperature and high concentrated temperature of the absorber pipe wall, which is one of the primary causes of parabolic trough solar receiver breakdown. In this study, a novel shape of the parabolic trough absorber pipe is proposed as a solution to well homogenize the solar flux distribution, as well as, the temperature in the absorber wall. The conventional straight absorber located along the focal line of the parabola is replaced by wavy one (invention patent by Y. Demagh [1]) for which the heat flux density distribution on the outer surface varies in both axial and azimuthal directions (3D) while it varies only in the azimuthal direction on the former (2D). As far as we know, there is not previous study which has used a longitudinally wavy pipe as an absorber into the parabolic trough collector unit.

  1. Exploring the surface reactivity of 3d metal endofullerenes: a density-functional theory study.

    PubMed

    Estrada-Salas, Rubén E; Valladares, Ariel A

    2009-09-24

    Changes in the preferential sites of electrophilic, nucleophilic, and radical attacks on the pristine C60 surface with endohedral doping using 3d transition metal atoms were studied via two useful reactivity indices, namely the Fukui functions and the molecular electrostatic potential. Both of these were calculated at the density functional BPW91 level of theory with the DNP basis set. Our results clearly show changes in the preferential reactivity sites on the fullerene surface when it is doped with Mn, Fe, Co, or Ni atoms, whereas there are no significant changes in the preferential reactivity sites on the C60 surface upon endohedral doping with Cu and Zn atoms. Electron affinities (EA), ionization potentials (IP), and HOMO-LUMO gaps (Eg) were also calculated to complete the study of the endofullerene's surface reactivity. These findings provide insight into endofullerene functionalization, an important issue in their application.

  2. SU-F-BRB-05: Collision Avoidance Mapping Using Consumer 3D Camera

    SciTech Connect

    Cardan, R; Popple, R

    2015-06-15

    Purpose: To develop a fast and economical method of scanning a patient’s full body contour for use in collision avoidance mapping without the use of ionizing radiation. Methods: Two consumer level 3D cameras used in electronic gaming were placed in a CT simulator room to scan a phantom patient set up in a high collision probability position. A registration pattern and computer vision algorithms were used to transform the scan into the appropriate coordinate systems. The cameras were then used to scan the surface of a gantry in the treatment vault. Each scan was converted into a polygon mesh for collision testing in a general purpose polygon interference algorithm. All clinically relevant transforms were applied to the gantry and patient support to create a map of all possible collisions. The map was then tested for accuracy by physically testing the collisions with the phantom in the vault. Results: The scanning fidelity of both the gantry and patient was sufficient to produce a collision prediction accuracy of 97.1% with 64620 geometry states tested in 11.5 s. The total scanning time including computation, transformation, and generation was 22.3 seconds. Conclusion: Our results demonstrate an economical system to generate collision avoidance maps. Future work includes testing the speed of the framework in real-time collision avoidance scenarios. Research partially supported by a grant from Varian Medical Systems.

  3. Indoor Localization Algorithms for an Ambulatory Human Operated 3D Mobile Mapping System

    SciTech Connect

    Corso, N; Zakhor, A

    2013-12-03

    Indoor localization and mapping is an important problem with many applications such as emergency response, architectural modeling, and historical preservation. In this paper, we develop an automatic, off-line pipeline for metrically accurate, GPS-denied, indoor 3D mobile mapping using a human-mounted backpack system consisting of a variety of sensors. There are three novel contributions in our proposed mapping approach. First, we present an algorithm which automatically detects loop closure constraints from an occupancy grid map. In doing so, we ensure that constraints are detected only in locations that are well conditioned for scan matching. Secondly, we address the problem of scan matching with poor initial condition by presenting an outlier-resistant, genetic scan matching algorithm that accurately matches scans despite a poor initial condition. Third, we present two metrics based on the amount and complexity of overlapping geometry in order to vet the estimated loop closure constraints. By doing so, we automatically prevent erroneous loop closures from degrading the accuracy of the reconstructed trajectory. The proposed algorithms are experimentally verified using both controlled and real-world data. The end-to-end system performance is evaluated using 100 surveyed control points in an office environment and obtains a mean accuracy of 10 cm. Experimental results are also shown on three additional datasets from real world environments including a 1500 meter trajectory in a warehouse sized retail shopping center.

  4. Detecting Genetic Association of Common Human Facial Morphological Variation Using High Density 3D Image Registration

    PubMed Central

    Hu, Sile; Zhou, Hang; Guo, Jing; Jin, Li; Tang, Kun

    2013-01-01

    Human facial morphology is a combination of many complex traits. Little is known about the genetic basis of common facial morphological variation. Existing association studies have largely used simple landmark-distances as surrogates for the complex morphological phenotypes of the face. However, this can result in decreased statistical power and unclear inference of shape changes. In this study, we applied a new image registration approach that automatically identified the salient landmarks and aligned the sample faces using high density pixel points. Based on this high density registration, three different phenotype data schemes were used to test the association between the common facial morphological variation and 10 candidate SNPs, and their performances were compared. The first scheme used traditional landmark-distances; the second relied on the geometric analysis of 15 landmarks and the third used geometric analysis of a dense registration of ∼30,000 3D points. We found that the two geometric approaches were highly consistent in their detection of morphological changes. The geometric method using dense registration further demonstrated superiority in the fine inference of shape changes and 3D face modeling. Several candidate SNPs showed potential associations with different facial features. In particular, one SNP, a known risk factor of non-syndromic cleft lips/palates, rs642961 in the IRF6 gene, was validated to strongly predict normal lip shape variation in female Han Chinese. This study further demonstrated that dense face registration may substantially improve the detection and characterization of genetic association in common facial variation. PMID:24339768

  5. 3D viscosity maps for Greenland and effect on GRACE mass balance estimates

    NASA Astrophysics Data System (ADS)

    van der Wal, Wouter; Xu, Zheng

    2016-04-01

    The GRACE satellite mission measures mass loss of the Greenland ice sheet. To correct for glacial isostatic adjustment numerical models are used. Although generally found to be a small signal, the full range of possible GIA models has not been explored yet. In particular, low viscosities due to a wet mantle and high temperatures due to the nearby Iceland hotspot could have a significant effect on GIA gravity rates. The goal of this study is to present a range of possible viscosity maps, and investigate the effect on GRACE mass balance estimates. Viscosity is derived using flow laws for olivine. Mantle temperature is computed from global seismology models, based on temperature derivatives for different mantle compositions. An indication for grain sizes is obtained by xenolith findings at a few locations. We also investigate the weakening effect of the presence of melt. To calculate gravity rates, we use a finite-element GIA model with the 3D viscosity maps and the ICE-5G loading history. GRACE mass balances for mascons in Greenland are derived with a least-squares inversion, using separate constraints for the inland and coastal areas in Greenland. Biases in the least-squares inversion are corrected using scale factors estimated from a simulation based on a surface mass balance model (Xu et al., submitted to The Cryosphere). Model results show enhanced gravity rates in the west and south of Greenland with 3D viscosity maps, compared to GIA models with 1D viscosity. The effect on regional mass balance is up to 5 Gt/year. Regional low viscosity can make present-day gravity rates sensitivity to ice thickness changes in the last decades. Therefore, an improved ice loading history for these time scales is needed.

  6. 2D/3D registration for X-ray guided bronchoscopy using distance map classification.

    PubMed

    Xu, Di; Xu, Sheng; Herzka, Daniel A; Yung, Rex C; Bergtholdt, Martin; Gutierrez, Luis F; McVeigh, Elliot R

    2010-01-01

    In X-ray guided bronchoscopy of peripheral pulmonary lesions, airways and nodules are hardly visible in X-ray images. Transbronchial biopsy of peripheral lesions is often carried out blindly, resulting in degraded diagnostic yield. One solution of this problem is to superimpose the lesions and airways segmented from preoperative 3D CT images onto 2D X-ray images. A feature-based 2D/3D registration method is proposed for the image fusion between the datasets of the two imaging modalities. Two stereo X-ray images are used in the algorithm to improve the accuracy and robustness of the registration. The algorithm extracts the edge features of the bony structures from both CT and X-ray images. The edge points from the X-ray images are categorized into eight groups based on the orientation information of their image gradients. An orientation dependent Euclidean distance map is generated for each group of X-ray feature points. The distance map is then applied to the edge points of the projected CT images whose gradient orientations are compatible with the distance map. The CT and X-ray images are registered by matching the boundaries of the projected CT segmentations to the closest edges of the X-ray images after the orientation constraint is satisfied. Phantom and clinical studies were carried out to validate the algorithm's performance, showing a registration accuracy of 4.19(± 0.5) mm with 48.39(± 9.6) seconds registration time. The algorithm was also evaluated on clinical data, showing promising registration accuracy and robustness.

  7. Visualization of high-density 3D graphs using nonlinear visual space transformations

    NASA Astrophysics Data System (ADS)

    Hao, Ming C.; Dayal, Umeshwar; Garg, Pankaj; Machiraju, Vijay

    2002-03-01

    The real world data distribution is seldom uniform. Clutter and sparsity commonly occur in visualization. Often, clutter results in overplotting, in which certain data items are not visible because other data items occlude them. Sparsity results in the inefficient use of the available display space. Common mechanisms to overcome this include reducing the amount of information displayed or using multiple representations with a varying amount of detail. This paper describes out experiments on Non-Linear Visual Space Transformations (NLVST). NLVST encompasses several innovative techniques: (1) employing a histogram for calculating the density of data distribution; (2) mapping the raw data values to a non-linear scale for stretching a high-density area; (3) tightening the sparse area to save the display space; (4) employing different color ranges of values on a non-linear scale according to the local density. We have applied NLVST to several web applications: market basket analysis, transactions observation, and IT search behavior analysis.

  8. 3D-Laser-Scanning Technique Applied to Bulk Density Measurements of Apollo Lunar Samples

    NASA Technical Reports Server (NTRS)

    Macke, R. J.; Kent, J. J.; Kiefer, W. S.; Britt, D. T.

    2015-01-01

    In order to better interpret gravimetric data from orbiters such as GRAIL and LRO to understand the subsurface composition and structure of the lunar crust, it is import to have a reliable database of the density and porosity of lunar materials. To this end, we have been surveying these physical properties in both lunar meteorites and Apollo lunar samples. To measure porosity, both grain density and bulk density are required. For bulk density, our group has historically utilized sub-mm bead immersion techniques extensively, though several factors have made this technique problematic for our work with Apollo samples. Samples allocated for measurement are often smaller than optimal for the technique, leading to large error bars. Also, for some samples we were required to use pure alumina beads instead of our usual glass beads. The alumina beads were subject to undesirable static effects, producing unreliable results. Other investigators have tested the use of 3d laser scanners on meteorites for measuring bulk volumes. Early work, though promising, was plagued with difficulties including poor response on dark or reflective surfaces, difficulty reproducing sharp edges, and large processing time for producing shape models. Due to progress in technology, however, laser scanners have improved considerably in recent years. We tested this technique on 27 lunar samples in the Apollo collection using a scanner at NASA Johnson Space Center. We found it to be reliable and more precise than beads, with the added benefit that it involves no direct contact with the sample, enabling the study of particularly friable samples for which bead immersion is not possible

  9. Non-destructive mapping of grain orientations in 3D by laboratory X-ray microscopy

    PubMed Central

    McDonald, S. A.; Reischig, P.; Holzner, C.; Lauridsen, E. M.; Withers, P. J.; Merkle, A. P.; Feser, M.

    2015-01-01

    The ability to characterise crystallographic microstructure, non-destructively and in three-dimensions, is a powerful tool for understanding many aspects related to damage and deformation mechanisms in polycrystalline materials. To this end, the technique of X-ray diffraction contrast tomography (DCT) using monochromatic synchrotron and polychromatic laboratory X-ray sources has been shown to be capable of mapping crystal grains and their orientations non-destructively in 3D. Here we describe a novel laboratory-based X-ray DCT modality (LabDCT), enabling the wider accessibility of the DCT technique for routine use and in-depth studies of, for example, temporal changes in crystallographic grain structure non-destructively over time through ‘4D’ in situ time-lapse studies. The capability of the technique is demonstrated by studying a titanium alloy (Ti-β21S) sample. In the current implementation the smallest grains that can be reliably detected are around 40 μm. The individual grain locations and orientations are reconstructed using the LabDCT method and the results are validated against independent measurements from phase contrast tomography and electron backscatter diffraction respectively. Application of the technique promises to provide important insights related to the roles of recrystallization and grain growth on materials properties as well as supporting 3D polycrystalline modelling of materials performance. PMID:26494523

  10. Mapping Nearby Terrain in 3D by Use of a Grid of Laser Spots

    NASA Technical Reports Server (NTRS)

    Padgett, Curtis; Liebe, Carl; Chang, Johnny; Brown, Kenneth

    2007-01-01

    A proposed optoelectronic system, to be mounted aboard an exploratory robotic vehicle, would be used to generate a three-dimensional (3D) map of nearby terrain and obstacles for purposes of navigating the vehicle across the terrain and avoiding the obstacles. The difference between this system and the other systems would lie in the details of implementation. In this system, the illumination would be provided by a laser. The beam from the laser would pass through a two-dimensional diffraction grating, which would divide the beam into multiple beams propagating in different, fixed, known directions. These beams would form a grid of bright spots on the nearby terrain and obstacles. The centroid of each bright spot in the image would be computed. For each such spot, the combination of (1) the centroid, (2) the known direction of the light beam that produced the spot, and (3) the known baseline would constitute sufficient information for calculating the 3D position of the spot.

  11. GPR data processing for 3D fracture mapping in a marble quarry (Thassos, Greece)

    NASA Astrophysics Data System (ADS)

    Grandjean, G.; Gourry, J. C.

    1996-11-01

    Ground Penetrating Radar (GPR) has been successfully applied to detect and map fractures in marble quarries. The aim was to distinguish quickly intact marketable marble areas from fractured ones in order to improve quarry management. The GPR profiling method was chosen because it is non destructive and quickly provides a detailed image of the subsurface. It was performed in domains corresponding to future working areas in real quarry-exploitation conditions. Field surveying and data processing were adapted to the local characteristics of the fractures: E-W orientation, sub-vertical dip, and karst features. After the GPR profiles had been processed, using methods adapted from seismics (amplitude compensation, filtering and Fourier migration), the interpreted fractures from a 12 × 24 × 15 m zone were incorporated into a 3D model. Due to the low electrical conductivity of the marble, GPR provides penetration depths of about 8 and 15 m, and resolutions of about 1 and 5 cm for frequencies of 900 and 300 MHz respectively. The detection power thus seems to be sufficient to recommend use of this method. As requested by the quarriers, the 3D representation can be used directly by themselves to locate high- or low-quality marble areas. Comparison between the observed surface fractures and the fractures detected using GPR showed reasonable correlation.

  12. Transient 3D numerical simulations of column collapse and pyroclastic density current scenarios at Vesuvius

    NASA Astrophysics Data System (ADS)

    Esposti Ongaro, T.; Neri, A.; Menconi, G.; de'Michieli Vitturi, M.; Marianelli, P.; Cavazzoni, C.; Erbacci, G.; Baxter, P. J.

    2008-12-01

    Numerical simulations of column collapse and pyroclastic density current (PDC) scenarios at Vesuvius were carried out using a transient 3D flow model based on multiphase transport laws. The model describes the dynamics of the collapse as well as the effects of the 3D topography of the volcano on PDC propagation. Source conditions refer to a medium-scale sub-Plinian event and consider a pressure-balanced jet. Simulation results provide new insights into the complex dynamics of these phenomena. In particular: 1) column collapse can be characterized by different regimes, from incipient collapse to partial or nearly total collapse, thus confirming the possibility of a transitional field of behaviour of the column characterized by the contemporaneous and/or intermittent occurrence of ash fallout and PDCs; 2) the collapse regime can be characterized by its fraction of eruptive mass reaching the ground and generating PDCs; 3) within the range of the investigated source conditions, the propagation and hazard potential of PDCs appear to be directly correlated with the flow-rate of the mass collapsing to the ground, rather than to the collapse height of the column (this finding is in contrast with predictions based on the energy-line concept, which simply correlates the PDC runout and kinetic energy with the collapse height of the column); 4) first-order values of hazard variables associated with PDCs (i.e., dynamic pressure, temperature, airborne ash concentration) can be derived from simulation results, thereby providing initial estimates for the quantification of damage scenarios; 5) for scenarios assuming a location of the central vent coinciding with that of the present Gran Cono, Mount Somma significantly influences the propagation of PDCs, largely reducing their propagation in the northern sector, and diverting mass toward the west and southeast, accentuating runouts and hazard variables for these sectors; 6) the 2D modelling approximation can force an artificial

  13. 3D mapping of nanoscale electric potentials in semiconductor structures using electron-holographic tomography

    NASA Astrophysics Data System (ADS)

    Wolf, Daniel; Lubk, Axel; Prete, Paola; Lovergine, Nico; Lichte, Hannes

    2016-09-01

    Off-axis electron holography (EH) is a powerful method for mapping projected electric potentials, such as built-in potentials in semiconductor devices, in two dimensions (2D) at nanometer resolution. However, not well-defined thickness profiles, surface effects, and composition changes of the sample under investigation complicate the interpretation of the projected potentials. Here, we demonstrate how these problems can be overcome by combining EH with tomographic techniques, that is, electron holographic tomography (EHT), reconstructing electric potentials in 3D. We present EHT reconstructions of an n-type MOSFET including its dopant-related built-in potentials inside the device, as well as of a GaAs/AlGaAs core-multishell nanowire containing a 5 nm thick quantum well tube.

  14. A 3-D reconstruction solution to current density imaging based on acoustoelectric effect by deconvolution: a simulation study.

    PubMed

    Yang, Renhuan; Li, Xu; Song, Aiguo; He, Bin; Yan, Ruqiang

    2013-05-01

    Hybrid imaging modality combining ultrasound scanning and electrical current density imaging through the acoustoelectric (AE) effect may potentially provide solutions to imaging electrical activities and properties of biological tissues with high spatial resolution. In this study, a 3-D reconstruction solution to ultrasound current source density imaging (UCSDI) by means of Wiener deconvolution is proposed and evaluated through computer simulations. As compared to previous 2-D UCSDI problem, in a 3-D volume conductor with broadly distributed current density field, the AE signal becomes a 3-D convolution between the electric field and the acoustic field, and effective 3-D reconstruction algorithm has not been developed so far. In the proposed method, a 3-D ultrasound scanning is performed while the corresponding AE signals are collected from multiple electrode pairs attached on the surface of the imaging object. From the collected AE signals, the acoustic field and electric field were first decoupled by Wiener deconvolution. Then, the current density distribution was reconstructed by inverse projection. Our simulations using artificial current fields in homogeneous phantoms suggest that the proposed method is feasible and robust against noise. It is also shown that using the proposed method, it is feasible to reconstruct 3-D current density distribution in an inhomogeneous conductive medium.

  15. 3D-Mapping of Dolomitized Structures in Lower Cambrian Phosphorites

    NASA Astrophysics Data System (ADS)

    Hippler, Dorothee; Stammeier, Jessica A.; Brunner, Roland; Rosc, Jördis; Franz, Gerhard; Dietzel, Martin

    2016-04-01

    Dolomitization is a widespread phenomenon in ancient sedimentary rocks, particularly close to the Precambrian-Cambrian boundary. Dolomite can form in synsedimentary or hydrothermal environments, preferentially via the replacement of solid carbonate precursor phases. Synsedimentary dolomite formation is often associated with microbial activity, such as bacterial sulfate reduction or methanogenesis. In this study, we investigate dolomitic phosphorites from the Lowermost Cambrian Tal Group, Mussoori Syncline, Lesser Himalaya, India, using micro-CT 3D-mapping, in order to unravel the complex diagenetic history of the rocks. The selected sample shows alternating layering of phosphatic mudstones and sparitic dolostone, in which brecciated layers of phosphorite or phosphatic mudstones are immersed in a dolomite-rich matrix. Lamination occurs on a sub-millimetre scale, with lamination sometimes wavy to crinkly. This fabric is interpreted as former microbial mats, providing the environment for early diagenetic phosphatization. Preliminary electron backscatter imaging with scanning microscopy revealed that dolomite crystals often occur in spherical to ellipsoidal structures, typically with a high porosity. This dolomite is associated with botryoidal apatite, organic matter and small amounts of calcite. Micro-CT 3D-mappings reveal that dolomite structures are cigar-shaped, elongated and up to 600 μm long. They are further arranged in a Mikado-like oriented framework spanning a layer thickness of a few millimetres. Analyses of ambient pore space, with similar elongated outlines and filled with organic matter, suggest a potential coherence of ambient pore space and shape of the dolomite structures. Allowing for other associated mineral phases, such as pyrite and silicates, and their spatial distribution, the present approach can be used to unravel distinct diagenetic reaction pathways, and might thus constrain the proxy potential of these Lower Cambrian dolomitic phosphorites

  16. True-3D accentuating of grids and streets in urban topographic maps enhances human object location memory.

    PubMed

    Edler, Dennis; Bestgen, Anne-Kathrin; Kuchinke, Lars; Dickmann, Frank

    2015-01-01

    Cognitive representations of learned map information are subject to systematic distortion errors. Map elements that divide a map surface into regions, such as content-related linear symbols (e.g. streets, rivers, railway systems) or additional artificial layers (coordinate grids), provide an orientation pattern that can help users to reduce distortions in their mental representations. In recent years, the television industry has started to establish True-3D (autostereoscopic) displays as mass media. These modern displays make it possible to watch dynamic and static images including depth illusions without additional devices, such as 3D glasses. In these images, visual details can be distributed over different positions along the depth axis. Some empirical studies of vision research provided first evidence that 3D stereoscopic content attracts higher attention and is processed faster. So far, the impact of True-3D accentuating has not yet been explored concerning spatial memory tasks and cartography. This paper reports the results of two empirical studies that focus on investigations whether True-3D accentuating of artificial, regular overlaying line features (i.e. grids) and content-related, irregular line features (i.e. highways and main streets) in official urban topographic maps (scale 1/10,000) further improves human object location memory performance. The memory performance is measured as both the percentage of correctly recalled object locations (hit rate) and the mean distances of correctly recalled objects (spatial accuracy). It is shown that the True-3D accentuating of grids (depth offset: 5 cm) significantly enhances the spatial accuracy of recalled map object locations, whereas the True-3D emphasis of streets significantly improves the hit rate of recalled map object locations. These results show the potential of True-3D displays for an improvement of the cognitive representation of learned cartographic information.

  17. True-3D Accentuating of Grids and Streets in Urban Topographic Maps Enhances Human Object Location Memory

    PubMed Central

    Edler, Dennis; Bestgen, Anne-Kathrin; Kuchinke, Lars; Dickmann, Frank

    2015-01-01

    Cognitive representations of learned map information are subject to systematic distortion errors. Map elements that divide a map surface into regions, such as content-related linear symbols (e.g. streets, rivers, railway systems) or additional artificial layers (coordinate grids), provide an orientation pattern that can help users to reduce distortions in their mental representations. In recent years, the television industry has started to establish True-3D (autostereoscopic) displays as mass media. These modern displays make it possible to watch dynamic and static images including depth illusions without additional devices, such as 3D glasses. In these images, visual details can be distributed over different positions along the depth axis. Some empirical studies of vision research provided first evidence that 3D stereoscopic content attracts higher attention and is processed faster. So far, the impact of True-3D accentuating has not yet been explored concerning spatial memory tasks and cartography. This paper reports the results of two empirical studies that focus on investigations whether True-3D accentuating of artificial, regular overlaying line features (i.e. grids) and content-related, irregular line features (i.e. highways and main streets) in official urban topographic maps (scale 1/10,000) further improves human object location memory performance. The memory performance is measured as both the percentage of correctly recalled object locations (hit rate) and the mean distances of correctly recalled objects (spatial accuracy). It is shown that the True-3D accentuating of grids (depth offset: 5 cm) significantly enhances the spatial accuracy of recalled map object locations, whereas the True-3D emphasis of streets significantly improves the hit rate of recalled map object locations. These results show the potential of True-3D displays for an improvement of the cognitive representation of learned cartographic information. PMID:25679208

  18. Enabling 3D-Liver Perfusion Mapping from MR-DCE Imaging Using Distributed Computing.

    PubMed

    Leporq, Benjamin; Camarasu-Pop, Sorina; Davila-Serrano, Eduardo E; Pilleul, Frank; Beuf, Olivier

    2013-01-01

    An MR acquisition protocol and a processing method using distributed computing on the European Grid Infrastructure (EGI) to allow 3D liver perfusion parametric mapping after Magnetic Resonance Dynamic Contrast Enhanced (MR-DCE) imaging are presented. Seven patients (one healthy control and six with chronic liver diseases) were prospectively enrolled after liver biopsy. MR-dynamic acquisition was continuously performed in free-breathing during two minutes after simultaneous intravascular contrast agent (MS-325 blood pool agent) injection. Hepatic capillary system was modeled by a 3-parameters one-compartment pharmacokinetic model. The processing step was parallelized and executed on the EGI. It was modeled and implemented as a grid workflow using the Gwendia language and the MOTEUR workflow engine. Results showed good reproducibility in repeated processing on the grid. The results obtained from the grid were well correlated with ROI-based reference method ran locally on a personal computer. The speed-up range was 71 to 242 with an average value of 126. In conclusion, distributed computing applied to perfusion mapping brings significant speed-up to quantification step to be used for further clinical studies in a research context. Accuracy would be improved with higher image SNR accessible on the latest 3T MR systems available today.

  19. The Derivation of Fault Volumetric Properties from 3D Trace Maps Using Outcrop Constrained Discrete Fracture Network Models

    NASA Astrophysics Data System (ADS)

    Hodgetts, David; Seers, Thomas

    2015-04-01

    Fault systems are important structural elements within many petroleum reservoirs, acting as potential conduits, baffles or barriers to hydrocarbon migration. Large, seismic-scale faults often serve as reservoir bounding seals, forming structural traps which have proved to be prolific plays in many petroleum provinces. Though inconspicuous within most seismic datasets, smaller subsidiary faults, commonly within the damage zones of parent structures, may also play an important role. These smaller faults typically form narrow, tabular low permeability zones which serve to compartmentalize the reservoir, negatively impacting upon hydrocarbon recovery. Though considerable improvements have been made in the visualization field to reservoir-scale fault systems with the advent of 3D seismic surveys, the occlusion of smaller scale faults in such datasets is a source of significant uncertainty during prospect evaluation. The limited capacity of conventional subsurface datasets to probe the spatial distribution of these smaller scale faults has given rise to a large number of outcrop based studies, allowing their intensity, connectivity and size distributions to be explored in detail. Whilst these studies have yielded an improved theoretical understanding of the style and distribution of sub-seismic scale faults, the ability to transform observations from outcrop to quantities that are relatable to reservoir volumes remains elusive. These issues arise from the fact that outcrops essentially offer a pseudo-3D window into the rock volume, making the extrapolation of surficial fault properties such as areal density (fracture length per unit area: P21), to equivalent volumetric measures (i.e. fracture area per unit volume: P32) applicable to fracture modelling extremely challenging. Here, we demonstrate an approach which harnesses advances in the extraction of 3D trace maps from surface reconstructions using calibrated image sequences, in combination with a novel semi

  20. Beyond optical molasses: 3D raman sideband cooling of atomic cesium to high phase-space density

    PubMed

    Kerman; Vuletic; Chin; Chu

    2000-01-17

    We demonstrate a simple, general purpose method to cool neutral atoms. A sample containing 3x10(8) cesium atoms prepared in a magneto-optical trap is cooled and simultaneously spin polarized in 10 ms at a density of 1.1x10(11) cm (-3) to a phase space density nlambda(3)(dB) = 1/500, which is almost 3 orders of magnitude higher than attainable in free space with optical molasses. The technique is based on 3D degenerate Raman sideband cooling in optical lattices and remains efficient even at densities where the mean lattice site occupation is close to unity.

  1. Determining the 3D Subsurface Density Structure of Taurus Littrow Valley Using Apollo 17 Gravity Data

    NASA Technical Reports Server (NTRS)

    Urbancic, N.; Ghent, R.; Stanley, S,; Johnson, C. L.; Carroll, K. A.; Hatch, D.; Williamson, M. C.; Garry, W. B.; Talwani, M.

    2016-01-01

    Surface gravity surveys can detect subsurface density variations that can reveal subsurface geologic features. In 1972, the Apollo 17 (A17) mission conducted the Traverse Gravimeter Experiment (TGE) using a gravimeter that measured the local gravity field near Taurus Littrow Valley (TLV), located on the south-eastern rim of the Serenitatis basin. TLV is hypothesized to be a basaltfilled radial graben resulting from the impact that formed Mare Serenitatis. It is bounded by both the North and South Massifs (NM and SM) as well as other smaller mountains to the East that are thought to be mainly composed of brecciated highland material. The TGE is the first and only successful gravity survey on the surface of the Moon. Other more recent satellite surveys, such as NASA's Gravity Recovery and Interior Laboratory (GRAIL) mission (2011- 2012), have produced the best global gravity field to date (approx. 13km resolution). However, these satellite surveys are not sensitive enough to detect fine-scale (<1km) lunar subsurface structures. This underscores the value of the data collected at the surface by A17. In the original analysis of the data a 2D forward-modelling approach was used to derive a thickness of the subsurface basalt layer of 1.0 km by assuming a simple flat-faced rectangular geometry and using densities derived from Apollo lunar samples. We are investigating whether modern 3D modelling techniques in combination with high-resolution topographical and image datasets can reveal additional fine-scale subsurface structure in TLV.

  2. First 3D thermal mapping of an active volcano using an advanced photogrammetric method

    NASA Astrophysics Data System (ADS)

    Antoine, Raphael; Baratoux, David; Lacogne, Julien; Lopez, Teodolina; Fauchard, Cyrille; Bretar, Frédéric; Arab-Sedze, Mélanie; Staudacher, Thomas; Jacquemoud, Stéphane; Pierrot-Deseilligny, Marc

    2014-05-01

    Thermal infrared data obtained in the [7-14 microns] spectral range are usually used in many Earth Science disciplines. These studies are exclusively based on the analysis of 2D information. In this case, a quantitative analysis of the surface energy budget remains limited, as it may be difficult to estimate the radiative contribution of the topography, the thermal influence of winds on the surface or potential imprints of subsurface flows on the soil without any precise DEM. The draping of a thermal image on a recent DEM is a common method to obtain a 3D thermal map of a surface. However, this method has many disadvantages i) errors can be significant in the orientation process of the thermal images, due to the lack of tie points between the images and the DEM; ii) the use of a recent DEM implies the use of another remote sensing technique to quantify the topography; iii) finally, the characterization of the evolution of a surface requires the simultaneous acquisition of thermal data and topographic information, which may be expensive in most cases. The stereophotogrammetry method allows to reconstitute the relief of an object from photos taken from different positions. Recently, substantial progress have been realized in the generation of high spatial resolution topographic surfaces using stereophotogrammetry. However, the presence of shadows, homogeneous textures and/or weak contrasts in the visible spectrum (e.g., flowing lavas, uniform lithologies) may prevent from the use of such method, because of the difficulties to find tie points on each image. Such situations are more favorable in the thermal infrared spectrum, as any variation in the thermal properties or geometric orientation of the surfaces may induce temperature contrasts that are detectable with a thermal camera. This system, usually functioning with a array sensor (Focal Plane Array) and an optical device, have geometric characteristics that are similar to digital cameras. Thus, it may be possible

  3. Developed Design for Humeral Head Replacement Using 3D Surface Mapping

    NASA Astrophysics Data System (ADS)

    Salah, H. R.

    2014-12-01

    Assessment of dimensional and geometrical data on the humeral head replacement (HHR) objects is essential for solving the relevant designing problems in the physics of reverse engineering (RE). In this work, 2D-assessment for human humerus was performed using the computed tomography (CT) technique within the RE plan, after which the 2D images of humeral objects were converted into 3D images. The conversion was successful and indicated a clear difference in the 2D and 3D estimates of sizes and geometry of the humerus. The authors have analyzed and confirmed experimentally the statistical information on the relevant anatomical objects. The results of finite-element simulation of the compressive stresses affecting the geometry of 3D surface mapping were analyzed using SolidWorks software. For developing the biomechanical design of an HHR object suitable biomaterials were selected, and different metal-based biomaterials are discussed as applied at various loads. New methodology is presented for the size estimation of humeral head - both anatomical and artificial - in 3D-shape. A detailed interpretation is given for the results of CT D-measurements. Izmēru un ģeometrisko datu novērtējums, kas attiecas uz pleca kaula galviņas nomaiņas (PKGN) objektiem, nepieciešams, lai risinātu virkni reversīvās inženierijas (RI) problēmu. Šajā darbā cilvēka pleca kaula galviņas divdimensiju novērtējums tika veikts ar datortomogrāfijas palīdzību (RI) ietvaros, un pēc tam objekta divdimensiju attēlojums tika pārveidots trīsdimensiju. Pārveidojums bija sekmīgs, parādot pleca kaula galviņas izmēru un ģeometrijas atšķirības starp 2D un 3D novērtējumiem. Autori izanalizēja un eksperimentāli apstiprināja statistisko informāciju pēc dotā veida anatomiskiem objektiem. Saspiešanas sasprindzinājumi, kuri ietekmē trīsdimensiju virsmas attēlojuma ģeometriju, tika analizēti ar gala-elementu simulācijas metodi, lietojot programmu Solid

  4. Calculation of the nuclear material inventory in a sealed vault by 3D radiation mapping

    SciTech Connect

    Adsley, Ian; Klepikov, Alexander; Tur, Yevgeniy; Wells, David

    2013-07-01

    The paper relates to the determination of the amount of nuclear material contained in a closed, concrete lined vault at the Aktau fast breeder reactor in Kazakhstan. This material had been disposed into the vault after examination in an experimental hot cell directly above the vault. In order to comply with IAEA Safeguards requirements it was necessary to determine the total quantities of nuclear materials - enriched uranium and plutonium - that were held with Kazakhstan. Although it was possible to determine the inventory of all of the accessible nuclear material - the quantity remaining in the vault was unknown. As part of the Global Threat Reduction Programme the UK Government funded a project to determine the inventory of these nuclear materials in this vault. This involved drilling three penetrations through the concrete lined roof of the vault; this enabled the placement of lights and a camera into the vault through two penetrations; while the third penetration enabled a lightweight manipulator arm to be introduced into the vault. This was used to provide a detailed 3D mapping of the dose rate within the vault and it also enabled the collection of samples for radionuclide analysis. The deconvolution of the 3D dose rate profile within the vault enabled the determination of the gamma emitting source distribution on the floor and walls of the vault. The samples were analysed to determine the fingerprint of those radionuclides producing the gamma dose - namely {sup 137}Cs and {sup 60}Co - to the nuclear materials. The combination of the dose rate source terms on the surfaces of the vault and the fingerprint then enabled the quantities of nuclear materials to be determined. The project was a major success and enabled the Kazakhstan Government to comply with IAEA Safeguards requirements. It also enabled the UK DECC Ministry to develop a technology of national (and international) use. Finally the technology was well received by IAEA Safeguards as an acceptable

  5. 3D Inversion of Gravity Anomalies for the Interpretation of Sedimentary Basins using Variable Density Contrast

    NASA Astrophysics Data System (ADS)

    Ekinci, Yunus Levent; Ertekin, Can

    2015-04-01

    Concern about sedimentary basins is generally related to their genetic and economic significance. Analysis of sedimentary basins requires the acquisition of data through outcrop studies and subsurface investigations that encompass drilling and geophysics. These data are commonly analysed by computer-assisted techniques. One of these methods is based on analysing gravity anomalies to compute the depth of sedimentary basin-basement rock interface. Sedimentary basins produce negative gravity anomalies, because they have mostly lower densities than that of the surrounding basement rocks. Density variations in a sedimentary fill increase rapidly at shallower depths then gradually reach the density of surrounding basement rocks due to the geostatic pressure i.e. compaction. The decrease of the density contrast can be easily estimated by a quadratic function. Hence, if the densities are chosen properly and the regional background is removed correctly, the topographical relief of the sedimentary basin-basement rock interface might be estimated by the inversion of the gravity data using an exponential density-depth relation. Three dimensional forward modelling procedure can be carried out by introducing a Cartesian coordinate system, and placing vertical prisms just below observation points on the grid plane. Depth to the basement, namely depths to the bottom of the vertical prisms are adjusted in an iterative manner by minimizing the differences between measured and calculated residual gravity anomalies. In this study, we present a MATLAB-based inversion code for the interpretation of sedimentary basins by approximating the topographical relief of sedimentary basin-basement rock interfaces. For a given gridded residual gravity anomaly map, the procedure estimates the bottom depths of vertical prisms by considering some published formulas and assumptions. The utility of the developed inversion code was successfully tested on theoretically produced gridded gravity data set

  6. Role of head of turbulent 3-D density currents in mixing during slumping regime

    NASA Astrophysics Data System (ADS)

    Bhaganagar, Kiran

    2017-02-01

    A fundamental study was conducted to shed light on entrainment and mixing in buoyancy-driven Boussinesq density currents. Large-eddy simulation was performed on lock-exchange (LE) release density currents—an idealized test bed to generate density currents. As dense fluid was released over a sloping surface into an ambient lighter fluid, the dense fluid slumps to the bottom and forms a characteristic head of the current. The dynamics of the head dictated the mixing processes in LE currents. The key contribution of this study is to resolve an ongoing debate on mixing: We demonstrate that substantial mixing occurs in the early stages of evolution in an LE experiment and that entrainment is highly inhomogeneous and unsteady during the slumping regime. Guided by the flow physics, entrainment is calculated using two different but related perspectives. In the first approach, the entrainment parameter (E) is defined as the fraction of ambient fluid displaced by the head that entrains into the current. It is an indicator of the efficiency in which ambient fluid is displaced into the current and it serves as an important metric to compare the entrainment of dense currents over different types of surfaces, e.g., roughness configuration. In the second approach, E measures the net entrainment in the current at an instantaneous time t over the length of the current. Net entrainment coefficient is a metric to compare the effects of flow dynamical conditions, i.e., lock-aspect ratio that dictates the fraction of buoyancy entering the head, and also the effect of the sloping angle. Together, the entrainment coefficient and the net entrainment coefficient provide an insight into the entrainment process. The "active" head of the current acts as an engine that mixes the ambient fluid with the existing dense fluid, the 3-D lobes and clefts on the frontal end of the current causes recirculation of the ambient fluid into the current, and Kelvin-Helmholtz rolls are the mixers that

  7. Observation of toroidal variation of density gradients and turbulence in DIII-D with 3D fields during ELM suppression

    NASA Astrophysics Data System (ADS)

    Wilcox, R. S.; Schafer, M. W.; Canik, J. M.; Unterberg, E. A.; Wingen, A.; Ferraro, N. M.; McKee, G. R.; Zeng, L.; Rhodes, T. L.

    2016-10-01

    Significant 3D variation in broadband density fluctuations is observed using beam emission spectroscopy and Doppler backscattering near the boundary of weakly 3D plasmas in DIII-D when non-axisymmetric fields are applied to suppress ELMs. The increase in fluctuations is concomitant with an increase in the density gradient measured using profile reflectometry, suggesting that this toroidally localized density gradient could be a mechanism for turbulence destabilization in localized flux tubes. Although changes to magnetic surface topology are shown to be too small to affect turbulence stability directly, two-fluid M3D-C1 simulations find that there is a significant 3D variation of density within flux surfaces in the pedestal. These modeled local density changes modify the local pressure- and density- gradient scale lengths, and measured turbulence is shown to increase on flux tubes with larger gradients. Work supported by the US DOE under contracts DE-AC05-00OR22725, DE-AC02-09CH11466, DE-FG02-08ER54999 and DE-FG02-08ER54984.

  8. The performance of semilocal and hybrid density functionals in 3d transition-metal chemistry

    NASA Astrophysics Data System (ADS)

    Furche, Filipp; Perdew, John P.

    2006-01-01

    We investigate the performance of contemporary semilocal and hybrid density functionals for bond energetics, structures, dipole moments, and harmonic frequencies of 3d transition-metal (TM) compounds by comparison with gas-phase experiments. Special attention is given to the nonempirical metageneralized gradient approximation (meta-GGA) of Tao, Perdew, Staroverov, and Scuseria (TPSS) [Phys. Rev. Lett. 91, 146401 (2003)], which has been implemented in TURBOMOLE for the present work. Trends and error patterns for classes of homologous compounds are analyzed, including dimers, monohydrides, mononitrides, monoxides, monofluorides, polyatomic oxides and halogenides, carbonyls, and complexes with organic π ligands such as benzene and cyclopentadienyl. Weakly bound systems such as Ca2, Mn2, and Zn2 are discussed. We propose a reference set of reaction energies for benchmark purposes. Our all-electron results with quadruple zeta valence basis sets validate semilocal density-functional theory as the workhorse of computational TM chemistry. Typical errors in bond energies are substantially larger than in (organic) main group chemistry, however. The Becke-Perdew'86 [Phys. Rev. A 38, 3098 (1988); Phys. Rev. B 33, 8822 (1986)] GGA and the TPSS meta-GGA have the best price/performance ratio, while the TPSS hybrid functional achieves a slightly lower mean absolute error in bond energies. The popular Becke three-parameter hybrid B3LYP underbinds significantly and tends to overestimate bond distances; we give a possible explanation for this. We further show that hybrid mixing does not reduce the width of the error distribution on our reference set. The error of a functional for the s-d transfer energy of a TM atom does not predict its error for TM bond energies and bond lengths. For semilocal functionals, self-interaction error in one- and three-electron bonds appears to be a major source of error in TM reaction energies. Nevertheless, TPSS predicts the correct ground

  9. Determination of a new uniform thorax density representative of the living population from 3D external body shape modeling.

    PubMed

    Amabile, Celia; Choisne, Julie; Nérot, Agathe; Pillet, Hélène; Skalli, Wafa

    2016-05-03

    Body segment parameters (BSP) for each body׳s segment are needed for biomechanical analysis. To provide population-specific BSP, precise estimation of body׳s segments volume and density are needed. Widely used uniform densities, provided by cadavers׳ studies, did not consider the air present in the lungs when determining the thorax density. The purpose of this study was to propose a new uniform thorax density representative of the living population from 3D external body shape modeling. Bi-planar X-ray radiographies were acquired on 58 participants allowing 3D reconstructions of the spine, rib cage and human body shape. Three methods of computing the thorax mass were compared for 48 subjects: (1) the Dempster Uniform Density Method, currently in use for BSPs calculation, using Dempster density data, (2) the Personalized Method using full-description of the thorax based on 3D reconstruction of the rib cage and spine and (3) the Improved Uniform Density Method using a uniform thorax density resulting from the Personalized Method. For 10 participants, comparison was made between the body mass obtained from a force-plate and the body mass computed with each of the three methods. The Dempster Uniform Density Method presented a mean error of 4.8% in the total body mass compared to the force-plate vs 0.2% for the Personalized Method and 0.4% for the Improved Uniform Density Method. The adjusted thorax density found from the 3D reconstruction was 0.74g/cm(3) for men and 0.73g/cm(3) for women instead of the one provided by Dempster (0.92g/cm(3)), leading to a better estimate of the thorax mass and body mass.

  10. New non-Doppler remote sensing technique for 3D wind field mapping

    NASA Astrophysics Data System (ADS)

    Belen'kii, Mikhail S.; Gimmestad, Gary G.; Gurvich, Alexander V.

    1994-06-01

    A new approach to the statistical analysis of fluctuating, photon-limited signals that permits us to accumulate and process the lidar returns without averaging of the reflected energy fluctuations is developed. This approach requires recording the photocounts for each pulse in a series of pulses and then determining photocount statistics. Based on the semiclassical theory of photodetection and Mandel's formula, a relationship has been obtained between the time-space cross correlation function and the cross spectrum of the lidar returns and corresponding photocount statistics. It is shown that the relative uncertainties of measuring the cross correlation or the cross spectrum of the lidar returns is determined by the general number of photocounts, but not by their mean value. A fast-scanning lidar system, which is based on a new photocounting analysis approach, is described for 3D wind field mapping in the atmosphere at altitudes up to 5 km. A program for the experimental verification of the new approach is presented.

  11. Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information

    PubMed Central

    Blouin, Christian; Boucher, Yan; Roger, Andrew J.

    2003-01-01

    Comparative sequence analysis has been used to study specific questions about the structure and function of proteins for many years. Here we propose a knowledge-based framework in which the maximum likelihood rate of evolution is used to quantify the level of constraint on the identity of a site. We demonstrate that site-rate mapping on 3D structures using datasets of rhodopsin-like G-protein receptors and α- and β-tubulins provides an excellent tool for pinpointing the functional features shared between orthologous and paralogous proteins. In addition, functional divergence within protein families can be inferred by examining the differences in the site rates, the differences in the chemical properties of the side chains or amino acid usage between aligned sites. Two novel analytical methods are introduced to characterize rate- independent functional divergence. These are tested using a dataset of two classes of HMG-CoA reductases for which only one class can perform both the forward and reverse reaction. We show that functionally divergent sites occur in a cluster of sites interacting with the catalytic residues and that this information should facilitate the design of experimental strategies to directly test functional properties of residues. PMID:12527789

  12. Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information.

    PubMed

    Blouin, Christian; Boucher, Yan; Roger, Andrew J

    2003-01-15

    Comparative sequence analysis has been used to study specific questions about the structure and function of proteins for many years. Here we propose a knowledge-based framework in which the maximum likelihood rate of evolution is used to quantify the level of constraint on the identity of a site. We demonstrate that site-rate mapping on 3D structures using datasets of rhodopsin-like G-protein receptors and alpha- and beta-tubulins provides an excellent tool for pinpointing the functional features shared between orthologous and paralogous proteins. In addition, functional divergence within protein families can be inferred by examining the differences in the site rates, the differences in the chemical properties of the side chains or amino acid usage between aligned sites. Two novel analytical methods are introduced to characterize rate- independent functional divergence. These are tested using a dataset of two classes of HMG-CoA reductases for which only one class can perform both the forward and reverse reaction. We show that functionally divergent sites occur in a cluster of sites interacting with the catalytic residues and that this information should facilitate the design of experimental strategies to directly test functional properties of residues.

  13. 3-D modeling useful tool for planning. [mapping groundwater and soil pollution and subsurface features

    SciTech Connect

    Calmbacher, C.W. )

    1992-12-01

    Visualizing and delineating subsurface geological features, groundwater contaminant plumes, soil contamination, geological faults, shears and other features can prove invaluable to environmental consultants, engineers, geologists and hydrogeologists. Three-dimensional modeling is useful for a variety of applications from planning remediation to site planning design. The problem often is figuring out how to convert drilling logs, map lists or contaminant levels from soil and groundwater into a 3-D model. Three-dimensional subsurface modeling is not a new requirement, but a flexible, easily applied method of developing such models has not always been readily available. LYNX Geosystems Inc. has developed the Geoscience Modeling System (GMS) in answer to the needs of those regularly having to do three-dimensional geostatistical modeling. The GMS program has been designed to allow analysis, interpretation and visualization of complex geological features and soil and groundwater contamination. This is a powerful program driven by a 30 volume modeling technology engine. Data can be entered, stored, manipulated and analyzed in ways that will present very few limitations to the user. The program has selections for Geoscience Data Management, Geoscience Data Analysis, Geological Modeling (interpretation and analysis), Geostatistical Modeling and an optional engineering component.

  14. Euro-Maps 3D- A Transnational, High-Resolution Digital Surface Model For Europe

    NASA Astrophysics Data System (ADS)

    Uttenthaler, A.; Barner, F.; Hass, T.; Makiola, J.; d'Angelo, P.; Reinartz, P.; Carl, S.; Steiner, K.

    2013-12-01

    Euro-Maps 3D is a homogeneous 5 m spaced digital surface model (DSM) semi-automatically derived by Euromap from 2.5 m in-flight stereo data provided by the Indian IRS-P5 Cartosat-1 satellite. This new and innovative product has been developed in close co- operation with the Remote Sensing Technology Institute (IMF) of the German Aerospace Center (DLR) and is being jointly exploited. The very detailed and accurate representation of the surface is achieved by using a sophisticated and well adapted algorithm implemented on the basis of the Semi-Global Matching approach. In addition, the final product includes detailed flanking information consisting of several pixel-based quality and traceability layers also including an ortho layer. The product is believed to provide maximum accuracy and transparency. The DSM product meets and exceeds HRE80 qualification standards. The DSM product will be made available transnational in a homogeneous quality for most parts of Europe, North Africa and Turkey by Euromap step-by-step. Other areas around the world are processed on demand.

  15. 3-D pain drawings and seating pressure maps: relationships and challenges.

    PubMed

    Spyridonis, Fotios; Ghinea, Gheorghita

    2011-05-01

    Mobility impaired people constitute a significant portion of the adult population, which often experience back pain at some point during their lifetime. Such pain is usually characterized by severe implications reflected on both their personal lives, as well as on a country's health and economic systems. The traditional 2-D representations of the human body often used can be limited in their ability to efficiently visualize such pain for diagnosis purposes. Yet, patients have been shown to prefer such drawings. However, considering that pain is a feeling or emotion that is subjective in nature, the pain drawings could be consequently regarded as a subjective means of communicating such pain. As a result, the study described in this paper proposes an alternative, which encompasses a 3-D pain visualization solution, developed in a previous work of ours. This alternative is complemented with the upcoming technique of pressure mapping for more objectivity in the pain data collection. The results of this study have shown that the proposed approach is a promising solution for the purpose intended, and it could generally prove to be a significant complementary method in the area of medical practice for the mobility impaired community.

  16. Denosumab rapidly increases cortical bone in key locations of the femur: a 3D bone mapping study in women with osteoporosis.

