BROCCOLI: Software for fast fMRI analysis on many-core CPUs and GPUs

PubMed Central

Eklund, Anders; Dufort, Paul; Villani, Mattias; LaConte, Stephen

2014-01-01

Analysis of functional magnetic resonance imaging (fMRI) data is becoming ever more computationally demanding as temporal and spatial resolutions improve, and large, publicly available data sets proliferate. Moreover, methodological improvements in the neuroimaging pipeline, such as non-linear spatial normalization, non-parametric permutation tests and Bayesian Markov Chain Monte Carlo approaches, can dramatically increase the computational burden. Despite these challenges, there do not yet exist any fMRI software packages which leverage inexpensive and powerful graphics processing units (GPUs) to perform these analyses. Here, we therefore present BROCCOLI, a free software package written in OpenCL (Open Computing Language) that can be used for parallel analysis of fMRI data on a large variety of hardware configurations. BROCCOLI has, for example, been tested with an Intel CPU, an Nvidia GPU, and an AMD GPU. These tests show that parallel processing of fMRI data can lead to significantly faster analysis pipelines. This speedup can be achieved on relatively standard hardware, but further, dramatic speed improvements require only a modest investment in GPU hardware. BROCCOLI (running on a GPU) can perform non-linear spatial normalization to a 1 mm3 brain template in 4–6 s, and run a second level permutation test with 10,000 permutations in about a minute. These non-parametric tests are generally more robust than their parametric counterparts, and can also enable more sophisticated analyses by estimating complicated null distributions. Additionally, BROCCOLI includes support for Bayesian first-level fMRI analysis using a Gibbs sampler. The new software is freely available under GNU GPL3 and can be downloaded from github (https://github.com/wanderine/BROCCOLI/). PMID:24672471

Software for analysis of chemical mixtures--composition, occurrence, distribution, and possible toxicity

USGS Publications Warehouse

Scott, Jonathon C.; Skach, Kenneth A.; Toccalino, Patricia L.

2013-01-01

The composition, occurrence, distribution, and possible toxicity of chemical mixtures in the environment are research concerns of the U.S. Geological Survey and others. The presence of specific chemical mixtures may serve as indicators of natural phenomena or human-caused events. Chemical mixtures may also have ecological, industrial, geochemical, or toxicological effects. Chemical-mixture occurrences vary by analyte composition and concentration. Four related computer programs have been developed by the National Water-Quality Assessment Program of the U.S. Geological Survey for research of chemical-mixture compositions, occurrences, distributions, and possible toxicities. The compositions and occurrences are identified for the user-supplied data, and therefore the resultant counts are constrained by the user’s choices for the selection of chemicals, reporting limits for the analytical methods, spatial coverage, and time span for the data supplied. The distribution of chemical mixtures may be spatial, temporal, and (or) related to some other variable, such as chemical usage. Possible toxicities optionally are estimated from user-supplied benchmark data. The software for the analysis of chemical mixtures described in this report is designed to work with chemical-analysis data files retrieved from the U.S. Geological Survey National Water Information System but can also be used with appropriately formatted data from other sources. Installation and usage of the mixture software are documented. This mixture software was designed to function with minimal changes on a variety of computer-operating systems. To obtain the software described herein and other U.S. Geological Survey software, visit http://water.usgs.gov/software/.

Application of GIS Rapid Mapping Technology in Disaster Monitoring

NASA Astrophysics Data System (ADS)

Wang, Z.; Tu, J.; Liu, G.; Zhao, Q.

2018-04-01

With the rapid development of GIS and RS technology, especially in recent years, GIS technology and its software functions have been increasingly mature and enhanced. And with the rapid development of mathematical statistical tools for spatial modeling and simulation, has promoted the widespread application and popularization of quantization in the field of geology. Based on the investigation of field disaster and the construction of spatial database, this paper uses remote sensing image, DEM and GIS technology to obtain the data information of disaster vulnerability analysis, and makes use of the information model to carry out disaster risk assessment mapping.Using ArcGIS software and its spatial data modeling method, the basic data information of the disaster risk mapping process was acquired and processed, and the spatial data simulation tool was used to map the disaster rapidly.

Stackfile Database

NASA Technical Reports Server (NTRS)

deVarvalho, Robert; Desai, Shailen D.; Haines, Bruce J.; Kruizinga, Gerhard L.; Gilmer, Christopher

2013-01-01

This software provides storage retrieval and analysis functionality for managing satellite altimetry data. It improves the efficiency and analysis capabilities of existing database software with improved flexibility and documentation. It offers flexibility in the type of data that can be stored. There is efficient retrieval either across the spatial domain or the time domain. Built-in analysis tools are provided for frequently performed altimetry tasks. This software package is used for storing and manipulating satellite measurement data. It was developed with a focus on handling the requirements of repeat-track altimetry missions such as Topex and Jason. It was, however, designed to work with a wide variety of satellite measurement data [e.g., Gravity Recovery And Climate Experiment -- GRACE). The software consists of several command-line tools for importing, retrieving, and analyzing satellite measurement data.

Integrating Spatial Components into FIA Models of Forest Resources: Some Technical Aspects

Treesearch

Pat Terletzky; Tracey Frescino

2005-01-01

We examined two software packages to determine their feasibility of implementing spatially explicit, forest resource models that integrate Forest Inventory and Analysis data (FIA). ARCINFO and Interactive Data Language (IDL) were examined for their input requirements, speed of processing, storage requirements, and flexibility of implementing. Implementations of two...

Where and Why There? Spatial Thinking with Geographic Information Systems

ERIC Educational Resources Information Center

Milson, Andrew J.; Curtis, Mary D.

2009-01-01

The authors developed and implemented a project for high school geography students that modeled the processes in a site selection analysis using Geographic Information Systems (GIS). They sought to explore how spatial thinking could be fostered by using the MyWorld GIS software that was designed specifically for educational uses. The task posed…

Integration of GIS and Bim for Indoor Geovisual Analytics

NASA Astrophysics Data System (ADS)

Wu, B.; Zhang, S.

2016-06-01

This paper presents an endeavour of integration of GIS (Geographical Information System) and BIM (Building Information Modelling) for indoor geovisual analytics. The merits of two types of technologies, GIS and BIM are firstly analysed in the context of indoor environment. GIS has well-developed capabilities of spatial analysis such as network analysis, while BIM has the advantages for indoor 3D modelling and dynamic simulation. This paper firstly investigates the important aspects for integrating GIS and BIM. Different data standards and formats such as the IFC (Industry Foundation Classes) and GML (Geography Markup Language) are discussed. Their merits and limitations in data transformation between GIS and BIM are analysed in terms of semantic and geometric information. An optimized approach for data exchange between GIS and BIM datasets is then proposed. After that, a strategy of using BIM for 3D indoor modelling, GIS for spatial analysis, and BIM again for visualization and dynamic simulation of the analysis results is presented. Based on the developments, this paper selects a typical problem, optimized indoor emergency evacuation, to demonstrate the integration of GIS and BIM for indoor geovisual analytics. The block Z of the Hong Kong Polytechnic University is selected as a test site. Detailed indoor and outdoor 3D models of the block Z are created using a BIM software Revit. The 3D models are transferred to a GIS software ArcGIS to carry out spatial analysis. Optimized evacuation plans considering dynamic constraints are generated based on network analysis in ArcGIS assuming there is a fire accident inside the building. The analysis results are then transferred back to BIM software for visualization and dynamic simulation. The developed methods and results are of significance to facilitate future development of GIS and BIM integrated solutions in various applications.

Spatial Paradigm for Information Retrieval and Exploration

DOE Office of Scientific and Technical Information (OSTI.GOV)

The SPIRE system consists of software for visual analysis of primarily text based information sources. This technology enables the content analysis of text documents without reading all the documents. It employs several algorithms for text and word proximity analysis. It identifies the key themes within the text documents. From this analysis, it projects the results onto a visual spatial proximity display (Galaxies or Themescape) where items (documents and/or themes) visually close to each other are known to have content which is close to each other. Innovative interaction techniques then allow for dynamic visual analysis of large text based information spaces.

SPIRE1.03. Spatial Paradigm for Information Retrieval and Exploration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adams, K.J.; Bohn, S.; Crow, V.

The SPIRE system consists of software for visual analysis of primarily text based information sources. This technology enables the content analysis of text documents without reading all the documents. It employs several algorithms for text and word proximity analysis. It identifies the key themes within the text documents. From this analysis, it projects the results onto a visual spatial proximity display (Galaxies or Themescape) where items (documents and/or themes) visually close to each other are known to have content which is close to each other. Innovative interaction techniques then allow for dynamic visual analysis of large text based information spaces.

A novel control software that improves the experimental workflow of scanning photostimulation experiments.

PubMed

Bendels, Michael H K; Beed, Prateep; Leibold, Christian; Schmitz, Dietmar; Johenning, Friedrich W

2008-10-30

Optical uncaging of caged compounds is a well-established method to study the functional anatomy of a brain region on the circuit level. We present an alternative approach to existing experimental setups. Using a low-magnification objective we acquire images for planning the spatial patterns of stimulation. Then high-magnification objectives are used during laser stimulation providing a laser spot between 2 microm and 20 microm size. The core of this system is a video-based control software that monitors and controls the connected devices, allows for planning of the experiment, coordinates the stimulation process and manages automatic data storage. This combines a high-resolution analysis of neuronal circuits with flexible and efficient online planning and execution of a grid of spatial stimulation patterns on a larger scale. The software offers special optical features that enable the system to achieve a maximum degree of spatial reliability. The hardware is mainly built upon standard laboratory devices and thus ideally suited to cost-effectively complement existing electrophysiological setups with a minimal amount of additional equipment. Finally, we demonstrate the performance of the system by mapping the excitatory and inhibitory connections of entorhinal cortex layer II stellate neurons and present an approach for the analysis of photo-induced synaptic responses in high spontaneous activity.

A study on spatial decision support systems for HIV/AIDS prevention based on COM GIS technology

NASA Astrophysics Data System (ADS)

Yang, Kun; Luo, Huasong; Peng, Shungyun; Xu, Quanli

2007-06-01

Based on the deeply analysis of the current status and the existing problems of GIS technology applications in Epidemiology, this paper has proposed the method and process for establishing the spatial decision support systems of AIDS epidemic prevention by integrating the COM GIS, Spatial Database, GPS, Remote Sensing, and Communication technologies, as well as ASP and ActiveX software development technologies. One of the most important issues for constructing the spatial decision support systems of AIDS epidemic prevention is how to integrate the AIDS spreading models with GIS. The capabilities of GIS applications in the AIDS epidemic prevention have been described here in this paper firstly. Then some mature epidemic spreading models have also been discussed for extracting the computation parameters. Furthermore, a technical schema has been proposed for integrating the AIDS spreading models with GIS and relevant geospatial technologies, in which the GIS and model running platforms share a common spatial database and the computing results can be spatially visualized on Desktop or Web GIS clients. Finally, a complete solution for establishing the decision support systems of AIDS epidemic prevention has been offered in this paper based on the model integrating methods and ESRI COM GIS software packages. The general decision support systems are composed of data acquisition sub-systems, network communication sub-systems, model integrating sub-systems, AIDS epidemic information spatial database sub-systems, AIDS epidemic information querying and statistical analysis sub-systems, AIDS epidemic dynamic surveillance sub-systems, AIDS epidemic information spatial analysis and decision support sub-systems, as well as AIDS epidemic information publishing sub-systems based on Web GIS.

Spatial problem-solving strategies of middle school students: Wayfinding with geographic information systems

NASA Astrophysics Data System (ADS)

Wigglesworth, John C.

2000-06-01

Geographic Information Systems (GIS) is a powerful computer software package that emphasizes the use of maps and the management of spatially referenced environmental data archived in a systems data base. Professional applications of GIS have been in place since the 1980's, but only recently has GIS gained significant attention in the K--12 classroom. Students using GIS are able to manipulate and query data in order to solve all manners of spatial problems. Very few studies have examined how this technological innovation can support classroom learning. In particular, there has been little research on how experience in using the software correlates with a child's spatial cognition and his/her ability to understand spatial relationships. This study investigates the strategies used by middle school students to solve a wayfinding (route-finding) problem using the ArcView GIS software. The research design combined an individual background questionnaire, results from the Group Assessment of Logical Thinking (GALT) test, and analysis of reflective think-aloud sessions to define the characteristics of the strategies students' used to solve this particular class of spatial problem. Three uniquely different spatial problem solving strategies were identified. Visual/Concrete Wayfinders used a highly visual strategy; Logical/Abstract Wayfinders used GIS software tools to apply a more analytical and systematic approach; Transitional Wayfinders used an approach that showed evidence of one that was shifting from a visual strategy to one that was more analytical. The triangulation of data sources indicates that this progression of wayfinding strategy can be correlated both to Piagetian stages of logical thought and to experience with the use of maps. These findings suggest that GIS teachers must be aware that their students' performance will lie on a continuum that is based on cognitive development, spatial ability, and prior experience with maps. To be most effective, GIS teaching strategies and curriculum development should also represent a progression that correlates to the learners' current skills and experience.

Fractals and Spatial Methods for Mining Remote Sensing Imagery

NASA Technical Reports Server (NTRS)

Lam, Nina; Emerson, Charles; Quattrochi, Dale

2003-01-01

The rapid increase in digital remote sensing and GIS data raises a critical problem -- how can such an enormous amount of data be handled and analyzed so that useful information can be derived quickly? Efficient handling and analysis of large spatial data sets is central to environmental research, particularly in global change studies that employ time series. Advances in large-scale environmental monitoring and modeling require not only high-quality data, but also reliable tools to analyze the various types of data. A major difficulty facing geographers and environmental scientists in environmental assessment and monitoring is that spatial analytical tools are not easily accessible. Although many spatial techniques have been described recently in the literature, they are typically presented in an analytical form and are difficult to transform to a numerical algorithm. Moreover, these spatial techniques are not necessarily designed for remote sensing and GIS applications, and research must be conducted to examine their applicability and effectiveness in different types of environmental applications. This poses a chicken-and-egg problem: on one hand we need more research to examine the usability of the newer techniques and tools, yet on the other hand, this type of research is difficult to conduct if the tools to be explored are not accessible. Another problem that is fundamental to environmental research are issues related to spatial scale. The scale issue is especially acute in the context of global change studies because of the need to integrate remote-sensing and other spatial data that are collected at different scales and resolutions. Extrapolation of results across broad spatial scales remains the most difficult problem in global environmental research. There is a need for basic characterization of the effects of scale on image data, and the techniques used to measure these effects must be developed and implemented to allow for a multiple scale assessment of the data before any useful process-oriented modeling involving scale-dependent data can be conducted. Through the support of research grants from NASA, we have developed a software module called ICAMS (Image Characterization And Modeling System) to address the need to develop innovative spatial techniques and make them available to the broader scientific communities. ICAMS provides new spatial techniques, such as fractal analysis, geostatistical functions, and multiscale analysis that are not easily available in commercial GIS/image processing software. By bundling newer spatial methods in a user-friendly software module, researchers can begin to test and experiment with the new spatial analysis methods and they can gauge scale effects using a variety of remote sensing imagery. In the following, we describe briefly the development of ICAMS and present application examples.

GIS Methodic and New Database for Magmatic Rocks. Application for Atlantic Oceanic Magmatism.

NASA Astrophysics Data System (ADS)

Asavin, A. M.

2001-12-01

There are several geochemical Databases in INTERNET available now. There one of the main peculiarities of stored geochemical information is geographical coordinates of each samples in those Databases. As rule the software of this Database use spatial information only for users interface search procedures. In the other side, GIS-software (Geographical Information System software),for example ARC/INFO software which using for creation and analyzing special geological, geochemical and geophysical e-map, have been deeply involved with geographical coordinates for of samples. We join peculiarities GIS systems and relational geochemical Database from special software. Our geochemical information system created in Vernadsky Geological State Museum and institute of Geochemistry and Analytical Chemistry from Moscow. Now we tested system with data of geochemistry oceanic rock from Atlantic and Pacific oceans, about 10000 chemical analysis. GIS information content consist from e-map covers Wold Globes. Parts of these maps are Atlantic ocean covers gravica map (with grid 2''), oceanic bottom hot stream, altimeteric maps, seismic activity, tectonic map and geological map. Combination of this information content makes possible created new geochemical maps and combination of spatial analysis and numerical geochemical modeling of volcanic process in ocean segment. Now we tested information system on thick client technology. Interface between GIS system Arc/View and Database resides in special multiply SQL-queries sequence. The result of the above gueries were simple DBF-file with geographical coordinates. This file act at the instant of creation geochemical and other special e-map from oceanic region. We used more complex method for geophysical data. From ARC\\View we created grid cover for polygon spatial geophysical information.

The Spectral Image Processing System (SIPS): Software for integrated analysis of AVIRIS data

NASA Technical Reports Server (NTRS)

Kruse, F. A.; Lefkoff, A. B.; Boardman, J. W.; Heidebrecht, K. B.; Shapiro, A. T.; Barloon, P. J.; Goetz, A. F. H.

1992-01-01

The Spectral Image Processing System (SIPS) is a software package developed by the Center for the Study of Earth from Space (CSES) at the University of Colorado, Boulder, in response to a perceived need to provide integrated tools for analysis of imaging spectrometer data both spectrally and spatially. SIPS was specifically designed to deal with data from the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) and the High Resolution Imaging Spectrometer (HIRIS), but was tested with other datasets including the Geophysical and Environmental Research Imaging Spectrometer (GERIS), GEOSCAN images, and Landsat TM. SIPS was developed using the 'Interactive Data Language' (IDL). It takes advantage of high speed disk access and fast processors running under the UNIX operating system to provide rapid analysis of entire imaging spectrometer datasets. SIPS allows analysis of single or multiple imaging spectrometer data segments at full spatial and spectral resolution. It also allows visualization and interactive analysis of image cubes derived from quantitative analysis procedures such as absorption band characterization and spectral unmixing. SIPS consists of three modules: SIPS Utilities, SIPS_View, and SIPS Analysis. SIPS version 1.1 is described below.

Army technology development. IBIS query. Software to support the Image Based Information System (IBIS) expansion for mapping, charting and geodesy

NASA Technical Reports Server (NTRS)

Friedman, S. Z.; Walker, R. E.; Aitken, R. B.

