Visualization Tools (visualization + tool)

Distribution by Scientific Domains

Selected Abstracts

Magnetic Resonance Microscopy Defines Ethanol-Induced Brain Abnormalities in Prenatal Mice: Effects of Acute Insult on Gestational Day 8

ALCOHOLISM, Issue 6 2009
Scott E. Parnell
Background:, Magnetic resonance microscopy (MRM), magnetic resonance imaging (MRI) at microscopic levels, provides unprecedented opportunities to aid in defining the full spectrum of ethanol's insult to the developing brain. This is the first in a series of reports that, collectively, will provide an MRM-based atlas of developmental stage-dependent structural brain abnormalities in a Fetal Alcohol Spectrum Disorders (FASD) mouse model. The ethanol exposure time and developmental stage examined for this report is gestational day (GD) 8 in mice, when the embryos are at early neurulation stages; stages present in humans early in the fourth week postfertilization. Methods:, For this study, pregnant C57Bl/6J mice were administered an ethanol dosage of 2.8 g/kg intraperitoneally at 8 days, 0 hour and again at 8 days, 4 hours postfertilization. On GD 17, fetuses that were selected for MRM analyses were immersion fixed in a Bouin's/Prohance® solution. Control fetuses from vehicle-treated dams were stage-matched to those that were ethanol-exposed. The fetal mice were scanned ex vivo at 7.0 T and 512 × 512 × 1024 image arrays were acquired using 3-D spin warp encoding. The resulting 29 ,m (isotropic) resolution images were processed using ITK-SNAP, a 3-D segmentation/visualization tool. Linear and volume measurements were determined for selected brain, head, and body regions of each specimen. Comparisons were made between control and treated fetuses, with an emphasis on determining (dis)proportionate changes in specific brain regions. Results:, As compared with controls, the crown-rump lengths of stage-matched ethanol-exposed GD 17 fetuses were significantly reduced, as were brain and whole body volumes. Volume reductions were notable in every brain region examined, with the exception of the pituitary and septal region, and were accompanied by increased ventricular volumes. Disproportionate regional brain volume reductions were most marked on the right side and were significant for the olfactory bulb, hippocampus, and cerebellum; the latter being the most severely affected. Additionally, the septal region and the pituitary were disproportionately large. Linear measures were consistent with those of volume. Other dysmorphologic features noted in the MR scans were choanal stenosis and optic nerve coloboma. Conclusions:, This study demonstrates that exposure to ethanol occurring in mice at stages corresponding to the human fourth week postfertilization results in structural brain abnormalities that are readily identifiable at fetal stages of development. In addition to illustrating the utility of MR microscopy for analysis of an FASD mouse model, this work provides new information that confirms and extends human clinical observations. It also provides a framework for comparison of structural brain abnormalities resulting from ethanol exposure at other developmental stages and dosages. [source]

A web-based tool for teaching neural network concepts

Aybars Ugur
Abstract Although neural networks (NN) are important especially for engineers, scientists, mathematicians and statisticians, they may also be hard to understand. In this article, application areas of NN are discussed, basic NN components are described and it is explained how an NN work. A web-based simulation and visualization tool (EasyLearnNN) is developed using Java and Java 2D for teaching NN concepts. Perceptron, ADALINE, Multilayer Perceptron, LVQ and SOM models and related training algorithms are implemented. As a result, comparison with other teaching methods of NN concepts is presented and discussed. © 2009 Wiley Periodicals, Inc. Comput Appl Eng Educ 18: 449,457, 2010; View this article online at; DOI 10.1002/cae.20184 [source]

A framework for performance analysis of Co-Array Fortran

Bernd Mohr
Abstract Co-Array Fortran (CAF) is a parallel programming extension to Fortran that provides a straightforward mechanism for representing distributed memory communication and, in particular, one-sided communication. Although this integration of communication primitives with the language improves programmer productivity, this new level of abstraction makes the analysis of CAF performance mode difficult. This situation is due, in part, to a lack of tools for the analysis of CAF applications. In this paper, we present an extension to the KOJAK toolkit based on a source-to-source translator that supports performance instrumentation, data collection, trace generation, and performance visualization of CAF applications. We illustrate this approach with a performance visualization of a CAF version of the Halo kernel benchmark using the VAMPIR event trace visualization tool. Copyright © 2007 John Wiley & Sons, Ltd. [source]