    PubMed

    Poole, Kenneth E S; Treece, Graham M; Gee, Andrew H; Brown, Jacques P; McClung, Michael R; Wang, Andrea; Libanati, Cesar

    2015-01-01

    Women with osteoporosis treated for 36 months with twice-yearly injections of denosumab sustained fewer hip fractures compared with placebo. Treatment might improve femoral bone at locations where fractures typically occur. To test this hypothesis, we used 3D cortical bone mapping of postmenopausal women with osteoporosis to investigate the timing and precise location of denosumab versus placebo effects in the hips. We analyzed clinical computed tomography scans from 80 female participants in FREEDOM, a randomized trial, wherein half of the study participants received subcutaneous denosumab 60 mg twice yearly and the others received placebo. Cortical 3D bone thickness maps of both hips were created from scans at baseline, 12, 24, and 36 months. Cortical mass surface density maps were also created for each visit. After registration of each bone to an average femur shape model followed by statistical parametric mapping, we visualized and quantified statistically significant treatment effects. The technique allowed us to pinpoint systematic differences between denosumab and control and to display the results on a 3D average femur model. Denosumab treatment led to an increase in femoral cortical mass surface density and thickness, already evident by the third injection (12 months). Overall, treatment with denosumab increased femoral cortical mass surface density by 5.4% over 3 years. One-third of the increase came from increasing cortical density, and two-thirds from increasing cortical thickness, relative to placebo. After 36 months, cortical mass surface density and thickness had increased by up to 12% at key locations such as the lateral femoral trochanter versus placebo. Most of the femoral cortex displayed a statistically significant relative difference by 36 months. Osteoporotic cortical bone responds rapidly to denosumab therapy, particularly in the hip trochanteric region. This mechanism may be involved in the robust decrease in hip fractures observed in

  17. Three-Dimensional Mapping of Soil Chemical Characteristics at Micrometric Scale by Combining 2D SEM-EDX Data and 3D X-Ray CT Images

    PubMed Central

    Hapca, Simona; Baveye, Philippe C.; Wilson, Clare; Lark, Richard Murray; Otten, Wilfred

    2015-01-01

    There is currently a significant need to improve our understanding of the factors that control a number of critical soil processes by integrating physical, chemical and biological measurements on soils at microscopic scales to help produce 3D maps of the related properties. Because of technological limitations, most chemical and biological measurements can be carried out only on exposed soil surfaces or 2-dimensional cuts through soil samples. Methods need to be developed to produce 3D maps of soil properties based on spatial sequences of 2D maps. In this general context, the objective of the research described here was to develop a method to generate 3D maps of soil chemical properties at the microscale by combining 2D SEM-EDX data with 3D X-ray computed tomography images. A statistical approach using the regression tree method and ordinary kriging applied to the residuals was developed and applied to predict the 3D spatial distribution of carbon, silicon, iron, and oxygen at the microscale. The spatial correlation between the X-ray grayscale intensities and the chemical maps made it possible to use a regression-tree model as an initial step to predict the 3D chemical composition. For chemical elements, e.g., iron, that are sparsely distributed in a soil sample, the regression-tree model provides a good prediction, explaining as much as 90% of the variability in some of the data. However, for chemical elements that are more homogenously distributed, such as carbon, silicon, or oxygen, the additional kriging of the regression tree residuals improved significantly the prediction with an increase in the R2 value from 0.221 to 0.324 for carbon, 0.312 to 0.423 for silicon, and 0.218 to 0.374 for oxygen, respectively. The present research develops for the first time an integrated experimental and theoretical framework, which combines geostatistical methods with imaging techniques to unveil the 3-D chemical structure of soil at very fine scales. The methodology presented

  18. Three-Dimensional Mapping of Soil Chemical Characteristics at Micrometric Scale by Combining 2D SEM-EDX Data and 3D X-Ray CT Images.

    PubMed

    Hapca, Simona; Baveye, Philippe C; Wilson, Clare; Lark, Richard Murray; Otten, Wilfred

    2015-01-01

    There is currently a significant need to improve our understanding of the factors that control a number of critical soil processes by integrating physical, chemical and biological measurements on soils at microscopic scales to help produce 3D maps of the related properties. Because of technological limitations, most chemical and biological measurements can be carried out only on exposed soil surfaces or 2-dimensional cuts through soil samples. Methods need to be developed to produce 3D maps of soil properties based on spatial sequences of 2D maps. In this general context, the objective of the research described here was to develop a method to generate 3D maps of soil chemical properties at the microscale by combining 2D SEM-EDX data with 3D X-ray computed tomography images. A statistical approach using the regression tree method and ordinary kriging applied to the residuals was developed and applied to predict the 3D spatial distribution of carbon, silicon, iron, and oxygen at the microscale. The spatial correlation between the X-ray grayscale intensities and the chemical maps made it possible to use a regression-tree model as an initial step to predict the 3D chemical composition. For chemical elements, e.g., iron, that are sparsely distributed in a soil sample, the regression-tree model provides a good prediction, explaining as much as 90% of the variability in some of the data. However, for chemical elements that are more homogenously distributed, such as carbon, silicon, or oxygen, the additional kriging of the regression tree residuals improved significantly the prediction with an increase in the R2 value from 0.221 to 0.324 for carbon, 0.312 to 0.423 for silicon, and 0.218 to 0.374 for oxygen, respectively. The present research develops for the first time an integrated experimental and theoretical framework, which combines geostatistical methods with imaging techniques to unveil the 3-D chemical structure of soil at very fine scales. The methodology presented

  19. Enhanced RGB-D Mapping Method for Detailed 3D Indoor and Outdoor Modeling

    PubMed Central

    Tang, Shengjun; Zhu, Qing; Chen, Wu; Darwish, Walid; Wu, Bo; Hu, Han; Chen, Min

    2016-01-01

    RGB-D sensors (sensors with RGB camera and Depth camera) are novel sensing systems that capture RGB images along with pixel-wise depth information. Although they are widely used in various applications, RGB-D sensors have significant drawbacks including limited measurement ranges (e.g., within 3 m) and errors in depth measurement increase with distance from the sensor with respect to 3D dense mapping. In this paper, we present a novel approach to geometrically integrate the depth scene and RGB scene to enlarge the measurement distance of RGB-D sensors and enrich the details of model generated from depth images. First, precise calibration for RGB-D Sensors is introduced. In addition to the calibration of internal and external parameters for both, IR camera and RGB camera, the relative pose between RGB camera and IR camera is also calibrated. Second, to ensure poses accuracy of RGB images, a refined false features matches rejection method is introduced by combining the depth information and initial camera poses between frames of the RGB-D sensor. Then, a global optimization model is used to improve the accuracy of the camera pose, decreasing the inconsistencies between the depth frames in advance. In order to eliminate the geometric inconsistencies between RGB scene and depth scene, the scale ambiguity problem encountered during the pose estimation with RGB image sequences can be resolved by integrating the depth and visual information and a robust rigid-transformation recovery method is developed to register RGB scene to depth scene. The benefit of the proposed joint optimization method is firstly evaluated with the publicly available benchmark datasets collected with Kinect. Then, the proposed method is examined by tests with two sets of datasets collected in both outside and inside environments. The experimental results demonstrate the feasibility and robustness of the proposed method. PMID:27690028

  20. Enhanced RGB-D Mapping Method for Detailed 3D Indoor and Outdoor Modeling.

    PubMed

    Tang, Shengjun; Zhu, Qing; Chen, Wu; Darwish, Walid; Wu, Bo; Hu, Han; Chen, Min

    2016-09-27

    RGB-D sensors (sensors with RGB camera and Depth camera) are novel sensing systems that capture RGB images along with pixel-wise depth information. Although they are widely used in various applications, RGB-D sensors have significant drawbacks including limited measurement ranges (e.g., within 3 m) and errors in depth measurement increase with distance from the sensor with respect to 3D dense mapping. In this paper, we present a novel approach to geometrically integrate the depth scene and RGB scene to enlarge the measurement distance of RGB-D sensors and enrich the details of model generated from depth images. First, precise calibration for RGB-D Sensors is introduced. In addition to the calibration of internal and external parameters for both, IR camera and RGB camera, the relative pose between RGB camera and IR camera is also calibrated. Second, to ensure poses accuracy of RGB images, a refined false features matches rejection method is introduced by combining the depth information and initial camera poses between frames of the RGB-D sensor. Then, a global optimization model is used to improve the accuracy of the camera pose, decreasing the inconsistencies between the depth frames in advance. In order to eliminate the geometric inconsistencies between RGB scene and depth scene, the scale ambiguity problem encountered during the pose estimation with RGB image sequences can be resolved by integrating the depth and visual information and a robust rigid-transformation recovery method is developed to register RGB scene to depth scene. The benefit of the proposed joint optimization method is firstly evaluated with the publicly available benchmark datasets collected with Kinect. Then, the proposed method is examined by tests with two sets of datasets collected in both outside and inside environments. The experimental results demonstrate the feasibility and robustness of the proposed method.

  1. 3D leaf water content mapping using terrestrial laser scanner backscatter intensity with radiometric correction

    NASA Astrophysics Data System (ADS)

    Zhu, Xi; Wang, Tiejun; Darvishzadeh, Roshanak; Skidmore, Andrew K.; Niemann, K. Olaf

    2015-12-01

    Leaf water content (LWC) plays an important role in agriculture and forestry management. It can be used to assess drought conditions and wildfire susceptibility. Terrestrial laser scanner (TLS) data have been widely used in forested environments for retrieving geometrically-based biophysical parameters. Recent studies have also shown the potential of using radiometric information (backscatter intensity) for estimating LWC. However, the usefulness of backscatter intensity data has been limited by leaf surface characteristics, and incidence angle effects. To explore the idea of using LiDAR intensity data to assess LWC we normalized (for both angular effects and leaf surface properties) shortwave infrared TLS data (1550 nm). A reflectance model describing both diffuse and specular reflectance was applied to remove strong specular backscatter intensity at a perpendicular angle. Leaves with different surface properties were collected from eight broadleaf plant species for modeling the relationship between LWC and backscatter intensity. Reference reflectors (Spectralon from Labsphere, Inc.) were used to build a look-up table to compensate for incidence angle effects. Results showed that before removing the specular influences, there was no significant correlation (R2 = 0.01, P > 0.05) between the backscatter intensity at a perpendicular angle and LWC. After the removal of the specular influences, a significant correlation emerged (R2 = 0.74, P < 0.05). The agreement between measured and TLS-derived LWC demonstrated a significant reduction of RMSE (root mean square error, from 0.008 to 0.003 g/cm2) after correcting for the incidence angle effect. We show that it is possible to use TLS to estimate LWC for selected broadleaved plants with an R2 of 0.76 (significance level α = 0.05) at leaf level. Further investigations of leaf surface and internal structure will likely result in improvements of 3D LWC mapping for studying physiology and ecology in vegetation.

  2. Seismic Hazard Maps for Seattle, Washington, Incorporating 3D Sedimentary Basin Effects, Nonlinear Site Response, and Rupture Directivity

    USGS Publications Warehouse

    Frankel, Arthur D.; Stephenson, William J.; Carver, David L.; Williams, Robert A.; Odum, Jack K.; Rhea, Susan

    2007-01-01

    This report presents probabilistic seismic hazard maps for Seattle, Washington, based on over 500 3D simulations of ground motions from scenario earthquakes. These maps include 3D sedimentary basin effects and rupture directivity. Nonlinear site response for soft-soil sites of fill and alluvium was also applied in the maps. The report describes the methodology for incorporating source and site dependent amplification factors into a probabilistic seismic hazard calculation. 3D simulations were conducted for the various earthquake sources that can affect Seattle: Seattle fault zone, Cascadia subduction zone, South Whidbey Island fault, and background shallow and deep earthquakes. The maps presented in this document used essentially the same set of faults and distributed-earthquake sources as in the 2002 national seismic hazard maps. The 3D velocity model utilized in the simulations was validated by modeling the amplitudes and waveforms of observed seismograms from five earthquakes in the region, including the 2001 M6.8 Nisqually earthquake. The probabilistic seismic hazard maps presented here depict 1 Hz response spectral accelerations with 10%, 5%, and 2% probabilities of exceedance in 50 years. The maps are based on determinations of seismic hazard for 7236 sites with a spacing of 280 m. The maps show that the most hazardous locations for this frequency band (around 1 Hz) are soft-soil sites (fill and alluvium) within the Seattle basin and along the inferred trace of the frontal fault of the Seattle fault zone. The next highest hazard is typically found for soft-soil sites in the Duwamish Valley south of the Seattle basin. In general, stiff-soil sites in the Seattle basin exhibit higher hazard than stiff-soil sites outside the basin. Sites with shallow bedrock outside the Seattle basin have the lowest estimated hazard for this frequency band.

  3. 3D electron density imaging using single scattered x rays with application to breast CT and mammographic screening

    NASA Astrophysics Data System (ADS)

    van Uytven, Eric Peter

    Screening mammography is the current standard in detecting breast cancer. However, its fundamental disadvantage is that it projects a 3D object into a 2D image. Small lesions are difficult to detect when superimposed over layers of normal tissue. Commercial Computed Tomography (CT) produces a true 3D image yet has a limited role in mammography due to relatively low resolution and contrast. With the intent of enhancing mammography and breast CT, we have developed an algorithm which can produce 3D electron density images using a single projection. Imaging an object with x rays produces a characteristic scattered photon spectrum at the detector plane. A known incident beam spectrum, beam shape, and arbitrary 3D matrix of electron density values enable a theoretical scattered photon distribution to be calculated. An iterative minimization algorithm is used to make changes to the electron density voxel matrix to reduce regular differences between the theoretical and the experimentally measured distributions. The object is characterized by the converged electron density image. This technique has been validated in simulation using data produced by the EGSnrc Monte Carlo code system. At both mammographic and CT energies, a scanning polychromatic pencil beam was used to image breast tissue phantoms containing lesion-like inhomogeneities. The resulting Monte Carlo data is processed using a Nelder-Mead iterative algorithm (MATLAB) to produce the 3D matrix of electron density values. Resulting images have confirmed the ability of the algorithm to detect various 1x1x2.5 mm3 lesions with calcification content as low as 0.5% (p<0.005) at a dose comparable to mammography.

  4. 3-D or median map? Earthquake scenario ground-motion maps from physics-based models versus maps from ground-motion prediction equations

    NASA Astrophysics Data System (ADS)

    Porter, K.

    2015-12-01

    There are two common ways to create a ground-motion map for a hypothetical earthquake: using ground motion prediction equations (by far the more common of the two) and using 3-D physics-based modeling. The former is very familiar to engineers, the latter much less so, and the difference can present a problem because engineers tend to trust the familiar and distrust novelty. Maps for essentially the same hypothetical earthquake using the two different methods can look very different, while appearing to present the same information. Using one or the other can lead an engineer or disaster planner to very different estimates of damage and risk. The reasons have to do with depiction of variability, spatial correlation of shaking, the skewed distribution of real-world shaking, and the upward-curving relationship between shaking and damage. The scientists who develop the two kinds of map tend to specialize in one or the other and seem to defend their turf, which can aggravate the problem of clearly communicating with engineers.The USGS Science Application for Risk Reduction's (SAFRR) HayWired scenario has addressed the challenge of explaining to engineers the differences between the two maps, and why, in a disaster planning scenario, one might want to use the less-familiar 3-D map.

  5. Inductively Driven, 3D Liner Compression of a Magnetized Plasma to Megabar Energy Densities

    SciTech Connect

    Slough, John

    2015-02-01

    modules. The additional energy and switching capability proposed will thus provide for optimal utilization of the liner energy. The following tasks were outlined for the three year effort: (1) Design and assemble the foil liner compression test structure and chamber including the compression bank and test foils [Year 1]. (2) Perform foil liner compression experiments and obtain performance data over a range on liner dimensions and bank parameters [Year 2]. (3) Carry out compression experiments of the FRC plasma to Megagauss fields and measure key fusion parameters [Year 3]. (4) Develop numerical codes and analyze experimental results, and determine the physics and scaling for future work [Year 1-3]. The principle task of the project was to design and assemble the foil liner FRC formation chamber, the full compression test structure and chamber including the compression bank. This task was completed successfully. The second task was to test foils in the test facility constructed in year one and characterize the performance obtained from liner compression. These experimental measurements were then compared with analytical predictions, and numerical code results. The liner testing was completed and compared with both the analytical results as well as the code work performed with the 3D structural dynamics package of ANSYS Metaphysics®. This code is capable of modeling the dynamic behavior of materials well into the non-linear regime (e.g. a bullet hit plate glass). The liner dynamic behavior was found to be remarkably close to that predicted by the 3D structural dynamics results. Incorporating a code that can also include the magnetics and plasma physics has also made significant progress at the UW. The remaining test bed construction and assembly task is was completed, and the FRC formation and merging experiments were carried out as planned. The liner compression of the FRC to Megagauss fields was not performed due to not obtaining a sufficiently long lived FRC during the

  6. NeuroMap: A Spline-Based Interactive Open-Source Software for Spatiotemporal Mapping of 2D and 3D MEA Data.

    PubMed

    Abdoun, Oussama; Joucla, Sébastien; Mazzocco, Claire; Yvert, Blaise

    2011-01-01

    A major characteristic of neural networks is the complexity of their organization at various spatial scales, from microscopic local circuits to macroscopic brain-scale areas. Understanding how neural information is processed thus entails the ability to study them at multiple scales simultaneously. This is made possible using microelectrodes array (MEA) technology. Indeed, high-density MEAs provide large-scale coverage (several square millimeters) of whole neural structures combined with microscopic resolution (about 50 μm) of unit activity. Yet, current options for spatiotemporal representation of MEA-collected data remain limited. Here we present NeuroMap, a new interactive Matlab-based software for spatiotemporal mapping of MEA data. NeuroMap uses thin plate spline interpolation, which provides several assets with respect to conventional mapping methods used currently. First, any MEA design can be considered, including 2D or 3D, regular or irregular, arrangements of electrodes. Second, spline interpolation allows the estimation of activity across the tissue with local extrema not necessarily at recording sites. Finally, this interpolation approach provides a straightforward analytical estimation of the spatial Laplacian for better current sources localization. In this software, coregistration of 2D MEA data on the anatomy of the neural tissue is made possible by fine matching of anatomical data with electrode positions using rigid-deformation-based correction of anatomical pictures. Overall, NeuroMap provides substantial material for detailed spatiotemporal analysis of MEA data. The package is distributed under GNU General Public License and available at http://sites.google.com/site/neuromapsoftware.

  7. Non-twist map bifurcation of drift-lines and drift-island formation in saturated 3D MHD equilibria

    NASA Astrophysics Data System (ADS)

    Pfefferle, David; Cooper, Wilfred A.; Graves, Jonathan P.

    2015-11-01

    Based on non-canonical perturbation theory, guiding-centre drift equations are identified as perturbed magnetic field-line equations. The topology of passing-particle orbits, called drift-lines, is completely determined by the magnetic configuration. In axisymmetric tokamak fields, drift-lines lie on shifted flux-surfaces, called drift-surfaces. Field-lines and drift-lines are subject to island structures at rational surfaces only when a non-axisymmetric component is added. The picture is different in the case of 3D saturated MHD equilibrium like the helical core associated with a non-resonant internal kink mode. In assuming nested flux-surfaces, these bifurcated states, expected for a reversed q-profile with qmin close yet above unity and conveniently obtained in VMEC, feature integrable field-lines. The helical drift-lines however become resonant with the axisymmetric component in the region of qmin and spontaneously generate drift-islands. Due to the locally reversed sheared q-profile, the drift-island structure follows the bifurcation/reconnection mechanism of non-twist maps. This result provides a theoretical interpretation of NBI fast ion helical hot-spots in Long-Lived Modes as well as snake-like impurity density accumulation in internal MHD activity.

  8. A method for 3D electron density imaging using single scattered x-rays with application to mammographic screening.

    PubMed

    Van Uytven, Eric; Pistorius, Stephen; Gordon, Richard

    2008-10-07

    Screening mammography is the current standard in detecting breast cancer. However, its fundamental disadvantage is that it projects a 3D object into a 2D image. Small lesions are difficult to detect when superimposed over layers of normal, heterogeneous tissue. In this work, we examine the potential of single scattered photon electron density imaging in a mammographic environment. Simulating a low-energy (<20 keV) scanning pencil beam, we have developed an algorithm capable of producing 3D electron density images from a single projection. We have tested the algorithm by imaging parts of a simulated mammographic accreditation phantom containing lesions of various sizes. The results indicate that the group of imaged lesions differ significantly from background breast tissue (p<0.005), confirming that electron density imaging may be a useful diagnostic test for the presence of breast cancer.

  9. Label-free characterization of white blood cells by measuring 3D refractive index maps

    PubMed Central

    Yoon, Jonghee; Kim, Kyoohyun; Park, HyunJoo; Choi, Chulhee; Jang, Seongsoo; Park, YongKeun

    2015-01-01

    The characterization of white blood cells (WBCs) is crucial for blood analyses and disease diagnoses. However, current standard techniques rely on cell labeling, a process which imposes significant limitations. Here we present three-dimensional (3D) optical measurements and the label-free characterization of mouse WBCs using optical diffraction tomography. 3D refractive index (RI) tomograms of individual WBCs are constructed from multiple two-dimensional quantitative phase images of samples illuminated at various angles of incidence. Measurements of the 3D RI tomogram of WBCs enable the separation of heterogeneous populations of WBCs using quantitative morphological and biochemical information. Time-lapse tomographic measurements also provide the 3D trajectory of micrometer-sized beads ingested by WBCs. These results demonstrate that optical diffraction tomography can be a useful and versatile tool for the study of WBCs. PMID:26504637

  10. a Review of Cooling Road Maps for 3d Chip Packages

    NASA Astrophysics Data System (ADS)

    Agonafer, Dereje

    The microelectronics industry has thrived through dimensional scaling and corresponding reduction in cost and increase in performance. It has been reported that the average selling price of a transistor has reduced from a few dollars in the early 50's to a billionth of a dollar in the early 2000. It has, however, become more difficult to sustain reduction in cost by scaling. Also, while new technology nodes results in reduced gate delay, it also effects an increase in the interconnect delay. One approach to delaying new technology node and improving performance is through reduction in interconnect delay through packaging. In particular, 3-D Through-Silicon-Via (3D TSV) technology is emerging as a powerful technology to reduce package footprint, decrease interconnection power, higher frequencies, and provide efficient integration of heterogeneous devices. TSVs provide high speed signal propagation due to reduced interconnect lengths as compared to wirebonding and SOC (system-on-chip). However, with many advantages of 3D ICs over conventional 2D counterpart, there are some inherent thermal-mechanical-electrical challenges that need to be addressed before 3D ICs could become mainstream. This chapter talks about a few of the 3D TSV IC challenges from the thermal, mechanical and the performance standpoint of view. It also discusses a novel technique for high powered 3D IC cooling to sub-ambient temperatures using thermo-electric cooler (TEC).

  11. 3D Euler equations and ideal MHD mapped to regular systems: Probing the finite-time blowup hypothesis

    NASA Astrophysics Data System (ADS)

    Bustamante, Miguel D.

    2011-06-01

    We prove by an explicit construction that solutions to incompressible 3D Euler equations defined in the periodic cube Ω=[0 can be mapped bijectively to a new system of equations whose solutions are globally regular. We establish that the usual Beale-Kato-Majda criterion for finite-time singularity (or blowup) of a solution to the 3D Euler system is equivalent to a condition on the corresponding regular solution of the new system. In the hypothetical case of Euler finite-time singularity, we provide an explicit formula for the blowup time in terms of the regular solution of the new system. The new system is amenable to being integrated numerically using similar methods as in Euler equations. We propose a method to simulate numerically the new regular system and describe how to use this to draw robust and reliable conclusions on the finite-time singularity problem of Euler equations, based on the conservation of quantities directly related to energy and circulation. The method of mapping to a regular system can be extended to any fluid equation that admits a Beale-Kato-Majda type of theorem, e.g. 3D Navier-Stokes, 2D and 3D magnetohydrodynamics, and 1D inviscid Burgers. We discuss briefly the case of 2D ideal magnetohydrodynamics. In order to illustrate the usefulness of the mapping, we provide a thorough comparison of the analytical solution versus the numerical solution in the case of 1D inviscid Burgers equation.

  12. High-Density 3D-Boron Nitride and 3D-Graphene for High-Performance Nano-Thermal Interface Material.

    PubMed

    Loeblein, Manuela; Tsang, Siu Hon; Pawlik, Matthieu; Phua, Eric Jian Rong; Yong, Han; Zhang, Xiao Wu; Gan, Chee Lip; Teo, Edwin Hang Tong

    2017-02-28

    Compression studies on three-dimensional foam-like graphene and h-BN (3D-C and 3D-BN) revealed their high cross-plane thermal conductivity (62-86 W m(-1) K(-1)) and excellent surface conformity, characteristics essential for thermal management needs. Comparative studies to state-of-the-art materials and other materials currently under research for heat dissipation revealed 3D-foam's improved performance (20-30% improved cooling, temperature decrease by ΔT of 44-24 °C).

  13. Developing Defined and Scalable 3D Culture Systems for Culturing Human Pluripotent Stem Cells at High Densities.

    PubMed

    Lei, Yuguo; Jeong, Daeun; Xiao, Jifang; Schaffer, David V

    2014-06-01

    Human pluripotent stem cells (hPSCs) - including embryonic stem cells (hESCs) and induced pluripotent stem cells (hiPSCs) - are very promising candidates for cell therapies, tissue engineering, high throughput pharmacology screens, and toxicity testing. These applications require large numbers of high quality cells; however, scalable production of human pluripotent stem cells and their derivatives at a high density and under well-defined conditions has been a challenge. We recently reported a simple, efficient, fully defined, scalable, and good manufacturing practice (GMP) compatible 3D culture system based on a thermoreversible hydrogel for hPSC expansion and differentiation. Here, we describe additional design rationale and characterization of this system. For instance, we have determined that culturing hPSCs as a suspension in a liquid medium can exhibit lower volumetric yields due to cell agglomeration and possible shear force-induced cell loss. By contrast, using hydrogels as 3D scaffolds for culturing hPSCs reduces aggregation and may insulate from shear forces. Additionally, hydrogel-based 3D culture systems can support efficient hPSC expansion and differentiation at a high density if compatible with hPSC biology. Finally, there are considerable opportunities for future development to further enhance hydrogel-based 3D culture systems for producing hPSCs and their progeny.

  14. Advances in animal ecology from 3D ecosystem mapping with LiDAR

    NASA Astrophysics Data System (ADS)

    Davies, A.; Asner, G. P.

    2015-12-01

    The advent and recent advances of Light Detection and Ranging (LiDAR) have enabled accurate measurement of 3D ecosystem structure. Although the use of LiDAR data is widespread in vegetation science, it has only recently (< 14 years) been applied to animal ecology. Despite such recent application, LiDAR has enabled new insights in the field and revealed the fundamental importance of 3D ecosystem structure for animals. We reviewed the studies to date that have used LiDAR in animal ecology, synthesising the insights gained. Structural heterogeneity is most conducive to increased animal richness and abundance, and increased complexity of vertical vegetation structure is more positively influential than traditionally measured canopy cover, which produces mixed results. However, different taxonomic groups interact with a variety of 3D canopy traits and some groups with 3D topography. LiDAR technology can be applied to animal ecology studies in a wide variety of environments to answer an impressive array of questions. Drawing on case studies from vastly different groups, termites and lions, we further demonstrate the applicability of LiDAR and highlight new understanding, ranging from habitat preference to predator-prey interactions, that would not have been possible from studies restricted to field based methods. We conclude with discussion of how future studies will benefit by using LiDAR to consider 3D habitat effects in a wider variety of ecosystems and with more taxa to develop a better understanding of animal dynamics.

  15. 3D Velocity and Density Model of the Los Angeles Basin and Spectral Element Method Earthquake Simulations

    NASA Astrophysics Data System (ADS)

    Suess, P.; Shaw, J. H.; Komatitsch, D.; Tromp, J.

    2001-12-01

    We present a 3D velocity model and a 3D density model of the LA basin. The LA basin velocity model was constructed using sonic log and stacking velocity information, provided by oil industry sources and not previously incorporated into southern California velocity models. The density model is based upon a new database of approximately 300 oil industry density logs from across the Los Angeles basin. These logs use gamma ray emissions to determine formation density at samples of about one meter. We have developed an empirical relation between sonic velocity and density by comparing data from approximately 30 wells in which we have both sonic and density logs. For the remaining wells, we have derived relationships between depth and density, and characterized this relationship for the three main stratigraphic sub-divisions of the SCEC Phase 2 model (Quaternary to base Pico Fm., top Repetto Fm. to top Mohnian, and top Mohnian to basement). The density-depth and density-velocity relations will provide independent rules that can be employed to define density and velocity structure in areas where data does not exist, or in other areas with similar lithology to the Los Angeles basin. We use a spectral element method (SEM) for simulation of seismic wave propagation which is currently being implemented on a 156-node Pentium PC cluster at Cal Tech. Preliminary work shows that SEM results using a 1D velocity model for southern California compare very well to discrete-wavenumber results. Both the density structure and velocity structure must be defined in a 3D model for its use in simulations of seismic wave propagation with a spectral element method, to predict the distribution of hazardous ground shaking during large events. Previous work has typically used density values which were predicted by the sonic velocity values; use of our measured density values should provide more accurate ground shaking predictions, and comparison to previous results will provide a useful

  16. True-3D Strain Mapping for Assessment of Material Deformation by Synchrotron X-Ray Microtomography

    SciTech Connect

    Ahn, J.J.; Toda, H.; Niinomi, M.; Kobayashi, T.; Akahori, T.; Uesugi, K.

    2005-04-09

    Downsizing of products with complex shapes has been accelerated thanks to the rapid development of electrodevice manufacturing technology. Micro electromechanical systems (MEMS) are one of such typical examples. 3D strain measurement of such miniature products is needed to ensure their reliability. In the present study, as preliminary trial for it 3D tensile deformation behavior of a pure aluminum wire is examined using the synchrotron X-ray microtomography technique at Spring-8, Japan. Multipurpose in-situ tester is used to investigate real-time tensile deformation behavior of the Al wire. Tensile tests are carried out under strokes of 0, 0.005, 0.01 and 0.015mm. It measures 3D local deformation of a region of interest by tracking a relative movement of a pair of particles at each point. Local deformation behavior of the Al wire is identified to be different from macroscopic deformation behavior. It may be closely associated with underlying microstructure.

  17. Edge-based intramode selection for depth-map coding in 3D-HEVC.

    PubMed

    Park, Chun-Su

    2015-01-01

    The 3D video extension of High Efficiency Video Coding (3D-HEVC) is the state-of-the-art video coding standard for the compression of the multiview video plus depth format. In the 3D-HEVC design, new depth-modeling modes (DMMs) are utilized together with the existing intraprediction modes for depth intracoding. The DMMs can provide more accurate prediction signals and thereby achieve better compression efficiency. However, testing the DMMs in the intramode decision process causes a drastic increase in the computational complexity. In this paper, we propose a fast mode decision algorithm for depth intracoding. The proposed algorithm first performs a simple edge classification in the Hadamard transform domain. Then, based on the edge classification results, the proposed algorithm selectively omits unnecessary DMMs in the mode decision process. Experimental results demonstrate that the proposed algorithm speeds up the mode decision process by up to 37.65% with negligible loss of coding efficiency.

  18. GIS prospectivity mapping and 3D modeling validation for potential uranium deposit targets in Shangnan district, China

    NASA Astrophysics Data System (ADS)

    Xie, Jiayu; Wang, Gongwen; Sha, Yazhou; Liu, Jiajun; Wen, Botao; Nie, Ming; Zhang, Shuai

    2017-04-01

    Integrating multi-source geoscience information (such as geology, geophysics, geochemistry, and remote sensing) using GIS mapping is one of the key topics and frontiers in quantitative geosciences for mineral exploration. GIS prospective mapping and three-dimensional (3D) modeling can be used not only to extract exploration criteria and delineate metallogenetic targets but also to provide important information for the quantitative assessment of mineral resources. This paper uses the Shangnan district of Shaanxi province (China) as a case study area. GIS mapping and potential granite-hydrothermal uranium targeting were conducted in the study area combining weights of evidence (WofE) and concentration-area (C-A) fractal methods with multi-source geoscience information. 3D deposit-scale modeling using GOCAD software was performed to validate the shapes and features of the potential targets at the subsurface. The research results show that: (1) the known deposits have potential zones at depth, and the 3D geological models can delineate surface or subsurface ore-forming features, which can be used to analyze the uncertainty of the shape and feature of prospectivity mapping at the subsurface; (2) single geochemistry anomalies or remote sensing anomalies at the surface require combining the depth exploration criteria of geophysics to identify potential targets; and (3) the single or sparse exploration criteria zone with few mineralization spots at the surface has high uncertainty in terms of the exploration target.

  19. Mapping the Extinction Curve in 3D: Structure on Kiloparsec Scales

    NASA Astrophysics Data System (ADS)

    Schlafly, E. F.; Peek, J. E. G.; Finkbeiner, D. P.; Green, G. M.

    2017-03-01

    Near-infrared spectroscopy from APOGEE and wide-field optical photometry from Pan-STARRS1 have recently made precise measurements of the shape of the extinction curve possible for tens of thousands of stars, parameterized by R(V). These measurements revealed structures in R(V) with large angular scales, which are challenging to explain in existing dust paradigms. In this work, we combine three-dimensional maps of dust column density with R(V) measurements to constrain the three-dimensional distribution of R(V) in the Milky Way. We find that the variations in R(V) are correlated on kiloparsec scales. In particular, most of the dust within one kiloparsec in the outer Galaxy, including many local molecular clouds (Orion, Taurus, Perseus, California, and Cepheus), has a significantly lower R(V) than more distant dust in the Milky Way. These results provide new input to models of dust evolution and processing, and complicate the application of locally derived extinction curves to more distant regions of the Milky Way and to other galaxies.

  20. A mapping of an ensemble of mitochondrial sequences for various organisms into 3D space based on the word composition.

    PubMed

    Aita, Takuyo; Nishigaki, Koichi

    2012-11-01

    To visualize a bird's-eye view of an ensemble of mitochondrial genome sequences for various species, we recently developed a novel method of mapping a biological sequence ensemble into Three-Dimensional (3D) vector space. First, we represented a biological sequence of a species s by a word-composition vector x(s), where its length [absolute value]x(s)[absolute value] represents the sequence length, and its unit vector x(s)/[absolute value]x(s)[absolute value] represents the relative composition of the K-tuple words through the sequence and the size of the dimension, N=4(K), is the number of all possible words with the length of K. Second, we mapped the vector x(s) to the 3D position vector y(s), based on the two following simple principles: (1) [absolute value]y(s)[absolute value]=[absolute value]x(s)[absolute value] and (2) the angle between y(s) and y(t) maximally correlates with the angle between x(s) and x(t). The mitochondrial genome sequences for 311 species, including 177 Animalia, 85 Fungi and 49 Green plants, were mapped into 3D space by using K=7. The mapping was successful because the angles between vectors before and after the mapping highly correlated with each other (correlation coefficients were 0.92-0.97). Interestingly, the Animalia kingdom is distributed along a single arc belt (just like the Milky Way on a Celestial Globe), and the Fungi and Green plant kingdoms are distributed in a similar arc belt. These two arc belts intersect at their respective middle regions and form a cross structure just like a jet aircraft fuselage and its wings. This new mapping method will allow researchers to intuitively interpret the visual information presented in the maps in a highly effective manner.

  1. Joint 2D and 3D phase processing for quantitative susceptibility mapping: application to 2D echo-planar imaging.

    PubMed

    Wei, Hongjiang; Zhang, Yuyao; Gibbs, Eric; Chen, Nan-Kuei; Wang, Nian; Liu, Chunlei

    2017-04-01

    Quantitative susceptibility mapping (QSM) measures tissue magnetic susceptibility and typically relies on time-consuming three-dimensional (3D) gradient-echo (GRE) MRI. Recent studies have shown that two-dimensional (2D) multi-slice gradient-echo echo-planar imaging (GRE-EPI), which is commonly used in functional MRI (fMRI) and other dynamic imaging techniques, can also be used to produce data suitable for QSM with much shorter scan times. However, the production of high-quality QSM maps is difficult because data obtained by 2D multi-slice scans often have phase inconsistencies across adjacent slices and strong susceptibility field gradients near air-tissue interfaces. To address these challenges in 2D EPI-based QSM studies, we present a new data processing procedure that integrates 2D and 3D phase processing. First, 2D Laplacian-based phase unwrapping and 2D background phase removal are performed to reduce phase inconsistencies between slices and remove in-plane harmonic components of the background phase. This is followed by 3D background phase removal for the through-plane harmonic components. The proposed phase processing was evaluated with 2D EPI data obtained from healthy volunteers, and compared against conventional 3D phase processing using the same 2D EPI datasets. Our QSM results were also compared with QSM values from time-consuming 3D GRE data, which were taken as ground truth. The experimental results show that this new 2D EPI-based QSM technique can produce quantitative susceptibility measures that are comparable with those of 3D GRE-based QSM across different brain regions (e.g. subcortical iron-rich gray matter, cortical gray and white matter). This new 2D EPI QSM reconstruction method is implemented within STI Suite, which is a comprehensive shareware for susceptibility imaging and quantification. Copyright © 2016 John Wiley & Sons, Ltd.

  2. Fluorescent stereo microscopy for 3D surface profilometry and deformation mapping.

    PubMed

    Hu, Zhenxing; Luo, Huiyang; Du, Yingjie; Lu, Hongbing

    2013-05-20

    Recently, mechanobiology has received increased attention. For investigation of biofilm and cellular tissue, measurements of the surface topography and deformation in real-time are a pre-requisite for understanding the growth mechanisms. In this paper, a novel three-dimensional (3D) fluorescent microscopic method for surface profilometry and deformation measurements is developed. In this technique a pair of cameras are connected to a binocular fluorescent microscope to acquire micrographs from two different viewing angles of a sample surface doped or sprayed with fluorescent microparticles. Digital image correlation technique is used to search for matching points in the pairing fluorescence micrographs. After calibration of the system, the 3D surface topography is reconstructed from the pair of planar images. When the deformed surface topography is compared with undeformed topography using fluorescent microparticles for movement tracking of individual material points, the full field deformation of the surface is determined. The technique is demonstrated on topography measurement of a biofilm, and also on surface deformation measurement of the biofilm during growth. The use of 3D imaging of the fluorescent microparticles eliminates the formation of bright parts in an image caused by specular reflections. The technique is appropriate for non-contact, full-field and real-time 3D surface profilometry and deformation measurements of materials and structures at the microscale.

  3. 2D map projections for visualization and quantitative analysis of 3D fluorescence micrographs

    PubMed Central

    Sendra, G. Hernán; Hoerth, Christian H.; Wunder, Christian; Lorenz, Holger

    2015-01-01

    We introduce Map3-2D, a freely available software to accurately project up to five-dimensional (5D) fluorescence microscopy image data onto full-content 2D maps. Similar to the Earth’s projection onto cartographic maps, Map3-2D unfolds surface information from a stack of images onto a single, structurally connected map. We demonstrate its applicability for visualization and quantitative analyses of spherical and uneven surfaces in fixed and dynamic live samples by using mammalian and yeast cells, and giant unilamellar vesicles. Map3-2D software is available at http://www.zmbh.uni-heidelberg.de//Central_Services/Imaging_Facility/Map3-2D.html. PMID:26208256

  4. Topographical guidance of 3D tumor cell migration at an interface of collagen densities.

    PubMed

    Bordeleau, Francois; Tang, Lauren N; Reinhart-King, Cynthia A

    2013-12-01

    During cancer progression, metastatic cells leave the primary tumor and invade into the fibrous extracellular matrix (ECM) within the surrounding stroma. This ECM network is highly heterogeneous, and interest in understanding how this network can affect cell behavior has increased in the past several decades. However, replicating this heterogeneity has proven challenging. Here, we designed and utilized a method to create a well-defined interface between two distinct regions of high- and low-density collagen gels to mimic the heterogeneities in density found in the tumor stroma. We show that cells will invade preferentially from the high-density side into the low-density side. We also demonstrate that the net cell migration is a function of the density of the collagen in which the cells are embedded, and the difference in density between the two regions has minimal effect on cell net displacement and distance travelled. Our data further indicate that a low-to-high density interface promotes directional migration and induces formation of focal adhesion on the interface surface. Together, the current results demonstrate how ECM heterogeneities, in the form of interfacial boundaries, can affect cell migration.

  5. Mapping molecular orientational distributions for biological sample in 3D (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    HE, Wei; Ferrand, Patrick; Richter, Benjamin; Bastmeyer, Martin; Brasselet, Sophie

    2016-04-01

    Measuring molecular orientation properties is very appealing for scientists in molecular and cell biology, as well as biomedical research. Orientational organization at the molecular scale is indeed an important brick to cells and tissues morphology, mechanics, functions and pathologies. Recent work has shown that polarized fluorescence imaging, based on excitation polarization tuning in the sample plane, is able to probe molecular orientational order in biological samples; however this applies only to information in 2D, projected in the sample plane. To surpass this limitation, we extended this approach to excitation polarization tuning in 3D. The principle is based on the decomposition of any arbitrary 3D linear excitation in a polarization along the longitudinal z-axis, and a polarization in the transverse xy-sample plane. We designed an interferometer with one arm generating radial polarization light (thus producing longitudinal polarization under high numerical aperture focusing), the other arm controlling a linear polarization in the transverse plane. The amplitude ratio between the two arms can vary so as to get any linear polarized excitation in 3D at the focus of a high NA objective. This technique has been characterized by polarimetry imaging at the back focal plane of the focusing objective, and modeled theoretically. 3D polarized fluorescence microscopy is demonstrated on actin stress fibers in non-flat cells suspended on synthetic polymer structures forming supporting pillars, for which heterogeneous actin orientational order could be identified. This technique shows a great potential in structural investigations in 3D biological systems, such as cell spheroids and tissues.

  6. Low-Amplitude Craniofacial EMG Power Spectral Density and 3D Muscle Reconstruction from MRI

    PubMed Central

    Wiedemann, Lukas; Chaberova, Jana; Edmunds, Kyle; Einarsdóttir, Guðrún; Ramon, Ceon

    2015-01-01

    Improving EEG signal interpretation, specificity, and sensitivity is a primary focus of many current investigations, and the successful application of EEG signal processing methods requires a detailed knowledge of both the topography and frequency spectra of low-amplitude, high-frequency craniofacial EMG. This information remains limited in clinical research, and as such, there is no known reliable technique for the removal of these artifacts from EEG data. The results presented herein outline a preliminary investigation of craniofacial EMG high-frequency spectra and 3D MRI segmentation that offers insight into the development of an anatomically-realistic model for characterizing these effects. The data presented highlights the potential for confounding signal contribution from around 60 to 200 Hz, when observed in frequency space, from both low and high-amplitude EMG signals. This range directly overlaps that of both low γ (30-50 Hz) and high γ (50-80 Hz) waves, as defined traditionally in standatrd EEG measurements, and mainly with waves presented in dense-array EEG recordings. Likewise, average EMG amplitude comparisons from each condition highlights the similarities in signal contribution of low-activity muscular movements and resting, control conditions. In addition to the FFT analysis performed, 3D segmentation and reconstruction of the craniofacial muscles whose EMG signals were measured was successful. This recapitulation of the relevant EMG morphology is a crucial first step in developing an anatomical model for the isolation and removal of confounding low-amplitude craniofacial EMG signals from EEG data. Such a model may be eventually applied in a clinical setting to ultimately help to extend the use of EEG in various clinical roles. PMID:26913150

  7. Mapping the Monoceros Ring in 3D with Pan-STARRS1

    NASA Astrophysics Data System (ADS)

    Morganson, Eric; Conn, Blair; Rix, Hans-Walter; Bell, Eric F.; Burgett, William S.; Chambers, Kenneth; Dolphin, Andrew; Draper, Peter W.; Flewelling, Heather; Hodapp, Klaus; Kaiser, Nick; Magnier, Eugene A.; Martin, Nicolas F.; Martinez-Delgado, David; Metcalfe, Nigel; Schlafly, Edward F.; Slater, Colin T.; Wainscoat, Richard J.; Waters, Christopher Z.

    2016-07-01

    Using the Pan-STARRS1 survey, we derive limiting magnitude, spatial completeness, and density maps that we use to probe the three-dimensional structure and estimate the stellar mass of the so-called Monoceros Ring. The Monoceros Ring is an enormous and complex stellar sub-structure in the outer Milky Way disk. It is most visible across the large Galactic Anticenter region, 120^\\circ \\lt l\\lt 240^\\circ , -30^\\circ \\lt b\\lt +40^\\circ . We estimate its stellar mass density profile along every line of sight in 2° × 2° pixels over the entire 30,000 deg2 Pan-STARRS1 survey using the previously developed match software. By parsing this distribution into a radially smooth component and the Monoceros Ring, we obtain its mass and distance from the Sun along each relevant line of sight. The Monoceros Ring is significantly closer to us in the south (6 kpc) than in the north (9 kpc). We also create 2D cross-sections parallel to the Galactic plane that show 135° of the Monoceros Ring in the south and 170° of the Monoceros Ring in the north. We show that the northern and southern structures are also roughly concentric circles, suggesting that they may be waves rippling from a common origin. Excluding the Galactic plane ˜ +/- 4^\\circ , we observe an excess mass of 4× {10}6{M}⊙ across 120^\\circ \\lt l\\lt 240^\\circ . If we interpolate across the Galactic plane, we estimate that this region contains 8× {10}6{M}⊙ . If we assume (somewhat boldly) that the Monoceros Ring is a set of two Galactocentric rings, its total mass is 6× {10}7{M}⊙ . Finally, if we assume that it is a set of two circles centered at a point 4 kpc from the Galactic center in the anti-central direction, as our data suggests, we estimate its mass to be 4× {10}7{M}⊙ .

  8. Diffraction effects incorporated design of a parallax barrier for a high-density multi-view autostereoscopic 3D display.

    PubMed

    Yoon, Ki-Hyuk; Ju, Heongkyu; Kwon, Hyunkyung; Park, Inkyu; Kim, Sung-Kyu

    2016-02-22

    We present optical characteristics of view image provided by a high-density multi-view autostereoscopic 3D display (HD-MVA3D) with a parallax barrier (PB). Diffraction effects that become of great importance in such a display system that uses a PB, are considered in an one-dimensional model of the 3D display, in which the numerical simulation of light from display panel pixels through PB slits to viewing zone is performed. The simulation results are then compared to the corresponding experimental measurements with discussion. We demonstrate that, as a main parameter for view image quality evaluation, the Fresnel number can be used to determine the PB slit aperture for the best performance of the display system. It is revealed that a set of the display parameters, which gives the Fresnel number of ∼ 0.7 offers maximized brightness of the view images while that corresponding to the Fresnel number of 0.4 ∼ 0.5 offers minimized image crosstalk. The compromise between the brightness and crosstalk enables optimization of the relative magnitude of the brightness to the crosstalk and lead to the choice of display parameter set for the HD-MVA3D with a PB, which satisfies the condition where the Fresnel number lies between 0.4 and 0.7.

  9. An Efficient Algorithm for Mapping Imaging Data to 3D Unstructured Grids in Computational Biomechanics

    SciTech Connect

    Einstein, Daniel R.; Kuprat, Andrew P.; Jiao, Xiangmin; Carson, James P.; Einstein, David M.; Corley, Richard A.; Jacob, Rick E.

    2013-01-01

    Geometries for organ scale and multiscale simulations of organ function are now routinely derived from imaging data. However, medical images may also contain spatially heterogeneous information other than geometry that are relevant to such simulations either as initial conditions or in the form of model parameters. In this manuscript, we present an algorithm for the efficient and robust mapping of such data to imaging based unstructured polyhedral grids in parallel. We then illustrate the application of our mapping algorithm to three different mapping problems: 1) the mapping of MRI diffusion tensor data to an unstuctured ventricular grid; 2) the mapping of serial cyro-section histology data to an unstructured mouse brain grid; and 3) the mapping of CT-derived volumetric strain data to an unstructured multiscale lung grid. Execution times and parallel performance are reported for each case.

  10. Crustal density structure in northwestern South America derived from analysis and 3-D modeling of gravity and seismicity data

    NASA Astrophysics Data System (ADS)

    Sanchez-Rojas, J.; Palma, M.

    2014-11-01

    This paper presents a three-dimensional (3-D) interpretation of new gravity and seismicity datasets for northern South America. A 3-D forward density model was constructed on the basis of deep wide-angle seismic refraction sections, Moho depth from receiver functions, and surface geology. Density values were estimated from published borehole data for sediments by using empirical velocity-density functions and considering mineralogical-chemical composition variations under typical pressure-temperature conditions for upper and lower crustal rocks. The modeled 3-D density structure was kept as simple as possible. The continental and oceanic plates were formed by two sedimentary bodies, one crustal body, and one mantle lithosphere body overlying a sub-lithospheric mantle. The Caribbean plate was modeled with an atypical crustal thickness of ~ 18 km (including sediments). The geometry of the Caribbean plate was modeled using a combination of gravity modeling and analyses of the seismicity and focal-mechanism solutions. Intermediate seismicity and the orientation of the T-axes appeared aligned along the predicted position of the slab. As a result, the estimated slab dip angle under Maracaibo and the Mérida Andes was ~ 15° and increases up to ~ 20° after 100 km depth. The model shows two orientations in the slab strike: ~ N150°E ± 5 in western Colombia and southward underneath the Maracaibo block. The modeling results suggest that the northern South American upper and lower crusts are relatively light and the density of the Caribbean crust is typical for an oceanic crust.

  11. Influence of Critical Current Density on Magnetic Force of Htsc Bulk above Pmr with 3D-MODELING Numerical Solutions

    NASA Astrophysics Data System (ADS)

    Lu, Yiyun; Lu, Bingjuan; Ge, Yunwang; Chen, Wenqing

    Numerical electromagnetic field simulations of high-temperature superconductors (HTSC) bulk were carried out to calculate the magnetic force between the HTSC bulk and the permanent magnet railway (PMR). A 3D-modeling numerical calculation method is proposed using the finite element method. The model is formulated with the magnetic field vector (H-method). The resulting code was written with FORTRAN language. The electric field intensity E and the current density J constitutive relation of HTSC were described with E-J power law. The Kim macro-model is used to describe critical current density Jc of HTSC bulk. Two virtual HTSC bulks were used to solve the critical current density Jc anisotropic properties of HTSC materials. A superconducting levitation system composed of one HTSC bulk and PMR is successfully investigated using the proposed method. By this method, the influence of critical current density on magnetic levitation force of the superconducting levitation system is mathematically studied.