1986-01-01

The Image Based Information System (IBIS) has been under development at the Jet Propulsion Laboratory (JPL) since 1975. It is a collection of more than 90 programs that enable processing of image, graphical, tabular data for spatial analysis. IBIS can be utilized to create comprehensive geographic data bases. From these data, an analyst can study various attributes describing characteristics of a given study area. Even complex combinations of disparate data types can be synthesized to obtain a new perspective on spatial phenomena. In 1984, new query software was developed enabling direct Boolean queries of IBIS data bases through the submission of easily understood expressions. An improved syntax methodology, a data dictionary, and display software simplified the analysts' tasks associated with building, executing, and subsequently displaying the results of a query. The primary purpose of this report is to describe the features and capabilities of the new query software. A secondary purpose of this report is to compare this new query software to the query software developed previously (Friedman, 1982). With respect to this topic, the relative merits and drawbacks of both approaches are covered.

Assessment of the spatial pattern of colorectal tumour perfusion estimated at perfusion CT using two-dimensional fractal analysis.

PubMed

Goh, Vicky; Sanghera, Bal; Wellsted, David M; Sundin, Josefin; Halligan, Steve

2009-06-01

The aim was to evaluate the feasibility of fractal analysis for assessing the spatial pattern of colorectal tumour perfusion at dynamic contrast-enhanced CT (perfusion CT). Twenty patients with colorectal adenocarcinoma underwent a 65-s perfusion CT study from which a perfusion parametric map was generated using validated commercial software. The tumour was identified by an experienced radiologist, segmented via thresholding and fractal analysis applied using in-house software: fractal dimension, abundance and lacunarity were assessed for the entire outlined tumour and for selected representative areas within the tumour of low and high perfusion. Comparison was made with ten patients with normal colons, processed in a similar manner, using two-way mixed analysis of variance with statistical significance at the 5% level. Fractal values were higher in cancer than normal colon (p < or = 0.001): mean (SD) 1.71 (0.07) versus 1.61 (0.07) for fractal dimension and 7.82 (0.62) and 6.89 (0.47) for fractal abundance. Fractal values were lower in 'high' than 'low' perfusion areas. Lacunarity curves were shifted to the right for cancer compared with normal colon. In conclusion, colorectal cancer mapped by perfusion CT demonstrates fractal properties. Fractal analysis is feasible, potentially providing a quantitative measure of the spatial pattern of tumour perfusion.

Spatial and temporal analysis of DIII-D 3D magnetic diagnostic data

DOE PAGES

Strait, E. J.; King, J. D.; Hanson, J. M.; ...

2016-08-11

An extensive set of magnetic diagnostics in DIII-D is aimed at measuring non-axisymmetric "3D" features of tokamak plasmas, with typical amplitudes ~10 -3 to 10 -5 of the total magnetic field. We describe hardware and software techniques used at DIII-D to condition the individual signals and analysis to estimate the spatial structure from an ensemble of discrete measurements. Lastly, applications of the analysis include detection of non-rotating MHD instabilities, plasma control, and validation of MHD stability and 3D equilibrium models.

Spatial information technologies for remote sensing today and tomorrow; Proceedings of the Ninth Pecora Symposium, Sioux Falls, SD, October 2-4, 1984

NASA Technical Reports Server (NTRS)

1984-01-01

Topics discussed at the symposium include hardware, geographic information system (GIS) implementation, processing remotely sensed data, spatial data structures, and NASA programs in remote sensing information systems. Attention is also given GIS applications, advanced techniques, artificial intelligence, graphics, spatial navigation, and classification. Papers are included on the design of computer software for geographic image processing, concepts for a global resource information system, algorithm development for spatial operators, and an application of expert systems technology to remotely sensed image analysis.

Potentials for Spatial Geometry Curriculum Development with Three-Dimensional Dynamic Geometry Software in Lower Secondary Mathematics

ERIC Educational Resources Information Center

Miyazaki, Mikio; Kimiho, Chino; Katoh, Ryuhei; Arai, Hitoshi; Ogihara, Fumihiro; Oguchi, Yuichi; Morozumi, Tatsuo; Kon, Mayuko; Komatsu, Kotaro

2012-01-01

Three-dimensional dynamic geometry software has the power to enhance students' learning of spatial geometry. The purpose of this research is to clarify what potential using three-dimensional dynamic geometry software can offer us in terms of how to develop the spatial geometry curriculum in lower secondary schools. By focusing on the impacts the…

A Modular GIS-Based Software Architecture for Model Parameter Estimation using the Method of Anchored Distributions (MAD)

NASA Astrophysics Data System (ADS)

Ames, D. P.; Osorio-Murillo, C.; Over, M. W.; Rubin, Y.

2012-12-01

The Method of Anchored Distributions (MAD) is an inverse modeling technique that is well-suited for estimation of spatially varying parameter fields using limited observations and Bayesian methods. This presentation will discuss the design, development, and testing of a free software implementation of the MAD technique using the open source DotSpatial geographic information system (GIS) framework, R statistical software, and the MODFLOW groundwater model. This new tool, dubbed MAD-GIS, is built using a modular architecture that supports the integration of external analytical tools and models for key computational processes including a forward model (e.g. MODFLOW, HYDRUS) and geostatistical analysis (e.g. R, GSLIB). The GIS-based graphical user interface provides a relatively simple way for new users of the technique to prepare the spatial domain, to identify observation and anchor points, to perform the MAD analysis using a selected forward model, and to view results. MAD-GIS uses the Managed Extensibility Framework (MEF) provided by the Microsoft .NET programming platform to support integration of different modeling and analytical tools at run-time through a custom "driver." Each driver establishes a connection with external programs through a programming interface, which provides the elements for communicating with core MAD software. This presentation gives an example of adapting the MODFLOW to serve as the external forward model in MAD-GIS for inferring the distribution functions of key MODFLOW parameters. Additional drivers for other models are being developed and it is expected that the open source nature of the project will engender the development of additional model drivers by 3rd party scientists.

GIS Tools For Improving Pedestrian & Bicycle Safety

DOT National Transportation Integrated Search

2000-07-01

Geographic Information System (GIS) software turns statistical data, such as accidents, and geographic data, such as roads and crash locations, into meaningful information for spatial analysis and mapping. In this project, GIS-based analytical techni...

Subband/Transform MATLAB Functions For Processing Images

NASA Technical Reports Server (NTRS)

Glover, D.

1995-01-01

SUBTRANS software is package of routines implementing image-data-processing functions for use with MATLAB*(TM) software. Provides capability to transform image data with block transforms and to produce spatial-frequency subbands of transformed data. Functions cascaded to provide further decomposition into more subbands. Also used in image-data-compression systems. For example, transforms used to prepare data for lossy compression. Written for use in MATLAB mathematical-analysis environment.

OpenMSI Arrayed Analysis Tools v2.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

BOWEN, BENJAMIN; RUEBEL, OLIVER; DE ROND, TRISTAN

2017-02-07

Mass spectrometry imaging (MSI) enables high-resolution spatial mapping of biomolecules in samples and is a valuable tool for the analysis of tissues from plants and animals, microbial interactions, high-throughput screening, drug metabolism, and a host of other applications. This is accomplished by desorbing molecules from the surface on spatially defined locations, using a laser or ion beam. These ions are analyzed by a mass spectrometry and collected into a MSI 'image', a dataset containing unique mass spectra from the sampled spatial locations. MSI is used in a diverse and increasing number of biological applications. The OpenMSI Arrayed Analysis Tool (OMAAT)more » is a new software method that addresses the challenges of analyzing spatially defined samples in large MSI datasets, by providing support for automatic sample position optimization and ion selection.« less

Recording and assessment of evoked potentials with electrode arrays.

PubMed

Miljković, N; Malešević, N; Kojić, V; Bijelić, G; Keller, T; Popović, D B

2015-09-01

In order to optimize procedure for the assessment of evoked potentials and to provide visualization of the flow of action potentials along the motor systems, we introduced array electrodes for stimulation and recording and developed software for the analysis of the recordings. The system uses a stimulator connected to an electrode array for the generation of evoked potentials, an electrode array connected to the amplifier, A/D converter and computer for the recording of evoked potentials, and a dedicated software application. The method has been tested for the assessment of the H-reflex on the triceps surae muscle in six healthy humans. The electrode array with 16 pads was positioned over the posterior aspect of the thigh, while the recording electrode array with 16 pads was positioned over the triceps surae muscle. The stimulator activated all the pads of the stimulation electrode array asynchronously, while the signals were recorded continuously at all the recording sites. The results are topography maps (spatial distribution of evoked potentials) and matrices (spatial visualization of nerve excitability). The software allows the automatic selection of the lowest stimulation intensity to achieve maximal H-reflex amplitude and selection of the recording/stimulation pads according to predefined criteria. The analysis of results shows that the method provides rich information compared with the conventional recording of the H-reflex with regard the spatial distribution.

An open source software for fast grid-based data-mining in spatial epidemiology (FGBASE).

PubMed

Baker, David M; Valleron, Alain-Jacques

2014-10-30

Examining whether disease cases are clustered in space is an important part of epidemiological research. Another important part of spatial epidemiology is testing whether patients suffering from a disease are more, or less, exposed to environmental factors of interest than adequately defined controls. Both approaches involve determining the number of cases and controls (or population at risk) in specific zones. For cluster searches, this often must be done for millions of different zones. Doing this by calculating distances can lead to very lengthy computations. In this work we discuss the computational advantages of geographical grid-based methods, and introduce an open source software (FGBASE) which we have created for this purpose. Geographical grids based on the Lambert Azimuthal Equal Area projection are well suited for spatial epidemiology because they preserve area: each cell of the grid has the same area. We describe how data is projected onto such a grid, as well as grid-based algorithms for spatial epidemiological data-mining. The software program (FGBASE), that we have developed, implements these grid-based methods. The grid based algorithms perform extremely fast. This is particularly the case for cluster searches. When applied to a cohort of French Type 1 Diabetes (T1D) patients, as an example, the grid based algorithms detected potential clusters in a few seconds on a modern laptop. This compares very favorably to an equivalent cluster search using distance calculations instead of a grid, which took over 4 hours on the same computer. In the case study we discovered 4 potential clusters of T1D cases near the cities of Le Havre, Dunkerque, Toulouse and Nantes. One example of environmental analysis with our software was to study whether a significant association could be found between distance to vineyards with heavy pesticide. None was found. In both examples, the software facilitates the rapid testing of hypotheses. Grid-based algorithms for mining spatial epidemiological data provide advantages in terms of computational complexity thus improving the speed of computations. We believe that these methods and this software tool (FGBASE) will lower the computational barriers to entry for those performing epidemiological research.

[Spatial distribution of occupational disease prevalence in Guangzhou and Foshan city by geographic information system].

PubMed

Tan, Q; Tu, H W; Gu, C H; Li, X D; Li, R Z; Wang, M; Chen, S G; Cheng, Y J; Liu, Y M

2017-11-20

Objective: To explore the occupational disease spatial distribution characteristics in Guangzhou and Foshan city in 2006-2013 with Geographic Information System and to provide evidence for making control strategy. Methods: The data on occupational disease diagnosis in Guangzhou and Foshan city from 2006 through 2013 were collected and linked to the digital map at administrative county level with Arc GIS12.0 software for spatial analysis. Results: The maps of occupational disease and Moran's spatial autocor-relation analysis showed that the spatial aggregation existed in Shunde and Nanhai region with Moran's index 1.727, -0.003. Local Moran's I spatial autocorrelation analysis pointed out the "positive high incidence re-gion" and the "negative high incidence region" during 2006~2013. Trend analysis showed that the diagnosis case increased slightly then declined from west to east, increase obviously from north to south, declined from? southwest to northeast, high in the middle and low on both sides in northwest-southeast direction. Conclusions: The occupational disease is obviously geographical distribution in Guangzhou and Foshan city. The corresponding prevention measures should be made according to the geographical distribution.

The GeoViz Toolkit: Using component-oriented coordination methods for geographic visualization and analysis

PubMed Central

Hardisty, Frank; Robinson, Anthony C.

2010-01-01

In this paper we present the GeoViz Toolkit, an open-source, internet-delivered program for geographic visualization and analysis that features a diverse set of software components which can be flexibly combined by users who do not have programming expertise. The design and architecture of the GeoViz Toolkit allows us to address three key research challenges in geovisualization: allowing end users to create their own geovisualization and analysis component set on-the-fly, integrating geovisualization methods with spatial analysis methods, and making geovisualization applications sharable between users. Each of these tasks necessitates a robust yet flexible approach to inter-tool coordination. The coordination strategy we developed for the GeoViz Toolkit, called Introspective Observer Coordination, leverages and combines key advances in software engineering from the last decade: automatic introspection of objects, software design patterns, and reflective invocation of methods. PMID:21731423

Using SaTScanTM spatial-scan software with national forest inventory data: a case study in South Carolina

Treesearch

KaDonna Randolph

2017-01-01

The USDA Forest Service Forest Inventory and Analysis (FIA) program makes and keeps current an inventory of all forest land in the United States. To comply with privacy laws while at the same time offering its data to the public, FIA makes approximate plot locations available through a process known as perturbing ("fuzzing") and swapping. The free spatial...

From fields to objects: A review of geographic boundary analysis

NASA Astrophysics Data System (ADS)

Jacquez, G. M.; Maruca, S.; Fortin, M.-J.

Geographic boundary analysis is a relatively new approach unfamiliar to many spatial analysts. It is best viewed as a technique for defining objects - geographic boundaries - on spatial fields, and for evaluating the statistical significance of characteristics of those boundary objects. This is accomplished using null spatial models representative of the spatial processes expected in the absence of boundary-generating phenomena. Close ties to the object-field dialectic eminently suit boundary analysis to GIS data. The majority of existing spatial methods are field-based in that they describe, estimate, or predict how attributes (variables defining the field) vary through geographic space. Such methods are appropriate for field representations but not object representations. As the object-field paradigm gains currency in geographic information science, appropriate techniques for the statistical analysis of objects are required. The methods reviewed in this paper are a promising foundation. Geographic boundary analysis is clearly a valuable addition to the spatial statistical toolbox. This paper presents the philosophy of, and motivations for geographic boundary analysis. It defines commonly used statistics for quantifying boundaries and their characteristics, as well as simulation procedures for evaluating their significance. We review applications of these techniques, with the objective of making this promising approach accessible to the GIS-spatial analysis community. We also describe the implementation of these methods within geographic boundary analysis software: GEM.

Open cyberGIS software for geospatial research and education in the big data era

NASA Astrophysics Data System (ADS)

Wang, Shaowen; Liu, Yan; Padmanabhan, Anand

CyberGIS represents an interdisciplinary field combining advanced cyberinfrastructure, geographic information science and systems (GIS), spatial analysis and modeling, and a number of geospatial domains to improve research productivity and enable scientific breakthroughs. It has emerged as new-generation GIS that enable unprecedented advances in data-driven knowledge discovery, visualization and visual analytics, and collaborative problem solving and decision-making. This paper describes three open software strategies-open access, source, and integration-to serve various research and education purposes of diverse geospatial communities. These strategies have been implemented in a leading-edge cyberGIS software environment through three corresponding software modalities: CyberGIS Gateway, Toolkit, and Middleware, and achieved broad and significant impacts.

Dynamic Analysis and Research on Environmental Pollution in China from 1992 to 2014

NASA Astrophysics Data System (ADS)

Sun, Fei; Yuan, Peng; Li, Huiting; Zhang, Moli

2018-01-01

The regular pattern of development of the environmental pollution events was analyzed from the perspective of statistical analysis of pollution events in recent years. The Moran, s I and spatial center-of-gravity shift curve of China, s environmental emergencies were calculated by ARCGIS software. And the method is global spatial analysis and spatial center of gravity shift. The results showed that the trend of China, s environmental pollution events from 1992 to 2014 was the first dynamic growth and then gradually reduced. Environmental pollution events showed spatial aggregation distribution in 1992-1994, 2001-2006, 2008-2014, and the rest of year was a random distribution of space. There were two stages in China, s environmental pollution events: The transition to the southwest from 1992 to 2006 and the transition to the northeast from the year of 2006 to 2014.

The deegree framework - Spatial Data Infrastructure solution for end-users and developers

NASA Astrophysics Data System (ADS)

Kiehle, Christian; Poth, Andreas

2010-05-01

The open source software framework deegree is a comprehensive implementa­tion of standards as defined by ISO and Open Geospatial Consortium (OGC). It has been developed with two goals in mind: provide a uniform framework for implementing Spatial Data Infrastructures (SDI) and adhering to standards as strictly as possible. Although being open source software (Lesser GNU Public Li­cense, LGPL), deegree has been developed with a business model in mind: providing the general building blocks of SDIs without license fees and offer cus­tomization, consulting and tailoring by specialized companies. The core of deegree is a comprehensive Java Application Programming Inter­face (API) offering access to spatial features, analysis, metadata and coordinate reference systems. As a library, deegree can and has been integrated as a core module inside spatial information systems. It is reference implementation for several OGC standards and based on an ISO 19107 geometry model. For end users, deegree is shipped as a web application providing easy-to-set-up components for web mapping and spatial analysis. Since 2000, deegree has been the backbone of many productive SDIs, first and foremost for governmental stakeholders (e.g. Federal Agency for Cartography and Geodesy in Germany, the Ministry of Housing, Spatial Planning and the En­vironment in the Netherlands, etc.) as well as for research and development projects as an early adoption of standards, drafts and discussion papers. Be­sides mature standards like Web Map Service, Web Feature Service and Cata­logue Services, deegree also implements rather new standards like the Sensor Observation Service, the Web Processing Service and the Web Coordinate Transformation Service (WCTS). While a robust background in standardization (knowledge and implementation) is a must for consultancy, standard-compliant services and encodings alone do not provide solutions for customers. The added value is comprised by a sophistic­ated set of client software, desktop and web environments. A focus lies on different client solutions for specific standards like the Web Pro­cessing Service and the Web Coordinate Transformation Service. On the other hand, complex geoportal solutions comprised of multiple standards and en­hanced by components for user management, security and map client function­ality show the demanding requirements of real world solutions. The XPlan-GML-standard as defined by the German spatial planing authorities is a good ex­ample of how complex real-world requirements can get. XPlan-GML is intended to provide a framework for digital spatial planning documents and requires complex Geography Markup Language (GML) features along with Symbology Encoding (SE), Filter Encoding (FE), Web Map Services (WMS), Web Feature Services (WFS). This complex in­frastructure should be used by urban and spatial planners and therefore re­quires a user-friendly graphical interface hiding the complexity of the underly­ing infrastructure. Based on challenges faced within customer projects, the importance of easy to use software components is focused. SDI solution should be build upon ISO/OGC-standards, but more important, should be user-friendly and support the users in spatial data management and analysis.

Earth-Science Data Co-Locating Tool

NASA Technical Reports Server (NTRS)

Lee, Seungwon; Pan, Lei; Block, Gary L.