SCALEA: a performance analysis tool for parallel programs

Hong-Linh Truong
Abstract Many existing performance analysis tools lack the flexibility to control instrumentation and performance measurement for code regions and performance metrics of interest. Performance analysis is commonly restricted to single experiments. In this paper we present SCALEA, which is a performance instrumentation, measurement, analysis, and visualization tool for parallel programs that supports post-mortem performance analysis. SCALEA currently focuses on performance analysis for OpenMP, MPI, HPF, and mixed parallel programs. It computes a variety of performance metrics based on a novel classification of overhead. SCALEA also supports multi-experiment performance analysis that allows one to compare and to evaluate the performance outcome of several experiments. A highly flexible instrumentation and measurement system is provided which can be controlled by command-line options and program directives. SCALEA can be interfaced by external tools through the provision of a full Fortran90 OpenMP/MPI/HPF frontend that allows one to instrument an abstract syntax tree at a very high-level with C-function calls and to generate source code. A graphical user interface is provided to view a large variety of performance metrics at the level of arbitrary code regions, threads, processes, and computational nodes for single- and multi-experiment performance analysis. Copyright © 2003 John Wiley & Sons, Ltd. [source]

MaSK: A visualization tool for teaching and research in computational chemistry

Yevgeniy Podolyan
Abstract The number of researchers using computational chemistry tools is growing every year. There are multiple programs used for calculation of various molecular and electronic properties such as optimized geometry, energy, vibrational spectra, and so forth. Another set of programs is used for the visualization of these properties. However, such programs are either too complex for a beginner or too simple for an intermediate user for everyday use. Molecular Modeling and Simulation Kit (MaSK) is designed to fill this gap by presenting an easy-to-use intuitive interface to quantum chemical programs such as GAMESS and Gaussian with an array of advanced tools. The program can be used as a postprocessor to visualize calculated properties or as a preprocessor to prepare the input files for quantum chemical programs. In addition, some properties such as the surfaces of molecular orbitals, electron and spin densities, and molecular electrostatic potentials are actually calculated by MaSK. If MaSK is combined with PC GAMESS, the preparation of the input, running of the calculations, and the display of the results can all be done without leaving the program's interface. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source]

Mercury CSD 2.0, new features for the visualization and investigation of crystal structures

Clare F. Macrae
The program Mercury, developed by the Cambridge Crystallographic Data Centre, is designed primarily as a crystal structure visualization tool. A new module of functionality has been produced, called the Materials Module, which allows highly customizable searching of structural databases for intermolecular interaction motifs and packing patterns. This new module also includes the ability to perform packing similarity calculations between structures containing the same compound. In addition to the Materials Module, a range of further enhancements to Mercury has been added in this latest release, including void visualization and links to ConQuest, Mogul and IsoStar. [source]

Interactive visualization of quantum-chemistry data

Yun Jang
Simulation and computation in chemistry studies have improved as computational power has increased over recent decades. Many types of chemistry simulation results are available, from atomic level bonding to volumetric representations of electron density. However, tools for the visualization of the results from quantum-chemistry computations are still limited to showing atomic bonds and isosurfaces or isocontours corresponding to certain isovalues. In this work, we study the volumetric representations of the results from quantum-chemistry computations, and evaluate and visualize the representations directly on a modern graphics processing unit without resampling the result in grid structures. Our visualization tool handles the direct evaluation of the approximated wavefunctions described as a combination of Gaussian-like primitive basis functions. For visualizations, we use a slice-based volume-rendering technique with a two-dimensional transfer function, volume clipping and illustrative rendering in order to reveal and enhance the quantum-chemistry structure. Since there is no need to resample the volume from the functional representations for the volume rendering, two issues, data transfer and resampling resolution, can be ignored; therefore, it is possible to explore interactively a large amount of different information in the computation results. [source]

Computed tomography virtual intravascular endoscopy in the evaluation of fenestrated stent graft repair of abdominal aortic aneurysms