  12. SU-C-213-02: Characterizing 3D Printing in the Fabrication of Variable Density Phantoms

    SciTech Connect

    Madamesila, J; McGeachy, P; Villarreal-Barajas, J; Khan, R

    2015-06-15

    Purpose: In this work, we present characterization, process flow, quality control and application of 3D fabricated low density phantoms for radiotherapy quality assurance. Methods: A Rostock delta 3D printer using polystyrene filament of diameter 1.75 mm was used to print geometric volumes of 2×2×1 cm{sup 3} of varying densities. The variable densities of 0.1 to 0.75 g/cm {sup 3} were created by modulating the infill. A computed tomography (CT) scan was performed to establish an infill-density calibration curve as well as characterize the quality of the print such as uniformity and the infill pattern. The time required to print these volumes was also recorded. Using the calibration, two low density cones (0.19, 0.52 g/cm{sup 3}) were printed and benchmarked against commercially available phantoms. The dosimetric validation of the low density scaling of Anisotropic Analytical Algorithm (AAA) was performed by using a 0.5 g/cm{sup 3} slab of 10×10×2.4 cm{sup 3} with EBT3 GafChromic film. The gamma analysis at 3%/3mm criteria were compared for the measured and computed dose planes. Results: Analysis of the volume of air pockets in the infill resulted in a reasonable uniformity for densities 0.4 to 0.75 g/cm{sup 3}. Printed phantoms with densities below 0.4 g/cm{sup 3} exhibited a higher ratio of air to polystyrene resulting in large non-uniformity. Compared to the commercial inserts, good agreement was observed only for the printed 0.52 g/cm{sup 3} cone. Dosimetric comparison for a printed low density volume placed in-between layers of solid water resulted in >95% gamma agreement between AAA calculated dose planes and measured EBT3 films for a 6MV 5×5 cm{sup 2} clinical beam. The comparison showed disagreement in the penumbra region. Conclusion: In conclusion, 3D printing technology opens the door to desktop fabrication of variable density phantoms at economical prices in an efficient manner for the quality assurance needs of a small clinic.

  13. Improving GOOGLE'S Cartographer 3d Mapping by Continuous-Time Slam

    NASA Astrophysics Data System (ADS)

    Nüchter, A.; Bleier, M.; Schauer, J.; Janotta, P.

    2017-02-01

    This paper shows how to use the result of Google's SLAM solution, called Cartographer, to bootstrap our continuous-time SLAM algorithm. The presented approach optimizes the consistency of the global point cloud, and thus improves on Google's results. We use the algorithms and data from Google as input for our continuous-time SLAM software. We also successfully applied our software to a similar backpack system which delivers consistent 3D point clouds even in absence of an IMU.

  14. High-density 3D graphene-based monolith and related materials, methods, and devices

    DOEpatents

    Worsley, Marcus A.; Baumann, Theodore F.; Biener, Juergen; Charnvanichborikarn, Supakit; Kucheyev, Sergei; Montalvo, Elizabeth; Shin, Swanee; Tylski, Elijah

    2017-03-21

    A composition comprising at least one high-density graphene-based monolith, said monolith comprising a three-dimensional structure of graphene sheets crosslinked by covalent carbon bonds and having a density of at least 0.1 g/cm.sup.3. Also provided is a method comprising: preparing a reaction mixture comprising a suspension and at least one catalyst, said suspension selected from a graphene oxide (GO) suspension and a carbon nanotube suspension; curing the reaction mixture to produce a wet gel; drying the wet gel to produce a dry gel, said drying step is substantially free of supercritical drying and freeze drying; and pyrolyzing the dry gel to produce a high-density graphene-based monolith. Exceptional combinations of properties are achieved including high conductive and mechanical properties.

  15. Pulmonary nodule classification based on CT density distribution using 3D thoracic CT images

    NASA Astrophysics Data System (ADS)

    Kawata, Yoshiki; Niki, Noboru; Ohamatsu, Hironobu; Kusumoto, Masahiko; Kakinuma, Ryutaro; Mori, Kiyoshi; Yamada, Kozo; Nishiyama, Hiroyuki; Eguchi, Kenji; Kaneko, Masahiro; Moriyama, Noriyuki

    2004-04-01

    Computer-aided diagnosis (CAD) has been investigated to provide physicians with quantitative information, such as estimates of the malignant likelihood, to aid in the classification of abnormalities detected at screening of lung cancers. The purpose of this study is to develop a method for classifying nodule density patterns that provides information with respect to nodule statuses such as lesion stage. This method consists of three steps, nodule segmentation, histogram analysis of CT density inside nodule, and classifying nodules into five types based on histogram patterns. In this paper, we introduce a two-dimensional (2-D) joint histogram with respect to distance from nodule center and CT density inside nodule and explore numerical features with respect to shape and position of the joint histogram.

  16. Active Free Surface Density Maps

    NASA Astrophysics Data System (ADS)

    Çelen, S.

    2016-10-01

    Percolation problems were occupied to many physical problems after their establishment in 1957 by Broadbent and Hammersley. They can be used to solve complex systems such as bone remodeling. Volume fraction method was adopted to set some algorithms in the literature. However, different rate of osteoporosis could be observed for different microstructures which have the same mass density, mechanical stimuli, hormonal stimuli and nutrition. Thus it was emphasized that the bone might have identical porosity with different specific surfaces. Active free surface density of bone refers the used total area for its effective free surface. The purpose of this manuscript is to consolidate a mathematical approach which can be called as “active free surface density maps” for different surface patterns and derive their formulations. Active free surface density ratios were calculated for different Archimedean lattice models according to Helmholtz free energy and they were compared with their site and bond percolation thresholds from the background studies to derive their potential probability for bone remodeling.

  17. A new approach to calculate Plant Area Density (PAD) using 3D ground-based lidar

    NASA Astrophysics Data System (ADS)

    Taheriazad, Leila; Moghadas, Hamid; Sanchez-Azofeifa, Arturo

    2016-10-01

    This paper presents a novel algorithm for calculation of plant area density based on surface and volume convex hull which is applied to each horizontal cut of a point cloud data. This method can be used as an alternative to conventional voxelization approaches to improve accuracy and computation efficiency. The terrestrial data was collected from a boreal forest at Peace River, Alberta, Canada during summer and fall in 2014. This technique can be applied to an arbitrary point cloud data to calculate all other metrics of forests including plant area index, leaf area density, and also leaf area index.

  18. Postprocessing of 3-D current density reconstruction results with equivalent ellipsoids.

    PubMed

    Ziolkowski, Marek; Haueisen, Jens; Leder, Uwe

    2002-11-01

    A method of postprocessing and visualizing three-dimensional vector fields, such as current density reconstruction results, is presented. This method is based on equivalent ellipsoids fitted to the vector fields. The technique has been tested with simulated data and current density reconstructions based on bioelectromagnetic data obtained from a physical thorax phantom. Three different approaches based on: 1) longest distance; 2) dominant direction; and 3) principal component analysis, for fitting the equivalent ellipsoids are proposed. Multiple foci in vector fields are extracted by multiple ellipsoids which are fitted iteratively. The method enables statistical postprocessing for the sake of comparisons of different source reconstructions algorithms or comparisons of groups of patients or volunteers.

  19. 5D Modelling: An Efficient Approach for Creating Spatiotemporal Predictive 3D Maps of Large-Scale Cultural Resources

    NASA Astrophysics Data System (ADS)

    Doulamis, A.; Doulamis, N.; Ioannidis, C.; Chrysouli, C.; Grammalidis, N.; Dimitropoulos, K.; Potsiou, C.; Stathopoulou, E.-K.; Ioannides, M.

    2015-08-01

    Outdoor large-scale cultural sites are mostly sensitive to environmental, natural and human made factors, implying an imminent need for a spatio-temporal assessment to identify regions of potential cultural interest (material degradation, structuring, conservation). On the other hand, in Cultural Heritage research quite different actors are involved (archaeologists, curators, conservators, simple users) each of diverse needs. All these statements advocate that a 5D modelling (3D geometry plus time plus levels of details) is ideally required for preservation and assessment of outdoor large scale cultural sites, which is currently implemented as a simple aggregation of 3D digital models at different time and levels of details. The main bottleneck of such an approach is its complexity, making 5D modelling impossible to be validated in real life conditions. In this paper, a cost effective and affordable framework for 5D modelling is proposed based on a spatial-temporal dependent aggregation of 3D digital models, by incorporating a predictive assessment procedure to indicate which regions (surfaces) of an object should be reconstructed at higher levels of details at next time instances and which at lower ones. In this way, dynamic change history maps are created, indicating spatial probabilities of regions needed further 3D modelling at forthcoming instances. Using these maps, predictive assessment can be made, that is, to localize surfaces within the objects where a high accuracy reconstruction process needs to be activated at the forthcoming time instances. The proposed 5D Digital Cultural Heritage Model (5D-DCHM) is implemented using open interoperable standards based on the CityGML framework, which also allows the description of additional semantic metadata information. Visualization aspects are also supported to allow easy manipulation, interaction and representation of the 5D-DCHM geometry and the respective semantic information. The open source 3DCity

  20. Comparative analysis of 3D expression patterns of transcription factor genes and digit fate maps in the developing chick wing.

    PubMed

    Fisher, Malcolm; Downie, Helen; Welten, Monique C M; Delgado, Irene; Bain, Andrew; Planzer, Thorsten; Sherman, Adrian; Sang, Helen; Tickle, Cheryll

    2011-04-22

    Hoxd13, Tbx2, Tbx3, Sall1 and Sall3 genes are candidates for encoding antero-posterior positional values in the developing chick wing and specifying digit identity. In order to build up a detailed profile of gene expression patterns in cell lineages that give rise to each of the digits over time, we compared 3 dimensional (3D) expression patterns of these genes during wing development and related them to digit fate maps. 3D gene expression data at stages 21, 24 and 27 spanning early bud to digital plate formation, captured from in situ hybridisation whole mounts using Optical Projection Tomography (OPT) were mapped to reference wing bud models. Grafts of wing bud tissue from GFP chicken embryos were used to fate map regions of the wing bud giving rise to each digit; 3D images of the grafts were captured using OPT and mapped on to the same models. Computational analysis of the combined computerised data revealed that Tbx2 and Tbx3 are expressed in digit 3 and 4 progenitors at all stages, consistent with encoding stable antero-posterior positional values established in the early bud; Hoxd13 and Sall1 expression is more dynamic, being associated with posterior digit 3 and 4 progenitors in the early bud but later becoming associated with anterior digit 2 progenitors in the digital plate. Sox9 expression in digit condensations lies within domains of digit progenitors defined by fate mapping; digit 3 condensations express Hoxd13 and Sall1, digit 4 condensations Hoxd13, Tbx3 and to a lesser extent Tbx2. Sall3 is only transiently expressed in digit 3 progenitors at stage 24 together with Sall1 and Hoxd13; then becomes excluded from the digital plate. These dynamic patterns of expression suggest that these genes may play different roles in digit identity either together or in combination at different stages including the digit condensation stage.

  1. A direct approach for instantaneous 3D density field reconstruction from background-oriented schlieren (BOS) measurements

    NASA Astrophysics Data System (ADS)

    Nicolas, F.; Todoroff, V.; Plyer, A.; Le Besnerais, G.; Donjat, D.; Micheli, F.; Champagnat, F.; Cornic, P.; Le Sant, Y.

    2016-01-01

    We present a new numerical method for reconstruction of instantaneous density volume from 3D background-oriented schlieren (3DBOS) measurements, with a validation on a dedicated flexible experimental BOS bench. In contrast to previous works, we use a direct formulation where density is estimated from measured deviation fields without the intermediate step of density gradient reconstruction. Regularization techniques are implemented to deal with the ill-posed problem encountered. The resulting high-dimensional optimization is conducted by conjugate gradient techniques. A parallel algorithm, implemented on graphics processing unit, helps to speed up the calculation. The resulting software is validated on synthetic BOS images of a 3D density field issued from a numerical simulation. Then, we describe a dedicated 3DBOS experimental facility which has been built to study various BOS settings and to assess the performance of the proposed numerical reconstruction process. Results on various datasets illustrate the potential of the method for flow characterization and measurement in real-world conditions.

  2. Lessons in modern digital field geology: Open source software, 3D techniques, and the new world of digital mapping

    NASA Astrophysics Data System (ADS)

    Pavlis, Terry; Hurtado, Jose; Langford, Richard; Serpa, Laura

    2014-05-01

    Although many geologists refuse to admit it, it is time to put paper-based geologic mapping into the historical archives and move to the full potential of digital mapping techniques. For our group, flat map digital geologic mapping is now a routine operation in both research and instruction. Several software options are available, and basic proficiency with the software can be learned in a few hours of instruction and practice. The first practical field GIS software, ArcPad, remains a viable, stable option on Windows-based systems. However, the vendor seems to be moving away from ArcPad in favor of mobile software solutions that are difficult to implement without GIS specialists. Thus, we have pursued a second software option based on the open source program QGIS. Our QGIS system uses the same shapefile-centric data structure as our ArcPad system, including similar pop-up data entry forms and generic graphics for easy data management in the field. The advantage of QGIS is that the same software runs on virtually all common platforms except iOS, although the Android version remains unstable as of this writing. A third software option we are experimenting with for flat map-based field work is Fieldmove, a derivative of the 3D-capable program Move developed by Midland Valley. Our initial experiments with Fieldmove are positive, particularly with the new, inexpensive (<300Euros) Windows tablets. However, the lack of flexibility in data structure makes for cumbersome workflows when trying to interface our existing shapefile-centric data structures to Move. Nonetheless, in spring 2014 we will experiment with full-3D immersion in the field using the full Move software package in combination with ground based LiDAR and photogrammetry. One new workflow suggested by our initial experiments is that field geologists should consider using photogrammetry software to capture 3D visualizations of key outcrops. This process is now straightforward in several software packages, and

  3. Electromechanical wave imaging (EWI) validation in all four cardiac chambers with 3D electroanatomic mapping in canines in vivo

    NASA Astrophysics Data System (ADS)

    Costet, Alexandre; Wan, Elaine; Bunting, Ethan; Grondin, Julien; Garan, Hasan; Konofagou, Elisa

    2016-11-01

    Characterization and mapping of arrhythmias is currently performed through invasive insertion and manipulation of cardiac catheters. Electromechanical wave imaging (EWI) is a non-invasive ultrasound-based imaging technique, which tracks the electromechanical activation that immediately follows electrical activation. Electrical and electromechanical activations were previously found to be linearly correlated in the left ventricle, but the relationship has not yet been investigated in the three other chambers of the heart. The objective of this study was to investigate the relationship between electrical and electromechanical activations and validate EWI in all four chambers of the heart with conventional 3D electroanatomical mapping. Six (n  =  6) normal adult canines were used in this study. The electrical activation sequence was mapped in all four chambers of the heart, both endocardially and epicardially using the St Jude’s EnSite 3D mapping system (St. Jude Medical, Secaucus, NJ). EWI acquisitions were performed in all four chambers during normal sinus rhythm, and during pacing in the left ventricle. Isochrones of the electromechanical activation were generated from standard echocardiographic imaging views. Electrical and electromechanical activation maps were co-registered and compared, and electrical and electromechanical activation times were plotted against each other and linear regression was performed for each pair of activation maps. Electromechanical and electrical activations were found to be directly correlated with slopes of the correlation ranging from 0.77 to 1.83, electromechanical delays between 9 and 58 ms and R 2 values from 0.71 to 0.92. The linear correlation between electrical and electromechanical activations and the agreement between the activation maps indicate that the electromechanical activation follows the pattern of propagation of the electrical activation. This suggests that EWI may be used as a novel non-invasive method

  4. Density Altitude Maps of Iran and Iraq

    DTIC Science & Technology

    1991-05-01

    standard, DA is lower than PA. DA can also be expressed as the altitude in the ICAO standard atmosphere at which a given density occurs. The maps...produced in this study show the altitude in the ICAO standard atmosphere at which surface density occurs.

  5. Visualization and mapping of neurosurgical functional brain data onto a 3-D MR-based model of the brain surface.

    PubMed

    Modayur, B R; Prothero, J; Rosse, C; Jakobovits, R; Brinkley, J F

    1996-01-01

    The Human Brain Project was initiated with the goal of developing methods for managing and sharing information about the brain. As a prototype Human Brain Project application we are developing a system for organizing, visualizing, integrating and sharing information about human language function. The goal of the brain mapping component of our work, described in this article, is to generate the 3D location and extent of cortical language sites with respect to a uniform, 3D patient coordinate system. The language sites of individual patients can then be combined with or related to other patient data in terms of a Talairach, surface-based, or other deformable coordinate systems. Language site mapping is done by visually comparing an intraoperative photograph with the rendered image (from MRI data). The techniques outlined in this article have been utilized to map cortical language sites of six patients. Preliminary results point to the adequacy of our volume visualizations for language mapping. The strength of the visualization scheme lies in the combination of interactive segmentation with volume and surface visualization. We are now in the process of acquiring more patient data to further validate the usefulness of our method.

  6. A simple, fast, and repeatable survey method for underwater visual 3D benthic mapping and monitoring.

    PubMed

    Pizarro, Oscar; Friedman, Ariell; Bryson, Mitch; Williams, Stefan B; Madin, Joshua

    2017-03-01

    Visual 3D reconstruction techniques provide rich ecological and habitat structural information from underwater imagery. However, an unaided swimmer or diver struggles to navigate precisely over larger extents with consistent image overlap needed for visual reconstruction. While underwater robots have demonstrated systematic coverage of areas much larger than the footprint of a single image, access to suitable robotic systems is limited and requires specialized operators. Furthermore, robots are poor at navigating hydrodynamic habitats such as shallow coral reefs. We present a simple approach that constrains the motion of a swimmer using a line unwinding from a fixed central drum. The resulting motion is the involute of a circle, a spiral-like path with constant spacing between revolutions. We test this survey method at a broad range of habitats and hydrodynamic conditions encircling Lizard Island in the Great Barrier Reef, Australia. The approach generates fast, structured, repeatable, and large-extent surveys (~110 m(2) in 15 min) that can be performed with two people and are superior to the commonly used "mow the lawn" method. The amount of image overlap is a design parameter, allowing for surveys that can then be reliably used in an automated processing pipeline to generate 3D reconstructions, orthographically projected mosaics, and structural complexity indices. The individual images or full mosaics can also be labeled for benthic diversity and cover estimates. The survey method we present can serve as a standard approach to repeatedly collecting underwater imagery for high-resolution 2D mosaics and 3D reconstructions covering spatial extents much larger than a single image footprint without requiring sophisticated robotic systems or lengthy deployment of visual guides. As such, it opens up cost-effective novel observations to inform studies relating habitat structure to ecological processes and biodiversity at scales and spatial resolutions not readily

  7. Improved 3D Look-Locker Acquisition Scheme and Angle Map Filtering Procedure for T1 Estimation

    PubMed Central

    Hui, CheukKai; Esparza-Coss, Emilio; Narayana, Ponnada A

    2013-01-01

    The 3D Look-Locker (LL) acquisition is a widely used fast and efficient T1 mapping method. However, the multi-shot approach of 3D LL acquisition can introduce reconstruction artifacts that result in intensity distortions. Traditional 3D LL acquisition generally utilizes centric encoding scheme that is limited to a single phase encoding direction in the k-space. To optimize the k-space segmentation, an elliptical scheme with two phase encoding directions is implemented for the LL acquisition. This elliptical segmentation can reduce the intensity errors in the reconstructed images and improve the final T1 estimation. One of the major sources of error in LL based T1 estimation is lack of accurate knowledge of the actual flip angle. Multi-parameter curve fitting procedure can account for some of the variability in the flip angle. However, curve fitting can also introduce errors in the estimated flip angle that can result in incorrect T1 values. A filtering procedure based on goodness of fit (GOF) is proposed to reduce the effect of false flip angle estimates. Filtering based on the GOF weighting can remove likely incorrect angles that result in bad curve fit. Simulation, phantom, and in-vivo studies have demonstrated that these techniques can improve the accuracy of 3D LL T1 estimation. PMID:23784967

  8. Interpretation and mapping of geological features using mobile devices for 3D outcrop modelling

    NASA Astrophysics Data System (ADS)

    Buckley, Simon J.; Kehl, Christian; Mullins, James R.; Howell, John A.

    2016-04-01

    Advances in 3D digital geometric characterisation have resulted in widespread adoption in recent years, with photorealistic models utilised for interpretation, quantitative and qualitative analysis, as well as education, in an increasingly diverse range of geoscience applications. Topographic models created using lidar and photogrammetry, optionally combined with imagery from sensors such as hyperspectral and thermal cameras, are now becoming commonplace in geoscientific research. Mobile devices (tablets and smartphones) are maturing rapidly to become powerful field computers capable of displaying and interpreting 3D models directly in the field. With increasingly high-quality digital image capture, combined with on-board sensor pose estimation, mobile devices are, in addition, a source of primary data, which can be employed to enhance existing geological models. Adding supplementary image textures and 2D annotations to photorealistic models is therefore a desirable next step to complement conventional field geoscience. This contribution reports on research into field-based interpretation and conceptual sketching on images and photorealistic models on mobile devices, motivated by the desire to utilise digital outcrop models to generate high quality training images (TIs) for multipoint statistics (MPS) property modelling. Representative training images define sedimentological concepts and spatial relationships between elements in the system, which are subsequently modelled using artificial learning to populate geocellular models. Photorealistic outcrop models are underused sources of quantitative and qualitative information for generating TIs, explored further in this research by linking field and office workflows through the mobile device. Existing textured models are loaded to the mobile device, allowing rendering in a 3D environment. Because interpretation in 2D is more familiar and comfortable for users, the developed application allows new images to be captured

  9. Assessing the performance of density functional theory for the electronic structure of metal-salens: the 3d(0)-metals.

    PubMed

    Sears, John S; Sherrill, C David

    2008-04-17

    A series of metal-salen complexes of the 3d(0) metals Sc(III), Ti(IV), V(V), Cr(VI), and Mn(VII) have been explored using high-level electronic structure methods including coupled-cluster theory with singles, doubles, and perturbative triples as well as complete active-space third-order perturbation theory. The performance of three common density functional theory approaches has been assessed for both the geometries and the relative energies of the low-lying electronic states. The nondynamical correlation effects are demonstrated to be extremely large in all of the systems examined. Although density functional theory provides reasonable results for some of the systems, the overall agreement is quite poor. This said, the density functional theory approaches are shown to outperform the single-reference perturbation theory and coupled-cluster theory approaches for cases of strong nondynamical correlation.

  10. GPU-based rapid reconstruction of cellular 3D refractive index maps from tomographic phase microscopy (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Dardikman, Gili; Shaked, Natan T.

    2016-03-01

    We present highly parallel and efficient algorithms for real-time reconstruction of the quantitative three-dimensional (3-D) refractive-index maps of biological cells without labeling, as obtained from the interferometric projections acquired by tomographic phase microscopy (TPM). The new algorithms are implemented on the graphic processing unit (GPU) of the computer using CUDA programming environment. The reconstruction process includes two main parts. First, we used parallel complex wave-front reconstruction of the TPM-based interferometric projections acquired at various angles. The complex wave front reconstructions are done on the GPU in parallel, while minimizing the calculation time of the Fourier transforms and phase unwrapping needed. Next, we implemented on the GPU in parallel the 3-D refractive index map retrieval using the TPM filtered-back projection algorithm. The incorporation of algorithms that are inherently parallel with a programming environment such as Nvidia's CUDA makes it possible to obtain real-time processing rate, and enables high-throughput platform for label-free, 3-D cell visualization and diagnosis.

  11. In vivo MEMRI characterization of brain metastases using a 3D Look-Locker T1-mapping sequence

    PubMed Central

    Castets, Charles R.; Koonjoo, Néha; Hertanu, Andreea; Voisin, Pierre; Franconi, Jean-Michel; Miraux, Sylvain; Ribot, Emeline J.

    2016-01-01

    Although MEMRI (Manganese Enhanced MRI) informations were obtained on primary tumors in small animals, MEMRI data on metastases are lacking. Thus, our goal was to determine if 3D Look-Locker T1 mapping was an efficient method to evaluate Mn ions transport in brain metastases in vivo. The high spatial resolution in 3D (156 × 156 × 218 μm) of the sequence enabled to detect metastases of 0.3 mm3. In parallel, the T1 quantitation enabled to distinguish three populations of MDA-MB-231 derived brain metastases after MnCl2 intravenous injection: one with a healthy blood-tumor barrier that did not internalize Mn2+ ions, and two others, which T1 shortened drastically by 54.2% or 24%. Subsequent scans of the mice, enabled by the fast acquisition (23 min), demonstrated that these T1 reached back their pre-injection values in 24 h. Contrarily to metastases, the T1 of U87-MG glioma remained 26.2% shorter for one week. In vitro results supported the involvement of the Transient Receptor Potential channels and the Calcium-Sensing Receptor in the uptake and efflux of Mn2+ ions, respectively. This study highlights the ability of the 3D Look-Locker T1 mapping sequence to study heterogeneities (i) amongst brain metastases and (ii) between metastases and glioma regarding Mn transport. PMID:27995976

  12. 3D-Pharmacophore mapping of thymidine-based inhibitors of TMPK as potential antituberculosis agents

    NASA Astrophysics Data System (ADS)

    Andrade, Carolina Horta; Pasqualoto, Kerly F. M.; Ferreira, Elizabeth I.; Hopfinger, Anton J.

    2010-02-01

    Tuberculosis (TB) is the primary cause of mortality among infectious diseases. Mycobacterium tuberculosis monophosphate kinase (TMPKmt) is essential to DNA replication. Thus, this enzyme represents a promising target for developing new drugs against TB. In the present study, the receptor-independent, RI, 4D-QSAR method has been used to develop QSAR models and corresponding 3D-pharmacophores for a set of 81 thymidine analogues, and two corresponding subsets, reported as inhibitors of TMPKmt . The resulting optimized models are not only statistically significant with r 2 ranging from 0.83 to 0.92 and q 2 from 0.78 to 0.88, but also are robustly predictive based on test set predictions. The most and the least potent inhibitors in their respective postulated active conformations, derived from each of the models, were docked in the active site of the TMPKmt crystal structure. There is a solid consistency between the 3D-pharmacophore sites defined by the QSAR models and interactions with binding site residues. Moreover, the QSAR models provide insights regarding a probable mechanism of action of the analogues.

  13. CheS-Mapper - Chemical Space Mapping and Visualization in 3D

    PubMed Central

    2012-01-01

    Analyzing chemical datasets is a challenging task for scientific researchers in the field of chemoinformatics. It is important, yet difficult to understand the relationship between the structure of chemical compounds, their physico-chemical properties, and biological or toxic effects. To that respect, visualization tools can help to better comprehend the underlying correlations. Our recently developed 3D molecular viewer CheS-Mapper (Chemical Space Mapper) divides large datasets into clusters of similar compounds and consequently arranges them in 3D space, such that their spatial proximity reflects their similarity. The user can indirectly determine similarity, by selecting which features to employ in the process. The tool can use and calculate different kind of features, like structural fragments as well as quantitative chemical descriptors. These features can be highlighted within CheS-Mapper, which aids the chemist to better understand patterns and regularities and relate the observations to established scientific knowledge. As a final function, the tool can also be used to select and export specific subsets of a given dataset for further analysis. PMID:22424447

  14. From Rice Bran to High Energy Density Supercapacitors: A New Route to Control Porous Structure of 3D Carbon

    PubMed Central

    Hou, Jianhua; Cao, Chuanbao; Ma, Xilan; Idrees, Faryal; Xu, Bin; Hao, Xin; Lin, Wei

    2014-01-01

    Controlled micro/mesopores interconnected structures of three-dimensional (3D) carbon with high specific surface areas (SSA) are successfully prepared by carbonization and activation of biomass (raw rice brans) through KOH. The highest SSA of 2475 m2 g−1 with optimized pore volume of 1.21 cm3 g−1 (40% for mesopores) is achieved for KOH/RBC = 4 mass ratio, than others. The as-prepared 3D porous carbon-based electrode materials for supercapacitors exhibit high specific capacitance specifically at large current densities of 10 A g−1 and 100 A g−1 i.e., 265 F g−1 and 182 F g−1 in 6 M KOH electrolyte, respectively. Moreover, a high power density ca. 1223 W kg−1 (550 W L−1) and energy density 70 W h kg−1 (32 W h L−1) are achieved on the base of active material loading (~10 mg cm2) in the ionic liquid. The findings can open a new avenue to use abundant agricultural by-products as ideal materials with promising applications in high-performance energy-storage devices. PMID:25434348

  15. In-situ biofouling assessment in spacer filled channels using optical coherence tomography (OCT): 3D biofilm thickness mapping.

    PubMed

    Fortunato, Luca; Leiknes, TorOve

    2017-04-01

    Membrane systems for water purification can be seriously hampered by biofouling. The use of optical coherence tomography (OCT) to investigate biofilms in membrane systems has recently increased due to the ability to do the characterization in-situ and non-destructively. The OCT biofilm thickness map is presented for the first time as a tool to assess biofilm spatial distribution on a surface. The map allows the visualization and evaluation of the biofilm formation and growth in membrane filtration systems through the use of a false color scale. The biofilm development was monitored with OCT to evaluate the suitability of the proposed approach. A 3D time series analysis of biofilm development in a spacer filled channel representative of a spiral-wound membrane element was performed. The biofilm thickness map enables the time-resolved and spatial-resolved evaluation and visualization of the biofilm deposition pattern in-situ non-destructively.

  16. Mapping of the C3d receptor (CR2)-binding site and a neoantigenic site in the C3d domain of the third component of complement.

    PubMed Central

    Lambris, J D; Ganu, V S; Hirani, S; Müller-Eberhard, H J

    1985-01-01

    The C3d domain of C3 contains the site that binds to the C3d receptor (CR2) which is expressed on B lymphocytes. It also contains a neoantigenic determinant that is recognized by monoclonal antibody (mAb) 130 and is expressed when C3b is cleaved to iC3b and subsequently to C3dg or C3d. mAb 130 inhibits the binding of C3d to CR2. In this study, the locations of the CR2-binding site and of the neoantigen recognized by mAb 130 within the C3d domain were investigated. Treatment of human C3d with CNBr generated two major fragments with Mrs of 12,500 and 8600. Binding studies showed that only the Mr 8600 fragment was capable of binding to both CR2 and mAb 130. Amino-terminal sequence analysis of the Mr 8600 fragment and comparison with the amino acid sequence derived from human C3 cDNA [de Bruijn, M. H. L. & Fey, G. H. (1985) Proc. Natl. Acad. Sci. USA 82, 708-712] placed it between residues 1199 and 1274 of the C3 sequence. Several peptides were synthesized according to the derived C3 sequence of amino acid residues 1209-1236. Based on their differential binding to CR2 and mAb 130, we localized the CR2-binding site and mAb 130 neoantigenic site, respectively, to residues 1227-1232 and 1217-1232 of the C3 sequence. PMID:2408276

  17. 3D-Printed High-Density Droplet Array Chip for Miniaturized Protein Crystallization Screening under Vapor Diffusion Mode.

    PubMed

    Liang, Yi-Ran; Zhu, Li-Na; Gao, Jie; Zhao, Hong-Xia; Zhu, Ying; Ye, Sheng; Fang, Qun

    2017-03-23

    Here we describe the combination of three-dimensional (3D) printed chip and automated microfluidic droplet-based screening techniques for achieving massively parallel, nanoliter-scale protein crystallization screening under vapor diffusion mode. We fabricated high-density microwell array chips for sitting-drop vapor diffusion crystallization utilizing the advantage of the 3D-printing technique in producing high-aspect-ratio chips. To overcome the obstacle of 3D-printed microchips in performing long-term reactions caused by their porousness and gas permeability properties in chip body, we developed a two-step postprocessing method, including paraffin filling and parylene coating, to achieve high sealability and stability. We also developed a simple method especially suitable for controlling the vapor diffusion speed of nanoliter-scale droplets by changing the layer thickness of covering oil. With the above methods, 84 tests of nanoliter-scale protein crystallization under vapor diffusion mode were successfully achieved in the 7 × 12 droplet array chip with a protein consumption of 10 nL for each test, which is 20-100 times lower than that in the conventional large-volume screening system. Such a nanoliter-scale vapor diffusion system was applied to two model proteins with commercial precipitants and displayed advantages over that under microbatch mode. It identified more crystallization conditions, especially for the protein samples with lower concentrations.

  18. Application of 3D scanned imaging methodology for volume, surface area, and envelope density evaluation of densified biomass.

    PubMed

    Igathinathane, C; Davis, J D; Purswell, J L; Columbus, E P

    2010-06-01

    Measurement of volume, surface area, and density is an essential for quantifying, evaluating, and designing the biomass densification, storage, and transport operations. Acquiring accurate and repeated measurements of these parameters for hygroscopic densified biomass are not straightforward and only a few methods are available. A 3D laser scanner was used as a measurement device and the 3D images were analyzed using image processing software. The validity of the method was verified using reference objects of known geometry and the accuracy obtained was in excess of 98%. Cotton gin trash briquettes, switchgrass pellets, switchgrass cubes, hardwood pellets, and softwood chips were tested. Most accurate results of the volume and surface area required the highest possible resolution of the scanner, which increased the total scan-process times, and image file size. Physical property determination using the 3D scanning and image analysis is highly repeatable (coefficient of variation <0.3%), non-invasive, accurate, and alternative methodology. The various limitations and merits of the developed method were also enumerated.

  19. Quenching of the beam-plasma instability by 3-D spectra of large scale density fluctuations

    NASA Technical Reports Server (NTRS)

    Muschietti, L.; Goldman, M. V.; Newman, D.

    1984-01-01

    A model is presented to explain the highly variable yet low level of Langmuir waves measured in situ by spacecraft when electron beams associated with Type III solar bursts are passing by; the low level of excited waves allows the propagation of such streams from the Sun to well past 1 AU without catastrophic energy losses. The model is based, first, on the existence of large scale density fluctuations that are able to efficiently diffuse small k beam unstable Langmuir waves in phase space, and, second, on the presence of a significantly isotropic nonthermal tail in the distribution function of the background electron population, which is capable of stabilizing larger k modes. The strength of the model lies in its ability to predict various levels of Langmuir waves depending on the parameters. This feature is consistent with the high variability actually observed in the measurements.

  20. Mapping snow avalanche risk using GIS technique and 3D modeling in Ceahlau Mountain

    NASA Astrophysics Data System (ADS)

    Covasnianu, A.; Grigoras, I. R.; State, L. E.; Balin, D.; Hogas, S.; Balin, I.

    2009-04-01

    This study consisted in a precise mapping project (GPS field campaign and on-screen digitization of the topographic maps at 1:5.000 scale) of the Ceahlau mountain area in Romanian Carpathians in order to address the snow avalanche risk management, surveying and monitoring. Thus we considered the slope, aspect, altitude, landforms and roughness derived from a high resolute numerical terrain model (31 km2 at 1: 5.000 scale resulted in a spatial resolution of 3 m by the help of Topo to Raster tool). These parameters were classified according to a model applied into Tatra Mountains and used over Ceahlau Massive. The results were adapted and interpreted considering to the European Avalanche Hazard Scale. This work was made in the context of the elaboration of Risk Map and is directly concerning both the security of tourism activities but also the management of the Natural Park Ceahlau. The extension of this method to similar mountain areas is ongoing.

  1. Evaluating the Potential of Rtk-Uav for Automatic Point Cloud Generation in 3d Rapid Mapping

    NASA Astrophysics Data System (ADS)

    Fazeli, H.; Samadzadegan, F.; Dadrasjavan, F.

    2016-06-01

    During disaster and emergency situations, 3D geospatial data can provide essential information for decision support systems. The utilization of geospatial data using digital surface models as a basic reference is mandatory to provide accurate quick emergency response in so called rapid mapping activities. The recipe between accuracy requirements and time restriction is considered critical in this situations. UAVs as alternative platforms for 3D point cloud acquisition offer potentials because of their flexibility and practicability combined with low cost implementations. Moreover, the high resolution data collected from UAV platforms have the capabilities to provide a quick overview of the disaster area. The target of this paper is to experiment and to evaluate a low-cost system for generation of point clouds using imagery collected from a low altitude small autonomous UAV equipped with customized single frequency RTK module. The customized multi-rotor platform is used in this study. Moreover, electronic hardware is used to simplify user interaction with the UAV as RTK-GPS/Camera synchronization, and beside the synchronization, lever arm calibration is done. The platform is equipped with a Sony NEX-5N, 16.1-megapixel camera as imaging sensor. The lens attached to camera is ZEISS optics, prime lens with F1.8 maximum aperture and 24 mm focal length to deliver outstanding images. All necessary calibrations are performed and flight is implemented over the area of interest at flight height of 120 m above the ground level resulted in 2.38 cm GSD. Earlier to image acquisition, 12 signalized GCPs and 20 check points were distributed in the study area and measured with dualfrequency GPS via RTK technique with horizontal accuracy of σ = 1.5 cm and vertical accuracy of σ = 2.3 cm. results of direct georeferencing are compared to these points and experimental results show that decimeter accuracy level for 3D points cloud with proposed system is achievable, that is suitable

  2. 3D model of small-scale density cavities in the auroral magnetosphere with field-aligned current

    NASA Astrophysics Data System (ADS)

    Bespalov, P. A.; Misonova, V. G.; Savina, O. N.

    2016-09-01

    We propose a 3D model of small-scale density cavities stimulated by an auroral field-aligned current and an oscillating field-aligned current of kinetic Alfvén waves. It is shown that when the field-aligned current increases so that the electron drift velocity exceeds a value of the order of the electron thermal velocity, the plasma becomes unstable to the formation of cavities with low density and strong electric field. The condition of instability is associated with the value of the background magnetic field. In the case of a relatively weak magnetic field (where the electron gyro-radius is greater than the ion acoustic wavelength), the current instability can lead to the formation of one-dimensional cavities along the magnetic field. In the case of a stronger magnetic field (where the ion acoustic wavelength is greater than the electron gyro-radius, but still is less than the ion gyro-radius), the instability can lead to the formation of 3D density cavities. In this case, the spatial scales of the cavity, both along and across the background magnetic field, can be comparable, and at the earlier stage of the cavity formation they are of the order of the ion acoustic wavelength. Rarefactions of the cavity density are accompanied by an increase in the electric field and are limited by the pressure of bipolar electric fields that occur within them. The estimates of typical density cavity characteristics and the results of numerical solutions agree with known experimental data: small-scale structures with a sufficiently strong electric field are observed in the auroral regions with strong field-aligned current.

  3. VizieR Online Data Catalog: 3D extinction map of northern Galactic plane (Sale+, 2014)

    NASA Astrophysics Data System (ADS)

    Sale, S. E.; Drew, J. E.; Barentsen, G.; Farnhill, H. J.; Raddi, R.; Barlow, M. J.; Eisloffel, J.; Vink, J. S.; Rodriguez-Gil, P.; Wright, N. J.

    2014-06-01

    We present a three dimensional map of extinction in the Northern Galactic Plane derived using photometry from the IPHAS survey. We construct the map using a method based on a hierarchical Bayesian model as previously described by Sale (2012MNRAS.427.2119S). In addition to mean extinction, we also measure differential extinction, which arises from the fractal nature of the ISM. The method applied also furnishes us with photometric estimates of the distance, extinction, effective temperature, surface gravity, and mass for ~38 million stars. Further details about the data as well as additional formats and data products are available via http://www.iphas.org/extinction. (2 data files).

  4. A 3D dust map from Pan-STARRS 1 photometry

    NASA Astrophysics Data System (ADS)

    Green, Gregory M.

    We have constructed a three-dimensional map of dust in the Milky Way, tracing reddening on ˜ 7' scales out to a distance of several kiloparsecs. We trace reddening using stars embedded in the dust, by simultaneously inferring stellar distance, stellar type, and the reddening along the line of sight. We use 5-band grizy Pan-STARRS 1 photometry of 800 million stars, augmented by 3-band 2MASS JHKs photometry when available. The full map is available at http://argonaut.skymaps.info. An online version of this talk is available at http://http://greg.ory.gr/present/ewass2015.

  5. EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy

    DOE PAGES

    Barad, Benjamin A.; Echols, Nathaniel; Wang, Ray Yu-Ruei; ...

    2015-08-17

    Advances in high-resolution cryo-electron microscopy (cryo-EM) require the development of validation metrics to independently assess map quality and model geometry. We report that EMRinger is a tool that assesses the precise fitting of an atomic model into the map during refinement and shows how radiation damage alters scattering from negatively charged amino acids. EMRinger (https://github.com/fraser-lab/EMRinger) will be useful for monitoring progress in resolving and modeling high-resolution features in cryo-EM.

  6. Mapping of the spontaneous deletion in the Ap3d1 gene of mocha mice: fast and reliable genotyping

    PubMed Central

    Drasbek, Kim Ryun; Holm, Mai Marie; Delenclos, Marion; Jensen, Kimmo

    2008-01-01

    Background The mocha mouse carries a spontaneous deletion in the Ap3d1 gene, encoding the delta 1 subunit of the adaptor related protein complex 3, (Ap3d1), and subsequently lack the expression of functional AP-3. This leads to a deficiency in vesicle transport and storage, which affects neurotransmitter vesicle turnover and release in the central nervous system. Since the genomic sequence of the Ap3d1 gene of mocha mouse is not known, precise mapping of the deletion as well as reliable genotyping protocols are lacking. Findings We sequenced the Ap3d1 gene (HGNC GeneID: 8943) around the deletion site in the mocha mouse and revealed a 10639 bp deletion covering exon 2 to 6. Subsequently, new PCR primers were designed yielding a reliable genotyping protocol of both newborn and adult tissue. To examine the genotypes further, hippocampal neurons were cultured from mocha and control mice. Patch-clamp recordings showed that mocha neurons had a higher input resistance, and that autaptic EPSC in mocha cultures depressed faster and stronger as compared with control cultures. Conclusion Our study reports the sequence of the deleted part of the Ap3d1 gene in mocha mice, as well as a reliable PCR-based genotyping protocol. We cultured hippocampal neurons from control and mocha mice, and found a difference in input resistance of the neurons, and in the synaptic short-term plasticity of glutamatergic autapses showing a larger synaptic depression than controls. The described procedures may be useful for the future utilization of the mocha mouse as a model of defective vesicle biogenesis. Importantly, as genotyping by eye color is complicated in newborn mice, the designed protocol is so fast and reliable that newborn mice could rapidly be genotyped and hippocampal neurons dissociated and cultured, which is normally best done at P0-P2. PMID:19032734

  7. Large Deformation Diffeomorphic Metric Mapping Registration of Reconstructed 3D Histological Section Images and in vivo MR Images

    PubMed Central

    Ceritoglu, Can; Wang, Lei; Selemon, Lynn D.; Csernansky, John G.; Miller, Michael I.; Ratnanather, J. Tilak

    2009-01-01

    Our current understanding of neuroanatomical abnormalities in neuropsychiatric diseases is based largely on magnetic resonance imaging (MRI) and post mortem histological analyses of the brain. Further advances in elucidating altered brain structure in these human conditions might emerge from combining MRI and histological methods. We propose a multistage method for registering 3D volumes reconstructed from histological sections to corresponding in vivo MRI volumes from the same subjects: (1) manual segmentation of white matter (WM), gray matter (GM) and cerebrospinal fluid (CSF) compartments in histological sections, (2) alignment of consecutive histological sections using 2D rigid transformation to construct a 3D histological image volume from the aligned sections, (3) registration of reconstructed 3D histological volumes to the corresponding 3D MRI volumes using 3D affine transformation, (4) intensity normalization of images via histogram matching, and (5) registration of the volumes via intensity based large deformation diffeomorphic metric (LDDMM) image matching algorithm. Here we demonstrate the utility of our method in the transfer of cytoarchitectonic information from histological sections to identify regions of interest in MRI scans of nine adult macaque brains for morphometric analyses. LDDMM improved the accuracy of the registration via decreased distances between GM/CSF surfaces after LDDMM (0.39 ± 0.13 mm) compared to distances after affine registration (0.76 ± 0.41 mm). Similarly, WM/GM distances decreased to 0.28 ± 0.16 mm after LDDMM compared to 0.54 ± 0.39 mm after affine registration. The multistage registration method may find broad application for mapping histologically based information, for example, receptor distributions, gene expression, onto MRI volumes. PMID:20577633

  8. 3D density model of the upper mantle of Asia based on inversion of gravity and seismic tomography data

    NASA Astrophysics Data System (ADS)

    Kaban, Mikhail K.; Stolk, Ward; Tesauro, Magdala; El Khrepy, Sami; Al-Arifi, Nassir; Beekman, Fred; Cloetingh, Sierd A. P. L.

    2016-11-01

    We construct a new-generation 3D density model of the upper mantle of Asia and its surrounding areas based on a joint interpretation of several data sets. A recent model of the crust combining nearly all available seismic data is employed to calculate the impact of the crust on the gravity anomalies and observed topography and to estimate the residual mantle anomalies and residual topography. These fields are jointly inverted to calculate the density variations in the lithosphere and upper mantle down to 325 km. As an initial approximation, we estimate density variations using a seismic tomography model. Seismic velocity variations are converted into temperatures and then to density variations based on mineral physics constraints. In the Occam-type inversion, we fit both the residual mantle gravity anomalies and residual topography by finding deviations to the initial model. The obtained corrections improve the resolution of the initial model and reflect important features of the mantle structure that are not well resolved by the seismic tomography. The most significant negative corrections of the upper mantle density, found in the Siberian and East European cratons, can be associated with depleted mantle material. The most pronounced positive density anomalies are found beneath the Tarim and South Caspian basins, Barents Sea, and Bay of Bengal. We attribute these anomalies to eclogites in the uppermost mantle, which have substantially affected the evolution of the basins. Furthermore, the obtained results provide evidence for the presence of eclogites in the oceanic subducting mantle lithosphere.

  9. Symmetry-plane model of 3D Euler flows: Mapping to regular systems and numerical solutions of blowup

    NASA Astrophysics Data System (ADS)

    Mulungye, Rachel M.; Lucas, Dan; Bustamante, Miguel D.

    2014-11-01

    We introduce a family of 2D models describing the dynamics on the so-called symmetry plane of the full 3D Euler fluid equations. These models depend on a free real parameter and can be solved analytically. For selected representative values of the free parameter, we apply the method introduced in [M.D. Bustamante, Physica D: Nonlinear Phenom. 240, 1092 (2011)] to map the fluid equations bijectively to globally regular systems. By comparing the analytical solutions with the results of numerical simulations, we establish that the numerical simulations of the mapped regular systems are far more accurate than the numerical simulations of the original systems, at the same spatial resolution and CPU time. In particular, the numerical integrations of the mapped regular systems produce robust estimates for the growth exponent and singularity time of the main blowup quantity (vorticity stretching rate), converging well to the analytically-predicted values even beyond the time at which the flow becomes under-resolved (i.e. the reliability time). In contrast, direct numerical integrations of the original systems develop unstable oscillations near the reliability time. We discuss the reasons for this improvement in accuracy, and explain how to extend the analysis to the full 3D case. Supported under the programme for Research in Third Level Institutions (PRTLI) Cycle 5 and co-funded by the European Regional Development Fund.

  10. Hard Copy to Digital Transfer: 3D Models that Match 2D Maps

    ERIC Educational Resources Information Center

    Kellie, Andrew C.

    2011-01-01

    This research describes technical drawing techniques applied in a project involving digitizing of existing hard copy subsurface mapping for the preparation of three dimensional graphic and mathematical models. The intent of this research was to identify work flows that would support the project, ensure the accuracy of the digital data obtained,…

  11. Learning Benefits of Using 2D versus 3D Maps: Evidence from a Randomized Controlled Experiment

    ERIC Educational Resources Information Center

    Niedomysl, Thomas; Ellder, Erik; Larsson, Anders; Thelin, Mikael; Jansund, Bodil

    2013-01-01

    The traditional important role of maps used for educational purposes has gained further potential with recent advances in GIS technology. But beyond specific courses in cartography this potential seems little realized in geography teaching. This article investigates the extent to which any learning benefits may be derived from the use of such…

  12. GPR Detection and 3D Mapping of Lateral Macropores II. Riparian Application

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The morphology and prevalence of 1-10 cm diameter macropores in forested riparian wetland buffers is largely unknown despite their importance as a source of preferential nutrient delivery to stream channels. Here, we validated in situ procedures for detecting and mapping the three-dimensional struct...

  13. Lab Experiments Probe Interactions Between Dilute Pyroclastic Density Currents and 3D Barriers

    NASA Astrophysics Data System (ADS)

    Fauria, K.; Andrews, B. J.; Manga, M.

    2014-12-01

    We conducted scaled laboratory experiments of unconfined dilute pyroclastic density currents (PDCs) to examine interactions between three - dimensional obstacles and dilute PDCs. While it is known that PDCs can surmount barriers by converting kinetic energy into potential energy, the signature of topography on PDC dynamics is unclear. To examine the interplay between PDCs and topography, we turbulently suspended heated and ambient-temperature 20 μm talc powder in air within an 8.5 x 6.1 x 2.6 m tank. Experimental parameters (Froude number, densimetric and thermal Richardson number, particle Stokes and Settling numbers) were scaled such that the experimental currents were dynamically similar to natural PCS. The Reynolds number, however, is much smaller than in natural currents, but still large enough for the flows to be turbulent. We placed cylindrical and ridge-like objects in the path of the currents, illuminated the currents with orthogonal laser sheets, and recorded each experiment with high definition cameras. We observed currents surmounting ridge-like barriers (barrier height = current height). Slanted ridges redirected the currents upward and parallel to the upstream face of the ridges (~45° from horizontal). Down stream of the slanted ridges, ambient-temperature currents reattached to the floor. By comparison, hot currents reversed buoyancy and lifted off. These observations suggest that obstacles enhance air entrainment, a process key to affecting runout distance and the depletion of fine particles in ignimbrites. Moreover, we observed vortex shedding in the wake of cylinders. Our experiments demonstrate that barriers of various shapes affect PDC dynamics and can shorten PDC runout distances. Understanding the effects of topography on PDCs is required for interpreting many deposits because processes such as vortex shedding and topographically-induced changes in turbulent length scales and entrainment likely leave depositional signatures.