2012-01-01

This software is used to locate Earth-science satellite data and climate-model analysis outputs in space and time. This enables the direct comparison of any set of data with different spatial and temporal resolutions. It is written in three separate modules that are clearly separated for their functionality and interface with other modules. This enables a fast development of supporting any new data set. In this updated version of the tool, several new front ends are developed for new products. This software finds co-locatable data pairs for given sets of data products and creates new data products that share the same spatial and temporal coordinates. This facilitates the direct comparison between the two heterogeneous datasets and the comprehensive and synergistic use of the datasets.

Program SPACECAP: software for estimating animal density using spatially explicit capture-recapture models

USGS Publications Warehouse

Gopalaswamy, Arjun M.; Royle, J. Andrew; Hines, James E.; Singh, Pallavi; Jathanna, Devcharan; Kumar, N. Samba; Karanth, K. Ullas

2012-01-01

1. The advent of spatially explicit capture-recapture models is changing the way ecologists analyse capture-recapture data. However, the advantages offered by these new models are not fully exploited because they can be difficult to implement. 2. To address this need, we developed a user-friendly software package, created within the R programming environment, called SPACECAP. This package implements Bayesian spatially explicit hierarchical models to analyse spatial capture-recapture data. 3. Given that a large number of field biologists prefer software with graphical user interfaces for analysing their data, SPACECAP is particularly useful as a tool to increase the adoption of Bayesian spatially explicit capture-recapture methods in practice.

GIS-Based System of Hydrologic and Hydraulic Applications for Highway Engineering

DOT National Transportation Integrated Search

1999-10-01

In this research project, a GIS has been developed to assist in the design of highway drainage facilities by utilizing hydrologic spatial data to calculate the input parameters for standard hydrologic software packages. This GIS reduces the analysis ...

MULTIMEDIA ENVIRONMENTAL DISTRIBUTION OF TOXICS (MEND-TOX): PART II, SOFTWARE IMPLEMENTATION AND CASE STUDIES

EPA Science Inventory

An integrated hybrid spatial-compartmental simulator is presented for analyzing the dynamic distribution of chemicals in the multimedia environment. Information obtained from such analysis, which includes temporal chemical concentration profiles in various media, mass distribu...

Is the spatial distribution of brain lesions associated with closed-head injury predictive of subsequent development of attention-deficit/hyperactivity disorder? Analysis with brain-image database

NASA Technical Reports Server (NTRS)

Herskovits, E. H.; Megalooikonomou, V.; Davatzikos, C.; Chen, A.; Bryan, R. N.; Gerring, J. P.

1999-01-01

PURPOSE: To determine whether there is an association between the spatial distribution of lesions detected at magnetic resonance (MR) imaging of the brain in children after closed-head injury and the development of secondary attention-deficit/hyperactivity disorder (ADHD). MATERIALS AND METHODS: Data obtained from 76 children without prior history of ADHD were analyzed. MR images were obtained 3 months after closed-head injury. After manual delineation of lesions, images were registered to the Talairach coordinate system. For each subject, registered images and secondary ADHD status were integrated into a brain-image database, which contains depiction (visualization) and statistical analysis software. Using this database, we assessed visually the spatial distributions of lesions and performed statistical analysis of image and clinical variables. RESULTS: Of the 76 children, 15 developed secondary ADHD. Depiction of the data suggested that children who developed secondary ADHD had more lesions in the right putamen than children who did not develop secondary ADHD; this impression was confirmed statistically. After Bonferroni correction, we could not demonstrate significant differences between secondary ADHD status and lesion burdens for the right caudate nucleus or the right globus pallidus. CONCLUSION: Closed-head injury-induced lesions in the right putamen in children are associated with subsequent development of secondary ADHD. Depiction software is useful in guiding statistical analysis of image data.

Spatial pattern recognition of seismic events in South West Colombia

NASA Astrophysics Data System (ADS)

Benítez, Hernán D.; Flórez, Juan F.; Duque, Diana P.; Benavides, Alberto; Lucía Baquero, Olga; Quintero, Jiber

2013-09-01

Recognition of seismogenic zones in geographical regions supports seismic hazard studies. This recognition is usually based on visual, qualitative and subjective analysis of data. Spatial pattern recognition provides a well founded means to obtain relevant information from large amounts of data. The purpose of this work is to identify and classify spatial patterns in instrumental data of the South West Colombian seismic database. In this research, clustering tendency analysis validates whether seismic database possesses a clustering structure. A non-supervised fuzzy clustering algorithm creates groups of seismic events. Given the sensitivity of fuzzy clustering algorithms to centroid initial positions, we proposed a methodology to initialize centroids that generates stable partitions with respect to centroid initialization. As a result of this work, a public software tool provides the user with the routines developed for clustering methodology. The analysis of the seismogenic zones obtained reveals meaningful spatial patterns in South-West Colombia. The clustering analysis provides a quantitative location and dispersion of seismogenic zones that facilitates seismological interpretations of seismic activities in South West Colombia.

Tissue-specific features of the X chromosome and nucleolus spatial dynamics in a malaria mosquito, Anopheles atroparvus

PubMed Central

Bondarenko, Semen M.; Artemov, Gleb N.; Stegniy, Vladimir N.

2017-01-01

Spatial organization of chromosome territories is important for maintenance of genomic stability and regulation of gene expression. Recent studies have shown tissue-specific features of chromosome attachments to the nuclear envelope in various organisms including malaria mosquitoes. However, other spatial characteristics of nucleus organization, like volume and shape of chromosome territories, have not been studied in Anopheles. We conducted a thorough analysis of tissue-specific features of the X chromosome and nucleolus volume and shape in follicular epithelium and nurse cells of the Anopheles atroparvus ovaries using a modern open-source software. DNA of the polytene X chromosome from ovarian nurse cells was obtained by microdissection and was used as a template for amplification with degenerate oligo primers. A fluorescently labeled X chromosome painting probe was hybridized with formaldehyde-fixed ovaries of mosquitoes using a 3D-FISH method. The nucleolus was stained by immunostaining with an anti-fibrillarin antibody. The analysis was conducted with TANGO—a software for a chromosome spatial organization analysis. We show that the volume and position of the X chromosome have tissue-specific characteristics. Unlike nurse cell nuclei, the growth of follicular epithelium nuclei is not accompanied with the proportional growth of the X chromosome. However, the shape of the X chromosome does not differ between the tissues. The dynamics of the X chromosome attachment regions location is tissue-specific and it is correlated with the process of nucleus growth in follicular epithelium and nurse cells. PMID:28158219

Tissue-specific features of the X chromosome and nucleolus spatial dynamics in a malaria mosquito, Anopheles atroparvus.

PubMed

Bondarenko, Semen M; Artemov, Gleb N; Sharakhov, Igor V; Stegniy, Vladimir N

2017-01-01

Spatial organization of chromosome territories is important for maintenance of genomic stability and regulation of gene expression. Recent studies have shown tissue-specific features of chromosome attachments to the nuclear envelope in various organisms including malaria mosquitoes. However, other spatial characteristics of nucleus organization, like volume and shape of chromosome territories, have not been studied in Anopheles. We conducted a thorough analysis of tissue-specific features of the X chromosome and nucleolus volume and shape in follicular epithelium and nurse cells of the Anopheles atroparvus ovaries using a modern open-source software. DNA of the polytene X chromosome from ovarian nurse cells was obtained by microdissection and was used as a template for amplification with degenerate oligo primers. A fluorescently labeled X chromosome painting probe was hybridized with formaldehyde-fixed ovaries of mosquitoes using a 3D-FISH method. The nucleolus was stained by immunostaining with an anti-fibrillarin antibody. The analysis was conducted with TANGO-a software for a chromosome spatial organization analysis. We show that the volume and position of the X chromosome have tissue-specific characteristics. Unlike nurse cell nuclei, the growth of follicular epithelium nuclei is not accompanied with the proportional growth of the X chromosome. However, the shape of the X chromosome does not differ between the tissues. The dynamics of the X chromosome attachment regions location is tissue-specific and it is correlated with the process of nucleus growth in follicular epithelium and nurse cells.

Aaron's Solution, Instructor's Problem: Teaching Surface Analysis Using GIS

ERIC Educational Resources Information Center

Koch, Tom; Denike, Ken

2007-01-01

Teaching GIS is relatively simple, a matter of helping students develop familiarity with the software. Mapping as an aid to thinking is harder to instruct. This article presents a laboratory and lecture package developed to teach the utility of mapping in a course on spatial data analysis. Following a historical review of the use of surface…

Students’ Spatial Ability through Open-Ended Approach Aided by Cabri 3D

NASA Astrophysics Data System (ADS)

Priatna, N.

2017-09-01

The use of computer software such as Cabri 3D for learning activities is very unlimited. Students can adjust their learning speed according to their level of ability. Open-ended approach strongly supports the use of computer software in learning, because the goal of open-ended learning is to help developing creative activities and mathematical mindset of students through problem solving simultaneously. In other words, creative activities and mathematical mindset of students should be developed as much as possible in accordance with the ability of spatial ability of each student. Spatial ability is the ability of students in constructing and representing geometry models. This study aims to determine the improvement of spatial ability of junior high school students who obtained learning with open-ended approach aided by Cabri 3D. It adopted a quasi-experimental method with the non-randomized control group pretest-posttest design and the 2×3 factorial model. The instrument of the study is spatial ability test. Based on analysis of the data, it is found that the improvement of spatial ability of students who received open-ended learning aided by Cabri 3D was greater than students who received expository learning, both as a whole and based on the categories of students’ initial mathematical ability.

Effects of Using Dynamic Mathematics Software on Preservice Mathematics Teachers' Spatial Visualization Skills: The Case of Spatial Analytic Geometry

ERIC Educational Resources Information Center

Kösa, Temel

2016-01-01

The purpose of this study was to investigate the effects of using dynamic geometry software on preservice mathematics teachers' spatial visualization skills and to determine whether spatial visualization skills can be a predictor of success in learning analytic geometry of space. The study used a quasi-experimental design with a control group.…

HydroDesktop as a Community Designed and Developed Resource for Hydrologic Data Discovery and Analysis

NASA Astrophysics Data System (ADS)

Ames, D. P.

2013-12-01

As has been seen in other informatics fields, well-documented and appropriately licensed open source software tools have the potential to significantly increase both opportunities and motivation for inter-institutional science and technology collaboration. The CUAHSI HIS (and related HydroShare) projects have aimed to foster such activities in hydrology resulting in the development of many useful community software components including the HydroDesktop software application. HydroDesktop is an open source, GIS-based, scriptable software application for discovering data on the CUAHSI Hydrologic Information System and related resources. It includes a well-defined plugin architecture and interface to allow 3rd party developers to create extensions and add new functionality without requiring recompiling of the full source code. HydroDesktop is built in the C# programming language and uses the open source DotSpatial GIS engine for spatial data management. Capabilities include data search, discovery, download, visualization, and export. An extension that integrates the R programming language with HydroDesktop provides scripting and data automation capabilities and an OpenMI plugin provides the ability to link models. Current revision and updates to HydroDesktop include migration of core business logic to cross platform, scriptable Python code modules that can be executed in any operating system or linked into other software front-end applications.

Simulation study on electric field intensity above train roof

NASA Astrophysics Data System (ADS)

Fan, Yizhe; Li, Huawei; Yang, Shasha

2018-04-01

In order to understand the distribution of electric field in the space above the train roof accurately and select the installation position of the detection device reasonably, in this paper, the 3D model of pantograph-catenary is established by using SolidWorks software, and the spatial electric field distribution of pantograph-catenary model is simulated based on Comsol software. According to the electric field intensity analysis within the 0.4m space above train roof, we give a reasonable installation of the detection device.

The pyramid system for multiscale raster analysis

USGS Publications Warehouse

De Cola, L.; Montagne, N.

1993-01-01

Geographical research requires the management and analysis of spatial data at multiple scales. As part of the U.S. Geological Survey's global change research program a software system has been developed that reads raster data (such as an image or digital elevation model) and produces a pyramid of aggregated lattices as well as various measurements of spatial complexity. For a given raster dataset the system uses the pyramid to report: (1) mean, (2) variance, (3) a spatial autocorrelation parameter based on multiscale analysis of variance, and (4) a monofractal scaling parameter based on the analysis of isoline lengths. The system is applied to 1-km digital elevation model (DEM) data for a 256-km2 region of central California, as well as to 64 partitions of the region. PYRAMID, which offers robust descriptions of data complexity, also is used to describe the behavior of topographic aspect with scale. ?? 1993.

The Effects of Computer-Aided Design Software on Engineering Students' Spatial Visualisation Skills

ERIC Educational Resources Information Center

Kösa, Temel; Karakus, Fatih

2018-01-01

The purpose of this study was to determine the influence of computer-aided design (CAD) software-based instruction on the spatial visualisation skills of freshman engineering students in a computer-aided engineering drawing course. A quasi-experimental design was applied, using the Purdue Spatial Visualization Test-Visualization of Rotations…

How Students Solve Problems in Spatial Geometry while Using a Software Application for Visualizing 3D Geometric Objects

ERIC Educational Resources Information Center

Widder, Mirela; Gorsky, Paul

2013-01-01

In schools, learning spatial geometry is usually dependent upon a student's ability to visualize three dimensional geometric configurations from two dimensional drawings. Such a process, however, often creates visual obstacles which are unique to spatial geometry. Useful software programs which realistically depict three dimensional geometric…

The design and implementation of urban earthquake disaster loss evaluation and emergency response decision support systems based on GIS

NASA Astrophysics Data System (ADS)

Yang, Kun; Xu, Quan-li; Peng, Shuang-yun; Cao, Yan-bo

2008-10-01

Based on the necessity analysis of GIS applications in earthquake disaster prevention, this paper has deeply discussed the spatial integration scheme of urban earthquake disaster loss evaluation models and visualization technologies by using the network development methods such as COM/DCOM, ActiveX and ASP, as well as the spatial database development methods such as OO4O and ArcSDE based on ArcGIS software packages. Meanwhile, according to Software Engineering principles, a solution of Urban Earthquake Emergency Response Decision Support Systems based on GIS technologies have also been proposed, which include the systems logical structures, the technical routes,the system realization methods and function structures etc. Finally, the testing systems user interfaces have also been offered in the paper.

Dynamic Hurricane Data Analysis Tool

NASA Technical Reports Server (NTRS)

Knosp, Brian W.; Li, Peggy; Vu, Quoc A.

2009-01-01

A dynamic hurricane data analysis tool allows users of the JPL Tropical Cyclone Information System (TCIS) to analyze data over a Web medium. The TCIS software is described in the previous article, Tropical Cyclone Information System (TCIS) (NPO-45748). This tool interfaces with the TCIS database to pull in data from several different atmospheric and oceanic data sets, both observed by instruments. Users can use this information to generate histograms, maps, and profile plots for specific storms. The tool also displays statistical values for the user-selected parameter for the mean, standard deviation, median, minimum, and maximum values. There is little wait time, allowing for fast data plots over date and spatial ranges. Users may also zoom-in for a closer look at a particular spatial range. This is version 1 of the software. Researchers will use the data and tools on the TCIS to understand hurricane processes, improve hurricane forecast models and identify what types of measurements the next generation of instruments will need to collect.

Integrated web system of geospatial data services for climate research

NASA Astrophysics Data System (ADS)

Okladnikov, Igor; Gordov, Evgeny; Titov, Alexander

2016-04-01

Georeferenced datasets are currently actively used for modeling, interpretation and forecasting of climatic and ecosystem changes on different spatial and temporal scales. Due to inherent heterogeneity of environmental datasets as well as their huge size (up to tens terabytes for a single dataset) a special software supporting studies in the climate and environmental change areas is required. An approach for integrated analysis of georefernced climatological data sets based on combination of web and GIS technologies in the framework of spatial data infrastructure paradigm is presented. According to this approach a dedicated data-processing web system for integrated analysis of heterogeneous georeferenced climatological and meteorological data is being developed. It is based on Open Geospatial Consortium (OGC) standards and involves many modern solutions such as object-oriented programming model, modular composition, and JavaScript libraries based on GeoExt library, ExtJS Framework and OpenLayers software. This work is supported by the Ministry of Education and Science of the Russian Federation, Agreement #14.613.21.0037.

Web-based access, aggregation, and visualization of future climate projections with emphasis on agricultural assessments

NASA Astrophysics Data System (ADS)

Villoria, Nelson B.; Elliott, Joshua; Müller, Christoph; Shin, Jaewoo; Zhao, Lan; Song, Carol

2018-01-01

Access to climate and spatial datasets by non-specialists is restricted by technical barriers involving hardware, software and data formats. We discuss an open-source online tool that facilitates downloading the climate data from the global circulation models used by the Inter-Sectoral Impacts Model Intercomparison Project. The tool also offers temporal and spatial aggregation capabilities for incorporating future climate scenarios in applications where spatial aggregation is important. We hope that streamlined access to these data facilitates analysis of climate related issues while considering the uncertainties derived from future climate projections and temporal aggregation choices.

Tularosa Basin Play Fairway Analysis Data and Models

DOE Data Explorer

Nash, Greg

2017-07-11

This submission includes raster datasets for each layer of evidence used for weights of evidence analysis as well as the deterministic play fairway analysis (PFA). Data representative of heat, permeability and groundwater comprises some of the raster datasets. Additionally, the final deterministic PFA model is provided along with a certainty model. All of these datasets are best used with an ArcGIS software package, specifically Spatial Data Modeler.

Geoinformatic subsystem for real estate market analysis). (Polish Title: Podsystem geoinformatyczny do analizy rynku nieruchomosci)

NASA Astrophysics Data System (ADS)

Basista, A.

2013-12-01

There are many tools to manage spatial data. They called Geographic Information System (GIS), which apart from data visualization in space, let users make various spatial analysis. Thanks to them, it is possible to obtain more, essential information for real estate market analysis. Many scientific research present GIS exploitation to future mass valuation, because it is necessary to use advanced tools to manage such a huge real estates' data sets gathered for mass valuation needs. In practice, appraisers use rarely these tools for single valuation, because there are not many available GIS tools to support real estate valuation. The paper presents the functionality of geoinformatic subsystem, that is used to support real estate market analysis and real estate valuation. There are showed a detailed description of the process relied to attributes' inputting into the database and the attributes' values calculation based on the proposed definition of attributes' scales. This work presents also the algorithm of similar properties selection that was implemented within the described subsystem. The main stage of this algorithm is the calculation of the price creative indicator for each real estate, using their attributes' values. The set of properties, chosen in this way, are visualized on the map. The geoinformatic subsystem is used for the un-built real estates and living premises. Geographic Information System software was used to worked out this project. The basic functionality of gvSIG software (open source software) was extended and some extra functions were added to support real estate market analysis.