Zhonghua Sun
Abstract Background:, This study aimed to investigate the diagnostic value of computed tomography virtual intravascular endoscopy (VIE) in the follow-up of patients with abdominal aortic aneurysm (AAA) treated with fenestrated stent grafts. Methods:, A total of 19 patients (17 males and 2 females; mean age: 75 years) with AAA undergoing fenestrated stent grafts were retrospectively studied. Pre- and post-fenestration computed tomography data were reconstructed for the generation of VIE images of aortic ostia and fenestrated stents and compared with two-dimensional axial and multiplanar reformation (MPR) images. Serum creatinine was measured pre and post fenestration to evaluate the renal function. Results:, The mean intra-aortic length measured by VIE, two-dimensional axial and MPR were 4.7, 4.4 and 4.6 mm, respectively, for the right renal stent; 5.0, 4.9 and 5.0 mm, respectively, for the left renal stent; and 5.9, 6.0 and 6.0 mm, respectively, for the superior mesenteric artery stent. Comparisons of these measurements did not show significant difference (P > 0.05). The mean diameters of renal artery ostia measured on VIE visualization pre and post fenestration were 9.2 × 8.3 and 10 × 8.9 mm for the right renal ostium; 8.3 × 7.1 and 9.9 × 8.9 mm for the left renal ostium, with significant changes observed (P < 0.01). No renal dysfunction was observed in this group. Conclusion:, VIE is a valuable visualization tool in the follow-up of fenestrated stent graft repair of AAA by providing intraluminal appearance of fenestrated stents and measuring the length of stent protrusion. [source]

A molecular viewer for the analysis of TLS rigid-body motion in macromolecules

Jay Painter
TLS (translation/libration/screw) models describe rigid-body vibrational motions of arbitrary objects. A single-group TLS model can be used to approximate the vibration of an entire protein molecule within a crystal lattice. More complex TLS models are broadly applicable to describing inter-domain and other internal vibrational modes of proteins. Such models can be derived and refined from crystallographic data, but they can also be used to describe the vibrational modes observed through other physical techniques or derived from molecular dynamics. The use of TLS models for protein motion has been relatively limited, partly because the physical meaning of the refined TLS parameters is not intuitive. Here, a molecular viewer, TLSView, is introduced using OpenGL and based on the mmLib library for describing and manipulating macromolecular structural models. This visualization tool allows an intuitive understanding of the physical significance of TLS models derived from crystallographic or other data and may be used as an interactive tool to display and interpret inter-domain or other motions in protein structural models. TLSView may also be used to prepare, analyze and validate TLS models for crystallographic refinement. [source]

A Time Model for Time-Varying Visualization

M. Wolter
I.3.6 [Computer Graphics]: Methodology and Techniques; I.6.6 [Simulation and Modelling]: Simulation Output Analysis Abstract The analysis of unsteady phenomena is an important topic for scientific visualization. Several time-dependent visualization techniques exist, as well as solutions for dealing with the enormous size of time-varying data in interactive visualization. Many current visualization toolkits support displaying time-varying data sets. However, for the interactive exploration of time-varying data in scientific visualization, no common time model that describes the temporal properties which occur in the visualization process has been established. In this work, we propose a general time model which classifies the time frames of simulation phenomena and the connections between different time scales in the analysis process. This model is designed for intuitive interaction with time in visualization applications for the domain expert as well as for the developer of visualization tools. We demonstrate the benefits of our model by applying it to two use cases with different temporal properties. [source]

Adaptive Zooming in Web Cartography

Alesandro Cecconi
Abstract Beyond any doubt much of the current web mapping and web GIS applications lack cartographic quality. Thereasons aren't only the technical limitations related to Internet delivery, but also the neglect of one of the maincartographic principles of digital mapping, namely adaptive zooming. Adaptive zooming describes the adjustmentof a map, its contents and the symbolization to target scale in consequence of a zooming operation. The approachdescribed in this paper proposes the combination of two commonly known concepts: on the one hand levelsof detail (LoD) for those object classes, that require high computational cost for the automated generalizationprocess (e.g. buildings, road network); on the other hand an on-the-fly generalization for those object classeswhich can be generalized by less complex methods and algorithms (e.g. rivers, lakes). Realizing such interactiveand dynamic concept for web mapping requires the use of vector based visualization tools. The data format bestmeeting the criteria is the W3C standard Scalable Vector Graphics (SVG). Thus, it has been used to implementthe presented ideas in a prototype application for topographic web mapping based on the landscape modelVECTOR25 of the Swiss Federal Office of Topography. [source]

High-throughput powder diffraction.