  14. Mapping tropical biodiversity using spectroscopic imagery : characterization of structural and chemical diversity with 3-D radiative transfer modeling

    NASA Astrophysics Data System (ADS)

    Feret, J. B.; Gastellu-Etchegorry, J. P.; Lefèvre-Fonollosa, M. J.; Proisy, C.; Asner, G. P.

    2014-12-01

    The accelerating loss of biodiversity is a major environmental trend. Tropical ecosystems are particularly threatened due to climate change, invasive species, farming and natural resources exploitation. Recent advances in remote sensing of biodiversity confirmed the potential of high spatial resolution spectroscopic imagery for species identification and biodiversity mapping. Such information bridges the scale-gap between small-scale, highly detailed field studies and large-scale, low-resolution satellite observations. In order to produce fine-scale resolution maps of canopy alpha-diversity and beta-diversity of the Peruvian Amazonian forest, we designed, applied and validated a method based on spectral variation hypothesis to CAO AToMS (Carnegie Airborne Observatory Airborne Taxonomic Mapping System) images, acquired from 2011 to 2013. There is a need to understand on a quantitative basis the physical processes leading to this spectral variability. This spectral variability mainly depends on canopy chemistry, structure, and sensor's characteristics. 3D radiative transfer modeling provides a powerful framework for the study of the relative influence of each of these factors in dense and complex canopies. We simulated series of spectroscopic images with the 3D radiative model DART, with variability gradients in terms of leaf chemistry, individual tree structure, spatial and spectral resolution, and applied methods for biodiversity mapping. This sensitivity study allowed us to determine the relative influence of these factors on the radiometric signal acquired by different types of sensors. Such study is particularly important to define the domain of validity of our approach, to refine requirements for the instrumental specifications, and to help preparing hyperspectral spatial missions to be launched at the horizon 2015-2025 (EnMAP, PRISMA, HISUI, SHALOM, HYSPIRI, HYPXIM). Simulations in preparation include topographic variations in order to estimate the robustness

  15. An ultra-high element density pMUT array with low crosstalk for 3-D medical imaging.

    PubMed

    Yang, Yi; Tian, He; Wang, Yu-Feng; Shu, Yi; Zhou, Chang-Jian; Sun, Hui; Zhang, Cang-Hai; Chen, Hao; Ren, Tian-Ling

    2013-07-26

    A ~1 MHz piezoelectric micromachined ultrasonic transducer (pMUT) array with ultra-high element density and low crosstalk is proposed for the first time. This novel pMUT array is based on a nano-layer spin-coating lead zirconium titanium film technique and can be fabricated with high element density using a relatively simple process. Accordingly, key fabrication processes such as thick piezoelectric film deposition, low-stress Si-SOI bonding and bulk silicon removal have been successfully developed. The novel fine-pitch 6 × 6 pMUT arrays can all work at the desired frequency (~1 MHz) with good uniformity, high performance and potential IC integration compatibility. The minimum interspace is ~20 μm, the smallest that has ever been achieved to the best of our knowledge. These arrays can be potentially used to steer ultrasound beams and implement high quality 3-D medical imaging applications.

  16. Biometric recognition via fixation density maps

    NASA Astrophysics Data System (ADS)

    Rigas, Ioannis; Komogortsev, Oleg V.

    2014-05-01

    This work introduces and evaluates a novel eye movement-driven biometric approach that employs eye fixation density maps for person identification. The proposed feature offers a dynamic representation of the biometric identity, storing rich information regarding the behavioral and physical eye movement characteristics of the individuals. The innate ability of fixation density maps to capture the spatial layout of the eye movements in conjunction with their probabilistic nature makes them a particularly suitable option as an eye movement biometrical trait in cases when free-viewing stimuli is presented. In order to demonstrate the effectiveness of the proposed approach, the method is evaluated on three different datasets containing a wide gamut of stimuli types, such as static images, video and text segments. The obtained results indicate a minimum EER (Equal Error Rate) of 18.3 %, revealing the perspectives on the utilization of fixation density maps as an enhancing biometrical cue during identification scenarios in dynamic visual environments.

  17. Gravity data for a 3-D density model of the Po plain and the surrounding region

    NASA Astrophysics Data System (ADS)

    Tondi, Rosaria; Borghi, Alessandra; Reguzzoni, Mirko; Vuan, Alessandro; Klin, Peter

    2015-04-01

    In order to properly localise earthquakes and define, especially in tectonically active areas, the seismic risk, there is the necessity to have reliable earth models. Unfortunately, conventional geophysical tomographic methods face the problem of irregular data coverage over the surface of the studied volume, which can produce irregular image resolution. This problem is difficult to address for each isolated geophysical technique, and it demands an effort for the integration of different geophysical methods into a single inversion scheme. In this work, we show how gravity information is a valuable tool in discriminating among possible models. An appropriate density starting model: a 10 layers 1D model which represents the mean geological structure below the Po plain and the surrounding region ([7.24E-12.80E], [43.78N-46.18N]), is tested upon two different gravity data sets, three different model parametrizations and two different seismic information.. The contribution given by ground based gravity data has been compared to the one, obtained by the combination of the GOCE satellite observation with the Italian terrestrial gravity data. This combination has been performed by means of a frequency analysis, using the very low frequencies from the GOCE data, the low frequency (between 181 and 240 degrees, in term of spherical harmonics) from the integration of the ground data with the GOCE data by least-square collocation, the high frequencies are obtained by residual terrain correction modelling. The 2012 Emilia seismic sequence, together with recent instrumentation deployed within the Po plain, allows to improve the existing crustal models by using a 2-20 s regional surface wave tomography. Isotropic reference S-wave velocity models up to 25 km of depth are calculated from the local dispersion curves for both the Love and Rayleigh fundamental mode using a linearized inversion scheme. Furtherly, seismological models and gravimetric data are exploited in the Sequential

  18. Real-time Process Monitoring and Temperature Mapping of the 3D Polymer Printing Process

    SciTech Connect

    Dinwiddie, Ralph Barton; Love, Lonnie J; Rowe, John C

    2013-01-01

    An extended range IR camera was used to make temperature measurements of samples as they are being manufactured. The objective is to quantify the temperature variation inside the system as parts are being fabricated, as well as quantify the temperature of a part during fabrication. The IR camera was used to map the temperature within the build volume of the oven and surface temperature measurement of a part as it was being manufactured. The development of the temperature map of the oven provides insight into the global temperature variation within the oven that may lead to understanding variations in the properties of parts as a function of location. The observation of the temperature variation of a part that fails during construction provides insight into how the deposition process itself impacts temperature distribution within a single part leading to failure.

  19. Dynamic 3-D chemical agent cloud mapping using a sensor constellation deployed on mobile platforms

    NASA Astrophysics Data System (ADS)

    Cosofret, Bogdan R.; Konno, Daisei; Rossi, David; Marinelli, William J.; Seem, Pete

    2014-05-01

    The need for standoff detection technology to provide early Chem-Bio (CB) threat warning is well documented. Much of the information obtained by a single passive sensor is limited to bearing and angular extent of the threat cloud. In order to obtain absolute geo-location, range to threat, 3-D extent and detailed composition of the chemical threat, fusion of information from multiple passive sensors is needed. A capability that provides on-the-move chemical cloud characterization is key to the development of real-time Battlespace Awareness. We have developed, implemented and tested algorithms and hardware to perform the fusion of information obtained from two mobile LWIR passive hyperspectral sensors. The implementation of the capability is driven by current Nuclear, Biological and Chemical Reconnaissance Vehicle operational tactics and represents a mission focused alternative of the already demonstrated 5-sensor static Range Test Validation System (RTVS).1 The new capability consists of hardware for sensor pointing and attitude information which is made available for streaming and aggregation as part of the data fusion process for threat characterization. Cloud information is generated using 2-sensor data ingested into a suite of triangulation and tomographic reconstruction algorithms. The approaches are amenable to using a limited number of viewing projections and unfavorable sensor geometries resulting from mobile operation. In this paper we describe the system architecture and present an analysis of results obtained during the initial testing of the system at Dugway Proving Ground during BioWeek 2013.

  20. Whole-brain 3D mapping of human neural transplant innervation

    PubMed Central

    Doerr, Jonas; Schwarz, Martin Karl; Wiedermann, Dirk; Leinhaas, Anke; Jakobs, Alina; Schloen, Florian; Schwarz, Inna; Diedenhofen, Michael; Braun, Nils Christian; Koch, Philipp; Peterson, Daniel A.; Kubitscheck, Ulrich; Hoehn, Mathias; Brüstle, Oliver

    2017-01-01

    While transplantation represents a key tool for assessing in vivo functionality of neural stem cells and their suitability for neural repair, little is known about the integration of grafted neurons into the host brain circuitry. Rabies virus-based retrograde tracing has developed into a powerful approach for visualizing synaptically connected neurons. Here, we combine this technique with light sheet fluorescence microscopy (LSFM) to visualize transplanted cells and connected host neurons in whole-mouse brain preparations. Combined with co-registration of high-precision three-dimensional magnetic resonance imaging (3D MRI) reference data sets, this approach enables precise anatomical allocation of the host input neurons. Our data show that the same neural donor cell population grafted into different brain regions receives highly orthotopic input. These findings indicate that transplant connectivity is largely dictated by the circuitry of the target region and depict rabies-based transsynaptic tracing and LSFM as efficient tools for comprehensive assessment of host–donor cell innervation. PMID:28102196

  1. Maps of clouds modeled with the IPSL Titan 3D-GCM

    NASA Astrophysics Data System (ADS)

    Burgalat, J.; Rannou, P.; Lebonnois, S.

    2011-10-01

    A new climate model for Titan's atmosphere has been developed at the IPSL. This model uses the current version of the LMDZ General Circulation Model (GCM) dynamical core with the physics part of the 2D Titan's IPSL-GCM. First simulations made at the LMD (Laboratoire de Météorologie Dynamique) used a version of the model with coupled haze microphysics only. We update the model with the implementation of the clouds microphysics scheme inherited frome the previous 2D version. The model is now fully coupled with clouds processes and is a full 3D extension of the Titan IPSL-GCM ([2], [3]). Currently the model is not optimized and is demanding in term of computational time (approximatively 17 days of execution for one Titan's year simulation) and the model can not be used with its full capacities. Therefore all the microphysics is still computed as zonal averages. Nevertheless, new simulations performed including clouds, shows some encouraging results. The lack of asymmetry of the clouds coverage in the results of the 2D simulations. seems to vanish using the new model which tends to show that dissipation process in the 2D model was too strong. With this new model, we intented to get a better tool to understand Titan's climate and to interpret the large amount of data collected by the probes.

  2. Maps of clouds modeled with the IPSL Titan 3D-GCM

    NASA Astrophysics Data System (ADS)

    Burgalat, J.; Rannou, P.; Lebonnois, S.

    2012-09-01

    A new climate model for Titan's atmosphere has been developed at the IPSL. This model uses the current version of the LMDZ General Circulation Model (GCM) dynamical core with the physics part of the 2D Titan's IPSL-GCM. First simulations made at the LMD (Laboratoire de Météorologie Dynamique) used a version of the model with coupled haze microphysics only. We update the model with the implementation of the clouds microphysics scheme inherited from the previous 2D version. The model is now fully coupled with clouds processes and is a full 3D extension of the Titan IPSL-GCM ([2], [3]). Currently the model is not optimized and is demanding in term of computational time (approximatively 17 days of execution for one Titan's year simulation) and the model can not be used with its full capacities. Therefore all the microphysics is still computed as zonal averages. Nevertheless, new simulations performed including clouds, shows some encouraging results. The lack of asymmetry of the clouds coverage in the results of the 2D simulations seems to vanish using the new model which tends to show that dissipation process in the 2D model was too strong. With this new model, we intented to get a better tool to understand Titan's climate and to interpret the large amount of data collected by the probes.

  3. Geo-Referenced Mapping Using AN Airborne 3d Time-Of Camera

    NASA Astrophysics Data System (ADS)

    Kohoutek, T. K.; Nitsche, M.; Eisenbeiss, H.

    2011-09-01

    This paper presents the first experience of a close range bird's eye view photogrammetry with range imaging (RIM) sensors for the real time generation of high resolution geo-referenced 3D surface models. The aim of this study was to develop a mobile, versatile and less costly outdoor survey methodology to measure natural surfaces compared to the terrestrial laser scanning (TLS). Two commercial RIM cameras (SR4000 by MESA Imaging AG and a CamCube 2.0 by PMDTechnologies GmbH) were mounted on a lightweight crane and on an unmanned aerial vehicle (UAV). The field experiments revealed various challenges in real time deployment of the two state-of-the-art RIM systems, e.g. processing of the large data volume. Acquisition strategy and data processing and first measurements are presented. The precision of the measured distances is less than 1 cm for good conditions. However, the measurement precision degraded under the test conditions due to direct sunlight, strong illumination contrasts and helicopter vibrations.

  4. Whole-brain 3D mapping of human neural transplant innervation.

    PubMed

    Doerr, Jonas; Schwarz, Martin Karl; Wiedermann, Dirk; Leinhaas, Anke; Jakobs, Alina; Schloen, Florian; Schwarz, Inna; Diedenhofen, Michael; Braun, Nils Christian; Koch, Philipp; Peterson, Daniel A; Kubitscheck, Ulrich; Hoehn, Mathias; Brüstle, Oliver

    2017-01-19

    While transplantation represents a key tool for assessing in vivo functionality of neural stem cells and their suitability for neural repair, little is known about the integration of grafted neurons into the host brain circuitry. Rabies virus-based retrograde tracing has developed into a powerful approach for visualizing synaptically connected neurons. Here, we combine this technique with light sheet fluorescence microscopy (LSFM) to visualize transplanted cells and connected host neurons in whole-mouse brain preparations. Combined with co-registration of high-precision three-dimensional magnetic resonance imaging (3D MRI) reference data sets, this approach enables precise anatomical allocation of the host input neurons. Our data show that the same neural donor cell population grafted into different brain regions receives highly orthotopic input. These findings indicate that transplant connectivity is largely dictated by the circuitry of the target region and depict rabies-based transsynaptic tracing and LSFM as efficient tools for comprehensive assessment of host-donor cell innervation.

  5. Development of a numerical procedure to map a general 3-d body onto a near-circle

    NASA Technical Reports Server (NTRS)

    Hommel, M. J.

    1986-01-01

    Conformal mapping is a classical technique utilized for solving problems in aerodynamics and hydrodynamics. Conformal mapping is utilized in the construction of grids around airfoils, engine inlets and other aircraft configurations. These shapes are transformed onto a near-circle image for which the equations of fluid motion are discretized on the mapped plane and solved numerically by utilizing the appropriate techniques. In comparison to other grid-generation techniques such as algerbraic or differential type, conformal mapping offers an analytical and accurate form even if the grid deformation is large. One of the most appealing features is that the grid can be constrained to remain orthogonal to the body after the transformation. Hence, the grid is suitable for analyzing the supersonic flow past a blunt object. The associated shock as a coordinate surface adjusts its position in the course of computation until convergence is reached. The present work applied conformal mapping to 3-D bodies with no axis of symmetry such as the Aerobraking Flight Experiment (AFE) vehicle, transforming the AFE shape onto a near-circle image. A numerical procedure and code are used to generate grids around the AFE body.

  6. Mapping tree density at a global scale.

    PubMed

    Crowther, T W; Glick, H B; Covey, K R; Bettigole, C; Maynard, D S; Thomas, S M; Smith, J R; Hintler, G; Duguid, M C; Amatulli, G; Tuanmu, M-N; Jetz, W; Salas, C; Stam, C; Piotto, D; Tavani, R; Green, S; Bruce, G; Williams, S J; Wiser, S K; Huber, M O; Hengeveld, G M; Nabuurs, G-J; Tikhonova, E; Borchardt, P; Li, C-F; Powrie, L W; Fischer, M; Hemp, A; Homeier, J; Cho, P; Vibrans, A C; Umunay, P M; Piao, S L; Rowe, C W; Ashton, M S; Crane, P R; Bradford, M A

    2015-09-10

    The global extent and distribution of forest trees is central to our understanding of the terrestrial biosphere. We provide the first spatially continuous map of forest tree density at a global scale. This map reveals that the global number of trees is approximately 3.04 trillion, an order of magnitude higher than the previous estimate. Of these trees, approximately 1.39 trillion exist in tropical and subtropical forests, with 0.74 trillion in boreal regions and 0.61 trillion in temperate regions. Biome-level trends in tree density demonstrate the importance of climate and topography in controlling local tree densities at finer scales, as well as the overwhelming effect of humans across most of the world. Based on our projected tree densities, we estimate that over 15 billion trees are cut down each year, and the global number of trees has fallen by approximately 46% since the start of human civilization.

  7. Techniques for Revealing 3d Hidden Archeological Features: Morphological Residual Models as Virtual-Polynomial Texture Maps

    NASA Astrophysics Data System (ADS)

    Pires, H.; Martínez Rubio, J.; Elorza Arana, A.

    2015-02-01

    The recent developments in 3D scanning technologies are not been accompanied by visualization interfaces. We are still using the same types of visual codes as when maps and drawings were made by hand. The available information in 3D scanning data sets is not being fully exploited by current visualization techniques. In this paper we present recent developments regarding the use of 3D scanning data sets for revealing invisible information from archaeological sites. These sites are affected by a common problem, decay processes, such as erosion, that never ceases its action and endangers the persistence of last vestiges of some peoples and cultures. Rock art engravings, or epigraphical inscriptions, are among the most affected by these processes because they are, due to their one nature, carved at the surface of rocks often exposed to climatic agents. The study and interpretation of these motifs and texts is strongly conditioned by the degree of conservation of the imprints left by our ancestors. Every single detail in the remaining carvings can make a huge difference in the conclusions taken by specialists. We have selected two case-studies severely affected by erosion to present the results of the on-going work dedicated to explore in new ways the information contained in 3D scanning data sets. A new method for depicting subtle morphological features in the surface of objects or sites has been developed. It allows to contrast human patterns still present at the surface but invisible to naked eye or by any other archaeological inspection technique. It was called Morphological Residual Model (MRM) because of its ability to contrast the shallowest morphological details, to which we refer as residuals, contained in the wider forms of the backdrop. Afterwards, we have simulated the process of building Polynomial Texture Maps - a widespread technique that as been contributing to archaeological studies for some years - in a 3D virtual environment using the results of MRM

  8. 3D modelling of soil texture: mapping and incertitude estimation in centre-France

    NASA Astrophysics Data System (ADS)

    Ciampalini, Rossano; Martin, Manuel P.; Saby, Nicolas P. A.; Richer de Forges, Anne C.; Nehlig, Pierre; Martelet, Guillaume; Arrouays, Dominique

    2014-05-01

    Soil texture is an important component of all soil physical-chemical processes. The spatial variability of soil texture plays a crucial role in the evaluation and modelling of all distributed processes. The object of this study is to determine the spatial variation of soil granulometric fractions (i.e., clay, silt, sand) in the region "Centre" of France in relation to the main controlling factors, and to create extended maps of these properties following GlobalSoilMap specifications. For this purpose we used 2487 soil profiles of the French soil database (IGCS - Inventory Management and Soil Conservation) and continuum depth values of the properties within the soil profiles have been calculated with a quadratic splines methodology optimising the spline parameters in each soil profile. We used environmental covariates to predict soil properties within the region at depth intervals 0-5, 5-15, 15-30, 30-60, 60-100, and 100-200 cm. Concerning environmental covariates, we used SRTM and ASTER DEM with 90m and 30m resolution, respectively, to generate terrain parameters and topographic indexes. Other covariates we used are Gamma Ray maps, Corine land cover, available geological and soil maps of the region at scales 1M, 250k and 50k. Soil texture is modeled with the application of the compositional data analysis theory namely, alr-transform (Aitchison, 1986) which considers in statistical calculation the complementary dependence between the different granulometric classes (i.e. 100% constraint). The prediction models of the alr-transformed variables have been developed with the use of boosting regression trees (BRT), then, using a LMM - Linear Mixed Model - that separates a fixed effect from a random effect related to the continuous spatially correlated variation of the property. In this case, the LMM is applied to the two co-regionalized properties (clay and sand alr-transforms). Model uncertainty mapping represents a practical way to describe efficiency and limits of

  9. Fusion of terrestrial LiDAR and tomographic mapping data for 3D karst landform investigation

    NASA Astrophysics Data System (ADS)

    Höfle, B.; Forbriger, M.; Siart, C.; Nowaczinski, E.

    2012-04-01

    Highly detailed topographic information has gained in importance for studying Earth surface landforms and processes. LiDAR has evolved into the state-of-the-art technology for 3D data acquisition on various scales. This multi-sensor system can be operated on several platforms such as airborne LS (ALS), mobile LS (MLS) from moving vehicles or stationary on ground (terrestrial LS, TLS). In karst research the integral investigation of surface and subsurface components of solution depressions (e.g. sediment-filled dolines) is required to gather and quantify the linked geomorphic processes such as sediment flux and limestone dissolution. To acquire the depth of the different subsurface layers, a combination of seismic refraction tomography (SRT) and electrical resistivity tomography (ERT) is increasingly applied. This multi-method approach allows modeling the extension of different subsurface media (i.e. colluvial fill, epikarst zone and underlying basal bedrock). Subsequent fusion of the complementary techniques - LiDAR surface and tomographic subsurface data - first-time enables 3D prospection and visualization as well as quantification of geomorphometric parameters (e.g. depth, volume, slope and aspect). This study introduces a novel GIS-based method for semi-automated fusion of TLS and geophysical data. The study area is located in the Dikti Mountains of East Crete and covers two adjacent dolines. The TLS data was acquired with a Riegl VZ-400 scanner from 12 scan positions located mainly at the doline divide. The scan positions were co-registered using the iterative closest point (ICP) algorithm of RiSCAN PRO. For the digital elevation rasters a resolution of 0.5 m was defined. The digital surface model (DSM) of the study was derived by moving plane interpolation of all laser points (including objects) using the OPALS software. The digital terrain model (DTM) was generated by iteratively "eroding" objects in the DSM by minimum filter, which additionally accounts for

  10. Development of kinematic 3D laser scanning system for indoor mapping and as-built BIM using constrained SLAM.

    PubMed

    Jung, Jaehoon; Yoon, Sanghyun; Ju, Sungha; Heo, Joon

    2015-10-16

    The growing interest and use of indoor mapping is driving a demand for improved data-acquisition facility, efficiency and productivity in the era of the Building Information Model (BIM). The conventional static laser scanning method suffers from some limitations on its operability in complex indoor environments, due to the presence of occlusions. Full scanning of indoor spaces without loss of information requires that surveyors change the scanner position many times, which incurs extra work for registration of each scanned point cloud. Alternatively, a kinematic 3D laser scanning system, proposed herein, uses line-feature-based Simultaneous Localization and Mapping (SLAM) technique for continuous mapping. Moreover, to reduce the uncertainty of line-feature extraction, we incorporated constrained adjustment based on an assumption made with respect to typical indoor environments: that the main structures are formed of parallel or orthogonal line features. The superiority of the proposed constrained adjustment is its reduction for uncertainties of the adjusted lines, leading to successful data association process. In the present study, kinematic scanning with and without constrained adjustment were comparatively evaluated in two test sites, and the results confirmed the effectiveness of the proposed system. The accuracy of the 3D mapping result was additionally evaluated by comparison with the reference points acquired by a total station: the Euclidean average distance error was 0.034 m for the seminar room and 0.043 m for the corridor, which satisfied the error tolerance for point cloud acquisition (0.051 m) according to the guidelines of the General Services Administration for BIM accuracy.

  11. Development of Kinematic 3D Laser Scanning System for Indoor Mapping and As-Built BIM Using Constrained SLAM

    PubMed Central

    Jung, Jaehoon; Yoon, Sanghyun; Ju, Sungha; Heo, Joon

    2015-01-01

    The growing interest and use of indoor mapping is driving a demand for improved data-acquisition facility, efficiency and productivity in the era of the Building Information Model (BIM). The conventional static laser scanning method suffers from some limitations on its operability in complex indoor environments, due to the presence of occlusions. Full scanning of indoor spaces without loss of information requires that surveyors change the scanner position many times, which incurs extra work for registration of each scanned point cloud. Alternatively, a kinematic 3D laser scanning system, proposed herein, uses line-feature-based Simultaneous Localization and Mapping (SLAM) technique for continuous mapping. Moreover, to reduce the uncertainty of line-feature extraction, we incorporated constrained adjustment based on an assumption made with respect to typical indoor environments: that the main structures are formed of parallel or orthogonal line features. The superiority of the proposed constrained adjustment is its reduction for uncertainties of the adjusted lines, leading to successful data association process. In the present study, kinematic scanning with and without constrained adjustment were comparatively evaluated in two test sites, and the results confirmed the effectiveness of the proposed system. The accuracy of the 3D mapping result was additionally evaluated by comparison with the reference points acquired by a total station: the Euclidean average distance error was 0.034 m for the seminar room and 0.043 m for the corridor, which satisfied the error tolerance for point cloud acquisition (0.051 m) according to the guidelines of the General Services Administration for BIM accuracy. PMID:26501292

  12. Energy Dispersive X-ray Tomography for 3D Elemental Mapping of Individual Nanoparticles

    PubMed Central

    Slater, Thomas J. A.; Lewis, Edward A.; Haigh, Sarah J.

    2016-01-01

    Energy dispersive X-ray spectroscopy within the scanning transmission electron microscope (STEM) provides accurate elemental analysis with high spatial resolution, and is even capable of providing atomically resolved elemental maps. In this technique, a highly focused electron beam is incident upon a thin sample and the energy of emitted X-rays is measured in order to determine the atomic species of material within the beam path. This elementally sensitive spectroscopy technique can be extended to three dimensional tomographic imaging by acquiring multiple spectrum images with the sample tilted along an axis perpendicular to the electron beam direction. Elemental distributions within single nanoparticles are often important for determining their optical, catalytic and magnetic properties. Techniques such as X-ray tomography and slice and view energy dispersive X-ray mapping in the scanning electron microscope provide elementally sensitive three dimensional imaging but are typically limited to spatial resolutions of > 20 nm. Atom probe tomography provides near atomic resolution but preparing nanoparticle samples for atom probe analysis is often challenging. Thus, elementally sensitive techniques applied within the scanning transmission electron microscope are uniquely placed to study elemental distributions within nanoparticles of dimensions 10-100 nm. Here, energy dispersive X-ray (EDX) spectroscopy within the STEM is applied to investigate the distribution of elements in single AgAu nanoparticles. The surface segregation of both Ag and Au, at different nanoparticle compositions, has been observed. PMID:27403838

  13. Microfluidic Gradients Reveal Enhanced Neurite Outgrowth but Impaired Guidance within 3D Matrices with High Integrin Ligand Densities

    PubMed Central

    Romano, Nicole H.; Lampe, Kyle J.; Xu, Hui; Ferreira, Meghaan M.

    2015-01-01

    The density of integrin-binding ligands in an extracellular matrix (ECM) is known to regulate cell migration speed by imposing a balance of traction forces between the leading and trailing edges of the cell, but the effect of cell-adhesive ligands on neurite chemoattraction is not well understood. We present a platform that combines gradient-generating microfluidic devices with three-dimensional (3D) protein-engineered hydrogels to study the effect of RGD ligand density on neurite pathfinding from chick dorsal root ganglia-derived spheroids. Spheroids are encapsulated in elastin-like polypeptide (ELP) hydrogels presenting either 3.2 or 1.6 mM RGD ligands and exposed to a microfluidic gradient of nerve growth factor (NGF). While the higher ligand density matrix enhanced neurite initiation and persistence of neurite outgrowth, the lower ligand density matrix significantly improved neurite pathfinding and increased the frequency of growth cone turning up the NGF gradient. The apparent trade-off between neurite extension and neurite guidance is reminiscent of the well-known parabolic relationship between cell adhesion and migration speed, implying that a similar matrix-mediated balance of forces regulate neurite elongation and growth cone turning. These results have implications in the design of engineered materials for in vitro models of neural tissue and in vivo nerve guidance channels. PMID:25315156

  14. 3D Stationary electric current density in a spherical tumor treated with low direct current: an analytical solution.

    PubMed

    Jiménez, Rolando Placeres; Pupo, Ana Elisa Bergues; Cabrales, Jesús Manuel Bergues; Joa, Javier Antonio González; Cabrales, Luis Enrique Bergues; Nava, Juan José Godina; Aguilera, Andrés Ramírez; Mateus, Miguel Angel O'Farril; Jarque, Manuel Verdecia; Brooks, Soraida Candida Acosta

    2011-02-01

    Electrotherapy with direct current delivered through implanted electrodes is used for local control of solid tumors in both preclinical and clinical studies. The aim of this research is to develop a solution method for obtaining a three-dimensional analytical expression for potential and electric current density as functions of direct electric current intensity, differences in conductivities between the tumor and the surrounding healthy tissue, and length, number and polarity of electrodes. The influence of these parameters on electric current density in both media is analyzed. The results show that the electric current density in the tumor is higher than that in the surrounding healthy tissue for any value of these parameters. The conclusion is that the solution method presented in this study is of practical interest because it provides, in a few minutes, a convenient way to visualize in 3D the electric current densities generated by a radial electrode array by means of the adequate selection of direct current intensity, length, number, and polarity of electrodes, and the difference in conductivity between the solid tumor and its surrounding healthy tissue.

  15. Gravity data inversion to determine 3D topographycal density contrast of Banten area, Indonesia based on fast Fourier transform

    NASA Astrophysics Data System (ADS)

    Windhari, Ayuty; Handayani, Gunawan

    2015-04-01

    The 3D inversion gravity anomaly to estimate topographical density using a matlab source code from gridded data provided by Parker Oldenburg algorithm based on fast Fourier transform was computed. We extend and improved the source code of 3DINVERT.M invented by Gomez Ortiz and Agarwal (2005) using the relationship between Fourier transform of the gravity anomaly and the sum of the Fourier transform from the topography density. We gave density contrast between the two media to apply the inversion. FFT routine was implemented to construct amplitude spectrum to the given mean depth. The results were presented as new graphics of inverted topography density, the gravity anomaly due to the inverted topography and the difference between the input gravity data and the computed ones. It terminates when the RMS error is lower than pre-assigned value used as convergence criterion or until maximum of iterations is reached. As an example, we used the matlab program on gravity data of Banten region, Indonesia.

  16. Scatterer size and concentration estimation technique based on a 3D acoustic impedance map from histologic sections

    NASA Astrophysics Data System (ADS)

    Mamou, Jonathan; Oelze, Michael L.; O'Brien, William D.; Zachary, James F.

    2004-05-01

    Accurate estimates of scatterer parameters (size and acoustic concentration) are beneficial adjuncts to characterize disease from ultrasonic backscatterer measurements. An estimation technique was developed to obtain parameter estimates from the Fourier transform of the spatial autocorrelation function (SAF). A 3D impedance map (3DZM) is used to obtain the SAF of tissue. 3DZMs are obtained by aligning digitized light microscope images from histologic preparations of tissue. Estimates were obtained for simulated 3DZMs containing spherical scatterers randomly located: relative errors were less than 3%. Estimates were also obtained from a rat fibroadenoma and a 4T1 mouse mammary tumor (MMT). Tissues were fixed (10% neutral-buffered formalin), embedded in paraffin, serially sectioned and stained with H&E. 3DZM results were compared to estimates obtained independently against ultrasonic backscatter measurements. For the fibroadenoma and MMT, average scatterer diameters were 91 and 31.5 μm, respectively. Ultrasonic measurements yielded average scatterer diameters of 105 and 30 μm, respectively. The 3DZM estimation scheme showed results similar to those obtained by the independent ultrasonic measurements. The 3D impedance maps show promise as a powerful tool to characterize ultrasonic scattering sites of tissue. [Work supported by the University of Illinois Research Board.

  17. 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture.

    PubMed

    Topp, Christopher N; Iyer-Pascuzzi, Anjali S; Anderson, Jill T; Lee, Cheng-Ruei; Zurek, Paul R; Symonova, Olga; Zheng, Ying; Bucksch, Alexander; Mileyko, Yuriy; Galkovskyi, Taras; Moore, Brad T; Harer, John; Edelsbrunner, Herbert; Mitchell-Olds, Thomas; Weitz, Joshua S; Benfey, Philip N

    2013-04-30

    Identification of genes that control root system architecture in crop plants requires innovations that enable high-throughput and accurate measurements of root system architecture through time. We demonstrate the ability of a semiautomated 3D in vivo imaging and digital phenotyping pipeline to interrogate the quantitative genetic basis of root system growth in a rice biparental mapping population, Bala × Azucena. We phenotyped >1,400 3D root models and >57,000 2D images for a suite of 25 traits that quantified the distribution, shape, extent of exploration, and the intrinsic size of root networks at days 12, 14, and 16 of growth in a gellan gum medium. From these data we identified 89 quantitative trait loci, some of which correspond to those found previously in soil-grown plants, and provide evidence for genetic tradeoffs in root growth allocations, such as between the extent and thoroughness of exploration. We also developed a multivariate method for generating and mapping central root architecture phenotypes and used it to identify five major quantitative trait loci (r(2) = 24-37%), two of which were not identified by our univariate analysis. Our imaging and analytical platform provides a means to identify genes with high potential for improving root traits and agronomic qualities of crops.

  18. Towards a high performance vertex detector based on 3D integration of deep N-well MAPS

    NASA Astrophysics Data System (ADS)

    Re, V.

    2010-06-01

    The development of deep N-Well (DNW) CMOS active pixel sensors was driven by the ambitious goal of designing a monolithic device with similar functionalities as in hybrid pixel readout chips, such as pixel-level sparsification and time stamping. The implementation of the DNW MAPS concept in a 3D vertical integration process naturally leads the designer towards putting more intelligence in the chip and in the pixels themselves, achieving novel device structures based on the interconnection of two or more layers fabricated in the same technology. These devices are read out with a data-push scheme that makes it possible to use pixel data for the generation of a flexible level 1 track trigger, based on associative memories, with short latency and high efficiency. This paper gives an update of the present status of DNW MAPS design in both 2D and 3D versions, and presents a discussion of the architectures that are being devised for the Layer 0 of the SuperB Silicon Vertex Tracker.

  19. 3D Vegetation Mapping Using UAVSAR, LVIS, and LIDAR Data Acquisition Methods

    NASA Technical Reports Server (NTRS)

    Calderon, Denice

    2011-01-01

    The overarching objective of this ongoing project is to assess the role of vegetation within climate change. Forests capture carbon, a green house gas, from the atmosphere. Thus, any change, whether, natural (e.g. growth, fire, death) or due to anthropogenic activity (e.g. logging, burning, urbanization) may have a significant impact on the Earth's carbon cycle. Through the use of Uninhabited Aerial Vehicle Synthetic Aperture Radar (UAVSAR) and NASA's Laser Vegetation Imaging Sensor (LVIS), which are airborne Light Detection and Ranging (LIDAR) remote sensing technologies, we gather data to estimate the amount of carbon contained in forests and how the content changes over time. UAVSAR and LVIS sensors were sent all over the world with the objective of mapping out terrain to gather tree canopy height and biomass data; This data is in turn used to correlate vegetation with the global carbon cycle around the world.

  20. Photocurrent mapping of 3D CdSe/CdTe windowless solar cells.

    PubMed

    Hangarter, Carlos M; Debnath, Ratan; Ha, Jong Y; Sahiner, Mehmet A; Reehil, Christopher J; Manners, William A; Josell, Daniel

    2013-09-25

    This paper details the use of scanning photocurrent microscopy to examine localized current collection efficiency of thin-film photovoltaic devices with in-plane patterning at a submicrometer length scale. The devices are based upon two interdigitated comb electrodes at the micrometer length scale prepatterned on a substrate, with CdSe electrodeposited on one electrode and CdTe deposited over the entire surface of the resulting structure by pulsed laser deposition. Photocurrent maps provide information on what limits the performance of the windowless CdSe/CdTe thin-film photovoltaic devices, revealing "dead zones" particularly above the electrodes contacting the CdTe which is interpreted as recombination over the back contact. Additionally, the impact of ammonium sulfide passivation is examined, which enables device efficiency to reach 4.3% under simulated air mass 1.5 illumination.

  1. A 3D map of the islet routes throughout the healthy human pancreas

    PubMed Central

    Ionescu-Tirgoviste, Constantin; Gagniuc, Paul A.; Gubceac, Elvira; Mardare, Liliana; Popescu, Irinel; Dima, Simona; Militaru, Manuella

    2015-01-01

    Islets of Langerhans are fundamental in understanding diabetes. A healthy human pancreas from a donor has been used to asses various islet parameters and their three-dimensional distribution. Here we show that islets are spread gradually from the head up to the tail section of the pancreas in the form of contracted or dilated islet routes. We also report a particular anatomical structure, namely the cluster of islets. Our observations revealed a total of 11 islet clusters which comprise of small islets that surround large blood vessels. Additional observations in the peripancreatic adipose tissue have shown lymphoid-like nodes and blood vessels captured in a local inflammatory process. Our observations are based on regional slice maps of the pancreas, comprising of 5,423 islets. We also devised an index of sphericity which briefly indicates various islet shapes that are dominant throughout the pancreas. PMID:26417671

  2. High-Resolution 3D Bathymetric Mapping for Small Streams Using Low-Altitude Aerial Photography

    NASA Astrophysics Data System (ADS)

    Dietrich, J. T.; Duffin, J.

    2015-12-01

    Geomorphic monitoring of river restoration projects is a critical component of measuring their success. In smaller streams, with depths less than 2 meters, one of the more difficult variables to map at high-resolution is bathymetry. In larger rivers, bathymetry can be measured with instruments like multi-beam sonar, bathymetric airborne LiDAR, or acoustic doppler current profilers (ADCP). However, these systems are often limited by their minimum operating depths, which makes them ineffective in shallow water. Remote sensing offers several potential solutions for collecting bathymetry, spectral depth mapping and photogrammetric measurement (e.g. Structure-from-Motion (SfM) multi-view photogrammetry). In this case study, we use SfM to produce both high-resolution above water topography and below water bathymetry for two reaches of a stream restoration project on the Middle Fork of the John Day River in eastern Oregon and one reach on the White River in Vermont. We collected low-allitude multispectral (RGB+NIR) aerial photography at all of the sites at altitudes of 30 to 50 meters. The SfM survey was georeferenced with RTK-GPS ground control points and the bathymetry was refraction-corrected using additional RTK-GPS sample points. The resulting raster data products have horizontal resolutions of ~4-8 centimeters for the topography and ~8-15 cm for the bathymetry. This methodology, like many fluvial remote sensing methods, will only work under ideal conditions (e.g. clear water), but it provides an additional tool for collecting high-resolution bathymetric datasets for geomorphic monitoring efforts.

  3. Stardust Under a Microscope - 3D maps of Wild 2/81P Cometary Samples in Aerogel

    NASA Astrophysics Data System (ADS)

    White, Amanda J.; Ebel, Denton

    2016-01-01

    The NASA Stardust mission to comet Wild 2 returned to Earth in 2006 with cometary and interstellar material captured in aerogel. Cometary particles impacted an aerogel collector at a relative velocity of 6.1 km/s, creating three-dimensional (3D) impact tracks of melted and crushed aerogel, void space, and fragmented cometary material. Each track represents the history of a unique hypervelocity capture event. The nature of each impact, including the original state of the impactor, is recorded in track morphology and material distribution. Using a combination of 3D morphological data, chemical data, and microphysical models, it is possible to reconstruct track formation events and a model of the original impactor.The focus of this work is to fully characterize whole tracks both morphologically and chemically using solely non-destructive methods. To achieve this, we combine high-resolution laser scanning confocal microscope (LSCM) 3D imaging with synchrotron X-ray fluorescence (SXRF) chemical mapping. We are also beginning to incorporate Raman spectroscopy to perform mineral phase analysis of fine track wall material. Using a Zeiss LSM 710 LSCM located in the American Museum of Natural History, we have imaged the morphology of over a dozen, whole Stardust tracks at high resolution (<80 nm/pixel in XY). We obtain the distribution of fine material along the track walls both quickly and without disturbing the sample. Complementary chemical data is acquired using the GSECARS X-ray microbe on beamline 13-IDE at the Advance Photon Source (APS) of Argonne National Laboratory. X-ray fluorescence maps of each track were collected with 100ms/pixel dwell time at a resolution of 1 or 2 micron/pixel. Many tracks were tilted and mapped a second time for stereo measurements.A thorough understanding of how cometary material and aerogel is distributed along tracks is required to understand the events which occurred after impact and to back-calculate properties of the original impactor

  4. Leveraging 3D Wheeler Diagrams and relative time mapping in seismic data to improve stratigraphic interpretation: Application, Assumptions, and Sequence Stratigraphic Revelations

    NASA Astrophysics Data System (ADS)

    Goggin, L. R.

    2014-12-01

    Our understanding of subsurface stratigraphic relationships is guided by stratigraphic concepts that were developed using many varieties and scales of data including paleontological samples, cuttings and core, outcrop analogs, well logs, and seismic. Subsurface stratigraphic correlations are strongly influenced by the type, density, and distribution of the data available. The exploration geologist typically interprets 2D and 3D seismic reflections to define prospects and plays. In structurally simple areas, he or she often assumes that seismic reflectors mark depositional boundaries that are essentially time-synchronous events represented by a single wavelet character. In reality, seismic reflectors usually display spatial wavelet variability, seldom resolve individual beds and are the product of the amplitude expression of a range of lithologic changes that encompasses a range of geologic time and depositional processes. Our assumption that seismic reflections are time-synchronous can lead to errors in stratigraphic correlation that only become evident when our prediction of well or field performance is unrealized. To mitigate the potential for this correlation error, we must modify how we interpret seismic data. In this presentation we will focus on the concept of defining or approximating time-correlative surfaces in seismic data, leverage concepts of the Wheeler transform to place these seismic reflectors into the relative time domain and then examine the diachronous nature of these time-mapped surfaces in 3D. We will then explore how the 3D mapping of time-correlative surfaces fits sequence stratigraphic concepts and discuss whether this new approach requires us to change our interpretation paradigms.

  5. SNW 2000 Proceedings. Oxide Thickness Variation Induced Threshold Voltage Fluctuations in Decanano MOSFETs: a 3D Density Gradient Simulation Study

    NASA Technical Reports Server (NTRS)

    Asenov, Asen; Kaya, S.; Davies, J. H.; Saini, S.

    2000-01-01

    We use the density gradient (DG) simulation approach to study, in 3D, the effect of local oxide thickness fluctuations on the threshold voltage of decanano MOSFETs in a statistical manner. A description of the reconstruction procedure for the random 2D surfaces representing the 'atomistic' Si-SiO2 interface variations is presented. The procedure is based on power spectrum synthesis in the Fourier domain and can include either Gaussian or exponential spectra. The simulations show that threshold voltage variations induced by oxide thickness fluctuation become significant when the gate length of the devices become comparable to the correlation length of the fluctuations. The extent of quantum corrections in the simulations with respect to the classical case and the dependence of threshold variations on the oxide thickness are examined.

  6. Maps of current density using density-functional methods

    NASA Astrophysics Data System (ADS)

    Soncini, A.; Teale, A. M.; Helgaker, T.; de Proft, F.; Tozer, D. J.

    2008-08-01

    The performance of several density-functional theory (DFT) methods for the calculation of current densities induced by a uniform magnetic field is examined. Calculations are performed using the BLYP and KT3 generalized-gradient approximations, together with the B3LYP hybrid functional. For the latter, both conventional and optimized effective potential (OEP) approaches are used. Results are also determined from coupled-cluster singles-and-doubles (CCSD) electron densities by a DFT constrained search procedure using the approach of Wu and Yang (WY). The current densities are calculated within the CTOCD-DZ2 distributed origin approach. Comparisons are made with results from Hartree-Fock (HF) theory. Several small molecules for which correlation is known to be especially important in the calculation of magnetic response properties are considered-namely, O3, CO, PN, and H2CO. As examples of aromatic and antiaromatic systems, benzene and planarized cyclooctatetraene molecules are considered, with specific attention paid to the ring current phenomenon and its Kohn-Sham orbital origin. Finally, the o-benzyne molecule is considered as a computationally challenging case. The HF and DFT induced current maps show qualitative differences, while among the DFT methods the maps show a similar qualitative structure. To assess quantitative differences in the calculated current densities with different methods, the maximal moduli of the induced current densities are compared and integration of the current densities to yield shielding constants is performed. In general, the maximal modulus is reduced in moving from HF to B3LYP and BLYP, and further reduced in moving to KT3, OEP(B3LYP), and WY(CCSD). The latter three methods offer the most accurate shielding constants in comparison with both experimental and ab initio data and hence the more reliable route to DFT calculation of induced current density in molecules.

  7. Temperature Mapping of 3D Printed Polymer Plates: Experimental and Numerical Study

    PubMed Central

    Kousiatza, Charoula; Chatzidai, Nikoleta; Karalekas, Dimitris

    2017-01-01

    In Fused Deposition Modeling (FDM), which is a common thermoplastic Additive Manufacturing (AM) method, the polymer model material that is in the form of a flexible filament is heated above its glass transition temperature (Tg) to a semi-molten state in the head’s liquefier. The heated material is extruded in a rastering configuration onto the building platform where it rapidly cools and solidifies with the adjoining material. The heating and rapid cooling cycles of the work materials exhibited during the FDM process provoke non-uniform thermal gradients and cause stress build-up that consequently result in part distortions, dimensional inaccuracy and even possible part fabrication failure. Within the purpose of optimizing the FDM technique by eliminating the presence of such undesirable effects, real-time monitoring is essential for the evaluation and control of the final parts’ quality. The present work investigates the temperature distributions developed during the FDM building process of multilayered thin plates and on this basis a numerical study is also presented. The recordings of temperature changes were achieved by embedding temperature measuring sensors at various locations into the middle-plane of the printed structures. The experimental results, mapping the temperature variations within the samples, were compared to the corresponding ones obtained by finite element modeling, exhibiting good correlation. PMID:28245557

  8. Robot-Aided Mapping of Wrist Proprioceptive Acuity across a 3D Workspace

    PubMed Central

    Marini, Francesca; Squeri, Valentina; Morasso, Pietro; Konczak, Jürgen; Masia, Lorenzo

    2016-01-01

    Proprioceptive signals from peripheral mechanoreceptors form the basis for bodily perception and are known to be essential for motor control. However we still have an incomplete understanding of how proprioception differs between joints, whether it differs among the various degrees-of-freedom (DoFs) within a particular joint, and how such differences affect motor control and learning. We here introduce a robot-aided method to objectively measure proprioceptive function: specifically, we systematically mapped wrist proprioceptive acuity across the three DoFs of the wrist/hand complex with the aim to characterize the wrist position sense. Thirty healthy young adults performed an ipsilateral active joint position matching task with their dominant wrist using a haptic robotic exoskeleton. Our results indicate that the active wrist position sense acuity is anisotropic across the joint, with the abduction/adduction DoF having the highest acuity (the error of acuity for flexion/extension is 4.64 ± 0.24°; abduction/adduction: 3.68 ± 0.32°; supination/pronation: 5.15 ± 0.37°) and they also revealed that proprioceptive acuity decreases for smaller joint displacements. We believe this knowledge is imperative in a clinical scenario when assessing proprioceptive deficits and for understanding how such sensory deficits relate to observable motor impairments. PMID:27536882

  9. 3D unmanned aerial vehicle radiation mapping for assessing contaminant distribution and mobility

    NASA Astrophysics Data System (ADS)

    Martin, P. G.; Kwong, S.; Smith, N. T.; Yamashiki, Y.; Payton, O. D.; Russell-Pavier, F. S.; Fardoulis, J. S.; Richards, D. A.; Scott, T. B.

    2016-10-01

    Following the events of March 2011 at the Fukushima Daiichi Nuclear Power Plant, significant quantities of radioactive material were released into the local and wider global environment. At five years since the incident, much expense is being currently devoted to the remediation of a large portion of eastern Japan contaminated primarily by radiocesium, yet further significant expenditure will be required over the succeeding decades to complete this clean-up. People displaced from their homes by the incident are now increasingly keen to return, making it more important than ever to provide accurate quantification and representation of any residual radiological contamination. Presented here is the use of an unmanned aerial vehicle equipped with a laser rangefinder unit to generate a three dimensional point-cloud of an area onto which a radiation contamination map, also obtained concurrently via the unmanned aerial platform, can be rendered. An exemplar site of an un-remediated farm consisting of multiple stepped rice paddy fields with a dedicated irrigation system was used for this work. The results obtained show that heightened radiological contamination exists around the site within the drainage network where material is observed to have collected, having been transported by transient water runoff events. These results obtained in May 2014 suggest that a proportion of the fallout material is highly mobile within the natural environment and is likely to be transported further through the system over the succeeding years.

  10. Electrical Structure Inferred by 3-D Lightning Mapping Observations During STEPS

    NASA Astrophysics Data System (ADS)

    Hamlin, T.; Krehbiel, P. R.; Zhang, Y.; Thomas, R. J.

    2002-12-01

    The Severe Thunderstorm Electrification and Precipitation Study (STEPS) provided numerous examples of storms which electrified anomalously, developing inverted tripole or quadrupole electrical structures. The storms were often supercells and cases where the lightning activity consisted primarily of IC flashes for substantial periods of time, only followed (if at all) much later by the onset of CG activity, were observed on several occasions. Radar comparisons for the tornadic storm of June 29 and the Bird City storm of June 3 during STEPS indicate that the main positive charge was localized in the precipitation core, but the electrification also had a definite horizontally extensive, multilayer structure extending away from the core. In these storms the upper positive charge region developed rapidly and produced intense lightning activity. The upper positive gradually evolved downward in altitude to become the dominant mid-level charge, forming an inverted tripole structure which appears to be stable for long periods of time. By assuming that a given polarity breakdown is moving into regions of opposite polarity charge (with exceptions) the total charge structure can be inferred and mapped based on information gleaned from the individual flashes; this allows use of the LMA data to detail the charge structure of storms. We take this approach to study the evolution of charge structures for storms during STEPS.