Designing Spatial Visualisation Tasks for Middle School Students with a 3D Modelling Software: An Instrumental Approach

ERIC Educational Resources Information Center

Turgut, Melih; Uygan, Candas

2015-01-01

In this work, certain task designs to enhance middle school students' spatial visualisation ability, in the context of an instrumental approach, have been developed. 3D modelling software, SketchUp®, was used. In the design process, software tools were focused on and, thereafter, the aim was to interpret the instrumental genesis and spatial…

Ricardo Oliveira | NREL

Science.gov Websites

the System Modeling & Geospatial Data Science Group in the Strategic Energy Analysis Center. Areas Publications Oliveira, R and Moreno, R. 2016. Harvesting, Integrating and Distributing Large Open Geospatial Datasets Using Free and Open-Source Software. Int. Arch. Photogramm. Remote Sens. Spatial Inf. Sci., XLI-B7

ENVIRONMENTAL TECHNOLOGY VERIFICATION REPORT, ENVIRONMENTAL DECISION SUPPORT SOFTWARE, UNIVERSITY OF TENNESSEE RESEARCH CORPORATION, SPATIAL ANALYSIS AND DECISION ASSISTANCE (SADA)

EPA Science Inventory

The U.S. Environmental Protection Agency (EPA) has created the Environmental Technology Verification Program (ETV) to facilitate the deployment of innovative or improved environmental technologies through performance verification and dissemination of information. The goal of the...

Mirion--a software package for automatic processing of mass spectrometric images.

PubMed

Paschke, C; Leisner, A; Hester, A; Maass, K; Guenther, S; Bouschen, W; Spengler, B

2013-08-01

Mass spectrometric imaging (MSI) techniques are of growing interest for the Life Sciences. In recent years, the development of new instruments employing ion sources that are tailored for spatial scanning allowed the acquisition of large data sets. A subsequent data processing, however, is still a bottleneck in the analytical process, as a manual data interpretation is impossible within a reasonable time frame. The transformation of mass spectrometric data into spatial distribution images of detected compounds turned out to be the most appropriate method to visualize the results of such scans, as humans are able to interpret images faster and easier than plain numbers. Image generation, thus, is a time-consuming and complex yet very efficient task. The free software package "Mirion," presented in this paper, allows the handling and analysis of data sets acquired by mass spectrometry imaging. Mirion can be used for image processing of MSI data obtained from many different sources, as it uses the HUPO-PSI-based standard data format imzML, which is implemented in the proprietary software of most of the mass spectrometer companies. Different graphical representations of the recorded data are available. Furthermore, automatic calculation and overlay of mass spectrometric images promotes direct comparison of different analytes for data evaluation. The program also includes tools for image processing and image analysis.

Structure and information in spatial segregation

PubMed Central

2017-01-01

Ethnoracial residential segregation is a complex, multiscalar phenomenon with immense moral and economic costs. Modeling the structure and dynamics of segregation is a pressing problem for sociology and urban planning, but existing methods have limitations. In this paper, we develop a suite of methods, grounded in information theory, for studying the spatial structure of segregation. We first advance existing profile and decomposition methods by posing two related regionalization methods, which allow for profile curves with nonconstant spatial scale and decomposition analysis with nonarbitrary areal units. We then formulate a measure of local spatial scale, which may be used for both detailed, within-city analysis and intercity comparisons. These methods highlight detailed insights in the structure and dynamics of urban segregation that would be otherwise easy to miss or difficult to quantify. They are computationally efficient, applicable to a broad range of study questions, and freely available in open source software. PMID:29078323

Structure and information in spatial segregation.

PubMed

Chodrow, Philip S

2017-10-31

Ethnoracial residential segregation is a complex, multiscalar phenomenon with immense moral and economic costs. Modeling the structure and dynamics of segregation is a pressing problem for sociology and urban planning, but existing methods have limitations. In this paper, we develop a suite of methods, grounded in information theory, for studying the spatial structure of segregation. We first advance existing profile and decomposition methods by posing two related regionalization methods, which allow for profile curves with nonconstant spatial scale and decomposition analysis with nonarbitrary areal units. We then formulate a measure of local spatial scale, which may be used for both detailed, within-city analysis and intercity comparisons. These methods highlight detailed insights in the structure and dynamics of urban segregation that would be otherwise easy to miss or difficult to quantify. They are computationally efficient, applicable to a broad range of study questions, and freely available in open source software. Published under the PNAS license.

Spatial information and modeling system for transportation (SIMST) : final report.

DOT National Transportation Integrated Search

1992-06-01

This project was directed toward research in the development of spatial information systems for transportation. The project and all software development was done in the Intergraph MGE environment. One objective was to investigate software tools for l...

Architecture of the local spatial data infrastructure for regional climate change research

NASA Astrophysics Data System (ADS)

Titov, Alexander; Gordov, Evgeny

2013-04-01

Georeferenced datasets (meteorological databases, modeling and reanalysis results, etc.) are actively used in modeling and analysis of climate change for various spatial and temporal scales. Due to inherent heterogeneity of environmental datasets as well as their size which might constitute up to tens terabytes for a single dataset studies in the area of climate and environmental change require a special software support based on SDI approach. A dedicated architecture of the local spatial data infrastructure aiming at regional climate change analysis using modern web mapping technologies is presented. Geoportal is a key element of any SDI, allowing searching of geoinformation resources (datasets and services) using metadata catalogs, producing geospatial data selections by their parameters (data access functionality) as well as managing services and applications of cartographical visualization. It should be noted that due to objective reasons such as big dataset volume, complexity of data models used, syntactic and semantic differences of various datasets, the development of environmental geodata access, processing and visualization services turns out to be quite a complex task. Those circumstances were taken into account while developing architecture of the local spatial data infrastructure as a universal framework providing geodata services. So that, the architecture presented includes: 1. Effective in terms of search, access, retrieval and subsequent statistical processing, model of storing big sets of regional georeferenced data, allowing in particular to store frequently used values (like monthly and annual climate change indices, etc.), thus providing different temporal views of the datasets 2. General architecture of the corresponding software components handling geospatial datasets within the storage model 3. Metadata catalog describing in detail using ISO 19115 and CF-convention standards datasets used in climate researches as a basic element of the spatial data infrastructure as well as its publication according to OGC CSW (Catalog Service Web) specification 4. Computational and mapping web services to work with geospatial datasets based on OWS (OGC Web Services) standards: WMS, WFS, WPS 5. Geoportal as a key element of thematic regional spatial data infrastructure providing also software framework for dedicated web applications development To realize web mapping services Geoserver software is used since it provides natural WPS implementation as a separate software module. To provide geospatial metadata services GeoNetwork Opensource (http://geonetwork-opensource.org) product is planned to be used for it supports ISO 19115/ISO 19119/ISO 19139 metadata standards as well as ISO CSW 2.0 profile for both client and server. To implement thematic applications based on geospatial web services within the framework of local SDI geoportal the following open source software have been selected: 1. OpenLayers JavaScript library, providing basic web mapping functionality for the thin client such as web browser 2. GeoExt/ExtJS JavaScript libraries for building client-side web applications working with geodata services. The web interface developed will be similar to the interface of such popular desktop GIS applications, as uDIG, QuantumGIS etc. The work is partially supported by RF Ministry of Education and Science grant 8345, SB RAS Program VIII.80.2.1 and IP 131.

Spatial resolution measurements by Radia diagnostic software with SEDENTEXCT image quality phantom in cone beam CT for dental use.

PubMed

Watanabe, Hiroshi; Nomura, Yoshikazu; Kuribayashi, Ami; Kurabayashi, Tohru

2018-02-01

We aimed to employ the Radia diagnostic software with the safety and efficacy of a new emerging dental X-ray modality (SEDENTEXCT) image quality (IQ) phantom in CT, and to evaluate its validity. The SEDENTEXCT IQ phantom and Radia diagnostic software were employed. The phantom was scanned using one medical full-body CT and two dentomaxillofacial cone beam CTs. The obtained images were imported to the Radia software, and the spatial resolution outputs were evaluated. The oversampling method was employed using our original wire phantom as a reference. The resultant modulation transfer function (MTF) curves were compared. The null hypothesis was that MTF curves generated using both methods would be in agreement. One-way analysis of variance tests were applied to the f50 and f10 values from the MTF curves. The f10 values were subjectively confirmed by observing the line pair modules. The Radia software reported the MTF curves on the xy-plane of the CT scans, but could not return f50 and f10 values on the z-axis. The null hypothesis concerning the reported MTF curves on the xy-plane was rejected. There were significant differences between the results of the Radia software and our reference method, except for f10 values in CS9300. These findings were consistent with our line pair observations. We evaluated the validity of the Radia software with the SEDENTEXCT IQ phantom. The data provided were semi-automatic, albeit with problems and statistically different from our reference. We hope the manufacturer will overcome these limitations.

SpatialEpiApp: A Shiny web application for the analysis of spatial and spatio-temporal disease data.

PubMed

Moraga, Paula

2017-11-01

During last years, public health surveillance has been facilitated by the existence of several packages implementing statistical methods for the analysis of spatial and spatio-temporal disease data. However, these methods are still inaccesible for many researchers lacking the adequate programming skills to effectively use the required software. In this paper we present SpatialEpiApp, a Shiny web application that integrate two of the most common approaches in health surveillance: disease mapping and detection of clusters. SpatialEpiApp is easy to use and does not require any programming knowledge. Given information about the cases, population and optionally covariates for each of the areas and dates of study, the application allows to fit Bayesian models to obtain disease risk estimates and their uncertainty by using R-INLA, and to detect disease clusters by using SaTScan. The application allows user interaction and the creation of interactive data visualizations and reports showing the analyses performed. Copyright © 2017 Elsevier Ltd. All rights reserved.

AITSO: A Tool for Spatial Optimization Based on Artificial Immune Systems

PubMed Central

Zhao, Xiang; Liu, Yaolin; Liu, Dianfeng; Ma, Xiaoya

2015-01-01

A great challenge facing geocomputation and spatial analysis is spatial optimization, given that it involves various high-dimensional, nonlinear, and complicated relationships. Many efforts have been made with regard to this specific issue, and the strong ability of artificial immune system algorithms has been proven in previous studies. However, user-friendly professional software is still unavailable, which is a great impediment to the popularity of artificial immune systems. This paper describes a free, universal tool, named AITSO, which is capable of solving various optimization problems. It provides a series of standard application programming interfaces (APIs) which can (1) assist researchers in the development of their own problem-specific application plugins to solve practical problems and (2) allow the implementation of some advanced immune operators into the platform to improve the performance of an algorithm. As an integrated, flexible, and convenient tool, AITSO contributes to knowledge sharing and practical problem solving. It is therefore believed that it will advance the development and popularity of spatial optimization in geocomputation and spatial analysis. PMID:25678911

Descriptions of Free and Freeware Software in the Mathematics Teaching

NASA Astrophysics Data System (ADS)

Antunes de Macedo, Josue; Neves de Almeida, Samara; Voelzke, Marcos Rincon

2016-05-01

This paper presents the analysis and the cataloging of free and freeware mathematical software available on the internet, a brief explanation of them, and types of licenses for use in teaching and learning. The methodology is based on the qualitative research. Among the different types of software found, it stands out in algebra, the Winmat, that works with linear algebra, matrices and linear systems. In geometry, the GeoGebra, which can be used in the study of functions, plan and spatial geometry, algebra and calculus. For graphing, can quote the Graph and Graphequation. With Graphmatica software, it is possible to build various graphs of mathematical equations on the same screen, representing cartesian equations, inequalities, parametric among other functions. The Winplot allows the user to build graphics in two and three dimensions functions and mathematical equations. Thus, this work aims to present the teachers some free math software able to be used in the classroom.

The Analysis of the Patterns of Radiation-Induced DNA Damage Foci by a Stochastic Monte Carlo Model of DNA Double Strand Breaks Induction by Heavy Ions and Image Segmentation Software

NASA Technical Reports Server (NTRS)

Ponomarev, Artem; Cucinotta, F.

2011-01-01

To create a generalized mechanistic model of DNA damage in human cells that will generate analytical and image data corresponding to experimentally observed DNA damage foci and will help to improve the experimental foci yields by simulating spatial foci patterns and resolving problems with quantitative image analysis. Material and Methods: The analysis of patterns of RIFs (radiation-induced foci) produced by low- and high-LET (linear energy transfer) radiation was conducted by using a Monte Carlo model that combines the heavy ion track structure with characteristics of the human genome on the level of chromosomes. The foci patterns were also simulated in the maximum projection plane for flat nuclei. Some data analysis was done with the help of image segmentation software that identifies individual classes of RIFs and colocolized RIFs, which is of importance to some experimental assays that assign DNA damage a dual phosphorescent signal. Results: The model predicts the spatial and genomic distributions of DNA DSBs (double strand breaks) and associated RIFs in a human cell nucleus for a particular dose of either low- or high-LET radiation. We used the model to do analyses for different irradiation scenarios. In the beam-parallel-to-the-disk-of-a-flattened-nucleus scenario we found that the foci appeared to be merged due to their high density, while, in the perpendicular-beam scenario, the foci appeared as one bright spot per hit. The statistics and spatial distribution of regions of densely arranged foci, termed DNA foci chains, were predicted numerically using this model. Another analysis was done to evaluate the number of ion hits per nucleus, which were visible from streaks of closely located foci. In another analysis, our image segmentaiton software determined foci yields directly from images with single-class or colocolized foci. Conclusions: We showed that DSB clustering needs to be taken into account to determine the true DNA damage foci yield, which helps to determine the DSB yield. Using the model analysis, a researcher can refine the DSB yield per nucleus per particle. We showed that purely geometric artifacts, present in the experimental images, can be analytically resolved with the model, and that the quantization of track hits and DSB yields can be provided to the experimentalists who use enumeration of radiation-induced foci in immunofluorescence experiments using proteins that detect DNA damage. An automated image segmentaiton software can prove useful in a faster and more precise object counting for colocolized foci images.

Locating Chicago's Charter Schools: A Socio-Spatial Analysis

ERIC Educational Resources Information Center

LaFleur, Jennifer C.

2016-01-01

This project contributes to the body of research examining the implications of the geographic location of charter schools for student access, especially in high-poverty communities. Using geographic information systems (GIS) software, this paper uses data from the U.S. Census American Community Survey to identify the socioeconomic characteristics…

Morphological Spatial Pattern Analysis of the Conterminous US

EPA Science Inventory

Six data layers, all created using GUIDOS 1.3 MSPA software to identify green infrastructure components (e.g. core, edge, corridor, etc.). Water was treated three different ways: 1) as foreground, 2) as background, and 3) as missing using both NLCD 2001 and 2006 for six total lay...

Students Investigate Local Communities with Geographic Information Systems (GIS).

ERIC Educational Resources Information Center

Carlstrom, Dick; Quinlan, Laurie A.

1997-01-01

Describes the use of Geographic Information Systems (GIS) in elementary and secondary school classrooms to analyze neighborhoods, cities, and regions. Discusses GIS software, databases, graphing data, and spatial analysis, and includes an example of a project for secondary school students investigating the local economy for summer jobs. (LRW)

Atlas-Guided Segmentation of Vervet Monkey Brain MRI

PubMed Central

Fedorov, Andriy; Li, Xiaoxing; Pohl, Kilian M; Bouix, Sylvain; Styner, Martin; Addicott, Merideth; Wyatt, Chris; Daunais, James B; Wells, William M; Kikinis, Ron

2011-01-01

The vervet monkey is an important nonhuman primate model that allows the study of isolated environmental factors in a controlled environment. Analysis of monkey MRI often suffers from lower quality images compared with human MRI because clinical equipment is typically used to image the smaller monkey brain and higher spatial resolution is required. This, together with the anatomical differences of the monkey brains, complicates the use of neuroimage analysis pipelines tuned for human MRI analysis. In this paper we developed an open source image analysis framework based on the tools available within the 3D Slicer software to support a biological study that investigates the effect of chronic ethanol exposure on brain morphometry in a longitudinally followed population of male vervets. We first developed a computerized atlas of vervet monkey brain MRI, which was used to encode the typical appearance of the individual brain structures in MRI and their spatial distribution. The atlas was then used as a spatial prior during automatic segmentation to process two longitudinal scans per subject. Our evaluation confirms the consistency and reliability of the automatic segmentation. The comparison of atlas construction strategies reveals that the use of a population-specific atlas leads to improved accuracy of the segmentation for subcortical brain structures. The contribution of this work is twofold. First, we describe an image processing workflow specifically tuned towards the analysis of vervet MRI that consists solely of the open source software tools. Second, we develop a digital atlas of vervet monkey brain MRIs to enable similar studies that rely on the vervet model. PMID:22253661

Maximizing Accessibility to Spatially Referenced Digital Data.

ERIC Educational Resources Information Center

Hunt, Li; Joselyn, Mark

1995-01-01

Discusses some widely available spatially referenced datasets, including raster and vector datasets. Strategies for improving accessibility include: acquisition of data in a software-dependent format; reorganization of data into logical geographic units; acquisition of intelligent retrieval software; improving computer hardware; and intelligent…

Accelerating Pathology Image Data Cross-Comparison on CPU-GPU Hybrid Systems

PubMed Central

Wang, Kaibo; Huai, Yin; Lee, Rubao; Wang, Fusheng; Zhang, Xiaodong; Saltz, Joel H.

2012-01-01

As an important application of spatial databases in pathology imaging analysis, cross-comparing the spatial boundaries of a huge amount of segmented micro-anatomic objects demands extremely data- and compute-intensive operations, requiring high throughput at an affordable cost. However, the performance of spatial database systems has not been satisfactory since their implementations of spatial operations cannot fully utilize the power of modern parallel hardware. In this paper, we provide a customized software solution that exploits GPUs and multi-core CPUs to accelerate spatial cross-comparison in a cost-effective way. Our solution consists of an efficient GPU algorithm and a pipelined system framework with task migration support. Extensive experiments with real-world data sets demonstrate the effectiveness of our solution, which improves the performance of spatial cross-comparison by over 18 times compared with a parallelized spatial database approach. PMID:23355955

A Comparison of the Critical Thinking Skills and Spatial Ability of Fifth Grade Children Using Simulation Software or Logo.

ERIC Educational Resources Information Center

Vasu, Ellen Storey; Tyler, Doris Kennedy

1997-01-01

Examined the effects of using Logo or problem-solving oriented simulation software on the spatial and critical thinking skills of fifth graders. Found that the Logo group had a significant pretest-posttest change in spatial scores, and the Simulation group had a significant pretest-posttest change in critical thinking scores. No significant change…

Planetary Spatial Analyst

NASA Technical Reports Server (NTRS)

Keely, Leslie

2008-01-01

This is a status report for the project entitled Planetary Spatial Analyst (PSA). This report covers activities from the project inception on October 1, 2007 to June 1, 2008. Originally a three year proposal, PSA was awarded funding for one year and required a revised work statement and budget. At the time of this writing the project is well on track both for completion of work as well as budget. The revised project focused on two objectives: build a solid connection with the target community and implement a prototype software application that provides 3D visualization and spatial analysis technologies for that community. Progress has been made for both of these objectives.