Powder pattern matching techniques, using all the experimentally measured data points, coupled with cluster analysis, fuzzy clustering and multivariate statistical methods are used, with appropriate visualization tools, to analyse a set of 27 powder diffraction patterns of alumina collected at seven different laboratories on different instruments as part of an International Center for Diffraction Data Grant-in-Aid program. In their original form, the data factor into six distinct clusters. However, when a non-linear shift of the form (where a0 and a1 are refinable constants) is applied to optimize the correlations between patterns, clustering produces a large 25-pattern set with two outliers. The first outlier is a synchrotron data set at a different wavelength from the other data, and the second is distinguished by the absence of K,2 lines, i.e. it uses Ge-monochromated incident X-rays. Fuzzy clustering, in which samples may belong to more than one cluster, is introduced as a complementary method of pinpointing problematic diffraction patterns. In contrast to the usual methodology associated with the analysis of round-robin data, this process is carried out in a routine way, with minimal user interaction or supervision, using the PolySNAP software. [source]

Phylogeographic information systems: putting the geography into phylogeography

David M. Kidd
Abstract Phylogeography is concerned with the observation, description and analysis of the spatial distribution of genotypes and the inference of historical scenarios. In the past, the discipline has concentrated on the historical ,phylo- ' component through the utilization of phylogenetic analyses. In contrast, the spatial , -geographic' component is not a prominent feature of many existing phylogenetic approaches and has often been dealt with in a relatively naive fashion. Recently, there has been a resurgence of interest in the importance of geography in evolutionary biology. Thus, we believe that it is time to assess how geographic information is currently handled and incorporated into phylogeographical analysis. Geographical information systems (GISs) are computer systems that facilitate the integration and interrelation of different geographically referenced data sets; however, so far they have been little utilized by the phylogeographical community to manage, analyse and disseminate phylogeographical data. However, the growth in individual studies and the resurgence of interest in the geographical components of genetic pattern and biodiversity should stimulate further uptake. Some advantages of GIS are the integration of disparate data sets via georeferencing, dynamic data base design and update, visualization tools and data mining. An important step in linking GIS to existing phylogeographical and historical biogeographical analysis software and the dissemination of spatial phylogenies will be the establishment of ,GeoPhylo' data standards. We hope that this paper will further stimulate the resurgence of geography as an equal partner in the symbiosis that is phylogeography as well as advertise some benefits that can be obtained from the application of GIS practices and technologies. [source]

Generation and visualization of large-scale three-dimensional reconstructions from underwater robotic surveys

Matthew Johnson-Roberson
Robust, scalable simultaneous localization and mapping (SLAM) algorithms support the successful deployment of robots in real-world applications. In many cases these platforms deliver vast amounts of sensor data from large-scale, unstructured environments. These data may be difficult to interpret by end users without further processing and suitable visualization tools. We present a robust, automated system for large-scale three-dimensional (3D) reconstruction and visualization that takes stereo imagery from an autonomous underwater vehicle (AUV) and SLAM-based vehicle poses to deliver detailed 3D models of the seafloor in the form of textured polygonal meshes. Our system must cope with thousands of images, lighting conditions that create visual seams when texturing, and possible inconsistencies between stereo meshes arising from errors in calibration, triangulation, and navigation. Our approach breaks down the problem into manageable stages by first estimating local structure and then combining these estimates to recover a composite georeferenced structure using SLAM-based vehicle pose estimates. A texture-mapped surface at multiple scales is then generated that is interactively presented to the user through a visualization engine. We adapt established solutions when possible, with an emphasis on quickly delivering approximate yet visually consistent reconstructions on standard computing hardware. This allows scientists on a research cruise to use our system to design follow-up deployments of the AUV and complementary instruments. To date, this system has been tested on several research cruises in Australian waters and has been used to reliably generate and visualize reconstructions for more than 60 dives covering diverse habitats and representing hundreds of linear kilometers of survey. © 2009 Wiley Periodicals, Inc. [source]