  11. Temperature Mapping of 3D Printed Polymer Plates: Experimental and Numerical Study.

    PubMed

    Kousiatza, Charoula; Chatzidai, Nikoleta; Karalekas, Dimitris

    2017-02-24

    In Fused Deposition Modeling (FDM), which is a common thermoplastic Additive Manufacturing (AM) method, the polymer model material that is in the form of a flexible filament is heated above its glass transition temperature (Tg) to a semi-molten state in the head's liquefier. The heated material is extruded in a rastering configuration onto the building platform where it rapidly cools and solidifies with the adjoining material. The heating and rapid cooling cycles of the work materials exhibited during the FDM process provoke non-uniform thermal gradients and cause stress build-up that consequently result in part distortions, dimensional inaccuracy and even possible part fabrication failure. Within the purpose of optimizing the FDM technique by eliminating the presence of such undesirable effects, real-time monitoring is essential for the evaluation and control of the final parts' quality. The present work investigates the temperature distributions developed during the FDM building process of multilayered thin plates and on this basis a numerical study is also presented. The recordings of temperature changes were achieved by embedding temperature measuring sensors at various locations into the middle-plane of the printed structures. The experimental results, mapping the temperature variations within the samples, were compared to the corresponding ones obtained by finite element modeling, exhibiting good correlation.

  12. 3D Mapping of calcite and a demonstration of its relevance to permeability evolution in reactive fractures

    NASA Astrophysics Data System (ADS)

    Ellis, Brian R.; Peters, Catherine A.

    2016-09-01

    There is a need to better understand reaction-induced changes in fluid transport in fractured shales, caprocks and reservoirs, especially in the context of emerging energy technologies, including geologic carbon sequestration, unconventional natural gas, and enhanced geothermal systems. We developed a method for 3D calcite mapping in rock specimens. Such information is critical in reactive transport modeling, which relies on information about the locations and accessible surface area of reactive minerals. We focused on calcite because it is a mineral whose dissolution could lead to substantial pathway alteration because of its high solubility, fast reactivity, and abundance in sedimentary rocks. Our approach combines X-ray computed tomography (XCT) and scanning electron microscopy. The method was developed and demonstrated for a fractured limestone core containing about 50% calcite, which was 2.5 cm in diameter and 3.5 cm in length and had been scanned using XCT. The core was subsequently sectioned and energy dispersive X-ray spectroscopy was used to determine elemental signatures for mineral identification and mapping. Back-scattered electron microscopy was used to identify features for co-location. Finally, image analysis resulted in characteristic grayscale intensities of X-ray attenuation that identify calcite. This attenuation mapping ultimately produced a binary segmented 3D image of the spatial distribution of calcite in the entire core. To demonstrate the value of this information, permeability changes were investigated for hypothetical fractures created by eroding calcite from 2D rock surfaces. Fluid flow was simulated using a 2D steady state model. The resulting increases in permeability were profoundly influenced by the degree to which calcite is contiguous along the flow path. If there are bands of less reactive minerals perpendicular to the direction of flow, fracture permeability may be an order of magnitude smaller than when calcite is contiguous

  13. Intrusion versus inversion—a 3D density model of the southern rim of the Northwest German Basin

    NASA Astrophysics Data System (ADS)

    Bilgili, Filiz; Götze, Hans-Jürgen; Pašteka, Roman; Schmidt, Sabine; Hackney, Ron

    2009-04-01

    An unsolved problem of regional importance for both the evolution and structure of the Northwest German Basin is the existence or non-existence of the so-called Bramsche Massif. Explaining the nature of this massif and the cause of a related strong, positive Bouguer anomaly (Bramsche Anomaly) is critical. In the study described here, we tested an existing “intrusion model” against a newer “inversion model” in the southern Northwest German Basin. In the intrusion model, the strongly-positive Bouguer anomaly represents the gravity effect of an intrusion at depths between 6 and 10 km. More recent interpretations invoke tectonic inversion rather than intrusion to explain increased burial and the low level of hydrocarbon maturity found in boreholes. We tested these different interpretations by constructing 3D forward density models to 15 km depth. The intrusion model was updated and adjusted to incorporate recent data and we also modelled pre-Zechstein structures using different scenarios. The final model has a very good fit between measured and modelled gravity fields. Based on currently available seismic and structural models, as well as borehole density measurements, we show that the positive Bouguer anomaly cannot be modeled without a high-density, intrusive-like body at depth. However, further in-sight into the crustal structures of the Bramsche region requires more detailed investigations.

  14. Spatial Density Maps from a Debris Cloud

    NASA Astrophysics Data System (ADS)

    Healy, L.; Kindl, S.; Binz, C.

    2016-09-01

    A debris cloud from a fragmentation on orbit may be modeled by transformation of variables from the instantaneous velocity distribution at the fragmentation time to the spatial distribution at some elapsed time later. There are no Gaussian distributions assumed and the evolution map is quite nonlinear, being derived from the solution of the Lambert, two-point boundary value, problem and the state transition matrix for unperturbed propagation, so the traditional tools of analysis that assume these qualities fail dramatically. The transformation of variables technique does not suffer from any such assumptions, and unlike the Monte Carlo method, is not subject to sampling errors or approximations. Structures and features are evident in the density maps, and these structures show promise for simplified approximation of the density map. Most prominent of the structures is the well-known pinch point at the fragmentation location in inertial space. The anti-pinch line, or wedge, is also observed. Bands on the opposite side of the fragmentation are very noticeable, and their existence may be motivated from simple orbit dynamics. These bands make the anti-pinch line actually more of a set of anti-pinch line segments. By computing these density maps over time, the evolution may be studied. There is a density generator, a density band at roughly the same altitude as the pinch point, that cycles around the earth and appears a source of the bands, with newly created bands moving radially outward and diminishing in density. Although the initial velocity distribution affects the final spatial distribution, the Lambert solutions, which are the most time consuming to compute, need only be computed once. Therefore, different initial distributions may be changed and the results recomputed with relative speed. A comparison of the effects of initial distributions is shown in this paper.

  15. Density Functional Theory of Open-Shell Systems. The 3d-Series Transition-Metal Atoms and Their Cations.

    PubMed

    Luo, Sijie; Averkiev, Boris; Yang, Ke R; Xu, Xuefei; Truhlar, Donald G

    2014-01-14

    The 3d-series transition metals (also called the fourth-period transition metals), Sc to Zn, are very important in industry and biology, but they provide unique challenges to computing the electronic structure of their compounds. In order to successfully describe the compounds by theory, one must be able to describe their components, in particular the constituent atoms and cations. In order to understand the ingredients required for successful computations with density functional theory, it is useful to examine the performance of various exchange-correlation functionals; we do this here for 4s(N)3d(N') transition-metal atoms and their cations. We analyze the results using three ways to compute the energy of the open-shell states: the direct variational method, the weighted-averaged broken symmetry (WABS) method, and a new broken-symmetry method called the reinterpreted broken symmetry (RBS) method. We find the RBS method to be comparable in accuracy with the WABS method. By examining the overall accuracy in treating 18 multiplicity-changing excitations and 10 ionization potentials with the RBS method, 10 functionals are found to have a mean-unsigned error of <5 kcal/mol, with ωB97X-D topping the list. For local density functionals, which are more practical for extended systems, the M06-L functional is the most accurate. And by combining the results with our previous studies of p-block and 4d-series elements as well as databases for alkyl bond dissociation, main-group atomization energies, and π-π noncovalent interactions, we find five functionals, namely, PW6B95, MPW1B95, M08-SO, SOGGA11-X, and MPWB1K, to be highly recommended. We also studied the performance of PW86 and C09 exchange functionals, which have drawn wide interest in recent studies due to their claimed ability to reproduce Hartree-Fock exchange at long distance. By combining them with four correlation functionals, we find the performance of the resulting functionals disappointing both for 3d

  16. Prospects of 3D mapping of the Galactic Centre clouds with X-ray polarimetry

    NASA Astrophysics Data System (ADS)

    Marin, F.; Karas, V.; Kunneriath, D.; Muleri, F.

    2014-07-01

    Despite past panchromatic observations of the innermost part of the Milky Way, the overall structure of the Galactic Centre (GC) remains enigmatic in terms of geometry. In this paper, we aim to show how polarimetry can probe the three-dimensional position of the molecular material in the central ˜100 pc of the GC. We investigate a model where the central supermassive black hole Sgr A* is radiatively coupled to a fragmented circumnuclear disc (CND), an elliptical twisted ring representative of the central molecular zone (CMZ), and the two main, bright molecular clouds Sgr B2 and Sgr C. 8-35 keV integrated polarization mapping reveals that Sgr B2 and Sgr C, situated at the two sides of the CMZ, present the highest polarization degrees (66.5 and 47.8 per cent, respectively), both associated with a polarization position angle ψ = 90° (normal to the scattering plane). The CND shows a lower polarization degree, 1.0 per cent with ψ = -20.5°, tracing the inclination of the CND with respect to the Galactic plane. The CMZ polarization is spatially variable. We also consider a range of spatial locations for Sgr A* and the reprocessing media, and investigate how the modelled three-dimensional geometry influences the resulting GC polarization. The two reflection nebulae are found to always produce high polarization degrees (≫10 per cent). We show that a 500 ks observation with a broad-band polarimeter could constrain the location and the morphology of the scattering material with respect to the emitting source, revealing the past activity of Sgr A*.

  17. Novel real-time 3D radiological mapping solution for ALARA maximization, D and D assessments and radiological management

    SciTech Connect

    Dubart, Philippe; Hautot, Felix; Morichi, Massimo; Abou-Khalil, Roger

    2015-07-01

    Good management of dismantling and decontamination (D and D) operations and activities is requiring safety, time saving and perfect radiological knowledge of the contaminated environment as well as optimization for personnel dose and minimization of waste volume. In the same time, Fukushima accident has imposed a stretch to the nuclear measurement operational approach requiring in such emergency situation: fast deployment and intervention, quick analysis and fast scenario definition. AREVA, as return of experience from his activities carried out at Fukushima and D and D sites has developed a novel multi-sensor solution as part of his D and D research, approach and method, a system with real-time 3D photo-realistic spatial radiation distribution cartography of contaminated premises. The system may be hand-held or mounted on a mobile device (robot, drone, e.g). In this paper, we will present our current development based on a SLAM technology (Simultaneous Localization And Mapping) and integrated sensors and detectors allowing simultaneous topographic and radiological (dose rate and/or spectroscopy) data acquisitions. This enabling technology permits 3D gamma activity cartography in real-time. (authors)

  18. Matrix density alters zyxin phosphorylation, which limits peripheral process formation and extension in endothelial cells invading 3D collagen matrices.

    PubMed

    Abbey, Colette A; Bayless, Kayla J

    2014-09-01

    This study was designed to determine the optimal conditions required for known pro-angiogenic stimuli to elicit successful endothelial sprouting responses. We used an established, quantifiable model of endothelial cell (EC) sprout initiation where ECs were tested for invasion in low (1 mg/mL) and high density (5 mg/mL) 3D collagen matrices. Sphingosine 1-phosphate (S1P) alone, or S1P combined with stromal derived factor-1α (SDF) and phorbol ester (TPA), elicited robust sprouting responses. The ability of these factors to stimulate sprouting was more effective in higher density collagen matrices. S1P stimulation resulted in a significant increase in invasion distance, and with the exception of treatment groups containing phorbol ester, invasion distance was longer in 1mg/mL compared to 5mg/mL collagen matrices. Closer examination of cell morphology revealed that increasing matrix density and supplementing with SDF and TPA enhanced the formation of multicellular structures more closely resembling capillaries. TPA enhanced the frequency and size of lumen formation and correlated with a robust increase in phosphorylation of p42/p44 Erk kinase, while S1P and SDF did not. Also, a higher number of significantly longer extended processes formed in 5mg/mL compared to 1mg/mL collagen matrices. Because collagen matrices at higher density have been reported to be stiffer, we tested for changes in the mechanosensitive protein, zyxin. Interestingly, zyxin phosphorylation levels inversely correlated with matrix density, while levels of total zyxin did not change significantly. Immunofluorescence and localization studies revealed that total zyxin was distributed evenly throughout invading structures, while phosphorylated zyxin was slightly more intense in extended peripheral processes. Silencing zyxin expression increased extended process length and number of processes, while increasing zyxin levels decreased extended process length. Altogether these data indicate that ECs

  19. C2SM: a mobile system for detecting and 3D mapping of chemical, radiological, and nuclear contamination

    NASA Astrophysics Data System (ADS)

    Jasiobedzki, Piotr; Ng, Ho-Kong; Bondy, Michel; McDiarmid, C. H.

    2009-05-01

    CBRN Crime Scene Modeler (C2SM) is a prototype mobile CBRN mapping system for First Responders in events where Chemical, Biological, Radiological and Nuclear agents where used. The prototype operates on board a small robotic platform, increases situational awareness of the robot operator by providing geo-located images and data, and current robot location. The sensor suite includes stereo and high resolution cameras, a long wave infra red (thermal) camera and gamma and chemical detectors. The system collects and sends geo-located data to a remote command post in near real-time and automatically creates 3D photorealistic model augmented with CBRN measurements. Two prototypes have been successfully tested in field trials and a fully ruggedised commercial version is expected in 2010.

  20. Monitoring and Simulating the 3-D Density Currents at the Confluence of the Snake and Clearwater Rivers

    SciTech Connect

    Cook, Chris B.; Richmond, Marshall C.

    2004-12-01

    Summer temperatures in the Lower Snake River can be altered by releasing cold waters that originate from deep depths within Dworshak Reservoir. These cold releases are used to lower temperatures in the Clearwater River, a major tributary to the Lower Snake River, and to improve hydrodynamic and water quality conditions for migrating aquatic species. This project monitored the complex three-dimensional density currents at the Clearwater and Snake River confluence and the processes that led to stratification of Lower Granite Reservoir (LGR) during the late spring, summer, and fall of 2002. In addition to monitoring the LGR environment, a three-dimensional hydrodynamic and water quality model was also applied. By utilizing both field data and a numerical model, a more holistic view of the 3-D density currents was discovered than by either method alone. During this process, it was discovered that several predictable stratification patterns would develop depending upon the discharge ratio and the thermal gradient between the two rivers. These results illustrate the complex hydrodynamic structure at the confluence of the Clearwater and Snake Rivers, which has previously been shown by fish biologists to be a difficult passage zone for migrating salmonids of various life stages.

  1. New ATCA, ALMA and VISIR observations of the candidate LBV SK -67 266 (S61): the nebular mass from modelling 3D density distributions

    NASA Astrophysics Data System (ADS)

    Agliozzo, C.; Nikutta, R.; Pignata, G.; Phillips, N. M.; Ingallinera, A.; Buemi, C.; Umana, G.; Leto, P.; Trigilio, C.; Noriega-Crespo, A.; Paladini, R.; Bufano, F.; Cavallaro, F.

    2017-04-01

    We present new observations of the nebula around the Magellanic candidate Luminous Blue Variable S61. These comprise high-resolution data acquired with the Australia Telescope Compact Array (ATCA), the Atacama Large Millimetre/Submillimetre Array (ALMA), and the VLT Imager and Spectrometer for mid Infrared (VISIR) at the Very Large Telescope. The nebula was detected only in the radio, up to 17 GHz. The 17 GHz ATCA map, with 0.8 arcsec resolution, allowed a morphological comparison with the Hα Hubble Space Telescope image. The radio nebula resembles a spherical shell, as in the optical. The spectral index map indicates that the radio emission is due to free-free transitions in the ionized, optically thin gas, but there are hints of inhomogeneities. We present our new public code RHOCUBE to model 3D density distributions and determine via Bayesian inference the nebula's geometric parameters. We applied the code to model the electron density distribution in the S61 nebula. We found that different distributions fit the data, but all of them converge to the same ionized mass, ∼ 0.1 M⊙, which is an order of magnitude smaller than previous estimates. We show how the nebula models can be used to derive the mass-loss history with high-temporal resolution. The nebula was probably formed through stellar winds, rather than eruptions. From the ALMA and VISIR non-detections, plus the derived extinction map, we deduce that the infrared emission observed by space telescopes must arise from extended, diffuse dust within the ionized region.

  2. Increase in the energy density of the pinch plasma in 3D implosion of quasi-spherical wire arrays

    SciTech Connect

    Aleksandrov, V. V.; Gasilov, V. A.; Grabovski, E. V.; Gritsuk, A. N. Laukhin, Ya. N.; Mitrofanov, K. N.; Oleinik, G. M.; Ol’khovskaya, O. G.; Sasorov, P. V.; Smirnov, V. P.; Frolov, I. N.; Shevel’ko, A. P.

    2014-12-15

    Results are presented from experimental studies of the characteristics of the soft X-ray (SXR) source formed in the implosion of quasi-spherical arrays made of tungsten wires and metalized kapron fibers. The experiments were carried out at the Angara-5-1 facility at currents of up to 3 MA. Analysis of the spatial distribution of hard X-ray emission with photon energies above 20 keV in the pinch images taken during the implosion of quasi-spherical tungsten wire arrays (QTWAs) showed that a compact quasi-spherical plasma object symmetric with respect to the array axis formed in the central region of the array. Using a diffraction grazing incidence spectrograph, spectra of SXR emission with wavelengths of 20–400 Å from the central, axial, and peripheral regions of the emission source were measured with spatial resolutions along the array radius and height in the implosion of QTWAs. It is shown that the emission spectra of the SXR sources formed under the implosion of quasi-spherical and cylindrical tungsten wire arrays at currents of up to 3 MA have a maximum in the wavelength range of 50–150 Å. It is found that, during the implosion of a QTWA with a profiled linear mass, a redistribution of energy in the emission spectrum takes place, which indicates that, during 3D implosion, the energy of longitudinal motion of the array material additionally contributes to the radiation energy. It is also found that, at close masses of the arrays and close values of the current in the range of 2.4{sup −3} MA, the average energy density in the emission source formed during the implosion of a quasi-spherical wire array is larger by a factor of 7 than in the source formed during the implosion of a cylindrical wire array. The experimental data were compared with results of 3D simulations of plasma dynamics and radiation generation during the implosion of quasi-spherical wire arrays with a profiled mass by using the MARPLE-3D radiative magnetohydrodynamic code, developed at the

  3. 3D geological modelling and geothermal mapping - the first results of the transboundary Polish - Saxon project "TransGeoTherm"

    NASA Astrophysics Data System (ADS)

    Kozdrój, Wiesław; Kłonowski, Maciej; Mydłowski, Adam; Ziółkowska-Kozdrój, Małgorzata; Badura, Janusz; Przybylski, Bogusław; Russ, Dorota; Zawistowski, Karol; Domańska, Urszula; Karamański, Paweł; Krentz, Ottomar; Hofmann, Karina; Riedel, Peter; Reinhardt, Silke; Bretschneider, Mario

    2014-05-01

    TransGeoTherm is a common project of the Polish Geological Institute - National Research Institute Lower Silesian Branch (Lead Partner) and the Saxon State Agency for Environment, Agriculture and Geology, co-financed by the European Union (EU) under the framework of the Operational Programme for Transboundary Co-operation Poland-Saxony 2007-2013. It started in October 2012 and will last until June 2014. The main goal of the project is to introduce and establish the use of low temperature geothermal energy as a low emission energy source in the Saxon-Polish transboundary project area. The numerous geological, hydrogeological and geothermal data have been gathered, analysed, combined and interpreted with respect to 3D numerical modelling and subsequently processed with use of the GOCAD software. The resulting geological model covers the transboundary project area exceeding 1.000 km2 and comprises around 70 units up to the depth of about 200 metres (locally deeper) below the terrain. The division of the above units has been based on their litho-stratigraphy as well as geological, hydrogeological and geothermal settings. The model includes two lignite deposits: Berzdorf deposit in Saxony-mined out and already recultivated and Radomierzyce deposit in Poland - documented but still not excavated. At the end of the modelling procedure the raster data sets of the top, bottom and thickness of every unit will be deduced from the 3D geological model with a gridsize of 25 by 25 metres. Based on the geothermal properties of the rocks and their groundwater content a specific value of geothermal conductivity will be allocated to each layer of every borehole. Thereafter for every section of a borehole, belonging to a certain unit of the 3D geological model, a weighted mean value will be calculated. Next the horizontal distribution of these values within every unit will be interpolated. This step / procedure has to be done for all units. As a result of further calculations a series

  4. Development of Inundation Map for Bantayan Island, Cebu Using Delft3D-Flow Storm Surge Simulations of Typhoon Haiyan

    NASA Astrophysics Data System (ADS)

    Cuadra, Camille; Suarez, John Kenneth; Biton, Nophi Ian; Cabacaba, Krichi May; Lapidez, John Phillip; Santiago, Joy; Mahar Francisco Lagmay, Alfredo; Malano, Vicente

    2014-05-01

    On average, 20 typhoons enter the Philippine area of responsibility annually, making it vulnerable to different storm hazards. Apart from the frequency of tropical cyclones, the archipelagic nature of the country makes it particularly prone to storm surges. On 08 November 2013, Haiyan, a Category 5 Typhoon with maximum one-minute sustained wind speed of 315 kph, hit the central region of the Philippines. In its path, the howler devastated Bantayan Island, a popular tourist destination. The island is located north of Cebu City, the second largest metropolis of the Philippines in terms of populace. Having been directly hit by Typhoon Haiyan, Bantayan Island was severely damaged by strong winds and storm surges, with more than 11,000 houses totally destroyed while 5,000 more suffered minor damage. The adverse impacts of possible future storm surge events in the island can only be mitigated if hazard maps that depict inundation of the coastal areas of Bantayan are generated. To create such maps, Delft3D-Flow, a hydrodynamic model was used to simulate storm surges. These simulations were made over a 10-m per pixel resolution Digital Elevation Model (DEM) and the General Bathymetric Chart of the Oceans (GEBCO) bathymetry. The results of the coastal inundation model for Typhoon Haiyan's storm surges were validated using data collected from field work and local government reports. The hydrodynamic model of Bantayan was then calibrated using the field data and further simulations were made with varying typhoon tracks. This was done to generate scenarios on the farthest possible inland incursion of storm surges. The output of the study is a detailed storm surge inundation map that depicts safe zones for development of infrastructure near coastal areas and for construction of coastal protection structures. The storm surge inundation map can also be used as basis for disaster preparedness plans of coastal communities threatened by approaching typhoons.

  5. A study of 3D structure of nighttime electron density enhancement in the mid-latitude ionosphere by GPS tomography

    NASA Astrophysics Data System (ADS)

    Chen, C.; Saito, A.

    2011-12-01

    The mid-latitude summer nighttime anomaly (MSNA) is a feature that the nighttime electron density larger than that in the daytime mid-latitude ionosphere. This anomaly was first detected in the southern hemisphere five decades ago and observed in the northern hemisphere recently by ionosondes and satellites. Previous studies presented the electron density structure of MSNA by using COSMIC occultation data and found that MSNA is clearly seen around 300 km altitude during local summer. However, due to lack of observation, the day-to-day variation of MSNA was not investigated. A GPS tomography method by SPEL of Kyoto University using the total electron content (TEC) data measured by the ground-based GPS receiver network is employed in this study. The wide coverage and continuous observation of GPS receivers are suitable for investigating the spatial and day-to-day variations of ionospheric electron densities. The algorithm of the GPS tomography developed by SPEL of Kyoto University use a constraint condition that the gradient of election density tends to be smooth in the horizontal direction and steep in the vicinity of the F2 peak, instead of inputting the initial conditions. Therefore, the algorithm is independent of any ionospheric and plasmaspheric electron density distribution models. The dense ground-based GPS receiver network around European region is used to study the three dimensional (3D) structure of MSNA with GPS tomography. Results show that the MSNA usually appear around the geomagnetic mid-latitude region during local summer nighttime. The feature of MSNA is most obvious at the ionospheric F2-peak altitudes. The result also shows a day-to-day variation in the formation of MSNA, in terms of the occurrence time, intensity, and spatial extent. The tomographic results are compared with the ionosondes, satellites, and radar measurements. A theoretical model simulation, SAMI2, is also used to further discuss the mechanism of MSNA. The comparison with other

  6. Documentation and Visualization of AN As-Built Tunnel by Combining 3d Laser Scanning and Web Mapping

    NASA Astrophysics Data System (ADS)

    Zhang, C.; Arditi, D.; Chen, Z.

    2013-08-01

    A new way to document and visualize the as-built condition of an urban tunnel project with high accuracy is described in this paper, based on recent developments of laser scanning technology. In traditional surveying, the components of a tunnel are organized on the basis of the location of stations and offsets along the project alignment specified in the drawings. It is difficult for people without an engineering background to understand the information involved in surveying reports, drawings, and engineering data. However, in the interest of transparency, public agencies that commission construction projects have to make project information available to government officials and to the general public. This paper discusses the combined use of laser scanning technology and web mapping services to improve the documentation and visualization of an urban metro tunnel. Laser scanning technology is introduced to perform the surveyor's task, document the as-built condition, and geo-reference the construction elements. A set of panoramic pictures is generated by laser scanning that allows for taking measurements and extracting 3D coordinates. An XML file that contains geo-reference information is appended to each panoramic picture. Using application programming interface (API), this information is referenced to a web mapping service. A case study of the CTA Red line Tunnel in Chicago, IL demonstrates this method in a real life project.

  7. Reconstructing 3-D maps of the local viscoelastic properties using a finite-amplitude modulated radiation force.

    PubMed

    Giannoula, Alexia; Cobbold, Richard; Bezerianos, Anastasios

    2014-02-01

    A modulated acoustic radiation force, produced by two confocal tone-burst ultrasound beams of slightly different frequencies (i.e. 2.0 MHz ± Δf/2, where Δf is the difference frequency), can be used to remotely generate modulated low-frequency (Δf ≤ 500 Hz) shear waves in attenuating media. By appropriately selecting the duration of the two beams, the energy of the generated shear waves can be concentrated around the difference frequency (i.e., Δf ± Δf/2). In this manner, neither their amplitude nor their phase information is distorted by frequency-dependent effects, thereby, enabling a more accurate reconstruction of the viscoelastic properties. Assuming a Voigt viscoelastic model, this paper describes the use of a finite-element-method model to simulate three-dimensional (3-D) shear-wave propagation in viscoelastic media containing a spherical inclusion. Nonlinear propagation is assumed for the two ultrasound beams, so that higher harmonics are developed in the force and shear spectrum. Finally, an inverse reconstruction algorithm is used to extract 3-D maps of the local shear modulus and viscosity from the simulated shear-displacement fields based on the fundamental and second-harmonic component. The quality of the reconstructed maps is evaluated using the contrast between the inclusion and the background and the contrast-to-noise ratio (CNR). It is shown that the shear modulus can be accurately reconstructed based on the fundamental component, such that the observed contrast deviates from the true contrast by a root-mean-square-error (RMSE) of only 0.38 and the CNR is greater than 30 dB. If the second-harmonic component is used, the RMSE becomes 1.54 and the corresponding CNR decreases by approximately 10-15 dB. The reconstructed shear viscosity maps based on the second harmonic are shown to be of higher quality than those based on the fundamental. The effects of noise are also investigated and a fusion operation between the two spectral components is

  8. Field Trial Results of a 14-channel GPR Integrated with a U.S. Program for 3-D Utility Mapping

    NASA Astrophysics Data System (ADS)

    Anspach, James H.

    2013-04-01

    utilities were mostly undetectable. Through a ground-truthing program of test holes to expose utilities, the depth values derived from the enhanced GPR were fairly consistent and within 15 cm of actual depth. The incomplete underground picture determined by the enhanced GPR reinforces previous studies that show that the mapping of existing underground utilities is a multi-tool effort that takes highly trained and skilled field technicians and data interpreters. The addition of a new GPR tool is valuable in determining continuous depth profiles of imaged utilities. A second and significant benefit is the interpretation of other geotechnical data that benefit project designers. This might include showing geometry, location, intensity, and depths of either areas of anomalies, or of known structures, such as paving thickness, substrate thickness, voids, water table, soil lenses, boulders, bedrock, and so forth. The Florida Department of Transportation has decided to take advantage of this new technology and has entered into an experimental contract with Cardno TBE to incorporate several enhanced GPR arrays with traditional utility detection tools. The goal of this contract will be to provide a 3-D model of existing underground utilities for use in automated construction. The GPR 3-D data model will be melded with conventional subsurface utility engineering and mapping practices and will be required to follow the ASCE 38 standard for utility data reliability.

  9. Vibrational density of states and thermodynamics at the nanoscale: the 3D-2D transition in gold nanostructures.

    PubMed

    Carles, R; Benzo, P; Pécassou, B; Bonafos, C

    2016-12-16

    Surface enhanced Raman scattering (SERS) is generally and widely used to enhance the vibrational fingerprint of molecules located at the vicinity of noble metal nanoparticles. In this work, SERS is originally used to enhance the own vibrational density of states (VDOS) of nude and isolated gold nanoparticles. This offers the opportunity of analyzing finite size effects on the lattice dynamics which remains unattainable with conventional techniques based on neutron or x-ray inelastic scattering. By reducing the size down to few nanometers, the role of surface atoms versus volume atoms become dominant, and the "text-book" 3D-2D transition on the dynamical behavior is experimentally emphasized. "Anomalies" that have been predicted by a large panel of simulations at the atomic scale, are really observed, like the enhancement of the VDOS at low frequencies or the occurrence of localized modes at frequencies beyond the cut-off in bulk. Consequences on the thermodynamic properties at the nanoscale, like the reduction of the Debye temperature or the excess of the specific heat, have been evaluated. Finally the high sensitivity of reminiscent bulk-like phonons on the arrangements at the atomic scale is used to access the morphology and internal disorder of the nanoparticles.

  10. Vibrational density of states and thermodynamics at the nanoscale: the 3D-2D transition in gold nanostructures

    NASA Astrophysics Data System (ADS)

    Carles, R.; Benzo, P.; Pécassou, B.; Bonafos, C.

    2016-12-01

    Surface enhanced Raman scattering (SERS) is generally and widely used to enhance the vibrational fingerprint of molecules located at the vicinity of noble metal nanoparticles. In this work, SERS is originally used to enhance the own vibrational density of states (VDOS) of nude and isolated gold nanoparticles. This offers the opportunity of analyzing finite size effects on the lattice dynamics which remains unattainable with conventional techniques based on neutron or x-ray inelastic scattering. By reducing the size down to few nanometers, the role of surface atoms versus volume atoms become dominant, and the “text-book” 3D-2D transition on the dynamical behavior is experimentally emphasized. “Anomalies” that have been predicted by a large panel of simulations at the atomic scale, are really observed, like the enhancement of the VDOS at low frequencies or the occurrence of localized modes at frequencies beyond the cut-off in bulk. Consequences on the thermodynamic properties at the nanoscale, like the reduction of the Debye temperature or the excess of the specific heat, have been evaluated. Finally the high sensitivity of reminiscent bulk-like phonons on the arrangements at the atomic scale is used to access the morphology and internal disorder of the nanoparticles.

  11. Vibrational density of states and thermodynamics at the nanoscale: the 3D-2D transition in gold nanostructures

    PubMed Central

    Carles, R.; Benzo, P.; Pécassou, B.; Bonafos, C.

    2016-01-01

    Surface enhanced Raman scattering (SERS) is generally and widely used to enhance the vibrational fingerprint of molecules located at the vicinity of noble metal nanoparticles. In this work, SERS is originally used to enhance the own vibrational density of states (VDOS) of nude and isolated gold nanoparticles. This offers the opportunity of analyzing finite size effects on the lattice dynamics which remains unattainable with conventional techniques based on neutron or x-ray inelastic scattering. By reducing the size down to few nanometers, the role of surface atoms versus volume atoms become dominant, and the “text-book” 3D-2D transition on the dynamical behavior is experimentally emphasized. “Anomalies” that have been predicted by a large panel of simulations at the atomic scale, are really observed, like the enhancement of the VDOS at low frequencies or the occurrence of localized modes at frequencies beyond the cut-off in bulk. Consequences on the thermodynamic properties at the nanoscale, like the reduction of the Debye temperature or the excess of the specific heat, have been evaluated. Finally the high sensitivity of reminiscent bulk-like phonons on the arrangements at the atomic scale is used to access the morphology and internal disorder of the nanoparticles. PMID:27982080

  12. Inverse current-source density method in 3D: reconstruction fidelity, boundary effects, and influence of distant sources.

    PubMed

    Łeski, Szymon; Wójcik, Daniel K; Tereszczuk, Joanna; Swiejkowski, Daniel A; Kublik, Ewa; Wróbel, Andrzej

    2007-01-01

    Estimation of the continuous current-source density in bulk tissue from a finite set of electrode measurements is a daunting task. Here we present a methodology which allows such a reconstruction by generalizing the one-dimensional inverse CSD method. The idea is to assume a particular plausible form of CSD within a class described by a number of parameters which can be estimated from available data, for example a set of cubic splines in 3D spanned on a fixed grid of the same size as the set of measurements. To avoid specificity of particular choice of reconstruction grid we add random jitter to the points positions and show that it leads to a correct reconstruction. We propose different ways of improving the quality of reconstruction which take into account the sources located outside the recording region through appropriate boundary treatment. The efficiency of the traditional CSD and variants of inverse CSD methods is compared using several fidelity measures on different test data to investigate when one of the methods is superior to the others. The methods are illustrated with reconstructions of CSD from potentials evoked by stimulation of a bunch of whiskers recorded in a slab of the rat forebrain on a grid of 4x5x7 positions.

  13. Dynamic deformation measurements of a rotating disc by twin-pulsed 3D digital holography and interpolation of phase maps

    NASA Astrophysics Data System (ADS)

    Perez-Lopez, Carlos; Mendoza Santoyo, Fernando

    2004-06-01

    This paper describes the application of twin-pulsed 3D digital holography to the measurement of the dynamic deformation of a disc while it rotates. Object rotation produces interferometric fringes that are related to deformations for instance, stress due to the centrifugal forces, out-to plane vibrations, and the object angular displacement. Furthermore an unbalanced disc that rotates may present a characteristic vibration amplitude pattern at a specific frequency. An optical arrangement that illuminates, with a twin pulsed laser, from three different positions the object was used to recover the x, y and z displacement components in a rotating object. The technique is able to distinguish the disc rotation from the displacement along the x-y plane and the out-of-plane z displacement. Two laser pulses are fired in order to take two digital holgrams with a time separation of 20 μs. This is done for each of the three object illumination positions. Triads of twin-pulsed digital holograms taken at different times during object rotation are processed independently, and their optical phase maps retrieved by the conventional Fourier transform method together with the combination of data from the three illumination positions. The phase term related to the deformation is found experimentally where the intrinsic sensitivity vector is related to the rotation via the vector cross product, forming parallel fringes. To recover the rotation and deformation data the unwrapped phase maps were used as 'tilt' phase planes an all three sensitivity vectors in order to recover the in-plane, and out-to plane displacements. An interpolation algorithm was developed to correlate the time depending phase maps, leading to obtain object vibration frequency data. Experimental results are presented, showing in particular that the rotating object has an unbalancing due to the detected vibration frequency.

  14. High-resolution 3-D T1*-mapping and quantitative image analysis of GRAY ZONE in chronic fibrosis.

    PubMed

    Pop, Mihaela; Ramanan, Venkat; Yang, Franklin; Zhang, Li; Newbigging, Susan; Ghugre, Nilesh R; Wright, Graham A

    2014-12-01

    The substrate of potentially lethal cardiac arrhythmias often resides in the gray zone (GZ), a mixture of viable myocytes and collagen strands found between healthy myocardium and infarct core (IC). The specific aims of this paper are to demonstrate correspondence between regions delineated in T1* (apparent T1) maps and tissue characteristics seen in histopathology and to determine the MR imaging resolution needed to adequately identify GZ-associated substrate in chronic infarct. For this, a novel 3-D multicontrast late enhancement (MCLE) MR method was used to image ex vivo swine hearts with chronic infarction, at high resolution ( 0.6×0.6×1.25 mm). Pixel-wise classified tissue maps were calculated using steady-state and T1* images as input to a fuzzy-clustering algorithm. Quantitative histology based on collagen stains was performed in n = 10 selected slabs and showed very good correlations between histologically-determined areas of heterogeneous and dense fibrosis, and the corresponding GZ ( R2 = 0.96) and IC ( R2 = 0.97 ) in tissue classified maps. Furthermore, in n = 24 slabs, we performed volumetric measurements of GZ and IC, at the original and decreased image resolutions. Our results demonstrated that the IC volume remained relatively unchanged across all resolutions, whereas the GZ volume progressively increased with diminished image resolution, with changes reaching significance at 1×1×5 mm resolution (p < 0.05 ) but not at 1×1×2.5 mm, suggesting that this resolution may be sufficient to adequately identify the GZ from MCLE images, enabling an effective MR probing of remodeled myocardium in late infarct. Future work will focus on translating these findings to optimizing the current in vivo MCLE imaging of the GZ.

  15. A 3D map of the hindlimb motor representation in the lumbar spinal cord in Sprague Dawley rats

    NASA Astrophysics Data System (ADS)

    Borrell, Jordan A.; Frost, Shawn B.; Peterson, Jeremy; Nudo, Randolph J.

    2017-02-01

    Objective. Spinal cord injury (SCI) is a devastating neurological trauma with a prevalence of about 282 000 people living with an SCI in the United States in 2016. Advances in neuromodulatory devices hold promise for restoring function by incorporating the delivery of electrical current directly into the spinal cord grey matter via intraspinal microstimulation (ISMS). In such designs, detailed topographic maps of spinal cord outputs are needed to determine ISMS locations for eliciting hindlimb movements. The primary goal of the present study was to derive a topographic map of functional motor outputs in the lumbar spinal cord to hindlimb skeletal muscles as defined by ISMS in a rat model. Approach. Experiments were carried out in nine healthy, adult, male, Sprague Dawley rats. After a laminectomy of the T13-L1 vertebrae and removal of the dura mater, a four-shank, 16-channel microelectrode array was inserted along a 3D (200 µm) stimulation grid. Trains of three biphasic current pulses were used to determine evoked movements and electromyographic (EMG) activity. Via fine wire EMG electrodes, stimulus-triggered averaging (StTA) was used on rectified EMG data to determine response latency. Main results. Hindlimb movements were elicited at a median current intensity of 6 µA, and thresholds were significantly lower in ventrolateral sites. Movements typically consisted of whole leg, hip, knee, ankle, toe, and trunk movements. Hip movements dominated rostral to the T13 vertebral segment, knee movements were evoked at the T13-L1 vertebral junction, while ankle and digit movements were found near the rostral L1 vertebra. Whole leg movements spanned the entire rostrocaudal region explored, while trunk movements dominated medially. StTAs of EMG activity demonstrated a latency of ~4 ms. Significance. The derived motor map provides insight into the parameters needed for future neuromodulatory devices.

  16. 3D-QSAR AND CONTOUR MAP ANALYSIS OF TARIQUIDAR ANALOGUES AS MULTIDRUG RESISTANCE PROTEIN-1 (MRP1) INHIBITORS

    PubMed Central

    Kakarla, Prathusha; Inupakutika, Madhuri; Devireddy, Amith R.; Gunda, Shravan Kumar; Willmon, Thomas Mark; Ranjana, KC; Shrestha, Ugina; Ranaweera, Indrika; Hernandez, Alberto J.; Barr, Sharla; Varela, Manuel F.

    2016-01-01

    One of the major obstacles to the successful chemotherapy towards several cancers is multidrug resistance of human cancer cells to anti-cancer drugs. An important contributor to multidrug resistance is the human multidrug resistance protein-1 transporter (MRP1), which is an efflux pump of the ABC (ATP binding cassette) superfamily. Thus, highly efficacious, third generation MRP1 inhibitors, like tariquidar analogues, are promising inhibitors of multidrug resistance and are under clinical trials. To maximize the efficacy of MRP1 inhibitors and to reduce systemic toxicity, it is important to limit the exposure of MRP1 inhibitors and anticancer drugs to normal tissues and to increase their co-localization with tumor cells. Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) associated with 3D-Quantitiative structure-activity relationship (3D-QSAR) studies were performed on a series of tariquidar analogues, as selective MDR modulators. Best predictability was obtained with CoMFA model r2(non-cross-validated square of correlation coefficient) = 0.968, F value = 151.768 with five components, standard error of estimate = 0.107 while the CoMSIA yielded r2 = 0.982, F value = 60.628 with six components, and standard error of estimate = 0.154. These results indicate that steric, electrostatic, hydrophobic (lipophilic), and hydrogen bond donor substituents play significant roles in multidrug resistance modulation of tariquidar analogues upon MRP1. The tariquidar analogue and MRP1 binding and stability data generated from CoMFA and CoMSIA based 3D–contour maps may further aid in study and design of tariquidar analogues as novel, potent and selective MDR modulator drug candidates. PMID:26913287

  17. Screening Method for the Discovery of Potential Bioactive Cysteine-Containing Peptides Using 3D Mass Mapping

    NASA Astrophysics Data System (ADS)

    van Oosten, Luuk N.; Pieterse, Mervin; Pinkse, Martijn W. H.; Verhaert, Peter D. E. M.

    2015-12-01

    Animal venoms and toxins are a valuable source of bioactive peptides with pharmacologic relevance as potential drug leads. A large subset of biologically active peptides discovered up till now contain disulfide bridges that enhance stability and activity. To discover new members of this class of peptides, we developed a workflow screening specifically for those peptides that contain inter- and intra-molecular disulfide bonds by means of three-dimensional (3D) mass mapping. Two intrinsic properties of the sulfur atom, (1) its relatively large negative mass defect, and (2) its isotopic composition, allow for differentiation between cysteine-containing peptides and peptides lacking sulfur. High sulfur content in a peptide decreases the normalized nominal mass defect (NMD) and increases the normalized isotopic shift (NIS). Hence in a 3D plot of mass, NIS, and NMD, peptides with sulfur appear in this plot with a distinct spatial localization compared with peptides that lack sulfur. In this study we investigated the skin secretion of two frog species; Odorrana schmackeri and Bombina variegata. Peptides from the crude skin secretions were separated by nanoflow LC, and of all eluting peptides high resolution zoom scans were acquired in order to accurately determine both monoisotopic mass and average mass. Both the NMD and the NIS were calculated from the experimental data using an in-house developed MATLAB script. Candidate peptides exhibiting a low NMD and high NIS values were selected for targeted de novo sequencing, and this resulted in the identification of several novel inter- and intra-molecular disulfide bond containing peptides.

  18. Performance of density functional theory for 3d transition metal-containing complexes: utilization of the correlation consistent basis sets.

    PubMed

    Tekarli, Sammer M; Drummond, Michael L; Williams, T Gavin; Cundari, Thomas R; Wilson, Angela K

    2009-07-30

    The performance of 44 density functionals used in conjunction with the correlation consistent basis sets (cc-pVnZ where n = T and Q) has been assessed for the gas-phase enthalpies of formation at 298.15 K of 3d transition metal (TM) containing systems. Nineteen molecules were examined: ScS, VO, VO(2), Cr(CO)(6), MnS, MnCl(2), Mn(CO)(5)Cl, FeCl(3), Fe(CO)(5), CoH(CO)(4), NiCl(2), Ni(CO)(4), CuH, CuF, CuCl, ZnH, ZnO, ZnCl, and Zn(CH(3))(2). Of the functionals examined, the functionals that resulted in the smallest mean absolute deviation (MAD, in parentheses, kcal mol(-1)) from experiment were B97-1 (6.9), PBE1KCIS (8.1), TPSS1KCIS (9.6), B97-2 (9.7), and B98 (10.7). All five of these functionals include some degree of Hartree-Fock (HF) exchange. The impact of increasing the basis set from cc-pVTZ to cc-pVQZ was found to be slight for the generalized gradient approximation (GGA) and meta-GGA (MGGA) functionals studied, indicating basis set saturation at the triple-zeta level. By contrast, for most of the generalized gradient exchange (GGE), hybrid GGA (HGGA), and hybrid meta-GGA (HMGGA) functionals considered, improvements in the average MAD of 2-3 kcal mol(-1) were seen upon progressing to a quadruple-zeta level basis set. Overall, it was found that the functionals that include Hartree-Fock exchange performed best overall, but those with greater than 40% HF exchange exhibit significantly poor performance for the prediction of enthalpies of formation for 3d TM complexes. Carbonyl-containing complexes, a mainstay in organometallic TM chemistry, are demonstrated to be exceedingly difficult to describe accurately with all but 2 of the 44 functionals considered. The most accurate functional, for both CO-containing and CO-free compounds, is B97-1/cc-pVQZ, which is shown to be capable of yielding results within 1 kcal mol(-1) of high-level ab initio composite methodologies.

  19. Development of a 3D Underground Cadastral System with Indoor Mapping for As-Built BIM: The Case Study of Gangnam Subway Station in Korea

    PubMed Central

    Kim, Sangmin; Kim, Jeonghyun; Jung, Jaehoon; Heo, Joon

    2015-01-01

    The cadastral system provides land ownership information by registering and representing land boundaries on a map. The current cadastral system in Korea, however, focuses mainly on the management of 2D land-surface boundaries. It is not yet possible to provide efficient or reliable land administration, as this 2D system cannot support or manage land information on 3D properties (including architectures and civil infrastructures) for both above-ground and underground facilities. A geometrical model of the 3D parcel, therefore, is required for registration of 3D properties. This paper, considering the role of the cadastral system, proposes a framework for a 3D underground cadastral system that can register various types of 3D underground properties using indoor mapping for as-built Building Information Modeling (BIM). The implementation consists of four phases: (1) geometric modeling of a real underground infrastructure using terrestrial laser scanning data; (2) implementation of as-built BIM based on geometric modeling results; (3) accuracy assessment for created as-built BIM using reference points acquired by total station; and (4) creation of three types of 3D underground cadastral map to represent underground properties. The experimental results, based on indoor mapping for as-built BIM, show that the proposed framework for a 3D underground cadastral system is able to register the rights, responsibilities, and restrictions corresponding to the 3D underground properties. In this way, clearly identifying the underground physical situation enables more reliable and effective decision-making in all aspects of the national land administration system. PMID:26690174

  20. Development of a 3D Underground Cadastral System with Indoor Mapping for As-Built BIM: The Case Study of Gangnam Subway Station in Korea.

    PubMed

    Kim, Sangmin; Kim, Jeonghyun; Jung, Jaehoon; Heo, Joon

    2015-12-09

    The cadastral system provides land ownership information by registering and representing land boundaries on a map. The current cadastral system in Korea, however, focuses mainly on the management of 2D land-surface boundaries. It is not yet possible to provide efficient or reliable land administration, as this 2D system cannot support or manage land information on 3D properties (including architectures and civil infrastructures) for both above-ground and underground facilities. A geometrical model of the 3D parcel, therefore, is required for registration of 3D properties. This paper, considering the role of the cadastral system, proposes a framework for a 3D underground cadastral system that can register various types of 3D underground properties using indoor mapping for as-built Building Information Modeling (BIM). The implementation consists of four phases: (1) geometric modeling of a real underground infrastructure using terrestrial laser scanning data; (2) implementation of as-built BIM based on geometric modeling results; (3) accuracy assessment for created as-built BIM using reference points acquired by total station; and (4) creation of three types of 3D underground cadastral map to represent underground properties. The experimental results, based on indoor mapping for as-built BIM, show that the proposed framework for a 3D underground cadastral system is able to register the rights, responsibilities, and restrictions corresponding to the 3D underground properties. In this way, clearly identifying the underground physical situation enables more reliable and effective decision-making in all aspects of the national land administration system.

  1. VizieR Online Data Catalog: 3D reddening map for stars from 2MASS phot. (Gontcharov, 2010)

    NASA Astrophysics Data System (ADS)

    Gontcharov, G. A.

    2016-07-01

    A three-dimensional reddening map for stars within 1100pc of the Sun are presented. Analysis of the distribution of 70 million stars from the 2MASS catalog with the most accurate photometry on the (J-Ks)-Ks diagram supplemented with Monte Carlo simulations has shown that one of the maxima of this distribution corresponds to F-type dwarfs and subgiants with a mean absolute magnitude MKs=2.5m. The shift of this maximum toward large (J-Ks) with increasing Ks reflects the reddening of these stars with increasing heliocentric distance. The distribution of the sample of stars over Ks, l, and b cells with a statistically significant number of stars in each cell corresponds to their distribution over three-dimensional spatial cells. As a result, the reddening E(J-Ks) has been determined with an accuracy of 0.03m for spatial cells with a side of 100pc. All of the known large absorbing clouds within 1100pc of the Sun have manifested themselves in the results obtained. The absorbing matter of the Gould Belt is shown to manifest itself at latitudes up to 40° and within 600pc of the Sun. The size and influence of the Gould Belt may have been underestimated thus far. The absorbing matter at latitudes up to 60° and within 1100pc of the Sun has been found to be distributed predominantly in the first and second quadrants in the southern hemisphere and in the third and fourth quadrants in the northern hemisphere. Also the data of the Rv (2012AstL...38...12G) and Av (2012AstL...38...87G) 3D maps are added. (1 data file).

  2. Using Lidar-derived 3-D Vegetation Structure Maps to Assist in the Search for the Ivory- billed Woodpecker

    NASA Astrophysics Data System (ADS)

    Hofton, M. A.; Blair, J. B.; Rabine, D.; Dubayah, R.; Greim, H.