Automating the evaluation of flood damages: methodology and potential gains

NASA Astrophysics Data System (ADS)

Eleutério, Julian; Martinez, Edgar Daniel

2010-05-01

The evaluation of flood damage potential consists of three main steps: assessing and processing data, combining data and calculating potential damages. The first step consists of modelling hazard and assessing vulnerability. In general, this step of the evaluation demands more time and investments than the others. The second step of the evaluation consists of combining spatial data on hazard with spatial data on vulnerability. Geographic Information System (GIS) is a fundamental tool in the realization of this step. GIS software allows the simultaneous analysis of spatial and matrix data. The third step of the evaluation consists of calculating potential damages by means of damage-functions or contingent analysis. All steps demand time and expertise. However, the last two steps must be realized several times when comparing different management scenarios. In addition, uncertainty analysis and sensitivity test are made during the second and third steps of the evaluation. The feasibility of these steps could be relevant in the choice of the extent of the evaluation. Low feasibility could lead to choosing not to evaluate uncertainty or to limit the number of scenario comparisons. Several computer models have been developed over time in order to evaluate the flood risk. GIS software is largely used to realise flood risk analysis. The software is used to combine and process different types of data, and to visualise the risk and the evaluation results. The main advantages of using a GIS in these analyses are: the possibility of "easily" realising the analyses several times, in order to compare different scenarios and study uncertainty; the generation of datasets which could be used any time in future to support territorial decision making; the possibility of adding information over time to update the dataset and make other analyses. However, these analyses require personnel specialisation and time. The use of GIS software to evaluate the flood risk requires personnel with a double professional specialisation. The professional should be proficient in GIS software and in flood damage analysis (which is already a multidisciplinary field). Great effort is necessary in order to correctly evaluate flood damages, and the updating and the improvement of the evaluation over time become a difficult task. The automation of this process should bring great advance in flood management studies over time, especially for public utilities. This study has two specific objectives: (1) show the entire process of automation of the second and third steps of flood damage evaluations; and (2) analyse the induced potential gains in terms of time and expertise needed in the analysis. A programming language is used within GIS software in order to automate hazard and vulnerability data combination and potential damages calculation. We discuss the overall process of flood damage evaluation. The main result of this study is a computational tool which allows significant operational gains on flood loss analyses. We quantify these gains by means of a hypothetical example. The tool significantly reduces the time of analysis and the needs for expertise. An indirect gain is that sensitivity and cost-benefit analyses can be more easily realized.

Circumnutation Tracker: novel software for investigation of circumnutation

PubMed Central

2014-01-01

Background An endogenous, helical plant organ movement named circumnutation is ubiquitous in the plant kingdom. Plant shoots, stems, tendrils, leaves, and roots commonly circumnutate but their appearance is still poorly described. To support such investigations, novel software Circumnutation Tracker (CT) for spatial-temporal analysis of circumnutation has been developed. Results CT works on time-lapse video and collected circumnutation parameters: period, length, rate, shape, angle, and clockwise- and counterclockwise directions. The CT combines a filtering algorithm with a graph-based method to describe the parameters of circumnutation. The parameters of circumnutation of Helianthus annuus hypocotyls and the relationship between cotyledon arrangement and circumnutation geometry are presented here to demonstrate the CT options. Conclusions We have established that CT facilitates and accelerates analysis of circumnutation. In combination with the physiological, molecular, and genetic methods, this software may be a powerful tool also for investigations of gravitropism, biological clock, and membrane transport, i.e. processes involved in the mechanism of circumnutation.

A Comparative Study of the Effects of Using Dynamic Geometry Software and Physical Manipulatives on the Spatial Visualisation Skills of Pre-Service Mathematics Teachers

ERIC Educational Resources Information Center

Baki, Adnan; Kosa, Temel; Guven, Bulent

2011-01-01

The study compared the effects of dynamic geometry software and physical manipulatives on the spatial visualisation skills of first-year pre-service mathematics teachers. A pre- and post-test quasi-experimental design was used. The Purdue Spatial Visualisation Test (PSVT) was used for the pre- and post-test. There were three treatment groups. The…

A Simplified Mesh Deformation Method Using Commercial Structural Analysis Software

NASA Technical Reports Server (NTRS)

Hsu, Su-Yuen; Chang, Chau-Lyan; Samareh, Jamshid

2004-01-01

Mesh deformation in response to redefined or moving aerodynamic surface geometries is a frequently encountered task in many applications. Most existing methods are either mathematically too complex or computationally too expensive for usage in practical design and optimization. We propose a simplified mesh deformation method based on linear elastic finite element analyses that can be easily implemented by using commercially available structural analysis software. Using a prescribed displacement at the mesh boundaries, a simple structural analysis is constructed based on a spatially varying Young s modulus to move the entire mesh in accordance with the surface geometry redefinitions. A variety of surface movements, such as translation, rotation, or incremental surface reshaping that often takes place in an optimization procedure, may be handled by the present method. We describe the numerical formulation and implementation using the NASTRAN software in this paper. The use of commercial software bypasses tedious reimplementation and takes advantage of the computational efficiency offered by the vendor. A two-dimensional airfoil mesh and a three-dimensional aircraft mesh were used as test cases to demonstrate the effectiveness of the proposed method. Euler and Navier-Stokes calculations were performed for the deformed two-dimensional meshes.

Use of Mapping and Spatial and Space-Time Modeling Approaches in Operational Control of Aedes aegypti and Dengue

PubMed Central

Eisen, Lars; Lozano-Fuentes, Saul

2009-01-01

The aims of this review paper are to 1) provide an overview of how mapping and spatial and space-time modeling approaches have been used to date to visualize and analyze mosquito vector and epidemiologic data for dengue; and 2) discuss the potential for these approaches to be included as routine activities in operational vector and dengue control programs. Geographical information system (GIS) software are becoming more user-friendly and now are complemented by free mapping software that provide access to satellite imagery and basic feature-making tools and have the capacity to generate static maps as well as dynamic time-series maps. Our challenge is now to move beyond the research arena by transferring mapping and GIS technologies and spatial statistical analysis techniques in user-friendly packages to operational vector and dengue control programs. This will enable control programs to, for example, generate risk maps for exposure to dengue virus, develop Priority Area Classifications for vector control, and explore socioeconomic associations with dengue risk. PMID:19399163

Environmental analysis using integrated GIS and remotely sensed data - Some research needs and priorities

NASA Technical Reports Server (NTRS)

Davis, Frank W.; Quattrochi, Dale A.; Ridd, Merrill K.; Lam, Nina S.-N.; Walsh, Stephen J.

1991-01-01

This paper discusses some basic scientific issues and research needs in the joint processing of remotely sensed and GIS data for environmental analysis. Two general topics are treated in detail: (1) scale dependence of geographic data and the analysis of multiscale remotely sensed and GIS data, and (2) data transformations and information flow during data processing. The discussion of scale dependence focuses on the theory and applications of spatial autocorrelation, geostatistics, and fractals for characterizing and modeling spatial variation. Data transformations during processing are described within the larger framework of geographical analysis, encompassing sampling, cartography, remote sensing, and GIS. Development of better user interfaces between image processing, GIS, database management, and statistical software is needed to expedite research on these and other impediments to integrated analysis of remotely sensed and GIS data.

Data Curation and Visualization for MuSIASEM Analysis of the Nexus

NASA Astrophysics Data System (ADS)

Renner, Ansel

2017-04-01

A novel software-based approach to relational analysis applying recent theoretical advancements of the Multi-Scale Integrated Analysis of Societal and Ecosystem Metabolism (MuSIASEM) accounting framework is presented. This research explores and explains underutilized ways software can assist complex system analysis across the stages of data collection, exploration, analysis and dissemination and in a transparent and collaborative manner. This work is being conducted as part of, and in support of, the four-year European Commission H2020 project: Moving Towards Adaptive Governance in Complexity: Informing Nexus Security (MAGIC). In MAGIC, theoretical advancements to MuSIASEM propose a powerful new approach to spatial-temporal WEFC relational analysis in accordance with a structural-functional scaling mechanism appropriate for biophysically relevant complex system analyses. Software is designed primarily with JavaScript using the Angular2 model-view-controller framework and the Data-Driven Documents (D3) library. These design choices clarify and modularize data flow, simplify research practitioner's work, allow for and assist stakeholder involvement and advance collaboration at all stages. Data requirements and scalable, robust yet light-weight structuring will first be explained. Following, algorithms to process this data will be explored. Data interfaces and data visualization approaches will lastly be presented and described.

An Analysis of Perturbed Quantization Steganography in the Spatial Domain

DTIC Science & Technology

2005-03-01

72 4.2.3 Hide v2.1 Steganographic Software & the Desaturate Function. ..................... 73 4.2.4 Studying the Effect of the Secret Message...Effect of the Secret Message Payload.......................................... 84 4.3.4 Performance Comparison of the Three Steganographic Systems...Epsilon .......................................................................... 89 4.4 Secrets for the Secret ............................................................................................... 90

Spectral and Spatial Coherent Emission of Thermal Radiation from Metal-Semiconductor Nanostructures

DTIC Science & Technology

2012-03-01

Coupled Wave Analysis (RCWA) numerical technique and Computer Simulation Technology (CST) electromagnetic modeling software, two structures were...Stephanie Gray, IR-VASE and modeling  Dr. Kevin Gross, FTIR  Mr. Richard Johnston, Cleanroom and Photolithography  Ms. Abbey Juhl, Nanoscribe...Appendix B. Supplemental IR-VASE Measurements and Modeling .............................114 Bibliography

User’s guide to SNAP for ArcGIS® :ArcGIS interface for scheduling and network analysis program

Treesearch

Woodam Chung; Dennis Dykstra; Fred Bower; Stephen O’Brien; Richard Abt; John. and Sessions

2012-01-01

This document introduces a computer software named SNAP for ArcGIS® , which has been developed to streamline scheduling and transportation planning for timber harvest areas. Using modern optimization techniques, it can be used to spatially schedule timber harvest with consideration of harvesting costs, multiple products, alternative...

STSE: Spatio-Temporal Simulation Environment Dedicated to Biology.

PubMed

Stoma, Szymon; Fröhlich, Martina; Gerber, Susanne; Klipp, Edda

2011-04-28

Recently, the availability of high-resolution microscopy together with the advancements in the development of biomarkers as reporters of biomolecular interactions increased the importance of imaging methods in molecular cell biology. These techniques enable the investigation of cellular characteristics like volume, size and geometry as well as volume and geometry of intracellular compartments, and the amount of existing proteins in a spatially resolved manner. Such detailed investigations opened up many new areas of research in the study of spatial, complex and dynamic cellular systems. One of the crucial challenges for the study of such systems is the design of a well stuctured and optimized workflow to provide a systematic and efficient hypothesis verification. Computer Science can efficiently address this task by providing software that facilitates handling, analysis, and evaluation of biological data to the benefit of experimenters and modelers. The Spatio-Temporal Simulation Environment (STSE) is a set of open-source tools provided to conduct spatio-temporal simulations in discrete structures based on microscopy images. The framework contains modules to digitize, represent, analyze, and mathematically model spatial distributions of biochemical species. Graphical user interface (GUI) tools provided with the software enable meshing of the simulation space based on the Voronoi concept. In addition, it supports to automatically acquire spatial information to the mesh from the images based on pixel luminosity (e.g. corresponding to molecular levels from microscopy images). STSE is freely available either as a stand-alone version or included in the linux live distribution Systems Biology Operational Software (SB.OS) and can be downloaded from http://www.stse-software.org/. The Python source code as well as a comprehensive user manual and video tutorials are also offered to the research community. We discuss main concepts of the STSE design and workflow. We demonstrate it's usefulness using the example of a signaling cascade leading to formation of a morphological gradient of Fus3 within the cytoplasm of the mating yeast cell Saccharomyces cerevisiae. STSE is an efficient and powerful novel platform, designed for computational handling and evaluation of microscopic images. It allows for an uninterrupted workflow including digitization, representation, analysis, and mathematical modeling. By providing the means to relate the simulation to the image data it allows for systematic, image driven model validation or rejection. STSE can be scripted and extended using the Python language. STSE should be considered rather as an API together with workflow guidelines and a collection of GUI tools than a stand alone application. The priority of the project is to provide an easy and intuitive way of extending and customizing software using the Python language.

Automated Liquid Microjunction Surface Sampling-HPLC-MS/MS Analysis of Drugs and Metabolites in Whole-Body Thin Tissue Sections

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kertesz, Vilmos; Van Berkel, Gary J

A fully automated liquid extraction-based surface sampling system utilizing a commercially available autosampler coupled to high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) detection is reported. Discrete spots selected for droplet-based sampling and automated sample queue generation for both the autosampler and MS were enabled by using in-house developed software. In addition, co-registration of spatially resolved sampling position and HPLC-MS information to generate heatmaps of compounds monitored for subsequent data analysis was also available in the software. The system was evaluated with whole-body thin tissue sections from propranolol dosed rat. The hands-free operation of the system was demonstrated by creating heatmapsmore » of the parent drug and its hydroxypropranolol glucuronide metabolites with 1 mm resolution in the areas of interest. The sample throughput was approximately 5 min/sample defined by the time needed for chromatographic separation. The spatial distributions of both the drug and its metabolites were consistent with previous studies employing other liquid extraction-based surface sampling methodologies.« less

Spatial and temporal patterns of dengue in Guangdong province of China.

PubMed

Wang, Chenggang; Yang, Weizhong; Fan, Jingchun; Wang, Furong; Jiang, Baofa; Liu, Qiyong

2015-03-01

The aim of the study was to describe the spatial and temporal patterns of dengue in Guangdong for 1978 to 2010. Time series analysis was performed using data on annual dengue incidence in Guangdong province for 1978-2010. Annual average dengue incidences for each city were mapped for 4 periods by using the geographical information system (GIS). Hot spot analysis was used to identify spatial patterns of dengue cases for 2005-2010 by using the CrimeStat III software. The incidence of dengue in Guangdong province had fallen steadily from 1978 to 2010. The time series was a random sequence without regularity and with no fixed cycle. The geographic range of dengue fever had expanded from 1978 to 2010. Cases were mostly concentrated in Zhanjiang and the developed regions of Pearl River Delta and Shantou. © 2013 APJPH.

Multispectral scanner system parameter study and analysis software system description, volume 2

NASA Technical Reports Server (NTRS)

Landgrebe, D. A. (Principal Investigator); Mobasseri, B. G.; Wiersma, D. J.; Wiswell, E. R.; Mcgillem, C. D.; Anuta, P. E.

1978-01-01

The author has identified the following significant results. The integration of the available methods provided the analyst with the unified scanner analysis package (USAP), the flexibility and versatility of which was superior to many previous integrated techniques. The USAP consisted of three main subsystems; (1) a spatial path, (2) a spectral path, and (3) a set of analytic classification accuracy estimators which evaluated the system performance. The spatial path consisted of satellite and/or aircraft data, data correlation analyzer, scanner IFOV, and random noise model. The output of the spatial path was fed into the analytic classification and accuracy predictor. The spectral path consisted of laboratory and/or field spectral data, EXOSYS data retrieval, optimum spectral function calculation, data transformation, and statistics calculation. The output of the spectral path was fended into the stratified posterior performance estimator.

PIRATE: pediatric imaging response assessment and targeting environment

NASA Astrophysics Data System (ADS)

Glenn, Russell; Zhang, Yong; Krasin, Matthew; Hua, Chiaho

2010-02-01

By combining the strengths of various imaging modalities, the multimodality imaging approach has potential to improve tumor staging, delineation of tumor boundaries, chemo-radiotherapy regime design, and treatment response assessment in cancer management. To address the urgent needs for efficient tools to analyze large-scale clinical trial data, we have developed an integrated multimodality, functional and anatomical imaging analysis software package for target definition and therapy response assessment in pediatric radiotherapy (RT) patients. Our software provides quantitative tools for automated image segmentation, region-of-interest (ROI) histogram analysis, spatial volume-of-interest (VOI) analysis, and voxel-wise correlation across modalities. To demonstrate the clinical applicability of this software, histogram analyses were performed on baseline and follow-up 18F-fluorodeoxyglucose (18F-FDG) PET images of nine patients with rhabdomyosarcoma enrolled in an institutional clinical trial at St. Jude Children's Research Hospital. In addition, we combined 18F-FDG PET, dynamic-contrast-enhanced (DCE) MR, and anatomical MR data to visualize the heterogeneity in tumor pathophysiology with the ultimate goal of adaptive targeting of regions with high tumor burden. Our software is able to simultaneously analyze multimodality images across multiple time points, which could greatly speed up the analysis of large-scale clinical trial data and validation of potential imaging biomarkers.

Geostatistics and GIS: tools for characterizing environmental contamination.

PubMed

Henshaw, Shannon L; Curriero, Frank C; Shields, Timothy M; Glass, Gregory E; Strickland, Paul T; Breysse, Patrick N

2004-08-01

Geostatistics is a set of statistical techniques used in the analysis of georeferenced data that can be applied to environmental contamination and remediation studies. In this study, the 1,1-dichloro-2,2-bis(p-chlorophenyl)ethylene (DDE) contamination at a Superfund site in western Maryland is evaluated. Concern about the site and its future clean up has triggered interest within the community because residential development surrounds the area. Spatial statistical methods, of which geostatistics is a subset, are becoming increasingly popular, in part due to the availability of geographic information system (GIS) software in a variety of application packages. In this article, the joint use of ArcGIS software and the R statistical computing environment are demonstrated as an approach for comprehensive geostatistical analyses. The spatial regression method, kriging, is used to provide predictions of DDE levels at unsampled locations both within the site and the surrounding areas where residential development is ongoing.

Water environmental management with the aid of remote sensing and GIS technology

NASA Astrophysics Data System (ADS)

Chen, Xiaoling; Yuan, Zhongzhi; Li, Yok-Sheung; Song, Hong; Hou, Yingzi; Xu, Zhanhua; Liu, Honghua; Wai, Onyx W.