Enhancing students' understanding of the concept of chemical bonding by using activities provided on an interactive website

Marcel Frailich
Abstract This study investigated the effectiveness of a web-based learning environment in enhancing 10th grade high-school students' understanding of the concept of chemical bonding. Two groups participated in this study: an experimental group (N,=,161) and a comparison one (N,=,93). The teachers in the experimental group were asked to implement four activities taken from a website, all dealing with the concept of chemical bonding. Computer-based visual models are utilized in all the activities in order to demonstrate bonding and the structure of matter, and are based on student-centered learning. The study incorporated both quantitative and qualitative research. The quantitative research consisted of achievement questionnaires administered to both the experimental and comparison groups. In contrast, the qualitative research included observations and interviews of students and teachers. Importantly, we found that the experimental group outperformed the comparison group significantly, in the achievement post-test, which examines students' understanding of the concept of chemical bonding. These results led us to conclude that the web-based learning activities which integrated visualization tools with active and cooperative learning strategies provided students with opportunities to construct their knowledge regarding the concept of chemical bonding. © 2008 Wiley Periodicals, Inc. J Res Sci Teach 46: 289,310, 2009 [source]

Disorderly reasoning in information design

Peter Hall
The importance of information visualization as a means of transforming data into visual, understandable form is now embraced across university campuses and research institutes world-wide. Yet, the role of designers in this field of activity is often overlooked by the dominant scientific and technological interests in data visualization, and a corporate culture reliant on off-the-shelf visualization tools. This article is an attempt to describe the value of design thinking in information visualization with reference to Horst Rittel's (1988) definition of "disorderly reasoning," and to frame design as a critical act of translating between scientific, technical, and aesthetic interests. [source]

From proteomics to systems biology of bacterial pathogens: Approaches, tools, and applications

Uwe Plikat Dr.
Abstract The hallmark of a systems biology approach is the integration of computational tools with experimental data encompassing multiple classes of biomolecules across different functional levels. Equally important as the availability of reasonably comprehensive information at the gene, protein, and metabolite levels is the development of adequate analysis and visualization tools to reduce the inherent complexity to interpretable dimensions. In this paper, we describe the integration of a 2-D gel-based proteome map of Staphylococcus aureus Mu50 with genomic and transcriptomic information through a customized data integration and user interface built on the Ensembl genome browser. We illustrate its application and potential through the analysis of a defined system perturbation caused by a mutation in the formyltransferase gene. We envision that this software package, which we called Insieme, can support the development of novel antibiotics by allowing a systems-based view of the bacterial response pathways. [source]

Strategic management of intangible assets and value drivers in R&D organizations

R & D MANAGEMENT, Issue 2 2005
Stephen Pike
This paper takes a resource-based view of the R&D process. Based on the literature, we forward a theory that allows us to predict the dynamic interaction and transformation of five key resources, namely human, relational, organizational, monetary, and physical. Utilizing visualization tools allows us to test this theory on various levels in order to draw insights from the data. The output of the analysis improves the strategic understanding of an organization. In particular, it improves the understanding of how intangible resources drive the value creation in an R&D organization. Further analysis of the data allows us to identify resources that are either under utilized or over utilized, which might indicate inefficiencies in the organizational performance. [source]

Using computers to teach biochemistry

Joyce P. Whitehead
Abstract This paper describes a symposium entitled "Using Computers to Teach Biochemistry," which was presented at the fall, 2001 National Meeting of the American Chemical Society in Chicago, IL. The use of computers has increased in all areas of chemical education; however, the visualization capabilities needed to convey some aspects of biochemistry are quite complex, so the upward trend in the use of computers for this purpose has been especially significant. The various speakers in this symposium discussed the use of a wide range of instructional technologies, including presentation software, Chime, online data exercises, interactive visualization tools, self-designed tutorial programs, and bioinformatics. [source]