    2006-12-01

    Averaging about 20 inches in length, the ivory-billed woodpecker is among the world's largest woodpeckers. It once ranged through swampy forests in the southeastern and lower Mississippi valley states, and until recently was believed to have become extinct in the 1940's when commercial logging destroyed its last known habitat. Recent sightings however, may indicate the birds' survival in remaining bottomland hardwood forest adjacent to the Cache and White Rivers in Arkansas. In June-July 2006, NASA's Laser Vegetation Imaging Sensor (LVIS) was used to map approximately 5000 km2 of the White River National Wildlife Refuge in Arkansas, including sites where recent possible sightings of the bird occurred. LVIS is an airborne, medium- footprint (5- to 25-meter diameter), full waveform-recording, airborne, scanning lidar system which has been used extensively for mapping forest structure, habitat, carbon and natural hazards. The system digitally records the shape of the returning laser echo, or waveform, after its interaction with the various reflecting surfaces of the earth (leaves, branches, ground, etc.), providing a true 3-dimensional record of the surface structure. Data collected included ground elevation and canopy height measurements for each laser footprint, as well as the vertical distribution of intercepted surfaces (the return waveform). Experimental metrics such as canopy structure metrics based on energy quartiles, as well as ground energy/canopy cover and waveform complexity metrics will be derived from each waveform. The project is a collaborative effort between the University of Maryland, NASA, USGS, and the US Fish and Wildlife Service. The LVIS-generated data of the 3- D vegetation structure and underlying terrain will be used as a means to guide local, ground-based search efforts in the upcoming field season as well as identify the remaining areas of habitat suitable for protection should the bird be found.

  3. Multigrid mapping and box relaxation for simulation of the whole process of flow transition in 3-D boundary layers

    SciTech Connect

    Liu, C.; Liu, Z.

    1994-12-31

    A new multilevel technology was developed in this study which provides a successful numerical simulation for the whole process of flow transition in 3-D flat plate boundary layers, including linear growth, secondary instability, breakdown, and transition on a relatively coarse grid with low CPU cost. A fourth-order finite difference scheme on stretched and staggered grids, a fully implicit time-marching technique, a semi-coarsening multigrid based on the so-called approximate line-box relaxation, and a buffer domain for the outflow boundary conditions were all employed for high-order accuracy, good stability, and fast convergence. A new fine-coarse-fine grid mapping technique was developed to catch the large eddies and represent main roles of small eddies to keep the code running after the laminar flow breaks down. The computational results are in good agreement with linear stability theory, secondary instability theory, and some experiments. The computation also reproduced the K-type and C-type transition observed by laboratory experiments. The CPU cost for a typical case is around 2-9 CRAY-YMP hours.

  4. Using Quasi-3D OSIRIS simulations of LWFA to study generating high brightness electron beams using ionization and density downramp injection

    NASA Astrophysics Data System (ADS)

    Dalichaouch, Thamine; Davidson, Asher; Xu, Xinlu; Yu, Peicheng; Tsung, Frank; Mori, Warren; Li, Fei; Zhang, Chaojie; Lu, Wei; Vieira, Jorge; Fonseca, Ricardo

    2016-10-01

    In the past few decades, there has been much progress in theory, simulation, and experiment towards using Laser wakefield acceleration (LWFA) as the basis for designing and building compact x-ray free-electron-lasers (XFEL) as well as a next generation linear collider. Recently, ionization injection and density downramp injection have been proposed and demonstrated as a controllable injection scheme for creating higher quality and ultra-bright relativistic electron beams using LWFA. However, full-3D simulations of plasma-based accelerators are computationally intensive, sometimes taking 100 millions of core-hours on today's computers. A more efficient quasi-3D algorithm was developed and implemented into OSIRIS using a particle-in-cell description with a charge conserving current deposition scheme in r - z and a gridless Fourier expansion in ϕ. Due to the azimuthal symmetry in LWFA, quasi-3D simulations are computationally more efficient than 3D cartesian simulations since only the first few harmonics in are needed ϕ to capture the 3D physics of LWFA. Using the quasi-3D approach, we present preliminary results of ionization and down ramp triggered injection and compare the results against 3D LWFA simulations. This work was supported by DOE and NSF.

  5. Polyphase tertiary fold-and-thrust tectonics in the Belluno Dolomites: new mapping, kinematic analysis, and 3D modelling

    NASA Astrophysics Data System (ADS)

    Chistolini, Filippo; Bistacchi, Andrea; Massironi, Matteo; Consonni, Davide; Cortinovis, Silvia

    2014-05-01

    performed a dip-domain analysis that allowed to categorize the different fold limbs and reduce the uncertainty in the reconstruction of the fault network topology in map view. This enabled us to reconstruct a high-quality, low-uncertainty 3D structural and geological model, which unambiguously proves that deformations with a top-to-WSW Dinaric transport direction propagate farther to the west than previously supposed in this part of the Southern Alps. Our new structural reconstruction of the Vajont valley have also clarified the structural control on the 1963 catastrophic landslide (which caused over 2000 losses). Besides being a challenging natural laboratory for testing analysis and modelling methodologies to be used when reconstructing in 3D this kind of complex interference structures, the Vajont area also provides useful clues on the still-enigmatic structures in the frontal part of the Friuli-Venetian Southern Alps, buried in the Venetian Plain foredeep. These include active seismogenic thrust-faults and, at the same time, represent a growing interest for the oil industry.

  6. Mapping the 3-D extent of the Northern Lobe of the Bushveld layered mafic intrusion from geophysical data

    USGS Publications Warehouse

    Finn, Carol A.; Bedrosian, Paul A.; Cole, Janine; Khoza, Tshepo David; Webb, Susan J.

    2015-01-01

    Geophysical models image the 3D geometry of the mafic portion of the Bushveld Complex north of the Thabazimbi-Murchison Lineament (TML), critical for understanding the origin of the world's largest layered mafic intrusion and platinum group element deposits. The combination of the gravity and magnetic data with recent seismic, MT, borehole and rock property measurements powerfully constrains the models. The intrusion north of the TML is generally shallowly buried (generally <1500 m) with a modeled area of ∼160 km × ∼125 km. The modeled thicknesses are not well constrained but vary from ∼<1000 to >12,000 m, averaging ∼4000 m. A feeder, suggested by a large modeled thickness (>10,000 m) and funnel shape, for Lower Zone magmas could have originated near the intersection of NS and NE trending TML faults under Mokopane. The TML has been thought to be the feeder zone for the entire Bushveld Complex but the identification of local feeders and/or dikes in the TML in the models is complicated by uncertainties on the syn- and post-Bushveld deformation history. However, modeled moderately thick high density material near the intersection of faults within the central and western TML may represent feeders for parts of the Bushveld Complex if deformation was minimal. The correspondence of flat, high resistivity and density regions reflect the sill-like geometry of the Bushveld Complex without evidence for feeders north of Mokopane. Magnetotelluric models indicate that the Transvaal sedimentary basin underlies much of the Bushveld Complex north of the TML, further than previously thought and important because the degree of reaction and assimilation of the Transvaal rocks with the mafic magmas resulted in a variety of mineralization zones.

  7. Mapping the North Sea base-Quaternary: using 3D seismic to fill a gap in the geological record

    NASA Astrophysics Data System (ADS)

    Lamb, Rachel; Huuse, Mads; Stewart, Margaret; Brocklehurst, Simon H.

    2014-05-01

    The identification and mapping of the base-Quaternary boundary in the central parts of the North Sea is problematic due to the change from an unconformable transition between Pliocene and Pleistocene deltaic deposits in the southern North Sea to a conformable one further north (Sejrup et al 1991; Gatliff et al 1994). The best estimates of the transition use seismic reflection data to identify a 'crenulated reflector' (Buckley 2012), or rely on correlating sparse biostratigraphy (Cameron et al 1987). Recent integration of biostratigraphy, pollen analysis, paleomagnetism and amino acid analysis in the Dutch and Danish sectors (Rasmussen et al 2005; Kuhlmann et al 2006) allows greater confidence in the correlation to a regional 3D seismic dataset and show that the base-Quaternary can be mapped across the entire basin. The base-Quaternary has been mapped using the PGS MegaSurvey dataset from wells in the Danish Sector along the initially unconformable horizon and down the delta front into the more conformable basin giving a high degree of confidence in the horizon pick. The mapped horizon is presented here alongside the difference between this new interpretation and the previously interpreted base-Quaternary (Buckley 2012). The revised base-Quaternary surface reaches a depth of 1248 ms TWT or approximately 1120 m (assuming average velocity of 1800 m/s) showing an elongate basin shape that follows the underlying structure of the Central Graben. The difference between the revised base-Quaternary and the traditional base-Quaternary reaches a maximum of over 600 ms TWT or approximately 540 m in the south-west with over 300 ms TWT or approximately 270 m at the Josephine well (56° 36.11'N, 2° 27.09'E) in the centre of the basin. Mapping this new base-Quaternary allows for the interpretation of the paleo-envionrment during the earliest Quaternary. Seismic attribute analysis indicates a deep water basin with sediment deposition from multiple deltas and redistribution by deep

  8. Comparison of radiotherapy dosimetry for 3D-CRT, IMRT, and SBRT based on electron density calibration

    NASA Astrophysics Data System (ADS)

    Kartutik, K.; Wibowo, W. E.; Pawiro, S. A.

    2016-03-01

    Accurate calculation of dose distribution affected by inhomogeneity tissue is required in radiotherapy planning. This study was performed to determine the ratio between radiotherapy planning using 3D-CRT, IMRT, and SBRT based on a calibrated curve of CT-number in the lung for different target's shape in 3D-CRT, IMRT, and spinal cord for SBRT. Calibration curves of CT-number were generated under measurement basis and introduced into TPS, then planning was performed for 3D-CRT, IMRT, and SBRT with 7, and 15 radiation fields. Afterwards, planning evaluation was performed by comparing the DVH curve, HI, and CI. 3D-CRT and IMRT produced the lowest HI at calibration curve of CIRS 002LFC with the value 0.24 and 10. Whereas SBRT produced the lowest HI on a linear calibration curve with a value of 0.361. The highest CI in IMRT and SBRT technique achieved using a linear calibration curve was 0.97 and 1.77 respectively. For 3D-CRT, the highest CI was obtained by using calibration curve of CIRS 062M with the value of 0.45. From the results of CI and HI, it is concluded that the calibration curve of CT-number does not significantly differ with Schneider's calibrated curve, and inverse planning gives a better result than forward planning.

  9. Accelerated mapping of magnetic susceptibility using 3D planes-on-a-paddlewheel (POP) EPI at ultra-high field strength.

    PubMed

    Stäb, Daniel; Bollmann, Steffen; Langkammer, Christian; Bredies, Kristian; Barth, Markus

    2017-04-01

    With the advent of ultra-high field MRI scanners in clinical research, susceptibility based MRI has recently gained increasing interest because of its potential to assess subtle tissue changes underlying neurological pathologies/disorders. Conventional, but rather slow, three-dimensional (3D) spoiled gradient-echo (GRE) sequences are typically employed to assess the susceptibility of tissue. 3D echo-planar imaging (EPI) represents a fast alternative but generally comes with echo-time restrictions, geometrical distortions and signal dropouts that can become severe at ultra-high fields. In this work we assess quantitative susceptibility mapping (QSM) at 7 T using non-Cartesian 3D EPI with a planes-on-a-paddlewheel (POP) trajectory, which is created by rotating a standard EPI readout train around its own phase encoding axis. We show that the threefold accelerated non-Cartesian 3D POP EPI sequence enables very fast, whole brain susceptibility mapping at an isotropic resolution of 1 mm and that the high image quality has sufficient signal-to-noise ratio in the phase data for reliable QSM processing. The susceptibility maps obtained were comparable with regard to QSM values and geometric distortions to those calculated from a conventional 4 min 3D GRE scan using the same QSM processing pipeline. Copyright © 2016 John Wiley & Sons, Ltd.

  10. Characterization of a subwavelength-scale 3D void structure using the FDTD-based confocal laser scanning microscopic image mapping technique.

    PubMed

    Choi, Kyongsik; Chon, James W; Gu, Min; Lee, Byoungho

    2007-08-20

    In this paper, a simple confocal laser scanning microscopic (CLSM) image mapping technique based on the finite-difference time domain (FDTD) calculation has been proposed and evaluated for characterization of a subwavelength-scale three-dimensional (3D) void structure fabricated inside polymer matrix. The FDTD simulation method adopts a focused Gaussian beam incident wave, Berenger's perfectly matched layer absorbing boundary condition, and the angular spectrum analysis method. Through the well matched simulation and experimental results of the xz-scanned 3D void structure, we first characterize the exact position and the topological shape factor of the subwavelength-scale void structure, which was fabricated by a tightly focused ultrashort pulse laser. The proposed CLSM image mapping technique based on the FDTD can be widely applied from the 3D near-field microscopic imaging, optical trapping, and evanescent wave phenomenon to the state-of-the-art bio- and nanophotonics.

  11. Phenotypic transition maps of 3D breast acini obtained by imaging-guided agent-based modeling

    SciTech Connect

    Tang, Jonathan; Enderling, Heiko; Becker-Weimann, Sabine; Pham, Christopher; Polyzos, Aris; Chen, Chen-Yi; Costes, Sylvain V

    2011-02-18

    We introduce an agent-based model of epithelial cell morphogenesis to explore the complex interplay between apoptosis, proliferation, and polarization. By varying the activity levels of these mechanisms we derived phenotypic transition maps of normal and aberrant morphogenesis. These maps identify homeostatic ranges and morphologic stability conditions. The agent-based model was parameterized and validated using novel high-content image analysis of mammary acini morphogenesis in vitro with focus on time-dependent cell densities, proliferation and death rates, as well as acini morphologies. Model simulations reveal apoptosis being necessary and sufficient for initiating lumen formation, but cell polarization being the pivotal mechanism for maintaining physiological epithelium morphology and acini sphericity. Furthermore, simulations highlight that acinus growth arrest in normal acini can be achieved by controlling the fraction of proliferating cells. Interestingly, our simulations reveal a synergism between polarization and apoptosis in enhancing growth arrest. After validating the model with experimental data from a normal human breast line (MCF10A), the system was challenged to predict the growth of MCF10A where AKT-1 was overexpressed, leading to reduced apoptosis. As previously reported, this led to non growth-arrested acini, with very large sizes and partially filled lumen. However, surprisingly, image analysis revealed a much lower nuclear density than observed for normal acini. The growth kinetics indicates that these acini grew faster than the cells comprising it. The in silico model could not replicate this behavior, contradicting the classic paradigm that ductal carcinoma in situ is only the result of high proliferation and low apoptosis. Our simulations suggest that overexpression of AKT-1 must also perturb cell-cell and cell-ECM communication, reminding us that extracellular context can dictate cellular behavior.

  12. 3D bone mineral density distribution and shape reconstruction of the proximal femur from a single simulated DXA image: an in vitro study

    NASA Astrophysics Data System (ADS)

    Whitmarsh, Tristan; Humbert, Ludovic; De Craene, Mathieu; del Río Barquero, Luis M.; Fritscher, Karl; Schubert, Rainer; Eckstein, Felix; Link, Thomas; Frangi, Alejandro F.

    2010-03-01

    Area Bone Mineral Density (aBMD) measured by Dual-energy X-ray Absorptiometry (DXA) is an established criterion in the evaluation of hip fracture risk. The evaluation from these planar images, however, is limited to 2D while it has been shown that proper 3D assessment of both the shape and the Bone Mineral Density (BMD) distribution improves the fracture risk estimation. In this work we present a method to reconstruct both the 3D bone shape and 3D BMD distribution of the proximal femur from a single DXA image. A statistical model of shape and a separate statistical model of the BMD distribution were automatically constructed from a set of Quantitative Computed Tomography (QCT) scans. The reconstruction method incorporates a fully automatic intensity based 3D-2D registration process, maximizing the similarity between the DXA and a digitally reconstructed radiograph of the combined model. For the construction of the models, an in vitro dataset of QCT scans of 60 anatomical specimens was used. To evaluate the reconstruction accuracy, experiments were performed on simulated DXA images from the QCT scans of 30 anatomical specimens. Comparisons between the reconstructions and the same subject QCT scans showed a mean shape accuracy of 1.2mm, and a mean density error of 81mg/cm3. The results show that this method is capable of accurately reconstructing both the 3D shape and 3D BMD distribution of the proximal femur from DXA images used in clinical routine, potentially improving the diagnosis of osteoporosis and fracture risk assessments at a low radiation dose and low cost.

  13. Advances in 3D soil mapping and water content estimation using multi-channel ground-penetrating radar

    NASA Astrophysics Data System (ADS)

    Moysey, S. M.

    2011-12-01

    Multi-channel ground-penetrating radar systems have recently become widely available, thereby opening new possibilities for shallow imaging of the subsurface. One advantage of these systems is that they can significantly reduce survey times by simultaneously collecting multiple lines of GPR reflection data. As a result, it is becoming more practical to complete 3D surveys - particularly in situations where the subsurface undergoes rapid changes, e.g., when monitoring infiltration and redistribution of water in soils. While 3D and 4D surveys can provide a degree of clarity that significantly improves interpretation of the subsurface, an even more powerful feature of the new multi-channel systems for hydrologists is their ability to collect data using multiple antenna offsets. Central mid-point (CMP) surveys have been widely used to estimate radar wave velocities, which can be related to water contents, by sequentially increasing the distance, i.e., offset, between the source and receiver antennas. This process is highly labor intensive using single-channel systems and therefore such surveys are often only performed at a few locations at any given site. In contrast, with multi-channel GPR systems it is possible to physically arrange an array of antennas at different offsets, such that a CMP-style survey is performed at every point along a radar transect. It is then possible to process this data to obtain detailed maps of wave velocity with a horizontal resolution on the order of centimeters. In this talk I review concepts underlying multi-channel GPR imaging with an emphasis on multi-offset profiling for water content estimation. Numerical simulations are used to provide examples that illustrate situations where multi-offset GPR profiling is likely to be successful, with an emphasis on considering how issues like noise, soil heterogeneity, vertical variations in water content and weak reflection returns affect algorithms for automated analysis of the data. Overall

  14. Investigation of the 2p_{32}-3d_{52} line emission of Au;{53+}-Au;{69+} for diagnosing high energy density plasmas.

    PubMed

    Brown, G V; Hansen, S B; Träbert, E; Beiersdorfer, P; Widmann, K; Chen, H; Chung, H K; Clementson, J H T; Gu, M F; Thorn, D B

    2008-06-01

    Measurements of the L -shell emission of highly charged gold ions were made under controlled laboratory conditions using the SuperEBIT electron beam ion trap, allowing detailed spectral observations of lines from Fe-like Au53+ through Ne-like Au69+ . Using atomic data from the Flexible Atomic Code, we have identified strong 3d_{52}-->2p_{32} emission features that can be used to diagnose the charge state distribution in high energy density plasmas, such as those found in the laser entrance hole of hot hohlraum radiation sources. We provide collisional-radiative calculations of the average ion charge Z as a function of temperature and density, which can be used to relate charge state distributions inferred from 3d_{52}-->2p_{32} emission features to plasma conditions, and investigate the effects of plasma density on calculated L -shell Au emission spectra.

  15. Experimental study of the maximum resolution and packing density achievable in sintered and non-sintered binder-jet 3D printed steel microchannels

    SciTech Connect

    Elliott, Amy M; Mehdizadeh Momen, Ayyoub; Benedict, Michael; Kiggans Jr, James O

    2015-01-01

    Developing high resolution 3D printed metallic microchannels is a challenge especially when there is an essential need for high packing density of the primary material. While high packing density could be achieved by heating the structure to the sintering temperature, some heat sensitive applications require other strategies to improve the packing density of primary materials. In this study the goal is to develop high green or pack densities microchannels on the scale of 2-300 microns which have a robust mechanical structure. Binder-jet 3D printing is an additive manufacturing process in which droplets of binder are deposited via inkjet into a bed of powder. By repeatedly spreading thin layers of powder and depositing binder into the appropriate 2D profiles, complex 3D objects can be created one layer at time. Microchannels with features on the order of 500 microns were fabricated via binder jetting of steel powder and then sintered and/or infiltrated with a secondary material. The average particle size of the steel powder was varied along with the droplet volume of the inkjet-deposited binder. The resolution of the process, packing density of the primary material, the subsequent features sizes of the microchannels, and the overall microchannel quality were characterized as a function of particle size distribution, droplet sizes and heat treatment temperatures.

  16. 3D analysis of synaptic vesicle density and distribution after acute foot-shock stress by using serial section transmission electron microscopy.

    PubMed

    Khanmohammadi, M; Darkner, S; Nava, N; Nyengaard, J R; Wegener, G; Popoli, M; Sporring, J

    2017-01-01

    Behavioural stress has shown to strongly affect neurotransmission within the neocortex. In this study, we analysed the effect of an acute stress model on density and distribution of neurotransmitter-containing vesicles within medial prefrontal cortex. Serial section transmission electron microscopy was employed to compare two groups of male rats: (1) rats subjected to foot-shock stress and (2) rats with sham stress as control group. Two-dimensional (2D) density measures are common in microscopic images and are estimated by following a 2D path in-section. However, this method ignores the slant of the active zone and thickness of the section. In fact, the active zone is a surface in three-dimension (3D) and the 2D measures do not accurately reflect the geometric configuration unless the active zone is perpendicular to the sectioning angle. We investigated synaptic vesicle density as a function of distance from the active zone in 3D. We reconstructed a 3D dataset by estimating the thickness of all sections and by registering all the image sections into a common coordinate system. Finally, we estimated the density as the average number of vesicles per area and volume and modelled the synaptic vesicle distribution by fitting a one-dimensional parametrized distribution that took into account the location uncertainty due to section thickness. Our results showed a clear structural difference in synaptic vesicle density and distribution between stressed and control group with improved separation by 3D measures in comparison to the 2D measures. Our results showed that acute foot-shock stress exposure significantly affected both the spatial distribution and density of the synaptic vesicles within the presynaptic terminal.

  17. Calculation of Local Water Densities in Biological Systems — A Comparison of Molecular Dynamics Simulations and the 3D-RISM-KH Molecular Theory of Solvation

    PubMed Central

    Stumpe, Martin C.; Blinov, Nikolay; Wishart, David; Kovalenko, Andriy; Pande, Vijay S.

    2010-01-01

    Water plays a unique role in all living organisms. Not only is it nature’s ubiquitous solvent, but it also actively takes part in many cellular processes. In particular, the structure and properties of interfacial water near biomolecules like proteins are often related to the function of the respective molecule. It can therefore be highly instructive to study the local water density around solutes in cellular systems, particularly when solvent-mediated forces like the hydrophobic effect are relevant. Computational methods like molecular dynamics (MD) simulations seem well suited to study these systems at the atomic level. However, due to sampling requirements, it is not clear that MD simulations are indeed the method of choice to obtain converged densities at a given level of precision. We here compare the calculation of local water densities with two different methods, MD simulations and the three-dimensional reference interaction site model with the Kovalenko-Hirata closure (3D-RISM-KH). In particular, we investigate the convergence of the local water density to assess the required simulation times for different levels of resolution. Moreover, we provide a quantitative comparison of the densities calculated with MD and with 3D-RISM-KH, and investigate the effect of the choice of the water model for both methods. Our results show that 3D-RISM-KH yields density distributions that are very similar to those from MD up to a 0.5 Å resolution, but for significantly reduced computational cost. The combined use of MD and 3D-RISM-KH emerges as an auspicious perspective for efficient solvent sampling in dynamical systems. PMID:21174421

  18. Exploring the Impact of Visual Complexity Levels in 3d City Models on the Accuracy of Individuals' Orientation and Cognitive Maps

    NASA Astrophysics Data System (ADS)

    Rautenbach, V.; Çöltekin, A.; Coetzee, S.

    2015-08-01

    In this paper we report results from a qualitative user experiment (n=107) designed to contribute to understanding the impact of various levels of complexity (mainly based on levels of detail, i.e., LoD) in 3D city models, specifically on the participants' orientation and cognitive (mental) maps. The experiment consisted of a number of tasks motivated by spatial cognition theory where participants (among other things) were given orientation tasks, and in one case also produced sketches of a path they `travelled' in a virtual environment. The experiments were conducted in groups, where individuals provided responses on an answer sheet. The preliminary results based on descriptive statistics and qualitative sketch analyses suggest that very little information (i.e., a low LoD model of a smaller area) might have a negative impact on the accuracy of cognitive maps constructed based on a virtual experience. Building an accurate cognitive map is an inherently desired effect of the visualizations in planning tasks, thus the findings are important for understanding how to develop better-suited 3D visualizations such as 3D city models. In this study, we specifically discuss the suitability of different levels of visual complexity for development planning (urban planning), one of the domains where 3D city models are most relevant.

  19. Increase in the Random Dopant Induced Threshold Fluctuations and Lowering in Sub 100 nm MOSFETs Due to Quantum Effects: A 3-D Density-Gradient Simulation Study

    NASA Technical Reports Server (NTRS)

    Asenov, Asen; Slavcheva, G.; Brown, A. R.; Davies, J. H.; Saini, S.

    2000-01-01

    In this paper we present a detailed simulation study of the influence of quantum mechanical effects in the inversion layer on random dopant induced threshold voltage fluctuations and lowering in sub 100 nm MOSFETs. The simulations have been performed using a 3-D implementation of the density gradient (DG) formalism incorporated in our established 3-D atomistic simulation approach. This results in a self-consistent 3-D quantum mechanical picture, which implies not only the vertical inversion layer quantisation but also the lateral confinement effects related to current filamentation in the 'valleys' of the random potential fluctuations. We have shown that the net result of including quantum mechanical effects, while considering statistical dopant fluctuations, is an increase in both threshold voltage fluctuations and lowering. At the same time, the random dopant induced threshold voltage lowering partially compensates for the quantum mechanical threshold voltage shift in aggressively scaled MOSFETs with ultrathin gate oxides.

  20. Soft Hydrogels Featuring In-Depth Surface Density Gradients for the Simple Establishment of 3D Tissue Models for Screening Applications.

    PubMed

    Zhang, Ning; Milleret, Vincent; Thompson-Steckel, Greta; Huang, Ning-Ping; Vörös, János; Simona, Benjamin R; Ehrbar, Martin

    2017-03-01

    Three-dimensional (3D) cell culture models are gaining increasing interest for use in drug development pipelines due to their closer resemblance to human tissues. Hydrogels are the first-choice class of materials to recreate in vitro the 3D extra-cellular matrix (ECM) environment, important in studying cell-ECM interactions and 3D cellular organization and leading to physiologically relevant in vitro tissue models. Here we propose a novel hydrogel platform consisting of a 96-well plate containing pre-cast synthetic PEG-based hydrogels for the simple establishment of 3D (co-)culture systems without the need for the standard encapsulation method. The in-depth density gradient at the surface of the hydrogel promotes the infiltration of cells deposited on top of it. The ability to decouple hydrogel production and cell seeding is intended to simplify the use of hydrogel-based platforms and thus increase their accessibility. Using this platform, we established 3D cultures relevant for studying stem cell differentiation, angiogenesis, and neural and cancer models.

  1. Mapping 3D Strains with Ultrasound Speckle Tracking: Method Validation and Initial Results in Porcine Scleral Inflation.

    PubMed

    Cruz Perez, Benjamin; Pavlatos, Elias; Morris, Hugh J; Chen, Hong; Pan, Xueliang; Hart, Richard T; Liu, Jun

    2016-07-01

    This study aimed to develop and validate a high frequency ultrasound method for measuring distributive, 3D strains in the sclera during elevations of intraocular pressure. A 3D cross-correlation based speckle-tracking algorithm was implemented to compute the 3D displacement vector and strain tensor at each tracking point. Simulated ultrasound radiofrequency data from a sclera-like structure at undeformed and deformed states with known strains were used to evaluate the accuracy and signal-to-noise ratio (SNR) of strain estimation. An experimental high frequency ultrasound (55 MHz) system was built to acquire 3D scans of porcine eyes inflated from 15 to 17 and then 19 mmHg. Simulations confirmed good strain estimation accuracy and SNR (e.g., the axial strains had less than 4.5% error with SNRs greater than 16.5 for strains from 0.005 to 0.05). Experimental data in porcine eyes showed increasing tensile, compressive, and shear strains in the posterior sclera during inflation, with a volume ratio close to one suggesting near-incompressibility. This study established the feasibility of using high frequency ultrasound speckle tracking for measuring 3D tissue strains and its potential to characterize physiological deformations in the posterior eye.

  2. Stroboscobic near-field scanning optical microscopy for 3D mapping of mode profiles of plasmonic nanostructures (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Dana, Aykutlu; Ozgur, Erol; Torunoglu, Gamze

    2016-09-01

    We present a dynamic approach to scanning near field optical microscopy that extends the measurement technique to the third dimension, by strobing the illumination in sync with the cantilever oscillation. Nitrogen vacancy (NV) centers in nanodiamonds placed on cantilever tips are used as stable emitters for emission enhancement. Local field enhancement and modulation of optical density states are mapped in three dimensions based on fluorescence intensity and spectrum changes as the tip is scanned over plasmonic nanostructures. The excitation of NV centers is done using a total internal reflection setup. Using a digital phase locked loop to pulse the excitation in various tip sample separations, 2D slices of fluorescence enhancement can be recorded. Alternatively, a conventional SNOM tip can be used to selectively couple wideband excitation to the collection path, with subdiffraction resolution of 60 nm in x and y and 10 nm in z directions. The approach solves the problem of tip-sample separation stabilization over extended periods of measurement time, required to collect data resolved in emission wavelength and three spatial dimensions. The method can provide a unique way of accessing the three dimensional field and mode profiles of nanophotonics structures.

  3. Low-resolution density maps from atomic models: how stepping "back" can be a step "forward".

    PubMed

    Belnap, D M; Kumar, A; Folk, J T; Smith, T J; Baker, T S

    1999-01-01

    Atomic-resolution structures have had a tremendous impact on modern biological science. Much useful information also has been gleaned by merging and correlating atomic-resolution structural details with lower-resolution (15-40 A), three-dimensional (3D) reconstructions computed from images recorded with cryo-transmission electron microscopy (cryoTEM) procedures. One way to merge these structures involves reducing the resolution of an atomic model to a level comparable to a cryoTEM reconstruction. A low-resolution density map can be derived from an atomic-resolution structure by retrieving a set of atomic coordinates editing the coordinate file, computing structure factors from the model coordinates, and computing the inverse Fourier transform of the structure factors. This method is a useful tool for structural studies primarily in combination with 3D cryoTEM reconstructions. It has been used to assess the quality of 3D reconstructions, to determine corrections for the phase-contrast transfer function of the transmission electron microscope, to calibrate the dimensions and handedness of 3D reconstructions, to produce difference maps, to model features in macromolecules or macromolecular complexes, and to generate models to initiate model-based determination of particle orientation and origin parameters for 3D reconstruction.

  4. Evaluation of the User Strategy on 2d and 3d City Maps Based on Novel Scanpath Comparison Method and Graph Visualization

    NASA Astrophysics Data System (ADS)

    Dolezalova, J.; Popelka, S.

    2016-06-01

    The paper is dealing with scanpath comparison of eye-tracking data recorded during case study focused on the evaluation of 2D and 3D city maps. The experiment contained screenshots from three map portals. Two types of maps were used - standard map and 3D visualization. Respondents' task was to find particular point symbol on the map as fast as possible. Scanpath comparison is one group of the eye-tracking data analyses methods used for revealing the strategy of the respondents. In cartographic studies, the most commonly used application for scanpath comparison is eyePatterns that output is hierarchical clustering and a tree graph representing the relationships between analysed sequences. During an analysis of the algorithm generating a tree graph, it was found that the outputs do not correspond to the reality. We proceeded to the creation of a new tool called ScanGraph. This tool uses visualization of cliques in simple graphs and is freely available at www.eyetracking.upol.cz/scangraph. Results of the study proved the functionality of the tool and its suitability for analyses of different strategies of map readers. Based on the results of the tool, similar scanpaths were selected, and groups of respondents with similar strategies were identified. With this knowledge, it is possible to analyse the relationship between belonging to the group with similar strategy and data gathered from the questionnaire (age, sex, cartographic knowledge, etc.) or type of stimuli (2D, 3D map).

  5. 3D Quantification of Low-Coordinate Surface Atom Density: Bridging Catalytic Activity to Concave Facets of Nanocatalysts in Fuel Cells.

    PubMed

    Xia, Ye; Zhong, Xiaoyan; Ke, Xiaoxing; Zhang, Gui-Rong; Cheng, Zhiying; Xu, Bo-Qing

    2016-12-01

    A protocol to quantify the distribution of surface atoms of concave nanocatalysts according to their coordination number is proposed. The 3D surface of an Au@Pd concave nanocube is reconstructed and segmented. The crystallographic coordinates and low-coordinate surface atom densities of the concave facets are determined. The result shows that 32% of the surface atoms are low-coordinated, which may contribute to the high activity.

  6. A Distributed Fiber Optic Sensor Network for Online 3-D Temperature and Neutron Fluence Mapping in a VHTR Environment

    SciTech Connect

    Tsvetkov, Pavel; Dickerson, Bryan; French, Joseph; McEachern, Donald; Ougouag, Abderrafi

    2014-04-30

    Robust sensing technologies allowing for 3D in-core performance monitoring in real time are of paramount importance for already established LWRs to enhance their reliability and availability per year, and therefore, to further facilitate their economic competitiveness via predictive assessment of the in-core conditions.

  7. SMEI 3D RECONSTRUCTION OF A CORONAL MASS EJECTION INTERACTING WITH A COROTATING SOLAR WIND DENSITY ENHANCEMENT: THE 2008 APRIL 26 CME

    SciTech Connect

    Jackson, B. V.; Buffington, A.; Hick, P. P.; Clover, J. M.; Bisi, M. M.; Webb, D. F.

    2010-12-01

    The Solar Mass Ejection Imager (SMEI) has recorded the brightness responses of hundreds of interplanetary coronal mass ejections (CMEs) in the interplanetary medium. Using a three-dimensional (3D) reconstruction technique that derives its perspective views from outward-flowing solar wind, analysis of SMEI data has revealed the shapes, extents, and masses of CMEs. Here, for the first time, and using SMEI data, we report on the 3D reconstruction of a CME that intersects a corotating region marked by a curved density enhancement in the ecliptic. Both the CME and the corotating region are reconstructed and demonstrate that the CME disrupts the otherwise regular density pattern of the corotating material. Most of the dense CME material passes north of the ecliptic and east of the Sun-Earth line: thus, in situ measurements in the ecliptic near Earth and at the Solar-TErrestrial RElations Observatory Behind spacecraft show the CME as a minor density increase in the solar wind. The mass of the dense portion of the CME is consistent with that measured by the Large Angle Spectrometric Coronagraph on board the Solar and Heliospheric Observatory spacecraft, and is comparable to the masses of many other three-dimensionally reconstructed solar wind features at 1 AU observed in SMEI 3D reconstructions.

  8. Chest wall segmentation in automated 3D breast ultrasound using rib shadow enhancement and multi-plane cumulative probability enhanced map

    NASA Astrophysics Data System (ADS)

    Kim, Hyeonjin; Kim, Hannah; Hong, Helen

    2015-03-01

    We propose an automatic segmentation method of chest wall in 3D ABUS images using rib shadow enhancement and multi-planar cumulative probability enhanced map. For the identification of individual dark rib shadows, each rib shadow is enhanced using intensity transfer function and 3D sheet-like enhancement filtering. Then, wrongly enhanced intercostal regions and small fatty tissues are removed using coronal and sagittal cumulative probability enhanced maps. The large fatty tissues with globular and sheet-like shapes at the top of rib shadow are removed using shape and orientation analysis based on moment matrix. Detected chest walls are connected with cubic B-spline interpolation. Experimental results show that the Dice similarity coefficient of proposed method as comparison with two manually outlining results provides over 90% in average.

  9. 3D Elevation Program—Virtual USA in 3D

    USGS Publications Warehouse

    Lukas, Vicki; Stoker, J.M.

    2016-04-14

    The U.S. Geological Survey (USGS) 3D Elevation Program (3DEP) uses a laser system called ‘lidar’ (light detection and ranging) to create a virtual reality map of the Nation that is very accurate. 3D maps have many uses with new uses being discovered all the time.  

  10. Application of 3D Scanned Imaging Methodology for Volume, Surface Area, and Envelope Density Evaluation of Densified Biomass

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Measurement of surface area, volume, and density is an essential for quantifying, evaluating, and designing the biomass densification, storage, and transport operations. Acquiring accurate and repeated measurements of these parameters for hygroscopic densified biomass are not straightforward and on...

  11. Development of Integrated 3D Terrain Maps for Unmanned Aerial Vehicle (UAV) Flight and Mission Control Support System (FMCSS)

    DTIC Science & Technology

    2006-03-01

    Direction Finding Payload DTAD Digital Terrain Analysis Data DTED Digital Terrain Elevation Data DTM Digital Terrain Model DVD Digital Video Disk...Environment Research Network (TERN), Silver Fox, Swift, Pointer , Raven, and Dragon Eye. The Hunter and the Shadow, by contrast, are larger and are usually...Available on DVD and on- line Library University of California, Berkley Library access based http://www.maps2any where.com/Maps/map s_index.htm Over

  12. Venus in 3D

    NASA Technical Reports Server (NTRS)

    Plaut, Jeffrey J.

    1993-01-01

    Stereographic images of the surface of Venus which enable geologists to reconstruct the details of the planet's evolution are discussed. The 120-meter resolution of these 3D images make it possible to construct digital topographic maps from which precise measurements can be made of the heights, depths, slopes, and volumes of geologic structures.

  13. Web-based 3D digital pathology framework for large-mapping data scanned by FF-OCT

    NASA Astrophysics Data System (ADS)

    Chang, ChiaKai; Tsai, Chien-Chung; Chien, Meng-Ting; Li, Yu-I.; Shun, Chia-Tung; Huang, Sheng-Lung

    2015-03-01

    Full-Field Optical Coherence Tomography (FF-OCT) is a high resolution instrument in 3 dimensional (3D) space, including lateral and longitudinal direction. With FF-OCT, we can perform 3D scanning for excised biopsy or cell culture sample to obtain cellular information. In this work, we have set up a high resolution FF-OCT scanning instrument that can perform cellular resolution tomography scanning of skin tissue for histopathology study. In a scan range of 1cm(x), 1cm(y), 106μm(z), for example, digital data occupies 253 GB capacity. Copying these materials is time consuming, not to mention efficient browsing and analyzing of these data. To solve the problem of information delivery, we have established a network service to browse and analyze the huge volume data.

  14. 3D Mapping of plasma effective areas via detection of cancer cell damage induced by atmospheric pressure plasma jets

    NASA Astrophysics Data System (ADS)

    Han, Xu; Liu, Yueing; Stack, M. Sharon; Ptasinska, Sylwia

    2014-12-01

    In the present study, a nitrogen atmospheric pressure plasma jet (APPJ) was used for irradiation of oral cancer cells. Since cancer cells are very susceptible to plasma treatment, they can be used as a tool for detection of APPJ-effective areas, which extended much further than the visible part of the APPJ. An immunofluorescence assay was used for DNA damage identification, visualization and quantification. Thus, the effective damage area and damage level were determined and plotted as 3D images.

  15. Arctic Research Mapping Application 3D Geobrowser: Accessing and Displaying Arctic Information From the Desktop to the Web

    NASA Astrophysics Data System (ADS)

    Johnson, G. W.; Gonzalez, J.; Brady, J. J.; Gaylord, A.; Manley, W. F.; Cody, R.; Dover, M.; Score, R.; Garcia-Lavigne, D.; Tweedie, C. E.

    2009-12-01

    ARMAP 3D allows users to dynamically interact with information about U.S. federally funded research projects in the Arctic. This virtual globe allows users to explore data maintained in the Arctic Research & Logistics Support System (ARLSS) database providing a very valuable visual tool for science management and logistical planning, ascertaining who is doing what type of research and where. Users can “fly to” study sites, view receding glaciers in 3D and access linked reports about specific projects. Custom “Search” tasks have been developed to query by researcher name, discipline, funding program, place names and year and display results on the globe with links to detailed reports. ARMAP 3D was created with ESRI’s free ArcGIS Explorer (AGX) new build 900 providing an updated application from build 500. AGX applications provide users the ability to integrate their own spatial data on various data layers provided by ArcOnline (http://resources.esri.com/arcgisonlineservices). Users can add many types of data including OGC web services without any special data translators or costly software. ARMAP 3D is part of the ARMAP suite (http://armap.org), a collection of applications that support Arctic science tools for users of various levels of technical ability to explore information about field-based research in the Arctic. ARMAP is funded by the National Science Foundation Office of Polar Programs Arctic Sciences Division and is a collaborative development effort between the Systems Ecology Lab at the University of Texas at El Paso, Nuna Technologies, the INSTAAR QGIS Laboratory, and CH2M HILL Polar Services.

  16. High density resolution synchrotron radiation based x-ray microtomography (SR μCT) for quantitative 3D-morphometrics in zoological sciences

    NASA Astrophysics Data System (ADS)

    Nickel, Michael; Hammel, Jörg U.; Herzen, Julia; Bullinger, Eric; Beckmann, Felix

    2008-08-01

    Zoological sciences widely rely on morphological data to reconstruct and understand body structures of animals. The best suitable methods like tomography allow for a direct representation of 3D-structures. In recent years, synchrotron radiation based x-ray microtomography (SR μCT) placed high resolutions to the disposal of morphologists. With the development of highly brilliant and collimated third generation synchrotron sources, phase contrast SR μCT became widely available. A number of scientific contributions stressed the superiority of phase contrast over absorption contrast. However, here we demonstrate the power of high density resolution methods based on absorption-contrast SRμCT for quantitative 3D-measurements of tissues and other delicate bio-structures in zoological sciences. We used beamline BW2 at DORIS III (DESY, Hamburg, Germany) to perform microtomography on tissue and mineral skeletons of marine sponges (Porifera) which were shock frozen and/or fixed in a glutamate osmium tetroxide solution, followed by critical point drying. High density resolution tomographic reconstructions allowed running quantitative 3D-image analyses in Matlab and ImageJ. By applying contrast and shape rule based algorithms we semi-automatically extracted and measured sponge body structures like mineral spicules, elements of the canal system or tissue structures. This lead to a better understanding of sponge biology: from skeleton functional morphology and internal water flow regimes to body contractility. Our high density resolution based quantitative approach can be applied to a wide variety of biological structures. However, two prerequisites apply: (1) maximum density resolution is necessary; (2) edge effects as seen for example in phase outline contrast SR μCT must not be present. As a consequence, to allow biological sciences to fully exploit the power of SR μCT further increase of density resolution in absorption contrast methods is desirable.

  17. 3D ELECTRON DENSITY DISTRIBUTIONS IN THE SOLAR CORONA DURING SOLAR MINIMA: ASSESSMENT FOR MORE REALISTIC SOLAR WIND MODELING

    SciTech Connect

    Patoul, Judith de; Foullon, Claire; Riley, Pete E-mail: c.foullon@exeter.ac.uk

    2015-11-20

    Knowledge of the electron density distribution in the solar corona put constraints on the magnetic field configurations for coronal modeling and on initial conditions for solar wind modeling. We work with polarized SOHO/LASCO-C2 images from the last two recent minima of solar activity (1996–1997 and 2008–2010), devoid of coronal mass ejections. The goals are to derive the 4D electron density distributions in the corona by applying a newly developed time-dependent tomographic reconstruction method and to compare the results between the two solar minima and with two magnetohydrodynamic models. First, we confirm that the values of the density distribution in thermodynamic models are more realistic than in polytropic ones. The tomography provides more accurate distributions in the polar regions, and we find that the density in tomographic and thermodynamic solutions varies with the solar cycle in both polar and equatorial regions. Second, we find that the highest-density structures do not always correspond to the predicted large-scale heliospheric current sheet or its helmet streamer but can follow the locations of pseudo-streamers. We deduce that tomography offers reliable density distributions in the corona, reproducing the slow time evolution of coronal structures, without prior knowledge of the coronal magnetic field over a full rotation. Finally, we suggest that the highest-density structures show a differential rotation well above the surface depending on how they are magnetically connected to the surface. Such valuable information on the rotation of large-scale structures could help to connect the sources of the solar wind to their in situ counterparts in future missions such as Solar Orbiter and Solar Probe Plus.

  18. Stiffness of the microenvironment upregulates ERBB2 expression in 3D cultures of MCF10A within the range of mammographic density

    PubMed Central

    Cheng, Qingsu; Bilgin, Cemal Cagatay; Fonteney, Gerald; Chang, Hang; Henderson, Matthew; Han, Ju; Parvin, Bahram

    2016-01-01

    The effects of the stiffness of the microenvironment on the molecular response of 3D colony organization, at the maximum level of mammographic density (MD), are investigated. Phenotypic profiling reveals that 3D colony formation is heterogeneous and increased stiffness of the microenvironment, within the range of the MD, correlates with the increased frequency of aberrant 3D colony formation. Further integrative analysis of the genome-wide transcriptome and phenotypic profiling hypothesizes overexpression of ERBB2 in the premalignant MCF10A cell lines at a stiffness value that corresponds to the collagen component at high mammographic density. Subsequently, ERBB2 overexpression has been validated in the same cell line. Similar experiments with a more genetically stable cell line of 184A1 also revealed an increased frequency of aberrant colony formation with the increased stiffness; however, 184A1 did not demonstrate overexpression of ERBB2 at the same stiffness value of the high MD. These results suggest that stiffness exacerbates premalignant cell line of MCF10A. PMID:27383056

  19. Characterization of 3D Trench PZT Capacitors for High Density FRAM Devices by Synchrotron X-ray Micro-diffraction

    SciTech Connect

    Shin, Sangmin; Park, Youngsoo; Han, Hee; Park, Yong Jun; Baik, Sunggi; Choi, Jae-Young

    2007-01-19

    3D trench PbZrxTi1-xO3 (PZT) capacitors for 256 Mbit 1T-1C FRAM devices were characterized by synchrotron X-ray micro-diffraction at Pohang Light Source. Three layers, Ir/PZT/Ir were deposited on SiO2 trench holes with different widths ranging from 180 nm to 810 nm and 400 nm in depth by ALD and MOCVD. Each hole is separated from neighboring holes by 200 nm. The cross sectional TEM analysis for the trenches revealed that the PZT layers were consisted of columnar grains at the trench entrance and changes to polycrystalline granular grains at the lower part of the trench. The transition from columnar to granular grains was dependent on the trench size. The smaller trenches were favorable to granular grain formation. High resolution synchrotron X-ray diffraction analysis was performed to determine the crystal structure of each region. The beam was focused to about 500 {mu}m and the diffraction patterns were obtained from a single trench. Only the peaks corresponding to ferroelectric tetragonal phases are observed for the trenches larger than 670 nm, which consist of fully columnar grains. However, the trenches smaller than 670 nm showed the peaks corresponding the pyrochlore phases, which suggested that the granular grains are of pyrochlore phases and non-ferroelectric.

  20. Effect of time-dependent 3-D electron density gradients on high angle of incidence HF radiowave propagation

    NASA Astrophysics Data System (ADS)

    Zawdie, K. A.; Drob, D. P.; Huba, J. D.; Coker, C.

    2016-07-01

    One of the challenges for the utilization of HF radiowaves in practical applications is to understand how the signals propagate in time- and range-dependent multipath environments. For typical quiescent ionospheric conditions it is often reasonably straightforward to interpret received HF signals. For disturbed ionospheric conditions, however, such as in the presence of large tilts, irregularities, and medium-scale traveling ionospheric disturbances (MSTIDs), data interpretation and utilization often becomes challenging. This paper presents a theoretical HF propagation modeling study that exploits the capabilities of a first principles, mesoscale resolution ionosphere code, SAMI3 (Sami3 is Another Model of the Ionosphere) and a new implementation of the 3-D ray trace equations, MoJo-15 (Modernized Jones Code) in order to examine the relationship between various HF propagation observables and MSTID characteristics. This paper demonstrates the implications of MSTIDS on high angle of incidence HF propagation during typical low-latitude, postsunset ionospheric conditions and examines the spatiotemporal evolution of multiple propagation paths that may connect a given source and receiver.

  1. Exoplanet Atmospheres in High Definition: 3D Eclipse Mapping of HD 209458b and HD 189733b

    NASA Astrophysics Data System (ADS)

    Lewis, Nikole; Cowan, Nicolas; Knutson, Heather; de Wit, Julien; Seager, Sara; Demory, Brice-Olivier; Fortney, Jonathan; Showman, Adam

    2013-10-01

    Eclipse mapping is a newly developed technique in the arsenal of observational methods aimed at the characterization of exoplanet atmospheres. This technique was first applied to HD189733b using multiple 8 micron secondary eclipse observations to create a high-resolution snapshot of the dayside of the planet. The eclipse map of HD189733b at 8 microns was able to resolve the dayside brightness distribution of the planet both in latitude and longitude giving key insights into the atmospheric circulation of HD189733b. Here we propose to use this eclipse mapping technique to produce dayside brightness maps of the benchmark exoplanets HD189733b and HD209458b at both 3.6 and 4.5 microns. By combining brightness maps at multiple wavelengths, we will create the first three-dimensional maps of an exoplanet atmosphere (latitude, longitude, and pressure). HD209458 and HD189733 are among the brightest (Ks~6) planet harboring system and represent our best opportunity to achieve a high signal-to-noise eclipse maps. Comparisons between the brightness maps of these two planets will highlight key differences in the atmospheric circulation patterns of planets with (HD209458b) and without (HD189733b) thermal inversions in their dayside atmospheres. The atmospheres of HD189733b and HD209458b have been previously probed at wavelengths from the infrared to the ultraviolet through transit, eclipse, and phase-curve observations. With the addition of the three-dimensional eclipse maps proposed here, we will answer many of the outstanding questions about the basic radiative, chemical, and advective processes at work in these key planetary atmospheres. The observations proposed here will allow us to make the first direct comparisons of the observed thermal structure of an exoplanet with the plethora of three-dimensional atmospheric circulation models developed specifically for HD189733b and HD209458b, thus both informing the models and gaining new insights into the complex circulation

  2. Feasibility of CT-based 3D anatomic mapping with a scanning-beam digital x-ray (SBDX) system

    NASA Astrophysics Data System (ADS)

    Slagowski, Jordan M.; Tomkowiak, Michael T.; Dunkerley, David A. P.; Speidel, Michael A.