2005-01-01

Water environment is associated with many disciplinary fields including sciences and management which makes it difficult to study. Timely observation, data getting and analysis on water environment are very important for decision makers who play an important role to maintain the sustainable development. This study focused on developing a plateform of water environment management based on remote sensing and GIS technology, and its main target is to provide with necessary information on water environment through spatial analysis and visual display in a suitable way. The work especially focused on three points, and the first one is related to technical issues of spatial data organization and communication with a combination of GIS and statistical software. A data-related model was proposed to solve the data communication between the mentioned systems. The second one is spatio-temporal analysis based on remote sensing and GIS. Water quality parameters of suspended sediment concentration and BOD5 were specially analyzed in this case, and the results suggested an obvious influence of land source pollution quantitatively in a spatial domain. The third one is 3D visualization of surface feature based on RS and GIS technology. The Pearl River estuary and HongKong's coastal waters in the South China Sea were taken as a case in this study. The software ARCGIS was taken as a basic platform to develop a water environmental management system. The sampling data of water quality in 76 monitoring stations of coastal water bodies and remote sensed images were selected in this study.

Improvement in Recursive Hierarchical Segmentation of Data

NASA Technical Reports Server (NTRS)

Tilton, James C.

2006-01-01

A further modification has been made in the algorithm and implementing software reported in Modified Recursive Hierarchical Segmentation of Data (GSC- 14681-1), NASA Tech Briefs, Vol. 30, No. 6 (June 2006), page 51. That software performs recursive hierarchical segmentation of data having spatial characteristics (e.g., spectral-image data). The output of a prior version of the software contained artifacts, including spurious segmentation-image regions bounded by processing-window edges. The modification for suppressing the artifacts, mentioned in the cited article, was addition of a subroutine that analyzes data in the vicinities of seams to find pairs of regions that tend to lie adjacent to each other on opposite sides of the seams. Within each such pair, pixels in one region that are more similar to pixels in the other region are reassigned to the other region. The present modification provides for a parameter ranging from 0 to 1 for controlling the relative priority of merges between spatially adjacent and spatially non-adjacent regions. At 1, spatially-adjacent-/spatially- non-adjacent-region merges have equal priority. At 0, only spatially-adjacent-region merges (no spectral clustering) are allowed. Between 0 and 1, spatially-adjacent- region merges have priority over spatially- non-adjacent ones.

"SABER": A new software tool for radiotherapy treatment plan evaluation.

PubMed

Zhao, Bo; Joiner, Michael C; Orton, Colin G; Burmeister, Jay

2010-11-01

Both spatial and biological information are necessary in order to perform true optimization of a treatment plan and for predicting clinical outcome. The goal of this work is to develop an enhanced treatment plan evaluation tool which incorporates biological parameters and retains spatial dose information. A software system is developed which provides biological plan evaluation with a novel combination of features. It incorporates hyper-radiosensitivity using the induced-repair model and applies the new concept of dose convolution filter (DCF) to simulate dose wash-out effects due to cell migration, bystander effect, and/or tissue motion during treatment. Further, the concept of spatial DVH (sDVH) is introduced to evaluate and potentially optimize the spatial dose distribution in the target volume. Finally, generalized equivalent uniform dose is derived from both the physical dose distribution (gEUD) and the distribution of equivalent dose in 2 Gy fractions (gEUD2) and the software provides three separate models for calculation of tumor control probability (TCP), normal tissue complication probability (NTCP), and probability of uncomplicated tumor control (P+). TCP, NTCP, and P+ are provided as a function of prescribed dose and multivariable TCP, NTCP, and P+ plots are provided to illustrate the dependence on individual parameters used to calculate these quantities. Ten plans from two clinical treatment sites are selected to test the three calculation models provided by this software. By retaining both spatial and biological information about the dose distribution, the software is able to distinguish features of radiotherapy treatment plans not discernible using commercial systems. Plans that have similar DVHs may have different spatial and biological characteristics and the application of novel tools such as sDVH and DCF within the software may substantially change the apparent plan quality or predicted plan metrics such as TCP and NTCP. For the cases examined, both the calculation method and the application of DCF can change the ranking order of competing plans. The voxel-by-voxel TCP model makes it feasible to incorporate spatial variations of clonogen densities (n), radiosensitivities (SF2), and fractionation sensitivities (alpha/beta) as those data become available. The new software incorporates both spatial and biological information into the treatment planning process. The application of multiple methods for the incorporation of biological and spatial information has demonstrated that the order of application of biological models can change the order of plan ranking. Thus, the results of plan evaluation and optimization are dependent not only on the models used but also on the order in which they are applied. This software can help the planner choose more biologically optimal treatment plans and potentially predict treatment outcome more accurately.

Environmental Assessment and Monitoring with ICAMS (Image Characterization and Modeling System) Using Multiscale Remote-Sensing Data

NASA Technical Reports Server (NTRS)

Lam, N.; Qiu, H.-I.; Quattrochi, Dale A.; Zhao, Wei

1997-01-01

With the rapid increase in spatial data, especially in the NASA-EOS (Earth Observing System) era, it is necessary to develop efficient and innovative tools to handle and analyze these data so that environmental conditions can be assessed and monitored. A main difficulty facing geographers and environmental scientists in environmental assessment and measurement is that spatial analytical tools are not easily accessible. We have recently developed a remote sensing/GIS software module called Image Characterization and Modeling System (ICAMS) to provide specialized spatial analytical tools for the measurement and characterization of satellite and other forms of spatial data. ICAMS runs on both the Intergraph-MGE and Arc/info UNIX and Windows-NT platforms. The main techniques in ICAMS include fractal measurement methods, variogram analysis, spatial autocorrelation statistics, textural measures, aggregation techniques, normalized difference vegetation index (NDVI), and delineation of land/water and vegetated/non-vegetated boundaries. In this paper, we demonstrate the main applications of ICAMS on the Intergraph-MGE platform using Landsat Thematic Mapper images from the city of Lake Charles, Louisiana. While the utilities of ICAMS' spatial measurement methods (e.g., fractal indices) in assessing environmental conditions remain to be researched, making the software available to a wider scientific community can permit the techniques in ICAMS to be evaluated and used for a diversity of applications. The findings from these various studies should lead to improved algorithms and more reliable models for environmental assessment and monitoring.

VideoHacking: Automated Tracking and Quantification of Locomotor Behavior with Open Source Software and Off-the-Shelf Video Equipment.

PubMed

Conklin, Emily E; Lee, Kathyann L; Schlabach, Sadie A; Woods, Ian G

2015-01-01

Differences in nervous system function can result in differences in behavioral output. Measurements of animal locomotion enable the quantification of these differences. Automated tracking of animal movement is less labor-intensive and bias-prone than direct observation, and allows for simultaneous analysis of multiple animals, high spatial and temporal resolution, and data collection over extended periods of time. Here, we present a new video-tracking system built on Python-based software that is free, open source, and cross-platform, and that can analyze video input from widely available video capture devices such as smartphone cameras and webcams. We validated this software through four tests on a variety of animal species, including larval and adult zebrafish (Danio rerio), Siberian dwarf hamsters (Phodopus sungorus), and wild birds. These tests highlight the capacity of our software for long-term data acquisition, parallel analysis of multiple animals, and application to animal species of different sizes and movement patterns. We applied the software to an analysis of the effects of ethanol on thigmotaxis (wall-hugging) behavior on adult zebrafish, and found that acute ethanol treatment decreased thigmotaxis behaviors without affecting overall amounts of motion. The open source nature of our software enables flexibility, customization, and scalability in behavioral analyses. Moreover, our system presents a free alternative to commercial video-tracking systems and is thus broadly applicable to a wide variety of educational settings and research programs.

Rapid Analysis of Mass Distribution of Radiation Shielding

NASA Technical Reports Server (NTRS)

Zapp, Edward

2007-01-01

Radiation Shielding Evaluation Toolset (RADSET) is a computer program that rapidly calculates the spatial distribution of mass of an arbitrary structure for use in ray-tracing analysis of the radiation-shielding properties of the structure. RADSET was written to be used in conjunction with unmodified commercial computer-aided design (CAD) software that provides access to data on the structure and generates selected three-dimensional-appearing views of the structure. RADSET obtains raw geometric, material, and mass data on the structure from the CAD software. From these data, RADSET calculates the distribution(s) of the masses of specific materials about any user-specified point(s). The results of these mass-distribution calculations are imported back into the CAD computing environment, wherein the radiation-shielding calculations are performed.

Spatially explicit spectral analysis of point clouds and geospatial data

USGS Publications Warehouse

Buscombe, Daniel D.

2015-01-01

The increasing use of spatially explicit analyses of high-resolution spatially distributed data (imagery and point clouds) for the purposes of characterising spatial heterogeneity in geophysical phenomena necessitates the development of custom analytical and computational tools. In recent years, such analyses have become the basis of, for example, automated texture characterisation and segmentation, roughness and grain size calculation, and feature detection and classification, from a variety of data types. In this work, much use has been made of statistical descriptors of localised spatial variations in amplitude variance (roughness), however the horizontal scale (wavelength) and spacing of roughness elements is rarely considered. This is despite the fact that the ratio of characteristic vertical to horizontal scales is not constant and can yield important information about physical scaling relationships. Spectral analysis is a hitherto under-utilised but powerful means to acquire statistical information about relevant amplitude and wavelength scales, simultaneously and with computational efficiency. Further, quantifying spatially distributed data in the frequency domain lends itself to the development of stochastic models for probing the underlying mechanisms which govern the spatial distribution of geological and geophysical phenomena. The software packagePySESA (Python program for Spatially Explicit Spectral Analysis) has been developed for generic analyses of spatially distributed data in both the spatial and frequency domains. Developed predominantly in Python, it accesses libraries written in Cython and C++ for efficiency. It is open source and modular, therefore readily incorporated into, and combined with, other data analysis tools and frameworks with particular utility for supporting research in the fields of geomorphology, geophysics, hydrography, photogrammetry and remote sensing. The analytical and computational structure of the toolbox is described, and its functionality illustrated with an example of a high-resolution bathymetric point cloud data collected with multibeam echosounder.

[Design and implementation of Geographical Information System on prevention and control of cholera].

PubMed

Li, Xiu-jun; Fang, Li-qun; Wang, Duo-chun; Wang, Lu-xi; Li, Ya-pin; Li, Yan-li; Yang, Hong; Kan, Biao; Cao, Wu-chun

2012-04-01

To build the Geographical Information System (GIS) database for prevention and control of cholera programs as well as using management analysis and function demonstration to show the spatial attribute of cholera. Data from case reporting system regarding diarrhoea, vibrio cholerae, serotypes of vibrio cholerae at the surveillance spots and seafoods, as well as surveillance data on ambient environment and climate were collected. All the data were imported to system database to show the incidence of vibrio cholerae in different provinces, regions and counties to support the spatial analysis through the spatial analysis of GIS. The epidemic trends of cholera, seasonal characteristics of the cholera and the variation of the vibrio cholerae with times were better understood. Information on hotspots, regions and time of epidemics was collected, and helpful in providing risk prediction on the incidence of vibrio cholerae. The exploitation of the software can predict and simulate the spatio-temporal risks, so as to provide guidance for the prevention and control of the disease.

RADSS: an integration of GIS, spatial statistics, and network service for regional data mining

NASA Astrophysics Data System (ADS)

Hu, Haitang; Bao, Shuming; Lin, Hui; Zhu, Qing

2005-10-01

Regional data mining, which aims at the discovery of knowledge about spatial patterns, clusters or association between regions, has widely applications nowadays in social science, such as sociology, economics, epidemiology, crime, and so on. Many applications in the regional or other social sciences are more concerned with the spatial relationship, rather than the precise geographical location. Based on the spatial continuity rule derived from Tobler's first law of geography: observations at two sites tend to be more similar to each other if the sites are close together than if far apart, spatial statistics, as an important means for spatial data mining, allow the users to extract the interesting and useful information like spatial pattern, spatial structure, spatial association, spatial outlier and spatial interaction, from the vast amount of spatial data or non-spatial data. Therefore, by integrating with the spatial statistical methods, the geographical information systems will become more powerful in gaining further insights into the nature of spatial structure of regional system, and help the researchers to be more careful when selecting appropriate models. However, the lack of such tools holds back the application of spatial data analysis techniques and development of new methods and models (e.g., spatio-temporal models). Herein, we make an attempt to develop such an integrated software and apply it into the complex system analysis for the Poyang Lake Basin. This paper presents a framework for integrating GIS, spatial statistics and network service in regional data mining, as well as their implementation. After discussing the spatial statistics methods involved in regional complex system analysis, we introduce RADSS (Regional Analysis and Decision Support System), our new regional data mining tool, by integrating GIS, spatial statistics and network service. RADSS includes the functions of spatial data visualization, exploratory spatial data analysis, and spatial statistics. The tool also includes some fundamental spatial and non-spatial database in regional population and environment, which can be updated by external database via CD or network. Utilizing this data mining and exploratory analytical tool, the users can easily and quickly analyse the huge mount of the interrelated regional data, and better understand the spatial patterns and trends of the regional development, so as to make a credible and scientific decision. Moreover, it can be used as an educational tool for spatial data analysis and environmental studies. In this paper, we also present a case study on Poyang Lake Basin as an application of the tool and spatial data mining in complex environmental studies. At last, several concluding remarks are discussed.

Geospatial-enabled Data Exploration and Computation through Data Infrastructure Building Blocks

NASA Astrophysics Data System (ADS)

Song, C. X.; Biehl, L. L.; Merwade, V.; Villoria, N.

2015-12-01

Geospatial data are present everywhere today with the proliferation of location-aware computing devices and sensors. This is especially true in the scientific community where large amounts of data are driving research and education activities in many domains. Collaboration over geospatial data, for example, in modeling, data analysis and visualization, must still overcome the barriers of specialized software and expertise among other challenges. The GABBs project aims at enabling broader access to geospatial data exploration and computation by developing spatial data infrastructure building blocks that leverage capabilities of end-to-end application service and virtualized computing framework in HUBzero. Funded by NSF Data Infrastructure Building Blocks (DIBBS) initiative, GABBs provides a geospatial data architecture that integrates spatial data management, mapping and visualization and will make it available as open source. The outcome of the project will enable users to rapidly create tools and share geospatial data and tools on the web for interactive exploration of data without requiring significant software development skills, GIS expertise or IT administrative privileges. This presentation will describe the development of geospatial data infrastructure building blocks and the scientific use cases that help drive the software development, as well as seek feedback from the user communities.

Describing spatial pattern in stream networks: A practical approach

USGS Publications Warehouse

Ganio, L.M.; Torgersen, C.E.; Gresswell, R.E.

2005-01-01

The shape and configuration of branched networks influence ecological patterns and processes. Recent investigations of network influences in riverine ecology stress the need to quantify spatial structure not only in a two-dimensional plane, but also in networks. An initial step in understanding data from stream networks is discerning non-random patterns along the network. On the other hand, data collected in the network may be spatially autocorrelated and thus not suitable for traditional statistical analyses. Here we provide a method that uses commercially available software to construct an empirical variogram to describe spatial pattern in the relative abundance of coastal cutthroat trout in headwater stream networks. We describe the mathematical and practical considerations involved in calculating a variogram using a non-Euclidean distance metric to incorporate the network pathway structure in the analysis of spatial variability, and use a non-parametric technique to ascertain if the pattern in the empirical variogram is non-random.

A geostatistical approach for describing spatial pattern in stream networks

USGS Publications Warehouse

Ganio, L.M.; Torgersen, C.E.; Gresswell, R.E.

2005-01-01

The shape and configuration of branched networks influence ecological patterns and processes. Recent investigations of network influences in riverine ecology stress the need to quantify spatial structure not only in a two-dimensional plane, but also in networks. An initial step in understanding data from stream networks is discerning non-random patterns along the network. On the other hand, data collected in the network may be spatially autocorrelated and thus not suitable for traditional statistical analyses. Here we provide a method that uses commercially available software to construct an empirical variogram to describe spatial pattern in the relative abundance of coastal cutthroat trout in headwater stream networks. We describe the mathematical and practical considerations involved in calculating a variogram using a non-Euclidean distance metric to incorporate the network pathway structure in the analysis of spatial variability, and use a non-parametric technique to ascertain if the pattern in the empirical variogram is non-random.

Computational Software for Fitting Seismic Data to Epidemic-Type Aftershock Sequence Models

NASA Astrophysics Data System (ADS)

Chu, A.

2014-12-01

Modern earthquake catalogs are often analyzed using spatial-temporal point process models such as the epidemic-type aftershock sequence (ETAS) models of Ogata (1998). My work introduces software to implement two of ETAS models described in Ogata (1998). To find the Maximum-Likelihood Estimates (MLEs), my software provides estimates of the homogeneous background rate parameter and the temporal and spatial parameters that govern triggering effects by applying the Expectation-Maximization (EM) algorithm introduced in Veen and Schoenberg (2008). Despite other computer programs exist for similar data modeling purpose, using EM-algorithm has the benefits of stability and robustness (Veen and Schoenberg, 2008). Spatial shapes that are very long and narrow cause difficulties in optimization convergence and problems with flat or multi-modal log-likelihood functions encounter similar issues. My program uses a robust method to preset a parameter to overcome the non-convergence computational issue. In addition to model fitting, the software is equipped with useful tools for examining modeling fitting results, for example, visualization of estimated conditional intensity, and estimation of expected number of triggered aftershocks. A simulation generator is also given with flexible spatial shapes that may be defined by the user. This open-source software has a very simple user interface. The user may execute it on a local computer, and the program also has potential to be hosted online. Java language is used for the software's core computing part and an optional interface to the statistical package R is provided.

GENERATING SOPHISTICATED SPATIAL SURROGATES USING THE MIMS SPATIAL ALLOCATOR

EPA Science Inventory

The Multimedia Integrated Modeling System (MIMS) Spatial Allocator is open-source software for generating spatial surrogates for emissions modeling, changing the map projection of Shapefiles, and performing other types of spatial allocation that does not require the use of a comm...

A Randomized Trial of an Elementary School Mathematics Software Intervention: Spatial-Temporal Math

ERIC Educational Resources Information Center

Rutherford, Teomara; Farkas, George; Duncan, Greg; Burchinal, Margaret; Kibrick, Melissa; Graham, Jeneen; Richland, Lindsey; Tran, Natalie; Schneider, Stephanie; Duran, Lauren; Martinez, Michael E.

2014-01-01

Fifty-two low performing schools were randomly assigned to receive Spatial-Temporal (ST) Math, a supplemental mathematics software and instructional program, in second/third or fourth/fifth grades or to a business-as-usual control. Analyses reveal a negligible effect of ST Math on mathematics scores, which did not differ significantly across…

Sonification Prototype for Space Physics

NASA Astrophysics Data System (ADS)

Candey, R. M.; Schertenleib, A. M.; Diaz Merced, W. L.

2005-12-01

As an alternative and adjunct to visual displays, auditory exploration of data via sonification (data controlled sound) and audification (audible playback of data samples) is promising for complex or rapidly/temporally changing visualizations, for data exploration of large datasets (particularly multi-dimensional datasets), and for exploring datasets in frequency rather than spatial dimensions (see also International Conferences on Auditory Display ). Besides improving data exploration and analysis for most researchers, the use of sound is especially valuable as an assistive technology for visually-impaired people and can make science and math more exciting for high school and college students. Only recently have the hardware and software come together to make a cross-platform open-source sonification tool feasible. We have developed a prototype sonification data analysis tool using the JavaSound API and NASA GSFC's ViSBARD software . Wanda Diaz Merced, a blind astrophysicist from Puerto Rico, is instrumental in advising on and testing the tool.

GUIDOS: tools for the assessment of pattern, connectivity, and fragmentation

NASA Astrophysics Data System (ADS)

Vogt, Peter

2013-04-01

Pattern, connectivity, and fragmentation can be considered as pillars for a quantitative analysis of digital landscape images. The free software toolbox GUIDOS (http://forest.jrc.ec.europa.eu/download/software/guidos) includes a variety of dedicated methodologies for the quantitative assessment of these features. Amongst others, Morphological Spatial Pattern Analysis (MSPA) is used for an intuitive description of image pattern structures and the automatic detection of connectivity pathways. GUIDOS includes tools for the detection and quantitative assessment of key nodes and links as well as to define connectedness in raster images and to setup appropriate input files for an enhanced network analysis using Conefor Sensinode. Finally, fragmentation is usually defined from a species point of view but a generic and quantifiable indicator is needed to measure fragmentation and its changes. Some preliminary results for different conceptual approaches will be shown for a sample dataset. Complemented by pre- and post-processing routines and a complete GIS environment the portable GUIDOS Toolbox may facilitate a holistic assessment in risk assessment studies, landscape planning, and conservation/restoration policies. Alternatively, individual analysis components may contribute to or enhance studies conducted with other software packages in landscape ecology.

A novel method for automated tracking and quantification of adult zebrafish behaviour during anxiety.

PubMed

Nema, Shubham; Hasan, Whidul; Bhargava, Anamika; Bhargava, Yogesh

2016-09-15

Behavioural neuroscience relies on software driven methods for behavioural assessment, but the field lacks cost-effective, robust, open source software for behavioural analysis. Here we propose a novel method which we called as ZebraTrack. It includes cost-effective imaging setup for distraction-free behavioural acquisition, automated tracking using open-source ImageJ software and workflow for extraction of behavioural endpoints. Our ImageJ algorithm is capable of providing control to users at key steps while maintaining automation in tracking without the need for the installation of external plugins. We have validated this method by testing novelty induced anxiety behaviour in adult zebrafish. Our results, in agreement with established findings, showed that during state-anxiety, zebrafish showed reduced distance travelled, increased thigmotaxis and freezing events. Furthermore, we proposed a method to represent both spatial and temporal distribution of choice-based behaviour which is currently not possible to represent using simple videograms. ZebraTrack method is simple and economical, yet robust enough to give results comparable with those obtained from costly proprietary software like Ethovision XT. We have developed and validated a novel cost-effective method for behavioural analysis of adult zebrafish using open-source ImageJ software. Copyright © 2016 Elsevier B.V. All rights reserved.

Geographic information systems: introduction.

PubMed

Calistri, Paolo; Conte, Annamaria; Freier, Jerome E; Ward, Michael P

2007-01-01

The recent exponential growth of the science and technology of geographic information systems (GIS) has made a tremendous contribution to epidemiological analysis and has led to the development of new powerful tools for the surveillance of animal diseases. GIS, spatial analysis and remote sensing provide valuable methods to collect and manage information for epidemiological surveys. Spatial patterns and trends of disease can be correlated with climatic and environmental information, thus contributing to a better understanding of the links between disease processes and explanatory spatial variables. Until recently, these tools were underexploited in the field of veterinary public health, due to the prohibitive cost of hardware and the complexity of GIS software that required a high level of expertise. The revolutionary developments in computer performance of the last decade have not only reduced the costs of equipment but have made available easy-to-use Web-based software which in turn have meant that GIS are more widely accessible by veterinary services at all levels. At the same time, the increased awareness of the possibilities offered by these tools has created new opportunities for decision-makers to enhance their planning, analysis and monitoring capabilities. These technologies offer a new way of sharing and accessing spatial and non-spatial data across groups and institutions. The series of papers included in this compilation aim to: - define the state of the art in the use of GIS in veterinary activities - identify priority needs in the development of new GIS tools at the international level for the surveillance of animal diseases and zoonoses - define practical proposals for their implementation. The topics addressed are presented in the following order in this book: - importance of GIS for the monitoring of animal diseases and zoonoses - GIS application in surveillance activities - spatial analysis in veterinary epidemiology - data collection and remote sensing applications - Web - GIS as a tool for data and knowledge sharing. All 43 manuscripts selected for this book have been peer-reviewed. These contributions were originally commissioned for the First international conference on the use of GIS in veterinary activities organised by the Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise 'G. Caporale', Teramo, Italy, and the World Organisation for Animal Health (OIE: Office International des Epizooties) that was held in Silvi Marina, Italy, from 8 to 11 October 2006. The editors would like to thank all authors for their valuable contributions.

Grave mapping in support of the search for missing persons in conflict contexts.

PubMed

Congram, Derek; Kenyhercz, Michael; Green, Arthur Gill

2017-09-01

We review the current and potential uses of Geographic Information Software (GIS) and "spatial thinking" for understanding body disposal behaviour in times of mass fatalities, particularly armed conflict contexts. The review includes observations made by the authors during the course of their academic research and professional consulting on the use of spatial analysis and GIS to support Humanitarian Forensic Action (HFA) to search for the dead, theoretical and statistical considerations in modelling grave site locations, and suggestions on how this work may be advanced further. Copyright © 2017 Elsevier B.V. All rights reserved.

Application of finite-element methods to dynamic analysis of flexible spatial and co-planar linkage systems, part 2

NASA Technical Reports Server (NTRS)

Dubowsky, Steven

1989-01-01

An approach is described to modeling the flexibility effects in spatial mechanisms and manipulator systems. The method is based on finite element representations of the individual links in the system. However, it should be noted that conventional finite element methods and software packages will not handle the highly nonlinear dynamic behavior of these systems which results form their changing geometry. In order to design high-performance lightweight systems and their control systems, good models of their dynamic behavior which include the effects of flexibility are required.

Software for Simulation of Hyperspectral Images

NASA Technical Reports Server (NTRS)

Richtsmeier, Steven C.; Singer-Berk, Alexander; Bernstein, Lawrence S.

2002-01-01

A package of software generates simulated hyperspectral images for use in validating algorithms that generate estimates of Earth-surface spectral reflectance from hyperspectral images acquired by airborne and spaceborne instruments. This software is based on a direct simulation Monte Carlo approach for modeling three-dimensional atmospheric radiative transport as well as surfaces characterized by spatially inhomogeneous bidirectional reflectance distribution functions. In this approach, 'ground truth' is accurately known through input specification of surface and atmospheric properties, and it is practical to consider wide variations of these properties. The software can treat both land and ocean surfaces and the effects of finite clouds with surface shadowing. The spectral/spatial data cubes computed by use of this software can serve both as a substitute for and a supplement to field validation data.

Computational Software to Fit Seismic Data Using Epidemic-Type Aftershock Sequence Models and Modeling Performance Comparisons

NASA Astrophysics Data System (ADS)

Chu, A.

2016-12-01

Modern earthquake catalogs are often analyzed using spatial-temporal point process models such as the epidemic-type aftershock sequence (ETAS) models of Ogata (1998). My work implements three of the homogeneous ETAS models described in Ogata (1998). With a model's log-likelihood function, my software finds the Maximum-Likelihood Estimates (MLEs) of the model's parameters to estimate the homogeneous background rate and the temporal and spatial parameters that govern triggering effects. EM-algorithm is employed for its advantages of stability and robustness (Veen and Schoenberg, 2008). My work also presents comparisons among the three models in robustness, convergence speed, and implementations from theory to computing practice. Up-to-date regional seismic data of seismic active areas such as Southern California and Japan are used to demonstrate the comparisons. Data analysis has been done using computer languages Java and R. Java has the advantages of being strong-typed and easiness of controlling memory resources, while R has the advantages of having numerous available functions in statistical computing. Comparisons are also made between the two programming languages in convergence and stability, computational speed, and easiness of implementation. Issues that may affect convergence such as spatial shapes are discussed.

[Analysis and spatial description to correlative factors on food hygiene appeal and food poison in restaurants of city zone in Qingdao].

PubMed

Liu, Ying; Guo, Xin-biao; Li, Hai-rong; Yang, Lin-sheng

2006-07-01

To study some factors that affected food poison and appeals in restaurants which were hidden danger on the cards. Data on food hygiene events from 2002 to 2004 in restaurants of 14 blocks which were located in the important city zone of Qingdao were collected and studied. The spatial distribution was conducted by means of Geographic Information System (GIS). Possible factors related to food hygiene events were investigated and analysed by NCSS Data statistics software. information of every block were marked on digitalized map by ARCVIEW3.2a software in order to show the spatial distribution of food hygiene events palpably in different areas in the course of three years. It was showed that air temperature, humidity, sunlight length were the important factors of food poison. Average amount of guests and floating population related to administration level of sanitation, the level of sanitation administration, geography location, business status of restaurants related to their status of food sanitation. This study showed the method that analysed and studied status of food sanitation from different areas by GIS were effective, simple and palpable.

Image Classification Workflow Using Machine Learning Methods

NASA Astrophysics Data System (ADS)

Christoffersen, M. S.; Roser, M.; Valadez-Vergara, R.; Fernández-Vega, J. A.; Pierce, S. A.; Arora, R.

2016-12-01

Recent increases in the availability and quality of remote sensing datasets have fueled an increasing number of scientifically significant discoveries based on land use classification and land use change analysis. However, much of the software made to work with remote sensing data products, specifically multispectral images, is commercial and often prohibitively expensive. The free to use solutions that are currently available come bundled up as small parts of much larger programs that are very susceptible to bugs and difficult to install and configure. What is needed is a compact, easy to use set of tools to perform land use analysis on multispectral images. To address this need, we have developed software using the Python programming language with the sole function of land use classification and land use change analysis. We chose Python to develop our software because it is relatively readable, has a large body of relevant third party libraries such as GDAL and Spectral Python, and is free to install and use on Windows, Linux, and Macintosh operating systems. In order to test our classification software, we performed a K-means unsupervised classification, Gaussian Maximum Likelihood supervised classification, and a Mahalanobis Distance based supervised classification. The images used for testing were three Landsat rasters of Austin, Texas with a spatial resolution of 60 meters for the years of 1984 and 1999, and 30 meters for the year 2015. The testing dataset was easily downloaded using the Earth Explorer application produced by the USGS. The software should be able to perform classification based on any set of multispectral rasters with little to no modification. Our software makes the ease of land use classification using commercial software available without an expensive license.

Geographic variations of ecosystem service intensity in Fuzhou City, China.

PubMed

Hu, Xisheng; Hong, Wei; Qiu, Rongzu; Hong, Tao; Chen, Can; Wu, Chengzhen

2015-04-15

Ecosystem services are strongly influenced by the landscape configuration of natural and human systems. So they are heterogeneous across landscapes. However lack of the knowledge of spatial variations of ecosystem services constrains the effective management and conservation of ecosystems. We presented a spatially explicit and quantitative assessment of the geographic variations in ecosystem services for the Fuzhou City in 2009 using exploratory spatial data analysis (ESDA) and semivariance analysis. Results confirmed a significant and positive spatial autocorrelation, and revealed several hot-spots and cold-spots for the spatial distribution of ecosystem service intensity (ESI) in the study area. Also the trend surface analysis indicated that the level of ESI tended to be reduced gradually from north to south and from west to east, with a trough in the urban central area, which was quite in accordance with land-use structure. A more precise cluster map was then developed using the range of lag distance, deriving from semivariance analysis, as neighborhood size instead of default value in the software of ESRI ArcGIS 10.0, and geographical clusters where population growth and land-use pressure varied significantly and positively with ESI across the city were also created by geographically weighted regression (GWR). This study has good policy implications applicable to prioritize areas for conservation or construction, and design ecological corridor to improve ecosystem service delivery to benefiting areas. Copyright © 2015 Elsevier B.V. All rights reserved.

MPATHav: A software prototype for multiobjective routing in transportation risk assessment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ganter, J.H.; Smith, J.D.

Most routing problems depend on several important variables: transport distance, population exposure, accident rate, mandated roads (e.g., HM-164 regulations), and proximity to emergency response resources are typical. These variables may need to be minimized or maximized, and often are weighted. `Objectives` to be satisfied by the analysis are thus created. The resulting problems can be approached by combining spatial analysis techniques from geographic information systems (GIS) with multiobjective analysis techniques from the field of operations research (OR); we call this hybrid multiobjective spatial analysis` (MOSA). MOSA can be used to discover, display, and compare a range of solutions that satisfymore » a set of objectives to varying degrees. For instance, a suite of solutions may include: one solution that provides short transport distances, but at a cost of high exposure; another solution that provides low exposure, but long distances; and a range of solutions between these two extremes.« less

Supporting NASA Facilities Through GIS

NASA Technical Reports Server (NTRS)

Ingham, Mary E.

2000-01-01

The NASA GIS Team supports NASA facilities and partners in the analysis of spatial data. Geographic Information System (G[S) is an integration of computer hardware, software, and personnel linking topographic, demographic, utility, facility, image, and other geo-referenced data. The system provides a graphic interface to relational databases and supports decision making processes such as planning, design, maintenance and repair, and emergency response.

Landscape Builder: software for the creation of initial landscapes for LANDIS from FIA data

Treesearch

William Dijak

2013-01-01

I developed Landscape Builder to create spatially explicit landscapes as starting conditions for LANDIS Pro 7.0 and LANDIS II landscape forest simulation models from classified satellite imagery and Forest Inventory and Analysis (FIA) data collected over multiple years. LANDIS Pro and LANDIS II models project future landscapes by simulating tree growth, tree species...

New geospatial approaches for efficiently mapping forest biomass logistics at high resolution over large areas

Treesearch

John Hogland; Nathaniel Anderson; Woodam Chung

2018-01-01

Adequate biomass feedstock supply is an important factor in evaluating the financial feasibility of alternative site locations for bioenergy facilities and for maintaining profitability once a facility is built. We used newly developed spatial analysis and logistics software to model the variables influencing feedstock supply and to estimate and map two components of...

Quantifying forest fragmentation using Geographic Information Systems and Forest Inventory and Analysis plot data

Treesearch

Dacia M. Meneguzzo; Mark H. Hansen

2009-01-01

Fragmentation metrics provide a means of quantifying and describing forest fragmentation. The most common method of calculating these metrics is through the use of Geographic Information System software to analyze raster data, such as a satellite or aerial image of the study area; however, the spatial resolution of the imagery has a significant impact on the results....

TASI: A software tool for spatial-temporal quantification of tumor spheroid dynamics.

PubMed

Hou, Yue; Konen, Jessica; Brat, Daniel J; Marcus, Adam I; Cooper, Lee A D

2018-05-08

Spheroid cultures derived from explanted cancer specimens are an increasingly utilized resource for studying complex biological processes like tumor cell invasion and metastasis, representing an important bridge between the simplicity and practicality of 2-dimensional monolayer cultures and the complexity and realism of in vivo animal models. Temporal imaging of spheroids can capture the dynamics of cell behaviors and microenvironments, and when combined with quantitative image analysis methods, enables deep interrogation of biological mechanisms. This paper presents a comprehensive open-source software framework for Temporal Analysis of Spheroid Imaging (TASI) that allows investigators to objectively characterize spheroid growth and invasion dynamics. TASI performs spatiotemporal segmentation of spheroid cultures, extraction of features describing spheroid morpho-phenotypes, mathematical modeling of spheroid dynamics, and statistical comparisons of experimental conditions. We demonstrate the utility of this tool in an analysis of non-small cell lung cancer spheroids that exhibit variability in metastatic and proliferative behaviors.

The Dynamic Interplay between Spatialization of Written Units in Writing Activity and Functions of Tools on the Computer

ERIC Educational Resources Information Center

Huh, Joo Hee

2012-01-01

I criticize the typewriting model and linear writing structure of Microsoft Word software for writing in the computer. I problematize bodily movement in writing that the error of the software disregards. In this research, writing activity is viewed as bodily, spatial and mediated activity under the premise of the unity of consciousness and…

LANDIS 4.0 users guide. LANDIS: a spatially explicit model of forest landscape disturbance, management, and succession

Treesearch

Hong S. He; Wei Li; Brian R. Sturtevant; Jian Yang; Bo Z. Shang; Eric J. Gustafson; David J. Mladenoff

2005-01-01

LANDIS 4.0 is new-generation software that simulates forest landscape change over large spatial and temporal scales. It is used to explore how disturbances, succession, and management interact to determine forest composition and pattern. Also describes software architecture, model assumptions and provides detailed instructions on the use of the model.

Development of digital reconstructed radiography software at new treatment facility for carbon-ion beam scanning of National Institute of Radiological Sciences.

PubMed

Mori, Shinichiro; Inaniwa, Taku; Kumagai, Motoki; Kuwae, Tsunekazu; Matsuzaki, Yuka; Furukawa, Takuji; Shirai, Toshiyuki; Noda, Koji

2012-06-01

To increase the accuracy of carbon ion beam scanning therapy, we have developed a graphical user interface-based digitally-reconstructed radiograph (DRR) software system for use in routine clinical practice at our center. The DRR software is used in particular scenarios in the new treatment facility to achieve the same level of geometrical accuracy at the treatment as at the imaging session. DRR calculation is implemented simply as the summation of CT image voxel values along the X-ray projection ray. Since we implemented graphics processing unit-based computation, the DRR images are calculated with a speed sufficient for the particular clinical practice requirements. Since high spatial resolution flat panel detector (FPD) images should be registered to the reference DRR images in patient setup process in any scenarios, the DRR images also needs higher spatial resolution close to that of FPD images. To overcome the limitation of the CT spatial resolution imposed by the CT voxel size, we applied image processing to improve the calculated DRR spatial resolution. The DRR software introduced here enabled patient positioning with sufficient accuracy for the implementation of carbon-ion beam scanning therapy at our center.

PLUS: open-source toolkit for ultrasound-guided intervention systems.