    2015-03-01

    This study investigates the feasibility of obtaining CT-derived 3D surfaces from data provided by the scanning-beam digital x-ray (SBDX) system. Simulated SBDX short-scan acquisitions of a Shepp-Logan and a thorax phantom containing a high contrast spherical volume were generated. 3D reconstructions were performed using a penalized weighted least squares method with total variation regularization (PWLS-TV), as well as a more efficient variant employing gridding of projection data to parallel rays (gPWLS-TV). Voxel noise, edge blurring, and surface accuracy were compared to gridded filtered back projection (gFBP). PWLS reconstruction of a noise-free reduced-size Shepp-Logan phantom had 1.4% rRMSE. In noisy gPWLS-TV reconstructions of a reduced-size thorax phantom, 99% of points on the segmented sphere perimeter were within 0.33, 0.47, and 0.70 mm of the ground truth, respectively, for fluences comparable to imaging through 18.0, 27.2, and 34.6 cm acrylic. Surface accuracies of gFBP and gPWLS-TV were similar at high fluences, while gPWLS-TV offered improvement at the lowest fluence. The gPWLS-TV voxel noise was reduced by 60% relative to gFBP, on average. High-contrast linespread functions measured 1.25 mm and 0.96 mm (FWHM) for gPWLS-TV and gFBP. In a simulation of gated and truncated projection data from a full-sized thorax, gPWLS-TV reconstruction yielded segmented surface points which were within 1.41 mm of ground truth. Results support the feasibility of 3D surface segmentation with SBDX. Further investigation of artifacts caused by data truncation and patient motion is warranted.

  3. Feasibility of CT-based 3D anatomic mapping with a scanning-beam digital x-ray (SBDX) system.

    PubMed

    Slagowski, Jordan M; Tomkowiak, Michael T; Dunkerley, David A P; Speidel, Michael A

    This study investigates the feasibility of obtaining CT-derived 3D surfaces from data provided by the scanning-beam digital x-ray (SBDX) system. Simulated SBDX short-scan acquisitions of a Shepp-Logan and a thorax phantom containing a high contrast spherical volume were generated. 3D reconstructions were performed using a penalized weighted least squares method with total variation regularization (PWLS-TV), as well as a more efficient variant employing gridding of projection data to parallel rays (gPWLS-TV). Voxel noise, edge blurring, and surface accuracy were compared to gridded filtered back projection (gFBP). PWLS reconstruction of a noise-free reduced-size Shepp-Logan phantom had 1.4% rRMSE. In noisy gPWLS-TV reconstructions of a reduced-size thorax phantom, 99% of points on the segmented sphere perimeter were within 0.33, 0.47, and 0.70 mm of the ground truth, respectively, for fluences comparable to imaging through 18.0, 27.2, and 34.6 cm acrylic. Surface accuracies of gFBP and gPWLS-TV were similar at high fluences, while gPWLS-TV offered improvement at the lowest fluence. The gPWLS-TV voxel noise was reduced by 60% relative to gFBP, on average. High-contrast linespread functions measured 1.25 mm and 0.96 mm (FWHM) for gPWLS-TV and gFBP. In a simulation of gated and truncated projection data from a full-sized thorax, gPWLS-TV reconstruction yielded segmented surface points which were within 1.41 mm of ground truth. Results support the feasibility of 3D surface segmentation with SBDX. Further investigation of artifacts caused by data truncation and patient motion is warranted.

  4. Mapping the Complement Factor H-Related Protein 1 (CFHR1):C3b/C3d Interactions

    PubMed Central

    Laskowski, Jennifer; Thurman, Joshua M.; Hageman, Gregory S.; Holers, V. Michael

    2016-01-01

    Complement factor H-related protein 1 (CFHR1) is a complement regulator which has been reported to regulate complement by blocking C5 convertase activity and interfering with C5b surface association. CFHR1 also competes with complement factor H (CFH) for binding to C3b, and may act as an antagonist of CFH-directed regulation on cell surfaces. We have employed site-directed mutagenesis in conjunction with ELISA-based and functional assays to isolate the binding interaction that CFHR1 undertakes with complement components C3b and C3d to a single shared interface. The C3b/C3d:CFHR1 interface is identical to that which occurs between the two C-terminal domains (SCR19-20) of CFH and C3b. Moreover, we have been able to corroborate that dimerization of CFHR1 is necessary for this molecule to bind effectively to C3b and C3d, or compete with CFH. Finally, we have established that CFHR1 competes with complement factor H-like protein 1 (CFHL-1) for binding to C3b. CFHL-1 is a CFH gene splice variant, which is almost identical to the N-terminal 7 domains of CFH (SCR1-7). CFHR1, therefore, not only competes with the C-terminus of CFH for binding to C3b, but also sterically blocks the interaction that the N-terminus of CFH undertakes with C3b, and which is required for CFH-regulation. PMID:27814381

  5. Multiple Baseline SAR Tomography's Performance Analysis in Forest 3-D Structure Mapping with long term ALOS L band repeat pass InSAR data

    NASA Astrophysics Data System (ADS)

    Lin, Q.; Zebker, H. A.

    2013-12-01

    Acquiring accurate measurement of three-dimensional structure of forest globally , is key to improve quantitative understanding of the state and dynamics of ecosystems, particularly global carbon cycle. Moreover, forest contains a large portion of Earth's renewable natural resources. All these require an accurate, timely and cost-effective global forest vertical structure mapping. Synthetic Aperture Radar Interferometry (InSAR) remote sensing is widely acknowledged as a powerful tool to accomplish this task. Within the last decade, a number of experimental demonstrations of 3-D InSAR techniques have suggested the possibility of remotely sensing global 3-D vegetation structure. Among all the 3-D InSAR techniques, Multiple Baseline SAR Tomography( MB Tomo-SAR) is a very promising one. Multiple baseline SAR tomography exploits InSAR images acquired from different baselines and form a synthetic aperture in the vertical direction in order to retrieval vertical structure. Though theoretical predictions and several laboratory experiments show great reconstruction results, applying the method in real world condition still face a lot of challenges, including low acquisition number, irregular sample distribution, atmospheric phase noise and time decorrelation effect. In this article, we use L band ALOS spaceborne SAR data in Hawaii area to test the performance of MB TomoSAR . In the process, advanced Fourier beamforming method, atmospheric phase screen removal algorithm and time decorrelation effect are all applied. In addition, we also utilize the Landsat vegetation index and the result with other 3-D reconstruction methods as comparison to validate its performance.

  6. 3-D density modeling of Mt. Paekdu (N Korea/China) stratovolcano and its evolution by a combination of EGM2008/terrestrial gravity field

    NASA Astrophysics Data System (ADS)

    Götze, Hans-Jürgen; Choi, Sungchan

    2015-04-01

    We combined the global gravity dataset EGM2008 and a local terrestrial gravity data survey to conduct constrained 3-D crustal density modeling of a strato-volcanic complex and the surrounding area located close to the border of North Korea and China. The independent geophysical (seismic, seismology, geochemistry) and petrological constraints will be presented together with the preprocessing of data base by curvature analysis and Euler deconvolution. The multiple data base is used to assist a general interpretation of the investigated area, and the 3D density model (modelled by the in-house IGMAS+ software). Mt. Paekdu is characterized by a low of Bouguer anomaly of some -110 × 10-5 m/s2, which is caused by the combined gravity effects of (1) Moho depth of about 40 km, (2) a zone with both lower P-wave velocity and density than the surrounding, (3) low density volcanic rocks at the surface, and (4) the presence of a magma chamber that has not previously been identified. The terrestrial gravity field measured along the seismic profile shows a remarkable anomaly descending from the southern- to the northern flank of the Mt. Paekdu volcano, which should be a typical anomaly pattern generally observed over the active volcanic area in the world (e.g. the Yellow Stone volcano). The trend is interpreted to be caused by a prominent density difference between a serious of high density mid crustal sill beneath the southern flank and a predicted partial melted zone locating in the northern flank. With the help of several geoscientific observations (seismic, electromagnetic, gravity and geochemistry) and the 3D density model we conclude that a high density sill was formed in Pliocene and early Pleistocene after pre-shield plateau-forming eruption. Since the Pliocene, volcanic activity in the Mt. Paekdu region might be migrated from the southeastern of North Korea to the northwest, following the path of NW-SE-trending faults. Recently observed seismic tremors can be explained

  7. 3-D Density Modeling of the Combined EGM2008/Terrestrial Gravity Field over the Mt. Paekdu (N Korea/China) Stratovolcano and Its Evolution

    NASA Astrophysics Data System (ADS)

    Goetze, H. J.; Choi, S.

    2014-12-01

    In the presentation we get use of the global gravity dataset EGM2008 and a local terrestrial gravity data survey for a constrained 3-D crustal density modeling of a stratovolcano and its surrounding area located close to the border of North Korea and China. The independent geophysical (seismic, seismology, geochemistry) and petrological constraints will be presented together with the preprocessing of data base by curvature analysis and Euler deconvolution. The multiple data base is used to assist a general interpretation of the investigated area in time, and the 3D density model (modelled by the inhouse IGMAS+ software). Mt. Paekdu is characterized by a low of Bouguer anomaly of some -110 ´ 10-5 m/s2, which is caused by the combined gravity effects of (1) Moho depth of about 40 km, (2) a zone with both lower P-wave velocity and density than the surrounding, (3) low density volcanic rocks at the surface, and (4) the presence of a magma chamber that has not previously been identified. The terrestrial gravity field measured along the seismic profile shows a remarkable anomaly descending from the southern- to the northern flank of the Mt. Paekdu volcano, which should be a typical anomaly pattern generally obsered over the active volcanic area in the world (e.g. the Yellow Stone volcano). The trend is interpreted to be caused by a prominent density difference between a serious of high density mid crustal sill beneath the southern flank and a predicted partial melted zone locating in the northern flank. With the help of several geoscientific observations (seismic, electromagnetic, gravity and geochemistry) and the 3D density model we conclude that a high density sill was formed in Pliocene and early Pleistocene after pre-shield plateau-forming eruption. Since the Pliocene, volcanic activity in the Mt. Paekdu region might be migrated from the southeastern of North Korea to the northwest, following the path of NW-SE-trending faults. Recently observed seismic tremors can

  8. 3D Density Modeling with Gravity and Muon-Radiographic Observations in Showa-Shinzan Lava Dome, Usu, Japan

    NASA Astrophysics Data System (ADS)

    Nishiyama, Ryuichi; Miyamoto, Seigo; Okubo, Shuhei; Oshima, Hiromitsu; Maekawa, Tokumitsu

    2017-03-01

    We performed three-dimensional density modeling of Showa-Shinzan lava dome, Usu, Japan, by joint inversion of the gravity anomaly and recently obtained muon radiography data. Our multilayer emulsion muon detector significantly reduces the background noise in our measurements of the muon flux through the dome. The high-quality muon data enables us to more accurately reconstruct the density structure of the lava dome compared with our own previous work. We find that the lava dome consists of a cylindrical column of massive lava with a diameter of 300 m, and that there is no evidence of magma intrusion in the shallow part of the plateau, located east of the dome.

  9. Highly-Ordered 3D Vertical Resistive Switching Memory Arrays with Ultralow Power Consumption and Ultrahigh Density.

    PubMed

    Al-Haddad, Ahmed; Wang, Chengliang; Qi, Haoyuan; Grote, Fabian; Wen, Liaoyong; Bernhard, Jörg; Vellacheri, Ranjith; Tarish, Samar; Nabi, Ghulam; Kaiser, Ute; Lei, Yong

    2016-09-07

    Resistive switching random access memories (RRAM) have attracted great scientific and industrial attention for next generation data storage because of their advantages of nonvolatile properties, high density, low power consumption, fast writing/erasing speed, good endurance, and simple and small operation system. Here, by using a template-assisted technique, we demonstrate a three-dimensional highly ordered vertical RRAM device array with density as high as that of the nanopores of the template (10(8)-10(9) cm(-2)), which can also be fabricated in large area. The high crystallinity of the materials, the large contact area and the intimate semiconductor/electrode interface (3 nm interfacial layer) make the ultralow voltage operation (millivolt magnitude) and ultralow power consumption (picowatt) possible. Our procedure for fabrication of the nanodevice arrays in large area can be used for producing many other different materials and such three-dimensional electronic device arrays with the capability to adjust the device densities can be extended to other applications of the next generation nanodevice technology.

  10. Investigation of the 2p3/2-3d5/2 line emission of Au53+ -- Au69+ for diagnosing high energy density plasmas

    SciTech Connect

    Brown, G V; Hansen, S B; Trabert, E; Beiersdorfer, P; Widmann, K; Chen, H; Chung, H K; Clementson, J T; Gu, M F; Thorn, D B

    2008-01-29

    Measurements of the L-shell emission of highly charged gold ions were made under controlled laboratory conditions using the SuperEBIT electron beam ion trap, allowing detailed spectral observations of lines from ironlike Au{sup 53+} through neonlike Au{sup 69+}. Using atomic data from the Flexible Atomic Code, we have identified strong 3d{sub 5/2} {yields} 2p{sub 3/2} emission features that can be used to diagnose the charge state distribution in high energy density plasmas, such as those found in the laser entrance hole of hot hohlraum radiation sources. We provide collisional-radiative calculations of the average ion charge as a function of temperature and density, which can be used to relate charge state distributions inferred from 3d{sub 5/2} {yields} 2p{sub 3/2} emission features to plasma conditions, and investigate the effects of plasma density on calculated L-shell Au emission spectra.

  11. Splitting of the Ti-3d bands of TiSe2 in the charge-density wave phase

    NASA Astrophysics Data System (ADS)

    Ghafari, A.; Petaccia, L.; Janowitz, C.

    2017-02-01

    Very high resolution angular resolved photoemission (ARPES) spectra on TiSe2 in two distinct polarization geometries (vertical and horizontal) at temperatures between 300 K and 22 K enabled the observation of details of bands near the Fermi level not reported so far. Calculations of the electronic band structure based on density functional theory (DFT) using B3LYP hybrid functional and MBJ potential (with and without spin-orbit coupling) were performed to obtain the orbital symmetry and dispersion. Two degenerate conduction bands (CB's) were observed at the Γ-point, a weak CB- emission at the A-point, and two non degenerate CB's (i.e. splitting of CB) at the M/L-point of the Brillouin Zone (BZ). The splitting was detected at L for both polarizations, while at M remarkably only for horizontal polarization. These results cannot be fully accounted for by current theories for the charge density wave (CDW) and point to a reduced symmetry of the electronic states, possibly due to the chiral CDW.

  12. Geomorphological activity at a rock glacier front detected with a 3D density-based clustering algorithm

    NASA Astrophysics Data System (ADS)

    Micheletti, Natan; Tonini, Marj; Lane, Stuart N.

    2017-02-01

    Acquisition of high density point clouds using terrestrial laser scanners (TLSs) has become commonplace in geomorphic science. The derived point clouds are often interpolated onto regular grids and the grids compared to detect change (i.e. erosion and deposition/advancement movements). This procedure is necessary for some applications (e.g. digital terrain analysis), but it inevitably leads to a certain loss of potentially valuable information contained within the point clouds. In the present study, an alternative methodology for geomorphological analysis and feature detection from point clouds is proposed. It rests on the use of the Density-Based Spatial Clustering of Applications with Noise (DBSCAN), applied to TLS data for a rock glacier front slope in the Swiss Alps. The proposed methods allowed the detection and isolation of movements directly from point clouds which yield to accuracies in the following computation of volumes that depend only on the actual registered distance between points. We demonstrated that these values are more conservative than volumes computed with the traditional DEM comparison. The results are illustrated for the summer of 2015, a season of enhanced geomorphic activity associated with exceptionally high temperatures.

  13. Reconstructing the 3D shape and bone mineral density distribution of the proximal femur from dual-energy X-ray absorptiometry.

    PubMed

    Whitmarsh, Tristan; Humbert, Ludovic; De Craene, Mathieu; Del Rio Barquero, Luis M; Frangi, Alejandro F

    2011-12-01

    The accurate diagnosis of osteoporosis has gained increasing importance due to the aging of our society. Areal bone mineral density (BMD) measured by dual-energy X-ray absorptiometry (DXA) is an established criterion in the diagnosis of osteoporosis. This measure, however, is limited by its two-dimensionality. This work presents a method to reconstruct both the 3D bone shape and 3D BMD distribution of the proximal femur from a single DXA image used in clinical routine. A statistical model of the combined shape and BMD distribution is presented, together with a method for its construction from a set of quantitative computed tomography (QCT) scans. A reconstruction is acquired in an intensity based 3D-2D registration process whereby an instance of the model is found that maximizes the similarity between its projection and the DXA image. Reconstruction experiments were performed on the DXA images of 30 subjects, with a model constructed from a database of QCT scans of 85 subjects. The accuracy was evaluated by comparing the reconstructions with the same subject QCT scans. The method presented here can potentially improve the diagnosis of osteoporosis and fracture risk assessment from the low radiation dose and low cost DXA devices currently used in clinical routine.

  14. About Non-Line-Of-Sight Satellite Detection and Exclusion in a 3D Map-Aided Localization Algorithm

    PubMed Central

    Peyraud, Sébastien; Bétaille, David; Renault, Stéphane; Ortiz, Miguel; Mougel, Florian; Meizel, Dominique; Peyret, François

    2013-01-01

    Reliable GPS positioning in city environment is a key issue actually, signals are prone to multipath, with poor satellite geometry in many streets. Using a 3D urban model to forecast satellite visibility in urban contexts in order to improve GPS localization is the main topic of the present article. A virtual image processing that detects and eliminates possible faulty measurements is the core of this method. This image is generated using the position estimated a priori by the navigation process itself, under road constraints. This position is then updated by measurements to line-of-sight satellites only. This closed-loop real-time processing has shown very first promising full-scale test results. PMID:23344379

  15. Mapping of the C3d ligand binding site on complement receptor 2 (CR2/CD21) using nuclear magnetic resonance and chemical shift analysis.

    PubMed

    Kovacs, James M; Hannan, Jonathan P; Eisenmesser, Elan Z; Holers, V Michael

    2009-04-03

    Complement receptor 2 (CR2, CD21) is a cell membrane protein, with 15 or 16 extracellular short consensus repeats (SCRs), that promotes B lymphocyte responses and bridges innate and acquired immunity. The most distally located SCRs (SCR1-2) mediate the interaction of CR2 with its four known ligands (C3d, Epstein-Barr virus gp350, interferon-alpha, and CD23). Inhibitory monoclonal antibodies against SCR1-2 block binding of all ligands. To develop ligand-specific inhibitors that would also assist in identifying residues unique to each receptor-ligand interaction, phage were selected from randomly generated libraries by panning with recombinant SCR1-2, followed by specific ligand-driven elution. Derived peptides were tested by competition ELISA. One peptide, C3dp1 (APQHLSSQYSRT) exhibited ligand-specific inhibition at midmicromolar IC(50). C3d was titrated into (15)N-labeled SCR1-2, which revealed chemical shift changes indicative of specific intermolecular interactions. With backbone assignments made, the chemical shift changes were mapped onto the crystal structure of SCR1-2. With regard to C3d, the binding surface includes regions of SCR1, SCR2, and the inter-SCR linker, specifically residues Arg(13), Tyr(16), Arg(28), Tyr(29), Ser(32), Thr(34), Lys(48), Asp(56), Lys(57), Tyr(68), Arg(83), Gly(84), Asn(101), Asn(105), and Ser(109). SCR1 and SCR2 demonstrated distinct binding modes. The CR2 binding surface incorporating SCR1 is inconsistent with a previous x-ray CR2-C3d co-crystal analysis but consistent with mutagenesis, x-ray neutron scattering, and inhibitory monoclonal antibody epitope mapping. Titration with C3dp1 yielded chemical shift changes (Arg(13), Tyr(16), Thr(34), Lys(48), Asp(56), Lys(57), Tyr(68), Arg(83), Gly(84), Asn(105), and Ser(109)) overlapping with C3d, indicating that C3dp1 interacts at the same CR2 site as C3d.

  16. Influence of critical current density on magnetic force of HTSC bulk above PMR with 3D-modeling numerical solutions

    NASA Astrophysics Data System (ADS)

    Lu, Yiyun; Qin, Yujie

    2015-09-01

    Numerical simulations of thermo-electromagnetic properties of a high temperature superconducting (HTS) bulk levitating over a permanent magnetic guideway (PMG) are performed by resorting to the quasistatic approximation of the H-method coupling with the classical description of the heat conduction equation. The numerical resolving codes are practiced with the help of the finite element program generation system (FEPG) platform using finite element method (FEM). The E-J power law is used to describe the electric current nonlinear characteristics of HTS bulk. The simulation results show that the heat conduction and the critical current density are tightly relative to the thermal effects of the HTS bulk over the PMG. The heat intensity which responds to the heat loss of the HTS bulk is mainly distributed at the two bottom-corners of the bulk sample.

  17. Lithospheric 3D gravity modelling using upper-mantle density constraints: Towards a characterization of the crustal configuration in the North Patagonian Massif area, Argentina

    NASA Astrophysics Data System (ADS)

    Gómez Dacal, María Laura; Tocho, Claudia; Aragón, Eugenio; Sippel, Judith; Scheck-Wenderoth, Magdalena; Ponce, Alexis

    2017-03-01

    The North Patagonian Massif is an Argentinean plateau that has an average height of 1200 m and stands from 500 to 700 m above the neighboring areas. During Paleogene, it suffered a sudden uplift of more than 1200 m without noticeable internal deformation; thus, it could be related to isostatic disequilibrium. To shed light on the geodynamic development of the area it is necessary to characterize the present-day configuration of the crust. In this study, a lithospheric-scale 3D density model was developed by integrating all the available data of the area with the objective of assessing the depth of the crust-mantle discontinuity (Moho). During the construction of the initial density model, we tested different mantle density scenarios obtained using P- and S-wave velocities from tomographic models, converting them into densities and comparing the conversions with densities obtained from xenoliths. Below the North Patagonian Massif plateau, we have derived a Moho depth between 40 and 50 km which is from 2 to 7 km deeper than its surroundings. There is an evident correlation between high topography and deep Moho that would indicate isostatic equilibrium at present. The model results provide a new approach to the Moho depth in an area where there is no seismic constraining information about this discontinuity. In addition, we found a spatial correlation between the variation of the mean crustal density and the location of the Paleozoic terranes that were proposed to constitute the basement of Argentina.

  18. Space Electron Density Gradient Studies using a 3D Embedded Reconfigurable Sounder and ESA/NASA CLUSTER Mission

    NASA Astrophysics Data System (ADS)

    Dekoulis, George

    2016-07-01

    This paper provides a direct comparison between data captured by a new embedded reconfigurable digital sounder, different ground-based ionospheric sounders spread around Europe and the ESA/NASA CLUSTER mission. The CLUSTER mission consists of four identical space probes flying in a formation that allows measurements of the electron density gradient in the local magnetic field. Both the ground-based and the spacecraft instrumentations assist in studying the motion, geometry and boundaries of the plasmasphere. The comparison results are in accordance to each other. Some slight deviations among the captured data were expected from the beginning of this investigation. These small discrepancies are reasonable and seriatim analyzed. The results of this research are significant, since the level of the plasma's ionization, which is related to the solar activity, dominates the propagation of electromagnetic waves through it. Similarly, unusually high solar activity presents serious hazards to orbiting satellites, spaceborne instrumentation, satellite communications and infrastructure located on the Earth's surface. Long-term collaborative study of the data is required to continue, in order to identify and determine the enhanced risk in advance. This would allow scientists to propose an immediate cure.

  19. Automated Quantification of DNA Demethylation Effects in Cells via 3D Mapping of Nuclear Signatures and Population Homogeneity Assessment1

    PubMed Central

    Gertych, Arkadiusz; Wawrowsky, Kolja A.; Lindsley, Erik; Vishnevsky, Eugene; Farkas, Daniel L.; Tajbakhsh, Jian

    2009-01-01

    Background Today’s advanced microscopic imaging applies to the preclinical stages of drug discovery that employ high-throughput and high-content three-dimensional (3D) analysis of cells to more efficiently screen candidate compounds. Drug efficacy can be assessed by measuring response homogeneity to treatment within a cell population. In this study topologically quantified nuclear patterns of methylated cytosine and global nuclear DNA are utilized as signatures of cellular response to the treatment of cultured cells with the demethylating anti-cancer agents: 5-azacytidine (5-AZA) and octreotide (OCT). Methods Mouse pituitary folliculostellate TtT-GF cells treated with 5-AZA and OCT for 48 hours, and untreated populations, were studied by immunofluorescence with a specific antibody against 5-methylcytosine (MeC), and 4,6-diamidino-2-phenylindole (DAPI) for delineation of methylated sites and global DNA in nuclei (n=163). Cell images were processed utilizing an automated 3D analysis software that we developed by combining seeded watershed segmentation to extract nuclear shells with measurements of Kullback-Leibler’s (K-L) divergence to analyze cell population homogeneity in the relative nuclear distribution patterns of MeC versus DAPI stained sites. Each cell was assigned to one of the four classes: similar, likely similar, unlikely similar and dissimilar. Results Evaluation of the different cell groups revealed a significantly higher number of cells with similar or likely similar MeC/DAPI patterns among untreated cells (~100%), 5-AZA-treated cells (90%), and a lower degree of same type of cells (64%) in the OCT-treated population. The latter group contained (28%) of unlikely similar or dissimilar (7%) cells. Conclusion Our approach was successful in the assessment of cellular behavior relevant to the biological impact of the applied drugs, i.e. the reorganization of MeC/DAPI distribution by demethylation. In a comparison with other metrics, K-L divergence has

  20. Interplay between spin-density wave and 3 d local moments with random exchange in a molecular conductor

    NASA Astrophysics Data System (ADS)

    Kawaguchi, Genta; Maesato, Mitsuhiko; Komatsu, Tokutaro; Imakubo, Tatsuro; Kitagawa, Hiroshi

    2016-02-01

    We present the results of high-pressure transport measurements on the anion-mixed molecular conductors (DIETSe)2M Br2Cl2 [DIETSe = diiodo(ethylenedithio)tetraselenafulvalene; M =Fe , Ga]. They undergo a metal-insulator (M-I) transition below 9 K at ambient pressure, which is suppressed by applying pressure, indicating a spin-density-wave (SDW) transition caused by a nesting instability of the quasi-one-dimensional (Q1D) Fermi surface, as observed in the parent compounds (DIETSe)2M Cl4 (M =Fe , Ga). In the metallic state, the existence of the Q1D Fermi surface is confirmed by observing the Lebed resonance. The critical pressures of the SDW, Pc, of the M Br2Cl2 (M =Fe , Ga) salts are significantly lower than those of the the M Cl4 (M = Fe, Ga) salts, suggesting chemical pressure effects. Above Pc, field-induced SDW transitions appear, as evidenced by kink structures in the magnetoresistance (MR) in both salts. The FeBr2Cl2 salt also shows antiferromagnetic (AF) ordering of d spins at 4 K, below which significant spin-charge coupling is observed. A large positive MR change up to 150% appears above the spin-flop field at high pressure. At low pressure, in particular below Pc, a dip or kink structure appears in MR at the spin-flop field, which shows unconventionally large hysteresis at low temperature (T <1 K). The hysteresis region clearly decreases with increasing pressure towards Pc, strongly indicating that the coexisting SDW plays an important role in the enhancement of magnetic hysteresis besides the random exchange interaction.

  1. Study of the 3D Geometric Structure and Temperature of a Coronal Cavity Using the Limb Synoptic Map Method

    NASA Astrophysics Data System (ADS)

    Karna, N.; Zhang, J.; Pesnell, W. Dean; Hess Webber, S. A.

    2015-09-01

    We present the three-dimensional geometric structure and thermal properties of a coronal cavity deduced from limb synoptic maps. The observations are extreme ultraviolet images from the Atmospheric Imager Assembly (AIA) and magnetic images from the Helioseismic Magnetic Imager instruments on board the Solar Dynamics Observatory. We describe a limb synoptic-map method used to effectively identify and measure cavities from annuli of radiance above the solar limb. We find that cavities are best seen in the 211, 193, and 171 Å passbands. The prominence associated with each cavity is best seen in the 304 Å synoptic maps. We also estimate the thermal properties of the cavity and surrounding plasma by combining the AIA radiances with a differential emission measure analysis. This paper focuses on one long cavity from a catalog of coronal cavities that we are developing. Cavities in this catalog are designated by a coded name using the Carrington Rotation number and position. Cavity C211347177N was observed during Carrington Rotation 2113 at the northwestern limb of the solar disk with an average latitude of 47° N and a central longitude of 177°. We showed the following. (1) The cavity is a long tube with an elliptical cross-section with ratios of the length to width and the length to height of 11:1 and 7:1, respectively. (2) The cavity is about 1360 Mm long, or 170° in longitude. (3) It is tilted in latitude. (4) And it is slightly hotter than its surroundings.

  2. STUDY OF THE 3D GEOMETRIC STRUCTURE AND TEMPERATURE OF A CORONAL CAVITY USING THE LIMB SYNOPTIC MAP METHOD

    SciTech Connect

    Karna, N.; Pesnell, W. Dean; Webber, S. A. Hess; Zhang, J.

    2015-09-10

    We present the three-dimensional geometric structure and thermal properties of a coronal cavity deduced from limb synoptic maps. The observations are extreme ultraviolet images from the Atmospheric Imager Assembly (AIA) and magnetic images from the Helioseismic Magnetic Imager instruments on board the Solar Dynamics Observatory. We describe a limb synoptic-map method used to effectively identify and measure cavities from annuli of radiance above the solar limb. We find that cavities are best seen in the 211, 193, and 171 Å passbands. The prominence associated with each cavity is best seen in the 304 Å synoptic maps. We also estimate the thermal properties of the cavity and surrounding plasma by combining the AIA radiances with a differential emission measure analysis. This paper focuses on one long cavity from a catalog of coronal cavities that we are developing. Cavities in this catalog are designated by a coded name using the Carrington Rotation number and position. Cavity C211347177N was observed during Carrington Rotation 2113 at the northwestern limb of the solar disk with an average latitude of 47° N and a central longitude of 177°. We showed the following. (1) The cavity is a long tube with an elliptical cross-section with ratios of the length to width and the length to height of 11:1 and 7:1, respectively. (2) The cavity is about 1360 Mm long, or 170° in longitude. (3) It is tilted in latitude. (4) And it is slightly hotter than its surroundings.

  3. Evolution of chemical bonding and electron density rearrangements during D(3h) → D(3d) reaction in monolayered TiS2: a QTAIM and ELF study.

    PubMed

    Ryzhikov, Maxim R; Slepkov, Vladimir A; Kozlova, Svetlana G; Gabuda, Svyatoslav P

    2014-08-15

    Monolayered titanium disulfide TiS2, a prospective nanoelectronic material, was previously shown to be subject to an exothermic solid-state D3h -D3d reaction that proceeds via a newly discovered transition state. Here, we study the reaction in detail using topological methods of quantum chemistry (quantum theory of atoms in molecules and electron localization function analysis) and show how electron density and chemical bonding between the atoms change in the course of the reaction. The reaction is shown to undergo a series of topological catastrophes, associated with elementary chemical events such as break and formation of bonds (including the unexpected formation of S-S bonding between sulfur layers), and rearrangement of electron density of outer valence and core shells.

  4. Classification of lung nodules in diagnostic CT: an approach based on 3D vascular features, nodule density distribution, and shape features

    NASA Astrophysics Data System (ADS)

    Lo, Shih-Chung B.; Hsu, Li-Yueh; Freedman, Matthew T.; Lure, Yuan Ming F.; Zhao, Hui

    2003-05-01

    We have developed various segmentation and analysis methods for the quantification of lung nodules in thoracic CT. Our methods include the enhancement of lung structures followed by a series of segmentation methods to extract the nodule and to form 3D configuration at an area of interest. The vascular index, aspect ratio, circularity, irregularity, extent, compactness, and convexity were also computed as shape features for quantifying the nodule boundary. The density distribution of the nodule was modeled based on its internal homogeneity and/or heterogeneity. We also used several density related features including entropy, difference entropy as well as other first and second order moments. We have collected 48 cases of lung nodules scanned by thin-slice diagnostic CT. Of these cases, 24 are benign and 24 are malignant. A jackknife experiment was performed using a standard back-propagation neural network as the classifier. The LABROC result showed that the Az of this preliminary study is 0.89.

  5. Simultaneous spatiotemporal mapping of in situ pH and bacterial activity within an intact 3D microcolony structure

    NASA Astrophysics Data System (ADS)

    Hwang, Geelsu; Liu, Yuan; Kim, Dongyeop; Sun, Victor; Aviles-Reyes, Alejandro; Kajfasz, Jessica K.; Lemos, Jose A.; Koo, Hyun

    2016-09-01

    Biofilms are comprised of bacterial-clusters (microcolonies) enmeshed in an extracellular matrix. Streptococcus mutans can produce exopolysaccharides (EPS)-matrix and assemble microcolonies with acidic microenvironments that can cause tooth-decay despite the surrounding neutral-pH found in oral cavity. How the matrix influences the pH and bacterial activity locally remains unclear. Here, we simultaneously analyzed in situ pH and gene expression within intact biofilms and measured the impact of damage to the surrounding EPS-matrix. The spatiotemporal changes of these properties were characterized at a single-microcolony level following incubation in neutral-pH buffer. The middle and bottom-regions as well as inner-section within the microcolony 3D structure were resistant to neutralization (vs. upper and peripheral-region), forming an acidic core. Concomitantly, we used a green fluorescent protein (GFP) reporter to monitor expression of the pH-responsive atpB (PatpB::gfp) by S. mutans within microcolonies. The atpB expression was induced in the acidic core, but sharply decreased at peripheral/upper microcolony regions, congruent with local pH microenvironment. Enzymatic digestion of the surrounding matrix resulted in nearly complete neutralization of microcolony interior and down-regulation of atpB. Altogether, our data reveal that biofilm matrix facilitates formation of an acidic core within microcolonies which in turn activates S. mutans acid-stress response, mediating both the local environment and bacterial activity in situ.

  6. Remote magnetic actuation of micrometric probes for in situ 3D mapping of bacterial biofilm physical properties.

    PubMed

    Galy, Olivier; Zrelli, Kais; Latour-Lambert, Patricia; Kirwan, Lyndsey; Henry, Nelly

    2014-05-02

    Bacterial adhesion and growth on interfaces lead to the formation of three-dimensional heterogeneous structures so-called biofilms. The cells dwelling in these structures are held together by physical interactions mediated by a network of extracellular polymeric substances. Bacterial biofilms impact many human activities and the understanding of their properties is crucial for a better control of their development - maintenance or eradication - depending on their adverse or beneficial outcome. This paper describes a novel methodology aiming to measure in situ the local physical properties of the biofilm that had been, until now, examined only from a macroscopic and homogeneous material perspective. The experiment described here involves introducing magnetic particles into a growing biofilm to seed local probes that can be remotely actuated without disturbing the structural properties of the biofilm. Dedicated magnetic tweezers were developed to exert a defined force on each particle embedded in the biofilm. The setup is mounted on the stage of a microscope to enable the recording of time-lapse images of the particle-pulling period. The particle trajectories are then extracted from the pulling sequence and the local viscoelastic parameters are derived from each particle displacement curve, thereby providing the 3D-spatial distribution of the parameters. Gaining insights into the biofilm mechanical profile is essential from an engineer's point of view for biofilm control purposes but also from a fundamental perspective to clarify the relationship between the architectural properties and the specific biology of these structures.

  7. Remote Magnetic Actuation of Micrometric Probes for in situ 3D Mapping of Bacterial Biofilm Physical Properties

    PubMed Central

    Galy, Olivier; Zrelli, Kais; Latour-Lambert, Patricia; Kirwan, Lyndsey; Henry, Nelly

    2014-01-01

    Bacterial adhesion and growth on interfaces lead to the formation of three-dimensional heterogeneous structures so-called biofilms. The cells dwelling in these structures are held together by physical interactions mediated by a network of extracellular polymeric substances. Bacterial biofilms impact many human activities and the understanding of their properties is crucial for a better control of their development — maintenance or eradication — depending on their adverse or beneficial outcome. This paper describes a novel methodology aiming to measure in situ the local physical properties of the biofilm that had been, until now, examined only from a macroscopic and homogeneous material perspective. The experiment described here involves introducing magnetic particles into a growing biofilm to seed local probes that can be remotely actuated without disturbing the structural properties of the biofilm. Dedicated magnetic tweezers were developed to exert a defined force on each particle embedded in the biofilm. The setup is mounted on the stage of a microscope to enable the recording of time-lapse images of the particle-pulling period. The particle trajectories are then extracted from the pulling sequence and the local viscoelastic parameters are derived from each particle displacement curve, thereby providing the 3D-spatial distribution of the parameters. Gaining insights into the biofilm mechanical profile is essential from an engineer's point of view for biofilm control purposes but also from a fundamental perspective to clarify the relationship between the architectural properties and the specific biology of these structures. PMID:24837001

  8. Reconstruction of 3D Coronal Magnetic Structures from THEMIS/MTR and Hinode/SOT Vector Maps

    NASA Astrophysics Data System (ADS)

    Schmieder, B.; Guo, Y.; Aulanier, G.; Démoulin, P.; Török, T.; Bommier, V.; Wiegelmann, T.; Gosain, S.

    2012-08-01

    Coordinated campaigns using THEMIS, Hinode, and other instruments have allowed us to study the magnetic fields of faculae, filaments, and active regions. In a first case, we modelled the 3D magnetic field in a flaring active region with a nonlinear force-free field extrapolation, using magnetic vectors observed by THEMIS/MTR as boundary condition. In order to construct a consistent bottom boundary for the model, we first removed the 180 degree ambiguity of the transverse fields and minimized the force and torque in the observed vector fields. We found a twisted magnetic flux rope, well aligned with the polarity inversion line and a part of an Hα filament, and located where a large flare is initiated about two hours later. In a second case, Hinode/SOT allowed us to detect fine flux concentrations in faculae, while MTR provided us with magnetic information at different levels in the atmosphere. The polarimetry analysis of the MTR and SOT data gave consistent results, using both UNNOFIT and MELANIE inversion codes.

  9. Simultaneous spatiotemporal mapping of in situ pH and bacterial activity within an intact 3D microcolony structure

    PubMed Central

    Hwang, Geelsu; Liu, Yuan; Kim, Dongyeop; Sun, Victor; Aviles-Reyes, Alejandro; Kajfasz, Jessica K.; Lemos, Jose A.; Koo, Hyun

    2016-01-01

    Biofilms are comprised of bacterial-clusters (microcolonies) enmeshed in an extracellular matrix. Streptococcus mutans can produce exopolysaccharides (EPS)-matrix and assemble microcolonies with acidic microenvironments that can cause tooth-decay despite the surrounding neutral-pH found in oral cavity. How the matrix influences the pH and bacterial activity locally remains unclear. Here, we simultaneously analyzed in situ pH and gene expression within intact biofilms and measured the impact of damage to the surrounding EPS-matrix. The spatiotemporal changes of these properties were characterized at a single-microcolony level following incubation in neutral-pH buffer. The middle and bottom-regions as well as inner-section within the microcolony 3D structure were resistant to neutralization (vs. upper and peripheral-region), forming an acidic core. Concomitantly, we used a green fluorescent protein (GFP) reporter to monitor expression of the pH-responsive atpB (PatpB::gfp) by S. mutans within microcolonies. The atpB expression was induced in the acidic core, but sharply decreased at peripheral/upper microcolony regions, congruent with local pH microenvironment. Enzymatic digestion of the surrounding matrix resulted in nearly complete neutralization of microcolony interior and down-regulation of atpB. Altogether, our data reveal that biofilm matrix facilitates formation of an acidic core within microcolonies which in turn activates S. mutans acid-stress response, mediating both the local environment and bacterial activity in situ. PMID:27604325

  10. Regional 3-D ionospheric electron density specification on the basis of data assimilation of ground-based GNSS and radio occultation data

    NASA Astrophysics Data System (ADS)

    Aa, Ercha; Liu, Siqing; Huang, Wengeng; Shi, Liqin; Gong, Jiancun; Chen, Yanhong; Shen, Hua; Li, Jianyong

    2016-06-01

    In this paper, a regional 3-D ionospheric electron density specification over China and adjacent areas (70°E-140°E in longitude, 15°N-55°N in latitude, and 100-900 km in altitude) is developed on the basis of data assimilation technique. The International Reference Ionosphere (IRI) is used as a background model, and a three-dimensional variational technique is used to assimilate both the ground-based Global Navigation Satellite System (GNSS) observations from the Crustal Movement Observation Network of China (CMONOC) and International GNSS Service (IGS) and the ionospheric radio occultation (RO) data from FORMOSAT-3/COSMIC (F3/C) satellites. The regional 3-D gridded ionospheric electron densities can be generated with temporal resolution of 5 min in universal time, horizontal resolution of 2° × 2° in latitude and longitude, and vertical resolution of 20 km between 100 and 500 km and 50 km between 500 and 900 km. The data assimilation results are validated through extensive comparison with several sources of electron density information, including (1) ionospheric total electron content (TEC); (2) Abel-retrieved F3/C electron density profiles (EDPs); (3) ionosonde foF2 and bottomside EDPs; and (4) the Utah State University Global Assimilation of Ionospheric Measurements (USU-GAIM) under both geomagnetic quiet and disturbed conditions. The validation results show that the data assimilation procedure pushes the climatological IRI model toward the observation, and a general accuracy improvement of 15-30% can be expected. Thecomparisons also indicate that the data assimilation results are more close to the Center for Orbit Determination of Europe (CODE) TEC and Madrigal TEC products than USU-GAIM. These initial results might demonstrate the effectiveness of the data assimilation technique in improving specification of local ionospheric morphology.

  11. Alterations of mass density and 3D osteocyte lacunar properties in bisphosphonate-related osteonecrotic human jaw bone, a synchrotron µCT study.

    PubMed

    Hesse, Bernhard; Langer, Max; Varga, Peter; Pacureanu, Alexandra; Dong, Pei; Schrof, Susanne; Männicke, Nils; Suhonen, Heikki; Olivier, Cecile; Maurer, Peter; Kazakia, Galateia J; Raum, Kay; Peyrin, Francoise

    2014-01-01

    Osteonecrosis of the jaw, in association with bisphosphonates (BRONJ) used for treating osteoporosis or cancer, is a severe and most often irreversible side effect whose underlying pathophysiological mechanisms remain largely unknown. Osteocytes are involved in bone remodeling and mineralization where they orchestrate the delicate equilibrium between osteoclast and osteoblast activity and through the active process called osteocytic osteolysis. Here, we hypothesized that (i) changes of the mineralized tissue matrix play a substantial role in the pathogenesis of BRONJ, and (ii) the osteocyte lacunar morphology is altered in BRONJ. Synchrotron µCT with phase contrast is an appropriate tool for assessing both the 3D morphology of the osteocyte lacunae and the bone matrix mass density. Here, we used this technique to investigate the mass density distribution and 3D osteocyte lacunar properties at the sub-micrometer scale in human bone samples from the jaw, femur and tibia. First, we compared healthy human jaw bone to human tibia and femur in order to assess the specific differences and address potential explanations of why the jaw bone is exclusively targeted by the necrosis as a side effect of BP treatment. Second, we investigated the differences between BRONJ and control jaw bone samples to detect potential differences which could aid an improved understanding of the course of BRONJ. We found that the apparent mass density of jaw bone was significantly smaller compared to that of tibia, consistent with a higher bone turnover in the jaw bone. The variance of the lacunar volume distribution was significantly different depending on the anatomical site. The comparison between BRONJ and control jaw specimens revealed no significant increase in mineralization after BP. We found a significant decrease in osteocyte-lacunar density in the BRONJ group compared to the control jaw. Interestingly, the osteocyte-lacunar volume distribution was not altered after BP treatment.

  12. Mapping motion from 4D-MRI to 3D-CT for use in 4D dose calculations: A technical feasibility study

    SciTech Connect

    Boye, Dirk; Lomax, Tony; Knopf, Antje

    2013-06-15

    Purpose: Target sites affected by organ motion require a time resolved (4D) dose calculation. Typical 4D dose calculations use 4D-CT as a basis. Unfortunately, 4D-CT images have the disadvantage of being a 'snap-shot' of the motion during acquisition and of assuming regularity of breathing. In addition, 4D-CT acquisitions involve a substantial additional dose burden to the patient making many, repeated 4D-CT acquisitions undesirable. Here the authors test the feasibility of an alternative approach to generate patient specific 4D-CT data sets. Methods: In this approach motion information is extracted from 4D-MRI. Simulated 4D-CT data sets [which the authors call 4D-CT(MRI)] are created by warping extracted deformation fields to a static 3D-CT data set. The employment of 4D-MRI sequences for this has the advantage that no assumptions on breathing regularity are made, irregularities in breathing can be studied and, if necessary, many repeat imaging studies (and consequently simulated 4D-CT data sets) can be performed on patients and/or volunteers. The accuracy of 4D-CT(MRI)s has been validated by 4D proton dose calculations. Our 4D dose algorithm takes into account displacements as well as deformations on the originating 4D-CT/4D-CT(MRI) by calculating the dose of each pencil beam based on an individual time stamp of when that pencil beam is applied. According to corresponding displacement and density-variation-maps the position and the water equivalent range of the dose grid points is adjusted at each time instance. Results: 4D dose distributions, using 4D-CT(MRI) data sets as input were compared to results based on a reference conventional 4D-CT data set capturing similar motion characteristics. Almost identical 4D dose distributions could be achieved, even though scanned proton beams are very sensitive to small differences in the patient geometry. In addition, 4D dose calculations have been performed on the same patient, but using 4D-CT(MRI) data sets based on

  13. The Performance Analysis of a 3d Map Embedded Ins/gps Fusion Algorithm for Seamless Vehicular Navigation in Elevated Highway Environments

    NASA Astrophysics Data System (ADS)

    Lee, Y. H.; Chiang, K. W.

    2012-07-01

    In this study, a 3D Map Matching (3D MM) algorithm is embedded to current INS/GPS fusion algorithm for enhancing the sustainability and accuracy of INS/GPS integration systems, especially the height component. In addition, this study propose an effective solutions to the limitation of current commercial vehicular navigation systems where they fail to distinguish whether the vehicle is moving on the elevated highway or the road under it because those systems don't have sufficient height resolution. To validate the performance of proposed 3D MM embedded INS/GPS integration algorithms, in the test area, two scenarios were considered, paths under the freeways and streets between tall buildings, where the GPS signal is obstacle or interfered easily. The test platform was mounted on the top of a land vehicle and also systems in the vehicle. The IMUs applied includes SPAN-LCI (0.1 deg/hr gyro bias) from NovAtel, which was used as the reference system, and two MEMS IMUs with different specifications for verifying the performance of proposed algorithm. The preliminary results indicate the proposed algorithms are able to improve the accuracy of positional components in GPS denied environments significantly with the use of INS/GPS integrated systems in SPP mode.

  14. Fingerprint recognition using model-based density map.

    PubMed

    Wan, Dingrui; Zhou, Jie

    2006-06-01

    Utilizing more information other than minutiae is much helpful for large-scale fingerprint recognition applications. In this paper, we proposed a polynomial model to approximate the density map of fingerprints and used the model's parameters as a novel kind of feature for fingerprint representation. Thus, the density information can be utilized into the matching stage with a low additional storage cost. A decision-level fusion scheme is further used to combine the density map matching with conventional minutiae-based matching and experimental results showed a much better performance than using single minutiae-based matching.

  15. Evolution of probability densities in stochastic coupled map lattices

    NASA Astrophysics Data System (ADS)

    Losson, Jérôme; Mackey, Michael C.

    1995-08-01

    This paper describes the statistical properties of coupled map lattices subjected to the influence of stochastic perturbations. The stochastic analog of the Perron-Frobenius operator is derived for various types of noise. When the local dynamics satisfy rather mild conditions, this equation is shown to possess either stable, steady state solutions (i.e., a stable invariant density) or density limit cycles. Convergence of the phase space densities to these limit cycle solutions explains the nonstationary behavior of statistical quantifiers at equilibrium. Numerical experiments performed on various lattices of tent, logistic, and shift maps with diffusivelike interelement couplings are examined in light of these theoretical results.

  16. Depth-varying density and organization of chondrocytes in immature and mature bovine articular cartilage assessed by 3d imaging and analysis

    NASA Technical Reports Server (NTRS)

    Jadin, Kyle D.; Wong, Benjamin L.; Bae, Won C.; Li, Kelvin W.; Williamson, Amanda K.; Schumacher, Barbara L.; Price, Jeffrey H.; Sah, Robert L.

    2005-01-01

    Articular cartilage is a heterogeneous tissue, with cell density and organization varying with depth from the surface. The objectives of the present study were to establish a method for localizing individual cells in three-dimensional (3D) images of cartilage and quantifying depth-associated variation in cellularity and cell organization at different stages of growth. Accuracy of nucleus localization was high, with 99% sensitivity relative to manual localization. Cellularity (million cells per cm3) decreased from 290, 310, and 150 near the articular surface in fetal, calf, and adult samples, respectively, to 120, 110, and 50 at a depth of 1.0 mm. The distance/angle to the nearest neighboring cell was 7.9 microm/31 degrees , 7.1 microm/31 degrees , and 9.1 microm/31 degrees for cells at the articular surface of fetal, calf, and adult samples, respectively, and increased/decreased to 11.6 microm/31 degrees , 12.0 microm/30 degrees , and 19.2 microm/25 degrees at a depth of 0.7 mm. The methodologies described here may be useful for analyzing the 3D cellular organization of cartilage during growth, maturation, aging, degeneration, and regeneration.

  17. Order parameter re-mapping algorithm for 3D phase field model of grain growth using FEM

    SciTech Connect

    Permann, Cody J.; Tonks, Michael R.; Fromm, Bradley; Gaston, Derek R.

    2016-01-14

    Phase field modeling (PFM) is a well-known technique for simulating microstructural evolution. To model grain growth using PFM, typically each grain is assigned a unique non-conserved order parameter and each order parameter field is evolved in time. Traditional approaches using a one-to-one mapping of grains to order parameters present a challenge when modeling large numbers of grains due to the computational expense of using many order parameters. This problem is exacerbated when using an implicit finite element method (FEM), as the global matrix size is proportional to the number of order parameters. While previous work has developed methods to reduce the number of required variables and thus computational complexity and run time, none of the existing approaches can be applied for an implicit FEM implementation of PFM. Here, we present a modular, dynamic, scalable reassignment algorithm suitable for use in such a system. Polycrystal modeling with grain growth and stress require careful tracking of each grain’s position and orientation which is lost when using a reduced order parameter set. In conclusion, the method presented in this paper maintains a unique ID for each grain even after reassignment, to allow the PFM to be tightly coupled to calculations of the stress throughout the polycrystal. Implementation details and comparative results of our approach are presented.

  18. A high performance biometric signal and image processing method to reveal blood perfusion towards 3D oxygen saturation mapping

    NASA Astrophysics Data System (ADS)

    Imms, Ryan; Hu, Sijung; Azorin-Peris, Vicente; Trico, Michaël.; Summers, Ron

    2014-03-01

    Non-contact imaging photoplethysmography (PPG) is a recent development in the field of physiological data acquisition, currently undergoing a large amount of research to characterize and define the range of its capabilities. Contact-based PPG techniques have been broadly used in clinical scenarios for a number of years to obtain direct information about the degree of oxygen saturation for patients. With the advent of imaging techniques, there is strong potential to enable access to additional information such as multi-dimensional blood perfusion and saturation mapping. The further development of effective opto-physiological monitoring techniques is dependent upon novel modelling techniques coupled with improved sensor design and effective signal processing methodologies. The biometric signal and imaging processing platform (bSIPP) provides a comprehensive set of features for extraction and analysis of recorded iPPG data, enabling direct comparison with other biomedical diagnostic tools such as ECG and EEG. Additionally, utilizing information about the nature of tissue structure has enabled the generation of an engineering model describing the behaviour of light during its travel through the biological tissue. This enables the estimation of the relative oxygen saturation and blood perfusion in different layers of the tissue to be calculated, which has the potential to be a useful diagnostic tool.

  19. Order parameter re-mapping algorithm for 3D phase field model of grain growth using FEM

    DOE PAGES

    Permann, Cody J.; Tonks, Michael R.; Fromm, Bradley; ...

    2016-01-14

    Phase field modeling (PFM) is a well-known technique for simulating microstructural evolution. To model grain growth using PFM, typically each grain is assigned a unique non-conserved order parameter and each order parameter field is evolved in time. Traditional approaches using a one-to-one mapping of grains to order parameters present a challenge when modeling large numbers of grains due to the computational expense of using many order parameters. This problem is exacerbated when using an implicit finite element method (FEM), as the global matrix size is proportional to the number of order parameters. While previous work has developed methods to reducemore » the number of required variables and thus computational complexity and run time, none of the existing approaches can be applied for an implicit FEM implementation of PFM. Here, we present a modular, dynamic, scalable reassignment algorithm suitable for use in such a system. Polycrystal modeling with grain growth and stress require careful tracking of each grain’s position and orientation which is lost when using a reduced order parameter set. In conclusion, the method presented in this paper maintains a unique ID for each grain even after reassignment, to allow the PFM to be tightly coupled to calculations of the stress throughout the polycrystal. Implementation details and comparative results of our approach are presented.« less

  20. Three-dimensional (3D) coseismic deformation map produced by the 2014 South Napa Earthquake estimated and modeled by SAR and GPS data integration

    NASA Astrophysics Data System (ADS)

    Polcari, Marco; Albano, Matteo; Fernández, José; Palano, Mimmo; Samsonov, Sergey; Stramondo, Salvatore; Zerbini, Susanna

    2016-04-01

    In this work we present a 3D map of coseismic displacements due to the 2014 Mw 6.0 South Napa earthquake, California, obtained by integrating displacement information data from SAR Interferometry (InSAR), Multiple Aperture Interferometry (MAI), Pixel Offset Tracking (POT) and GPS data acquired by both permanent stations and campaigns sites. This seismic event produced significant surface deformation along the 3D components causing several damages to vineyards, roads and houses. The remote sensing results, i.e. InSAR, MAI and POT, were obtained from the pair of SAR images provided by the Sentinel-1 satellite, launched on April 3rd, 2014. They were acquired on August 7th and 31st along descending orbits with an incidence angle of about 23°. The GPS dataset includes measurements from 32 stations belonging to the Bay Area Regional Deformation Network (BARDN), 301 continuous stations available from the UNAVCO and the CDDIS archives, and 13 additional campaign sites from Barnhart et al, 2014 [1]. These data constrain the horizontal and vertical displacement components proving to be helpful for the adopted integration method. We exploit the Bayes theory to search for the 3D coseismic displacement components. In particular, for each point, we construct an energy function and solve the problem to find a global minimum. Experimental results are consistent with a strike-slip fault mechanism with an approximately NW-SE fault plane. Indeed, the 3D displacement map shows a strong North-South (NS) component, peaking at about 15 cm, a few kilometers far from the epicenter. The East-West (EW) displacement component reaches its maximum (~10 cm) south of the city of Napa, whereas the vertical one (UP) is smaller, although a subsidence in the order of 8 cm on the east side of the fault can be observed. A source modelling was performed by inverting the estimated displacement components. The best fitting model is given by a ~N330° E-oriented and ~70° dipping fault with a prevailing

  1. Systematic mapping of the subchondral bone 3D microarchitecture in the human tibial plateau: Variations with joint alignment.

    PubMed

    Roberts, Bryant C; Thewlis, Dominic; Solomon, Lucian B; Mercer, Graham; Reynolds, Karen J; Perilli, Egon

    2016-11-07

    Tibial subchondral bone plays an important role in knee osteoarthritis (OA). Microarchitectural characterization of subchondral bone plate (SBP), underlying subchondral trabecular bone (STB) and relationships between these compartments, however, is limited. The aim of this study was to characterize the spatial distribution of SBP thickness, SBP porosity and STB microarchitecture, and relationships among them, in OA tibiae of varying joint alignment. Twenty-five tibial plateaus from end-stage knee-OA patients, with varus (n = 17) or non-varus (n = 8) alignment were micro-CT scanned (17 μm/voxel). SBP and STB microarchitecture was quantified via a systematic mapping in 22 volumes of interest per knee (11 medial, 11 lateral). Significant within-condylar and between-condylar (medial vs. lateral) differences (p < 0.05) were found. In varus, STB bone volume fraction (BV/TV) was consistently high throughout the medial condyle, whereas in non-varus, medially, it was more heterogeneously distributed. Regions of high SBP thickness were co-located with regions of high STB BV/TV underneath. In varus, BV/TV was significantly higher medially than laterally, however, not so in non-varus. Moreover, region-specific significant associations between the SBP thickness and SBP porosity and the underlying STB microarchitecture were detected, which in general were not captured when considering the values averaged for each condyle. As subchondral bone changes reflect responses to local mechanical and biochemical factors within the joint, our results suggest that joint alignment influences both the medial-to-lateral and the within-condyle distribution of force across the tibia, generating corresponding local bony responses (adaptation) of both the subchondral bone plate and underlying subchondral trabecular bone microarchitecture. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res.

  2. Turbulence computations with 3-D small-scale additive turbulent decomposition and data-fitting using chaotic map combinations

    SciTech Connect

    Mukerji, Sudip

    1997-01-01

    Although the equations governing turbulent fluid flow, the Navier-Stokes (N.S.) equations, have been known for well over a century and there is a clear technological necessity in obtaining solutions to these equations, turbulence remains one of the principal unsolved problems in physics today. It is still not possible to make accurate quantitative predictions about turbulent flows without relying heavily on empirical data. In principle, it is possible to obtain turbulent solutions from a direct numerical simulation (DNS) of the N.-S. equations. The author first provides a brief introduction to the dynamics of turbulent flows. The N.-S. equations which govern fluid flow, are described thereafter. Then he gives a brief overview of DNS calculations and where they stand at present. He next introduces the two most popular approaches for doing turbulent computations currently in use, namely, the Reynolds averaging of the N.-S. equations (RANS) and large-eddy simulation (LES). Approximations, often ad hoc ones, are present in these methods because use is made of heuristic models for turbulence quantities (the Reynolds stresses) which are otherwise unknown. They then introduce a new computational method called additive turbulent decomposition (ATD), the small-scale version of which is the topic of this research. The rest of the thesis is organized as follows. In Chapter 2 he describes the ATD procedure in greater detail; how dependent variables are split and the decomposition into large- and small-scale sets of equations. In Chapter 3 the spectral projection of the small-scale momentum equations are derived in detail. In Chapter 4 results of the computations with the small-scale ATD equations are presented. In Chapter 5 he describes the data-fitting procedure which can be used to directly specify the parameters of a chaotic-map turbulence model.

  3. Mapping 3D thin shale and permeability pathway within a reservoir system: Case study from the Sleipner Field

    NASA Astrophysics Data System (ADS)

    Ponfa Bitrus, Roy; Iacopini, David; Bond, Clare

    2016-04-01

    Reservoir architecture plays an integral part of seismic reservoir characterization. The characteristics of a reservoir which includes its external and internal geometry are important as they influence the production and development strategy employed in the oil and gas sector. Reservoir architecture is defined by the interpretation of seismic data, thus identifying the basic structural and stratigraphic geometrical framework of a trapping and flow system for hydrocarbon and fluids. One major issue though is the interpretation of thin shales and identification of permeability pathways within the reservoir system. This paper employs a method using attributes to map thin shales and identify permeability pathways or transmissitives that exist within a reservoir taking into consideration the seismic resolution and available data. Case study is the Utsira Formation in the Sleipner field, Norwegian North sea. The Utsira formation presents a classic case of thin beds within a sandstone formation and transmissitives that exist as chimneys within the formation. A total of 10 intra reservoir horizon units of shales where interpreted using complex trace seismic attributes. These interpreted horizons where further analysed through spectral decomposition to reveal possible facies distribution and unit thickness within the horizon. Reservoir transmissitives identified as vertical curvilinear structures were also analysed using unique seismic attributes in other to delineate their extent and characterise their occurrence These interpreted shales and pathway transmissitives illuminate the geometry of the formation, the reservoir heterogeneities on a finer-scale and, in the long term, constrain the migration prediction of reservoir fluids, hydrocarbons and injected CO2 when matched across a 4D seismic data survey. As such, useful insights into the key elements operating within the reservoir can be provided, giving a good indication of the long and short term reservoir performance.

  4. Use of stereoscopic satellite imagery for 3D mapping of bedrock structure in West Antarctica: An example from the northern Ford Ranges

    NASA Astrophysics Data System (ADS)

    Contreras, A.; Siddoway, C. S.; Porter, C.; Gottfried, M.

    2012-12-01

    In coastal West Antarctica, crustal-scale faults have been minimally mapped using traditional ground-based methods but regional scale structures are inferred mainly on the basis of low resolution potential fields data from airborne geophysical surveys (15 km flightline spacing). We use a new approach to detailed mapping of faults, shear zones, and intrusive relationships using panchromatic and multispectral imagery draped upon a digital elevation model (DEM). Our work focuses on the Fosdick Mountains, a culmination of lower middle crustal rocks exhumed at c. 100 Ma by dextral oblique detachment faulting. Ground truth exists for extensive areas visited during field studies in 2005-2011, providing a basis for spectral analysis of 8-band WorldView-02 imagery for detailed mapping of complex granite- migmatite relationships on the north side of the Fosdick range. A primary aim is the creation of a 3D geological map using the results of spectral analysis merged with a DEM computed from a stereographic pair of high resolution panchromatic images (sequential scenes, acquired 45 seconds apart). DEMs were computed using ERDAS Imagine™ LPS eATE, refined by MATLAB-based interpolation scripts to remove artifacts in the terrain model according to procedures developed by the Polar Geospatial Center (U. Minnesota). Orthorectified satellite imagery that covers the area of the DEMs was subjected to principal component analysis in ESRI ArcGIS™ 10.1, then the different rock types were identified using various combinations of spectral bands in order to map the geology of rock exposures that could not be accessed directly from the ground. Renderings in 3D of the satellite scenes draped upon the DEMs were created using Global Mapper™. The 3D perspective views reveal structural and geological features that are not observed in either the DEM nor the satellite imagery alone. The detailed map is crucial for an ongoing petrological / geochemical investigation of Cretaceous crustal

  5. SNP-based high density genetic map and mapping of btwd1 dwarfing gene in barley

    PubMed Central

    Ren, Xifeng; Wang, Jibin; Liu, Lipan; Sun, Genlou; Li, Chengdao; Luo, Hong; Sun, Dongfa

    2016-01-01

    A high-density linkage map is a valuable tool for functional genomics and breeding. A newly developed sequence-based marker technology, restriction site associated DNA (RAD) sequencing, has been proven to be powerful for the rapid discovery and genotyping of genome-wide single nucleotide polymorphism (SNP) markers and for the high-density genetic map construction. The objective of this research was to construct a high-density genetic map of barley using RAD sequencing. 1894 high-quality SNP markers were developed and mapped onto all seven chromosomes together with 68 SSR markers. These 1962 markers constituted a total genetic length of 1375.8 cM and an average of 0.7 cM between adjacent loci. The number of markers within each linkage group ranged from 209 to 396. The new recessive dwarfing gene btwd1 in Huaai 11 was mapped onto the high density linkage maps. The result showed that the btwd1 is positioned between SNP marks 7HL_6335336 and 7_249275418 with a genetic distance of 0.9 cM and 0.7 cM on chromosome 7H, respectively. The SNP-based high-density genetic map developed and the dwarfing gene btwd1 mapped in this study provide critical information for position cloning of the btwd1 gene and molecular breeding of barley. PMID:27530597

  6. Data Integration Acquired from Micro-Uav and Terrestrial Laser Scanner for the 3d Mapping of Jesuit Ruins of São Miguel das Missões

    NASA Astrophysics Data System (ADS)

    Reiss, M. L. L.; da Rocha, R. S.; Ferraz, R. S.; Cruz, V. C.; Morador, L. Q.; Yamawaki, M. K.; Rodrigues, E. L. S.; Cole, J. O.; Mezzomo, W.

    2016-06-01

    The Jesuit Missions the Guaranis were one of the great examples of cultural, social, and scientific of the eighteenth century, which had its decline from successive wars that followed the exchange of territories domain occupied by Portugal and Spain with the Madrid Treaty of January 13, 1750. One of the great examples of this development is materialized in the ruins of 30 churches and villages that remain in a territory that now comprises part of Brazil, Argentina and Paraguay. These Churches, São Miguel das Missões is among the Brazilian ruins, the best preserved. The ruins of São Miguel das Missões were declared a UNESCO World Cultural Heritage in 1983 and the Institute of National Historical Heritage (IPHAN) is the Brazilian Federal agency that manages and maintains this heritage. In order to produce a geographic database to assist the IPHAN in the management of the Ruins of São Miguel das Missões it was proposed a three-dimensional mapping of these ruins never performed in this location before. The proposal is integrated data acquired from multiple sensors: two micro-UAV, an Asctec Falcon 8 (rotary wing) and a Sensefly e-Bee (fixed wing); photos from terrestrial cameras; two terrestrial LIDAR sensors, one Faro Focus 3D S-120 and Optec 3D-HD ILRIS. With this abundance of sensors has been possible to perform comparisons and integration of the acquired data, and produce a 3D reconstruction of the church with high completeness and accuracy (better than 25 mm), as can be seen in the presentation of this work.

  7. Accurate and Fully Automatic Hippocampus Segmentation Using Subject-Specific 3D Optimal Local Maps Into a Hybrid Active Contour Model

    PubMed Central

    Gkontra, Polyxeni; Daras, Petros; Maglaveras, Nicos

    2014-01-01

    Assessing the structural integrity of the hippocampus (HC) is an essential step toward prevention, diagnosis, and follow-up of various brain disorders due to the implication of the structural changes of the HC in those disorders. In this respect, the development of automatic segmentation methods that can accurately, reliably, and reproducibly segment the HC has attracted considerable attention over the past decades. This paper presents an innovative 3-D fully automatic method to be used on top of the multiatlas concept for the HC segmentation. The method is based on a subject-specific set of 3-D optimal local maps (OLMs) that locally control the influence of each energy term of a hybrid active contour model (ACM). The complete set of the OLMs for a set of training images is defined simultaneously via an optimization scheme. At the same time, the optimal ACM parameters are also calculated. Therefore, heuristic parameter fine-tuning is not required. Training OLMs are subsequently combined, by applying an extended multiatlas concept, to produce the OLMs that are anatomically more suitable to the test image. The proposed algorithm was tested on three different and publicly available data sets. Its accuracy was compared with that of state-of-the-art methods demonstrating the efficacy and robustness of the proposed method. PMID:27170866

  8. Combining sedimentological and geophysical data for high-resolution 3-D mapping of fluvial architectural elements in the Quaternary Po plain (Italy)

    NASA Astrophysics Data System (ADS)

    Bersezio, R.; Giudici, M.; Mele, M.

    2007-11-01

    Current approaches to the reconstruction of the geometry of fluvial sediments of Quaternary alluvial plains and the characterization of their internal architecture are strongly dependent on core data (1-D). Accurate 2-D and 3-D reconstructions and maps of the subsurface are needed in hydrostratigraphy, hydrogeology and geotechnical studies. The present study aims to: 1) improve current methods for geophysical imaging of the subsurface by means of VES, ERGI and GPR data, and calibration with geomorphological and geological reconstructions, 2) optimize the horizontal and vertical resolution of subsurface imaging in order to resolve sedimentary heterogeneity, and 3) check the reliability/uncertainty of the results (maps and architectural reconstructions) by comparison with exposed analogues. The method was applied to shallow (0 to 15 m) aquifers of the fluvial plain of southern Lombardy (Northern Italy). At two sites we studied fluvial sediments of meandering systems of the Last Glacial Maximum and post-glacial historical age. These sediments comprise juxtaposed and superimposed gravel-sand units with fining-upward sequences (channel-bar depositional elements), which are separated by thin and laterally discontinuous silty and sandy clay units (overbank and flood plain deposits). The sedimentary architecture has been studied at different scales in the two areas. At the scale of the depositional system, we reconstructed the subsurface over an area of 4 km 2 to a depth of 18 m (study site 1). Reconstructed sequences based on 10 boreholes and water-well stratigraphic logs were integrated with the interpretation of 10 vertical electrical soundings (VES) with Schlumberger arrays and 1570 m long dipole-dipole electrical resistivity ground imaging profiles (ERGI). In unsaturated sediments, vertical and horizontal transitions between gravel-sand units and fine-grained sediments could be mapped respectively at the meter- to decameter scale after calibration of the VES with

  9. Using a modified 3D-printer for mapping the magnetic field of RF coils designed for fetal and neonatal imaging.

    PubMed

    Vavoulas, Alexander; Vaiopoulos, Nicholas; Hedström, Erik; Xanthis, Christos G; Sandalidis, Harilaos G; Aletras, Anthony H

    2016-08-01

    An experimental setup for characterizing the magnetic field of MRI RF coils was proposed and tested. The setup consisted of a specially configured 3D-printer, a network analyzer and a mid-performance desktop PC. The setup was tested on a single loop RF coil, part of a phased array for fetal imaging. Then, the setup was used for determining the magnetic field characteristics of a high-pass birdcage coil used for neonatal MR imaging with a vertical static field. The scattering parameter S21, converted into power ratio, was used for mapping the B1 magnetic field. The experimental measurements from the loop coil were close to the theoretical results (R=0.924). A high degree of homogeneity was measured for the neonatal birdcage RF coil. The development of MR RF coils is time consuming and resource intensive. The proposed experimental setup provides an alternative method for magnetic field characterization of RF coils used in MRI.

  10. Using a modified 3D-printer for mapping the magnetic field of RF coils designed for fetal and neonatal imaging

    NASA Astrophysics Data System (ADS)

    Vavoulas, Alexander; Vaiopoulos, Nicholas; Hedström, Erik; Xanthis, Christos G.; Sandalidis, Harilaos G.; Aletras, Anthony H.

    2016-08-01

    An experimental setup for characterizing the magnetic field of MRI RF coils was proposed and tested. The setup consisted of a specially configured 3D-printer, a network analyzer and a mid-performance desktop PC. The setup was tested on a single loop RF coil, part of a phased array for fetal imaging. Then, the setup was used for determining the magnetic field characteristics of a high-pass birdcage coil used for neonatal MR imaging with a vertical static field. The scattering parameter S21, converted into power ratio, was used for mapping the B1 magnetic field. The experimental measurements from the loop coil were close to the theoretical results (R = 0.924). A high degree of homogeneity was measured for the neonatal birdcage RF coil. The development of MR RF coils is time consuming and resource intensive. The proposed experimental setup provides an alternative method for magnetic field characterization of RF coils used in MRI.

  11. 3D mapping of water in oolithic limestone at atmospheric and vacuum saturation using X-ray micro-CT differential imaging

    SciTech Connect

    Boone, M.A.; De Kock, T.; Bultreys, T.; De Schutter, G.; Vontobel, P.; Van Hoorebeke, L.; Cnudde, V.

    2014-11-15

    Determining the distribution of fluids in porous sedimentary rocks is of great importance in many geological fields. However, this is not straightforward, especially in the case of complex sedimentary rocks like limestone, where a multidisciplinary approach is often needed to capture its broad, multimodal pore size distribution and complex pore geometries. This paper focuses on the porosity and fluid distribution in two varieties of Massangis limestone, a widely used natural building stone from the southeast part of the Paris basin (France). The Massangis limestone shows locally varying post-depositional alterations, resulting in different types of pore networks and very different water distributions within the limestone. Traditional techniques for characterizing the porosity and pore size distribution are compared with state-of-the-art neutron radiography and X-ray computed microtomography to visualize the distribution of water inside the limestone at different imbibition conditions. X-ray computed microtomography images have the great advantage to non-destructively visualize and analyze the pore space inside of a rock, but are often limited to the larger macropores in the rock due to resolution limitations. In this paper, differential imaging is successfully applied to the X-ray computed microtomography images to obtain sub-resolution information about fluid occupancy and to map the fluid distribution in three dimensions inside the scanned limestone samples. The detailed study of the pore space with differential imaging allows understanding the difference in the water uptake behavior of the limestone, a primary factor that affects the weathering of the rock. - Highlights: • The water distribution in a limestone was visualized in 3D with micro-CT. • Differential imaging allowed to map both macro and microporous zones in the rock. • The 3D study of the pore space clarified the difference in water uptake behavior. • Trapped air is visualized in the moldic

  12. SUTRA: A model for 2D or 3D saturated-unsaturated, variable-density ground-water flow with solute or energy transport

    USGS Publications Warehouse

    Voss, Clifford I.; Provost, A.M.

    2002-01-01

    SUTRA (Saturated-Unsaturated Transport) is a computer program that simulates fluid movement and the transport of either energy or dissolved substances in a subsurface environment. This upgraded version of SUTRA adds the capability for three-dimensional simulation to the former code (Voss, 1984), which allowed only two-dimensional simulation. The code employs a two- or three-dimensional finite-element and finite-difference method to approximate the governing equations that describe the two interdependent processes that are simulated: 1) fluid density-dependent saturated or unsaturated ground-water flow; and 2) either (a) transport of a solute in the ground water, in which the solute may be subject to: equilibrium adsorption on the porous matrix, and both first-order and zero-order production or decay; or (b) transport of thermal energy in the ground water and solid matrix of the aquifer. SUTRA may also be used to simulate simpler subsets of the above processes. A flow-direction-dependent dispersion process for anisotropic media is also provided by the code and is introduced in this report. As the primary calculated result, SUTRA provides fluid pressures and either solute concentrations or temperatures, as they vary with time, everywhere in the simulated subsurface system. SUTRA flow simulation may be employed for two-dimensional (2D) areal, cross sectional and three-dimensional (3D) modeling of saturated ground-water flow systems, and for cross sectional and 3D modeling of unsaturated zone flow. Solute-transport simulation using SUTRA may be employed to model natural or man-induced chemical-species transport including processes of solute sorption, production, and decay. For example, it may be applied to analyze ground-water contaminant transport problems and aquifer restoration designs. In addition, solute-transport simulation with SUTRA may be used for modeling of variable-density leachate movement, and for cross sectional modeling of saltwater intrusion in

  13. Pushing the Limits of Geological Mapping Outside the Earth: 3D Modeling of Strike-Slip and Extensional Fault Systems in Meridiani Planum Region, Mars.

    NASA Astrophysics Data System (ADS)

    Vidal Royo, O.

    2014-12-01

    GIS and geological modeling software have radically changed the means by which geological mapping is produced, published and visualized. This type of software environment normally requires a spatially aware reference system to position data and interpretation, often referred as georeferenced data (i.e. geographic data referenced on the Earth). However, for this study we coin the term areoreferenced data (i.e. Mars-referenced "geographic" data). Thanks to the wealth of areoreferenced data made available by the NASA and the HiRise at University of Arizona it is now possible to carry out 3D areographic and areologic (i.e. related to the topography and geology of Mars, respectively) reconstructions in great detail. The present work benefits from the availability of software and areographic data, and presents the results of an areologic map and 3D model of the fault systems in the Meridiani Planum of Mars. The work has been carried out in Move™ (developed by Midland Valley Exploration), a geological modeling toolkit that allows for easy data loading in a wide range of formats as well as straightforward 2D/3D model building tools of geological bodies. Initial data consisted of Digital Terrain Model and orthoimages (NASA/JPL/University of Arizona/USGS). From these we have interpreted several structural domains: right-lateral strike-slip systems with associated releasing bends, which gave room to an extensional event causing a horizontal-axis rotation of the bedding. Bedding ranges from subhorizontal in the southern domain where strike-slip prevails to nearly 40º in the central and northern domains, where a more complex interaction between strike-slip and extensional faults is described. The stratigraphic sequence is mainly composed by moderately rounded well laminated basaltic sandstones (Squyres et al., 2004) in which a high component of sulfurs (e.g. sulfate anhydrate, hexahydrite, epsomite, gypsum) and salts (e.g. halite) has been described (Squyres et al., 2004

  14. Seafloor surface processes and subsurface paleo-channel unconformities mapped using multi-channel seismic and multi-beam sonar data from the Galicia 3D seismic experiment.

    NASA Astrophysics Data System (ADS)

    Gibson, J. C.; Shillington, D. J.; Sawyer, D. S.; Jordan, B.; Morgan, J. K.; Ranero, C.; Reston, T. J.

    2015-12-01

    In this study we use geophysical methods, stratigraphic relationships, and coring/drilling leg results to assess possible controls on deep-sea channel formation in order to further constrain paleo-channel (PC) and associated unconformity timing/source processes. A series of cut and fill PC are mapped in 3D multi-channel seismic (MCS) data and compared with multi-beam (MB) sonar bathymetry/backscatter data collected during the Galicia 3D survey with the R/V Marcus G. Langseth (2013). The MCS data were collected using four 6 km streamers spaced at 200 m resulting in 25 m x 25 m common mid-point bins within the ~67 km x 20 km 3D volume. The MB data were collected at an average depth of ~4900 m with a constrained swath width of 4.5 km resulting in 11.25x overlap while enabling 25-m bathymetry and 10-m backscatter grids. The PC lie below the mouth of a submarine canyon at the edge of the Galicia abyssal plain and cut pre/syn-rift sediments; they are bound by a rift block to the north and paleo-levees to the south (maximum height of ~180m). From drilling results, the most recent PC is late Miocene in age. In this study, four PC are traced into the basin as unconformities. Several of the PC/unconformities are tentatively correlated with previously interpreted Pyrenean orogeny/compressional Miocene/Oligocene tectonic events. However, one PC/unconformity within this interval has not been previously interpreted. In order test the hypothesis that the unconformities are the result of a significant change in base level indicated by a low shale/sand (SS) ratio, we use seismic surface attributes to calculate the SS ratio and trace the horizontal extent of the unconformities. Additionally, the MB/MCS seafloor morphology reveals sedimentary waves outboard of the canyon mouth. We use backscatter data to compare the extent of recent processes (e.g., Pleistocene glaciation/de-glaciation) with the unconformities by mapping the surface/shallow subsurface SS ratio (volume scattering).

  15. Identification of novel histone deacetylase 1 inhibitors by combined pharmacophore modeling, 3D-QSAR analysis, in silico screening and Density Functional Theory (DFT) approaches

    NASA Astrophysics Data System (ADS)

    Choubey, Sanjay K.; Mariadasse, Richard; Rajendran, Santhosh; Jeyaraman, Jeyakanthan

    2016-12-01

    Overexpression of HDAC1, a member of Class I histone deacetylase is reported to be implicated in breast cancer. Epigenetic alteration in carcinogenesis has been the thrust of research for few decades. Increased deacetylation leads to accelerated cell proliferation, cell migration, angiogenesis and invasion. HDAC1 is pronounced as the potential drug target towards the treatment of breast cancer. In this study, the biochemical potential of 6-aminonicotinamide derivatives was rationalized. Five point pharmacophore model with one hydrogen-bond acceptor (A3), two hydrogen-bond donors (D5, D6), one ring (R12) and one hydrophobic group (H8) was developed using 6-aminonicotinamide derivatives. The pharmacophore hypothesis yielded a 3D-QSAR model with correlation-coefficient (r2 = 0.977, q2 = 0.801) and it was externally validated with (r2pred = 0.929, r2cv = 0.850 and r2m = 0.856) which reveals the statistical significance of the model having high predictive power. The model was then employed as 3D search query for virtual screening against compound libraries (Zinc, Maybridge, Enamine, Asinex, Toslab, LifeChem and Specs) in order to identify novel scaffolds which can be experimentally validated to design future drug molecule. Density Functional Theory (DFT) at B3LYP/6-31G* level was employed to explore the electronic features of the ligands involved in charge transfer reaction during receptor ligand interaction. Binding free energy (ΔGbind) calculation was done using MM/GBSA which defines the affinity of ligands towards the receptor.

  16. Photoemission spectra and density functional theory calculations of 3d transition metal-aqua complexes (Ti-Cu) in aqueous solution.

    PubMed

    Yepes, Diana; Seidel, Robert; Winter, Bernd; Blumberger, Jochen; Jaque, Pablo

    2014-06-19

    Photoelectron spectroscopy measurements and density functional calculations are combined to determine the lowest electron binding energies of first-row transition-metal aqua ions, titanium through copper, with 3d(1) through 3d(9) electronic configurations, in their most common oxidation states. Vertical ionization energies are found to oscillate considerably between 6.76 and 9.65 eV for the dications and between 7.05 and 10.28 eV for the respective trivalent cations. The metal cations are modeled as [M(H2O)n](q+) clusters (q = 2, 3, and 4; n = 6 and 18) surrounded by continuum solvent. The performance of 10 exchange-correlation functionals, two GGAs, three MGGAs, two HGGAs and three HMGGAs, combined with the MDF10(ECP)/6-31+G(d,p) basis set is assessed for 11 M-O bond distances, 10 vertical ionization energies, 6 adiabatic ionization energies, and the associated reorganization free energies. We find that for divalent cations the HGGA and HMGGA functionals in combination with the 18 water model show the best agreement with experimental vertical ionization energies and geometries; for trivalent ions, the MGGA functionals perform best. The corresponding reorganization free energies (λo) of the oxidized ions are significantly underestimated with all DFT functionals and cluster models. This indicates that the structural reorganization of the solvation shell upon ionization is not adequately accounted for by the simple solvation models used, emphasizing the importance of extended sampling of thermally accessible solvation structures for an accurate computation of this quantity. The photoelectron spectroscopy measurements reported herein provide a comprehensive set of transition-metal redox energetic quantities for future electronic structure benchmarks.

  17. A mechanistic approach to explore novel HDAC1 inhibitor using pharmacophore modeling, 3D- QSAR analysis, molecular docking, density functional and molecular dynamics simulation study.

    PubMed

    Choubey, Sanjay K; Jeyaraman, Jeyakanthan

    2016-11-01

    Deregulated epigenetic activity of Histone deacetylase 1 (HDAC1) in tumor development and carcinogenesis pronounces it as promising therapeutic target for cancer treatment. HDAC1 has recently captured the attention of researchers owing to its decisive role in multiple types of cancer. In the present study a multistep framework combining ligand based 3D-QSAR, molecular docking and Molecular Dynamics (MD) simulation studies were performed to explore potential compound with good HDAC1 binding affinity. Four different pharmacophore hypotheses Hypo1 (AADR), Hypo2 (AAAH), Hypo3 (AAAR) and Hypo4 (ADDR) were obtained. The hypothesis Hypo1 (AADR) with two hydrogen bond acceptors (A), one hydrogen bond donor (D) and one aromatics ring (R) was selected to build 3D-QSAR model on the basis of statistical parameter. The pharmacophore hypothesis produced a statistically significant QSAR model, with co-efficient of correlation r(2)=0.82 and cross validation correlation co-efficient q(2)=0.70. External validation result displays high predictive power with r(2) (o) value of 0.88 and r(2) (m) value of 0.58 to carry out further in silico studies. Virtual screening result shows ZINC70450932 as the most promising lead where HDAC1 interacts with residues Asp99, His178, Tyr204, Phe205 and Leu271 forming seven hydrogen bonds. A high docking score (-11.17kcal/mol) and lower docking energy -37.84kcal/mol) displays the binding efficiency of the ligand. Binding free energy calculation was done using MM/GBSA to access affinity of ligands towards protein. Density Functional Theory was employed to explore electronic features of the ligands describing intramolcular charge transfer reaction. Molecular dynamics simulation studies at 50ns display metal ion (Zn)-ligand interaction which is vital to inhibit the enzymatic activity of the protein.

  18. ESammon: A Computationaly Enhanced Sammon Mapping based on Data Density.

    PubMed

    Wang, Chanpaul Jin; Fang, Hua; Wang, Honggang

    2016-02-01

    Sammon mapping is a widely used visualization technique to display complex data from high- to low-dimensional space. However, its extensive computational cost may pose potential computational challenges to big data visualization. This paper proposes a computationally-enhanced Sammon mapping (ESammon) by leveraging the characteristics of spatial data density. Unlike the conventional Sammon, ESammon preserves critical pairwise distances between data points in the process of projection, instead of all distances. Specifically, we integrated the Directed-Acyclic-Graph (DAG) based data density characterization method to select the critical distances. The numerical results demonstrated that our ESammon can achieve comparable projection results as the conventional Sammon mapping while reducing the computational cost from O(N(2)) toO(N).

  19. High Energy Density Asymmetric Supercapacitor Based on NiOOH/Ni3S2/3D Graphene and Fe3O4/Graphene Composite Electrodes

    PubMed Central

    Lin, Tsung-Wu; Dai, Chao-Shuan; Hung, Kuan-Chung

    2014-01-01

    The application of the composite of Ni3S2 nanoparticles and 3D graphene as a novel cathode material for supercapacitors is systematically investigated in this study. It is found that the electrode capacitance increases by up to 111% after the composite electrode is activated by the consecutive cyclic voltammetry scanning in 1 M KOH. Due to the synergistic effect, the capacitance and the diffusion coefficient of electrolyte ions of the activated composite electrode are ca. 3.7 and 6.5 times higher than those of the Ni3S2 electrode, respectively. Furthermore, the activated composite electrode exhibits an ultrahigh specific capacitance of 3296 F/g and great cycling stability at a current density of 16 A/g. To obtain the reasonable matching of cathode/anode electrodes, the composite of Fe3O4 nanoparticles and chemically reduced graphene oxide (Fe3O4/rGO) is synthesized as the anode material. The Fe3O4/rGO electrode exhibits the specific capacitance of 661 F/g at 1 A/g and excellent rate capability. More importantly, an asymmetric supercapacitor fabricated by two different composite electrodes can be operated reversibly between 0 and 1.6 V and obtain a high specific capacitance of 233 F/g at 5 mV/s, which delivers a maximum energy density of 82.5 Wh/kg at a power density of 930 W/kg. PMID:25449978

  20. 3D-DXA: Assessing the Femoral Shape, the Trabecular Macrostructure and the Cortex in 3D from DXA images.

    PubMed

    Humbert, Ludovic; Martelli, Yves; Fonolla, Roger; Steghofer, Martin; Di Gregorio, Silvana; Malouf, Jorge; Romera, Jordi; Barquero, Luis Miguel Del Rio

    2017-01-01

    The 3D distribution of the cortical and trabecular bone mass in the proximal femur is a critical component in determining fracture resistance that is not taken into account in clinical routine Dual-energy X-ray Absorptiometry (DXA) examination. In this paper, a statistical shape and appearance model together with a 3D-2D registration approach are used to model the femoral shape and bone density distribution in 3D from an anteroposterior DXA projection. A model-based algorithm is subsequently used to segment the cortex and build a 3D map of the cortical thickness and density. Measurements characterising the geometry and density distribution were computed for various regions of interest in both cortical and trabecular compartments. Models and measurements provided by the "3D-DXA" software algorithm were evaluated using a database of 157 study subjects, by comparing 3D-DXA analyses (using DXA scanners from three manufacturers) with measurements performed by Quantitative Computed Tomography (QCT). The mean point-to-surface distance between 3D-DXA and QCT femoral shapes was 0.93 mm. The mean absolute error between cortical thickness and density estimates measured by 3D-DXA and QCT was 0.33 mm and 72 mg/cm(3). Correlation coefficients (R) between the 3D-DXA and QCT measurements were 0.86, 0.93, and 0.95 for the volumetric bone mineral density at the trabecular, cortical, and integral compartments respectively, and 0.91 for the mean cortical thickness. 3D-DXA provides a detailed analysis of the proximal femur, including a separate assessment of the cortical layer and trabecular macrostructure, which could potentially improve osteoporosis management while maintaining DXA as the standard routine modality.

  1. Spherical 3D isotropic wavelets

    NASA Astrophysics Data System (ADS)

    Lanusse, F.; Rassat, A.; Starck, J.-L.

    2012-04-01

    Context. Future cosmological surveys will provide 3D large scale structure maps with large sky coverage, for which a 3D spherical Fourier-Bessel (SFB) analysis in spherical coordinates is natural. Wavelets are particularly well-suited to the analysis and denoising of cosmological data, but a spherical 3D isotropic wavelet transform does not currently exist to analyse spherical 3D data. Aims: The aim of this paper is to present a new formalism for a spherical 3D isotropic wavelet, i.e. one based on the SFB decomposition of a 3D field and accompany the formalism with a public code to perform wavelet transforms. Methods: We describe a new 3D isotropic spherical wavelet decomposition based on the undecimated wavelet transform (UWT) described in Starck et al. (2006). We also present a new fast discrete spherical Fourier-Bessel transform (DSFBT) based on both a discrete Bessel transform and the HEALPIX angular pixelisation scheme. We test the 3D wavelet transform and as a toy-application, apply a denoising algorithm in wavelet space to the Virgo large box cosmological simulations and find we can successfully remove noise without much loss to the large scale structure. Results: We have described a new spherical 3D isotropic wavelet transform, ideally suited to analyse and denoise future 3D spherical cosmological surveys, which uses a novel DSFBT. We illustrate its potential use for denoising using a toy model. All the algorithms presented in this paper are available for download as a public code called MRS3D at http://jstarck.free.fr/mrs3d.html

  2. Ag Nanoparticle-Grafted PAN-Nanohump Array Films with 3D High-Density Hot Spots as Flexible and Reliable SERS Substrates.

    PubMed

    Li, Zhongbo; Meng, Guowen; Huang, Qing; Hu, Xiaoye; He, Xuan; Tang, Haibin; Wang, Zhiwei; Li, Fadi

    2015-10-28

    A facile fabrication approach of large-scale flexible films is reported, with one surface side consisting of Ag-nanoparticle (Ag-NP) decorated polyacrylonitrile (PAN) nanohump (denoted as Ag-NPs@PAN-nanohump) arrays. This is achieved via molding PAN films with ordered nanohump arrays on one side and then sputtering much smaller Ag-NPs onto each of the PAN-nanohumps. Surface-enhanced Raman scattering (SERS) activity of the Ag-NPs@PAN-nanohump array films can be improved by curving the flexible PAN film with ordered nanohump arrays during the Ag-sputtering process to increase the density of the Ag-NPs on the sidewalls of the PAN-nanohumps. More 3D hot spots are thus achieved on a large-scale. The Ag-NPs@PAN-nanohump array films show high SERS activity with good Raman signal reproducibility for Rhodamine 6G probe molecules. To trial their practical application, the Ag-NPs@PAN-nanohump array films are employed as SERS substrates for trace detection of trinitrotoluene and a congener of polychlorinated biphenyls. A lower detection limit of 10(-12) m and 10(-5) m can be achieved, respectively. Furthermore, the flexible Ag-NPs@PAN-nanohump array films can also be utilized as swabs to probe traces of methyl parathion on the surface of fruits such as apples. The as-fabricated SERS substrates therefore have promising potential for applications in rapid safety inspection and environmental protection.

  3. Numerical Solution of 3D Poisson-Nernst-Planck Equations Coupled with Classical Density Functional Theory for Modeling Ion and Electron Transport in a Confined Environment

    SciTech Connect

    Meng, Da; Zheng, Bin; Lin, Guang; Sushko, Maria L.

    2014-08-29

    We have developed efficient numerical algorithms for the solution of 3D steady-state Poisson-Nernst-Planck equations (PNP) with excess chemical potentials described by the classical density functional theory (cDFT). The coupled PNP equations are discretized by finite difference scheme and solved iteratively by Gummel method with relaxation. The Nernst-Planck equations are transformed into Laplace equations through the Slotboom transformation. Algebraic multigrid method is then applied to efficiently solve the Poisson equation and the transformed Nernst-Planck equations. A novel strategy for calculating excess chemical potentials through fast Fourier transforms is proposed which reduces computational complexity from O(N2) to O(NlogN) where N is the number of grid points. Integrals involving Dirac delta function are evaluated directly by coordinate transformation which yields more accurate result compared to applying numerical quadrature to an approximated delta function. Numerical results for ion and electron transport in solid electrolyte for Li ion batteries are shown to be in good agreement with the experimental data and the results from previous studies.

  4. 3D pharmacophore-based virtual screening, docking and density functional theory approach towards the discovery of novel human epidermal growth factor receptor-2 (HER2) inhibitors.

    PubMed

    Gogoi, Dhrubajyoti; Baruah, Vishwa Jyoti; Chaliha, Amrita Kashyap; Kakoti, Bibhuti Bhushan; Sarma, Diganta; Buragohain, Alak Kumar

    2016-12-21

    Human epidermal growth factor receptor 2 (HER2) is one of the four members of the epidermal growth factor receptor (EGFR) family and is expressed to facilitate cellular proliferation across various tissue types. Therapies targeting HER2, which is a transmembrane glycoprotein with tyrosine kinase activity, offer promising prospects especially in breast and gastric/gastroesophageal cancer patients. Persistence of both primary and acquired resistance to various routine drugs/antibodies is a disappointing outcome in the treatment of many HER2 positive cancer patients and is a challenge that requires formulation of new and improved strategies to overcome the same. Identification of novel HER2 inhibitors with improved therapeutics index was performed with a highly correlating (r=0.975) ligand-based pharmacophore model (Hypo1) in this study. Hypo1 was generated from a training set of 22 compounds with HER2 inhibitory activity and this well-validated hypothesis was subsequently used as a 3D query to screen compounds in a total of four databases of which two were natural product databases. Further, these compounds were analyzed for compliance with Veber's drug-likeness rule and optimum ADMET parameters. The selected compounds were then subjected to molecular docking and Density Functional Theory (DFT) analysis to discern their molecular interactions at the active site of HER2. The findings thus presented would be an important starting point towards the development of novel HER2 inhibitors using well-validated computational techniques.

  5. Heat map visualization of high-density clinical chemistry data.

    PubMed

    Auman, J Todd; Boorman, Gary A; Wilson, Ralph E; Travlos, Gregory S; Paules, Richard S

    2007-10-22

    Clinical chemistry data are routinely generated as part of preclinical animal toxicity studies and human clinical studies. With large-scale studies involving hundreds or even thousands of samples in multiple treatment groups, it is currently difficult to interpret the resulting complex, high-density clinical chemistry data. Accordingly, we conducted this study to investigate methods for easy visualization of complex, high-density data. Clinical chemistry data were obtained from male rats each treated with one of eight different acute hepatotoxicants from a large-scale toxicogenomics study. The raw data underwent a Z-score transformation comparing each individual animal's clinical chemistry values to that of reference controls from all eight studies and then were visualized in a single graphic using a heat map. The utility of using a heat map to visualize high-density clinical chemistry data was explored by clustering changes in clinical chemistry values for >400 animals. A clear distinction was observed in animals displaying hepatotoxicity from those that did not. Additionally, while animals experiencing hepatotoxicity showed many similarities in the observed clinical chemistry alterations, distinct differences were noted in the heat map profile for the different compounds. Using a heat map to visualize complex, high-density clinical chemistry data in a single graphic facilitates the identification of previously unrecognized trends. This method is simple to implement and maintains the biological integrity of the data. The value of this clinical chemistry data transformation and visualization will manifest itself through integration with other high-density data, such as genomics data, to study physiology at the systems level.

  6. A high-density genetic map and growth related QTL mapping in bighead carp (Hypophthalmichthys nobilis)

    PubMed Central

    Fu, Beide; Liu, Haiyang; Yu, Xiaomu; Tong, Jingou

    2016-01-01

    Growth related traits in fish are controlled by quantitative trait loci (QTL), but no QTL for growth have been detected in bighead carp (Hypophthalmichthys nobilis) due to the lack of high-density genetic map. In this study, an ultra-high density genetic map was constructed with 3,121 SNP markers by sequencing 117 individuals in a F1 family using 2b-RAD technology. The total length of the map was 2341.27 cM, with an average marker interval of 0.75 cM. A high level of genomic synteny between our map and zebrafish was detected. Based on this genetic map, one genome-wide significant and 37 suggestive QTL for five growth-related traits were identified in 6 linkage groups (i.e. LG3, LG11, LG15, LG18, LG19, LG22). The phenotypic variance explained (PVE) by these QTL varied from 15.4% to 38.2%. Marker within the significant QTL region was surrounded by CRP1 and CRP2, which played an important role in muscle cell division. These high-density map and QTL information provided a solid base for QTL fine mapping and comparative genomics in bighead carp. PMID:27345016

  7. Gap Opening in 3D: Single-planet Gaps

    NASA Astrophysics Data System (ADS)

    Fung, Jeffrey; Chiang, Eugene

    2016-12-01

    Giant planets can clear deep gaps when embedded in 2D (razor-thin) viscous circumstellar disks. We show by direct simulation that giant planets are just as capable of carving out gaps in 3D. Surface density maps are similar between 2D and 3D, even in detail. In particular, the scaling {{{Σ }}}{gap}\\propto {q}-2 of gap surface density with planet mass, derived from a global “zero-dimensional” balance of Lindblad and viscous torques, applies equally well to results obtained at higher dimensions. Our 3D simulations reveal extensive, near-sonic, meridional flows both inside and outside the gaps; these large-scale circulations might bear on disk compositional gradients, in dust or other chemical species. At high planet mass, gap edges are mildly Rayleigh unstable and intermittently shed streams of material into the gap—less so in 3D than in 2D.

  8. Selective mapping: a strategy for optimizing the construction of high-density linkage maps.

    PubMed Central

    Vision, T J; Brown, D G; Shmoys, D B; Durrett, R T; Tanksley, S D

    2000-01-01

    Historically, linkage mapping populations have consisted of large, randomly selected samples of progeny from a given pedigree or cell lines from a panel of radiation hybrids. We demonstrate that, to construct a map with high genome-wide marker density, it is neither necessary nor desirable to genotype all markers in every individual of a large mapping population. Instead, a reduced sample of individuals bearing complementary recombinational or radiation-induced breakpoints may be selected for genotyping subsequent markers from a large, but sparsely genotyped, mapping population. Choosing such a sample can be reduced to a discrete stochastic optimization problem for which the goal is a sample with breakpoints spaced evenly throughout the genome. We have developed several different methods for selecting such samples and have evaluated their performance on simulated and actual mapping populations, including the Lister and Dean Arabidopsis thaliana recombinant inbred population and the GeneBridge 4 human radiation hybrid panel. Our methods quickly and consistently find much-reduced samples with map resolution approaching that of the larger populations from which they are derived. This approach, which we have termed selective mapping, can facilitate the production of high-quality, high-density genome-wide linkage maps. PMID:10790413

  9. Density equalizing map projections (cartograms) in public health applications

    SciTech Connect

    Merrill, D.W.

    1998-05-01

    In studying geographic disease distributions, one normally compares rates among arbitrarily defined geographic subareas (e.g. census tracts), thereby sacrificing some of the geographic detail of the original data. The sparser the data, the larger the subareas must be in order to calculate stable rates. This dilemma is avoided with the technique of Density Equalizing Map Projections (DEMP){copyright}. Boundaries of geographic subregions are adjusted to equalize population density over the entire study area. Case locations plotted on the transformed map should have a uniform distribution if the underlying disease risk is constant. On the transformed map, the statistical analysis of the observed distribution is greatly simplified. Even for sparse distributions, the statistical significance of a supposed disease cluster can be calculated with validity. The DEMP algorithm was applied to a data set previously analyzed with conventional techniques; namely, 401 childhood cancer cases in four counties of California. The distribution of cases on the transformed map was analyzed visually and statistically. To check the validity of the method, the identical analysis was performed on 401 artificial cases randomly generated under the assumption of uniform risk. No statistically significant evidence for geographic non-uniformity of rates was found, in agreement with the original analysis performed by the California Department of Health Services.

  10. FINDMOL: automated identification of macromolecules in electron-density maps.

    PubMed

    McKee, E W; Kanbi, L D; Childs, K L; Grosse-Kunstleve, R W; Adams, P D; Sacchettini, J C; Ioerger, T R

    2005-11-01

    Automating the determination of novel macromolecular structures via X-ray crystallographic methods involves building a model into an electron-density map. Unfortunately, the conventional crystallographic asymmetric unit volumes are usually not well matched to the biological molecular units. In most cases, the facets of the asymmetric unit cut the molecules into a number of disconnected fragments, rendering interpretation b