PubMed

Lasso, Andras; Heffter, Tamas; Rankin, Adam; Pinter, Csaba; Ungi, Tamas; Fichtinger, Gabor

2014-10-01

A variety of advanced image analysis methods have been under the development for ultrasound-guided interventions. Unfortunately, the transition from an image analysis algorithm to clinical feasibility trials as part of an intervention system requires integration of many components, such as imaging and tracking devices, data processing algorithms, and visualization software. The objective of our paper is to provide a freely available open-source software platform-PLUS: Public software Library for Ultrasound-to facilitate rapid prototyping of ultrasound-guided intervention systems for translational clinical research. PLUS provides a variety of methods for interventional tool pose and ultrasound image acquisition from a wide range of tracking and imaging devices, spatial and temporal calibration, volume reconstruction, simulated image generation, and recording and live streaming of the acquired data. This paper introduces PLUS, explains its functionality and architecture, and presents typical uses and performance in ultrasound-guided intervention systems. PLUS fulfills the essential requirements for the development of ultrasound-guided intervention systems and it aspires to become a widely used translational research prototyping platform. PLUS is freely available as open source software under BSD license and can be downloaded from http://www.plustoolkit.org.

Image sequence analysis workstation for multipoint motion analysis

NASA Astrophysics Data System (ADS)

Mostafavi, Hassan

1990-08-01

This paper describes an application-specific engineering workstation designed and developed to analyze motion of objects from video sequences. The system combines the software and hardware environment of a modem graphic-oriented workstation with the digital image acquisition, processing and display techniques. In addition to automation and Increase In throughput of data reduction tasks, the objective of the system Is to provide less invasive methods of measurement by offering the ability to track objects that are more complex than reflective markers. Grey level Image processing and spatial/temporal adaptation of the processing parameters is used for location and tracking of more complex features of objects under uncontrolled lighting and background conditions. The applications of such an automated and noninvasive measurement tool include analysis of the trajectory and attitude of rigid bodies such as human limbs, robots, aircraft in flight, etc. The system's key features are: 1) Acquisition and storage of Image sequences by digitizing and storing real-time video; 2) computer-controlled movie loop playback, freeze frame display, and digital Image enhancement; 3) multiple leading edge tracking in addition to object centroids at up to 60 fields per second from both live input video or a stored Image sequence; 4) model-based estimation and tracking of the six degrees of freedom of a rigid body: 5) field-of-view and spatial calibration: 6) Image sequence and measurement data base management; and 7) offline analysis software for trajectory plotting and statistical analysis.

Mississippi Company Using NASA Software Program to Provide Unique Imaging Service: DATASTAR Success Story

NASA Technical Reports Server (NTRS)

2001-01-01

DATASTAR, Inc., of Picayune, Miss., has taken NASA's award-winning Earth Resources Laboratory Applications (ELAS) software program and evolved it to the point that the company is now providing a unique, spatial imagery service over the Internet. ELAS was developed in the early 80's to process satellite and airborne sensor imagery data of the Earth's surface into readable and useable information. While there are several software packages on the market that allow the manipulation of spatial data into useable products, this is usually a laborious task. The new program, called the DATASTAR Image Processing Exploitation, or DIPX, Delivery Service, is a subscription service available over the Internet that takes the work out of the equation and provides normalized geo-spatial data in the form of decision products.

Knickpoint finder: A software tool that improves neotectonic analysis

NASA Astrophysics Data System (ADS)

Queiroz, G. L.; Salamuni, E.; Nascimento, E. R.

2015-03-01

This work presents a new software tool for morphometric analysis of drainage networks based on the methods of Hack (1973) and Etchebehere et al. (2004). This tool is applicable to studies of morphotectonics and neotectonics. The software used a digital elevation model (DEM) to identify the relief breakpoints along drainage profiles (knickpoints). The program was coded in Python for use on the ArcGIS platform and is called Knickpoint Finder. A study area was selected to test and evaluate the software's ability to analyze and identify neotectonic morphostructures based on the morphology of the terrain. For an assessment of its validity, we chose an area of the James River basin, which covers most of the Piedmont area of Virginia (USA), which is an area of constant intraplate seismicity and non-orogenic active tectonics and exhibits a relatively homogeneous geodesic surface currently being altered by the seismogenic features of the region. After using the tool in the chosen area, we found that the knickpoint locations are associated with the geologic structures, epicenters of recent earthquakes, and drainages with rectilinear anomalies. The regional analysis demanded the use of a spatial representation of the data after processing using Knickpoint Finder. The results were satisfactory in terms of the correlation of dense areas of knickpoints with active lineaments and the rapidity of the identification of deformed areas. Therefore, this software tool may be considered useful in neotectonic analyses of large areas and may be applied to any area where there is DEM coverage.

Development of a Heterogenic Distributed Environment for Spatial Data Processing Using Cloud Technologies

NASA Astrophysics Data System (ADS)

Garov, A. S.; Karachevtseva, I. P.; Matveev, E. V.; Zubarev, A. E.; Florinsky, I. V.

2016-06-01

We are developing a unified distributed communication environment for processing of spatial data which integrates web-, desktop- and mobile platforms and combines volunteer computing model and public cloud possibilities. The main idea is to create a flexible working environment for research groups, which may be scaled according to required data volume and computing power, while keeping infrastructure costs at minimum. It is based upon the "single window" principle, which combines data access via geoportal functionality, processing possibilities and communication between researchers. Using an innovative software environment the recently developed planetary information system (http://cartsrv.mexlab.ru/geoportal) will be updated. The new system will provide spatial data processing, analysis and 3D-visualization and will be tested based on freely available Earth remote sensing data as well as Solar system planetary images from various missions. Based on this approach it will be possible to organize the research and representation of results on a new technology level, which provides more possibilities for immediate and direct reuse of research materials, including data, algorithms, methodology, and components. The new software environment is targeted at remote scientific teams, and will provide access to existing spatial distributed information for which we suggest implementation of a user interface as an advanced front-end, e.g., for virtual globe system.

PROS: An IRAF based system for analysis of x ray data

NASA Technical Reports Server (NTRS)

Conroy, M. A.; Deponte, J.; Moran, J. F.; Orszak, J. S.; Roberts, W. P.; Schmidt, D.

1992-01-01

PROS is an IRAF based software package for the reduction and analysis of x-ray data. The use of a standard, portable, integrated environment provides for both multi-frequency and multi-mission analysis. The analysis of x-ray data differs from optical analysis due to the nature of the x-ray data and its acquisition during constantly varying conditions. The scarcity of data, the low signal-to-noise ratio and the large gaps in exposure time make data screening and masking an important part of the analysis. PROS was developed to support the analysis of data from the ROSAT and Einstein missions but many of the tasks have been used on data from other missions. IRAF/PROS provides a complete end-to-end system for x-ray data analysis: (1) a set of tools for importing and exporting data via FITS format -- in particular, IRAF provides a specialized event-list format, QPOE, that is compatible with its IMAGE (2-D array) format; (2) a powerful set of IRAF system capabilities for both temporal and spatial event filtering; (3) full set of imaging and graphics tasks; (4) specialized packages for scientific analysis such as spatial, spectral and timing analysis -- these consist of both general and mission specific tasks; and (5) complete system support including ftp and magnetic tape releases, electronic and conventional mail hotline support, electronic mail distribution of solutions to frequently asked questions and current known bugs. We will discuss the philosophy, architecture and development environment used by PROS to generate a portable, multimission software environment. PROS is available on all platforms that support IRAF, including Sun/Unix, VAX/VMS, HP, and Decstations. It is available on request at no charge.

Comparison of existing digital image analysis systems for the analysis of Thematic Mapper data

NASA Technical Reports Server (NTRS)

Likens, W. C.; Wrigley, R. C.

1984-01-01

Most existing image analysis systems were designed with the Landsat Multi-Spectral Scanner in mind, leaving open the question of whether or not these systems could adequately process Thematic Mapper data. In this report, both hardware and software systems have been evaluated for compatibility with TM data. Lack of spectral analysis capability was not found to be a problem, though techniques for spatial filtering and texture varied. Computer processing speed and data storage of currently existing mini-computer based systems may be less than adequate. Upgrading to more powerful hardware may be required for many TM applications.

MOLNs: A CLOUD PLATFORM FOR INTERACTIVE, REPRODUCIBLE, AND SCALABLE SPATIAL STOCHASTIC COMPUTATIONAL EXPERIMENTS IN SYSTEMS BIOLOGY USING PyURDME.

PubMed

Drawert, Brian; Trogdon, Michael; Toor, Salman; Petzold, Linda; Hellander, Andreas

2016-01-01

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools and a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments.

Characterization of Fragment Spatial Distribution From Arena Testing Using Photo Analysis Software

DTIC Science & Technology

2013-03-01

This created an imperfect representation of the area the capture packs covered so empty sections of the canvas in Photoshop were filled in black. This...Arlington, VA 22202-4302. Respondents should be aware that notwithstanding any other provision of law, no person shall be subject to any penalty for...AFCEC-1316, 12 April 2013 TABLE OF CONTENTS LIST OF FIGURES

Cost Analysis of Spatial Data Production as Part of Business Intelligence Within the Mapping Department

NASA Astrophysics Data System (ADS)

Kisa, A.; Erkek, B.; Çolak, S.

2012-07-01

Business intelligence is becoming an important strategic tool for business management. Companies have invested significant resources in applications for customer relationship management (CRM), supply chain management (SCM), enterprise resource planning (ERP), e-commerce, among others, which collect vast amounts of data. Today, these same companies are realizing that no matter how robust their application feature sets are, without an equally robust BI mechanism to make use of the collected data, these applications are ultimately coming up short. They do not provide actionable information to end users nor can they give a global understanding among all the organization's information from the various databases for accounting, CRM, and so on. General Directorate of Land Registry and Cadastre (GDLRC) is the leader organizations in Turkey on the field of mapping-land registry-cadastre. GDLRC has executed spatial based projects on the way National Spatial Data Infrastructure especially from the beginnings of 2000s. such as; Continuously Operating GPS Reference Stations (TUSAGA-Aktif), Geo-Metadata Portal (HBB), Orthophoto-Base Map Production and web services, Completion of Initial Cadastre, Cadastral Renovation Project (TKMP), Land Registry and Cadastre Information System (TAKBIS), Turkish National Spatial Data Infrastructure Project (TNSDI), Ottoman Land Registry Archive Information System (TARBIS). Most of this project has been completed. Some software has been developed within the mentioned project, especially reporting for management level to take decision. In the year of 2010 a new law launched and forced to reorganization of General Directorate of Land Registry and Cadastre. The new structural changes effected to whole organization, management understanding, carrier understanding so on. Even in mapping department which is spatial data producer, now there is no technician, there is no section; there are new carrier as experts. Because of that, all procedures and performance critters are redefined, improvement of existing software are defined, cost analysis implemented as a part of business intelligence. This paper indicated some activities such as cost analysis and its reflection in Mapping Department as an example to share in the concept of reorganization.

Demand-supply dynamics in tourism systems: A spatio-temporal GIS analysis. The Alberta ski industry case study

NASA Astrophysics Data System (ADS)

Bertazzon, Stefania

The present research focuses on the interaction of supply and demand of down-hill ski tourism in the province of Alberta. The main hypothesis is that the demand for skiing depends on the socio-economic and demographic characteristics of the population living in the province and outside it. A second, consequent hypothesis is that the development of ski resorts (supply) is a response to the demand for skiing. From the latter derives the hypothesis of a dynamic interaction between supply (ski resorts) and demand (skiers). Such interaction occurs in space, within a range determined by physical distance and the means available to overcome it. The above hypotheses implicitly define interactions that take place in space and evolve over time. The hypotheses are tested by temporal, spatial, and spatio-temporal regression models, using the best available data and the latest commercially available software. The main purpose of this research is to explore analytical techniques to model spatial, temporal, and spatio-temporal dynamics in the context of regional science. The completion of the present research has produced more significant contributions than was originally expected. Many of the unexpected contributions resulted from theoretical and applied needs arising from the application of spatial regression models. Spatial regression models are a new and largely under-applied technique. The models are fairly complex and a considerable amount of preparatory work is needed, prior to their specification and estimation. Most of this work is specific to the field of application. The originality of the solutions devised is increased by the lack of applications in the field of tourism. The scarcity of applications in other fields adds to their value for other applications. The estimation of spatio-temporal models has been only partially attained in the present research. This apparent limitation is due to the novelty and complexity of the analytical methods applied. This opens new directions for further work in the field of spatial analysis, in conjunction with the development of specific software.

Utilization of Solar Dynamics Observatory space weather digital image data for comparative analysis with application to Baryon Oscillation Spectroscopic Survey

NASA Astrophysics Data System (ADS)

Shekoyan, V.; Dehipawala, S.; Liu, Ernest; Tulsee, Vivek; Armendariz, R.; Tremberger, G.; Holden, T.; Marchese, P.; Cheung, T.

2012-10-01

Digital solar image data is available to users with access to standard, mass-market software. Many scientific projects utilize the Flexible Image Transport System (FITS) format, which requires specialized software typically used in astrophysical research. Data in the FITS format includes photometric and spatial calibration information, which may not be useful to researchers working with self-calibrated, comparative approaches. This project examines the advantages of using mass-market software with readily downloadable image data from the Solar Dynamics Observatory for comparative analysis over with the use of specialized software capable of reading data in the FITS format. Comparative analyses of brightness statistics that describe the solar disk in the study of magnetic energy using algorithms included in mass-market software have been shown to give results similar to analyses using FITS data. The entanglement of magnetic energy associated with solar eruptions, as well as the development of such eruptions, has been characterized successfully using mass-market software. The proposed algorithm would help to establish a publicly accessible, computing network that could assist in exploratory studies of all FITS data. The advances in computer, cell phone and tablet technology could incorporate such an approach readily for the enhancement of high school and first-year college space weather education on a global scale. Application to ground based data such as that contained in the Baryon Oscillation Spectroscopic Survey is discussed.

`spup' - An R Package for Analysis of Spatial Uncertainty Propagation and Application to Trace Gas Emission Simulations

NASA Astrophysics Data System (ADS)

Sawicka, K.; Breuer, L.; Houska, T.; Santabarbara Ruiz, I.; Heuvelink, G. B. M.

2016-12-01

Computer models have become a crucial tool in engineering and environmental sciences for simulating the behaviour of complex static and dynamic systems. However, while many models are deterministic, the uncertainty in their predictions needs to be estimated before they are used for decision support. Advances in uncertainty propagation analysis and assessment have been paralleled by a growing number of software tools for uncertainty analysis, but none has gained recognition for a universal applicability, including case studies with spatial models and spatial model inputs. Due to the growing popularity and applicability of the open source R programming language we undertook a project to develop an R package that facilitates uncertainty propagation analysis in spatial environmental modelling. In particular, the `spup' package provides functions for examining the uncertainty propagation starting from input data and model parameters, via the environmental model onto model predictions. The functions include uncertainty model specification, stochastic simulation and propagation of uncertainty using Monte Carlo techniques, as well as several uncertainty visualization functions. Here we will demonstrate that the 'spup' package is an effective and easy-to-use tool to be applied even in a very complex study case, and that it can be used in multi-disciplinary research and model-based decision support. As an example, we use the ecological LandscapeDNDC model to analyse propagation of uncertainties associated with spatial variability of the model driving forces such as rainfall, nitrogen deposition and fertilizer inputs. The uncertainty propagation is analysed for the prediction of emissions of N2O and CO2 for a German low mountainous, agriculturally developed catchment. The study tests the effect of spatial correlations on spatially aggregated model outputs, and could serve as an advice for developing best management practices and model improvement strategies.

A framework for incorporating DTI Atlas Builder registration into Tract-Based Spatial Statistics and a simulated comparison to standard TBSS.

PubMed

Leming, Matthew; Steiner, Rachel; Styner, Martin

2016-02-27

Tract-based spatial statistics (TBSS) 6 is a software pipeline widely employed in comparative analysis of the white matter integrity from diffusion tensor imaging (DTI) datasets. In this study, we seek to evaluate the relationship between different methods of atlas registration for use with TBSS and different measurements of DTI (fractional anisotropy, FA, axial diffusivity, AD, radial diffusivity, RD, and medial diffusivity, MD). To do so, we have developed a novel tool that builds on existing diffusion atlas building software, integrating it into an adapted version of TBSS called DAB-TBSS (DTI Atlas Builder-Tract-Based Spatial Statistics) by using the advanced registration offered in DTI Atlas Builder 7 . To compare the effectiveness of these two versions of TBSS, we also propose a framework for simulating population differences for diffusion tensor imaging data, providing a more substantive means of empirically comparing DTI group analysis programs such as TBSS. In this study, we used 33 diffusion tensor imaging datasets and simulated group-wise changes in this data by increasing, in three different simulations, the principal eigenvalue (directly altering AD), the second and third eigenvalues (RD), and all three eigenvalues (MD) in the genu, the right uncinate fasciculus, and the left IFO. Additionally, we assessed the benefits of comparing the tensors directly using a functional analysis of diffusion tensor tract statistics (FADTTS 10 ). Our results indicate comparable levels of FA-based detection between DAB-TBSS and TBSS, with standard TBSS registration reporting a higher rate of false positives in other measurements of DTI. Within the simulated changes investigated here, this study suggests that the use of DTI Atlas Builder's registration enhances TBSS group-based studies.

Systems, methods, and software for determining spatially variable distributions of the dielectric properties of a heterogeneous material

DOE Office of Scientific and Technical Information (OSTI.GOV)

Farrington, Stephen P.

Systems, methods, and software for measuring the spatially variable relative dielectric permittivity of materials along a linear or otherwise configured sensor element, and more specifically the spatial variability of soil moisture in one dimension as inferred from the dielectric profile of the soil matrix surrounding a linear sensor element. Various methods provided herein combine advances in the processing of time domain reflectometry data with innovations in physical sensing apparatuses. These advancements enable high temporal (and thus spatial) resolution of electrical reflectance continuously along an insulated waveguide that is permanently emplaced in contact with adjacent soils. The spatially resolved reflectance ismore » directly related to impedance changes along the waveguide that are dominated by electrical permittivity contrast due to variations in soil moisture. Various methods described herein are thus able to monitor soil moisture in profile with high spatial resolution.« less

Hail Size Distribution Mapping

NASA Technical Reports Server (NTRS)

2008-01-01

A 3-D weather radar visualization software program was developed and implemented as part of an experimental Launch Pad 39 Hail Monitor System. 3DRadPlot, a radar plotting program, is one of several software modules that form building blocks of the hail data processing and analysis system (the complete software processing system under development). The spatial and temporal mapping algorithms were originally developed through research at the University of Central Florida, funded by NASA s Tropical Rainfall Measurement Mission (TRMM), where the goal was to merge National Weather Service (NWS) Next-Generation Weather Radar (NEXRAD) volume reflectivity data with drop size distribution data acquired from a cluster of raindrop disdrometers. In this current work, we adapted these algorithms to process data from a cluster of hail disdrometers positioned around Launch Pads 39A or 39B, along with the corresponding NWS radar data. Radar data from all NWS NEXRAD sites is archived at the National Climatic Data Center (NCDC). That data can be readily accessed at . 3DRadPlot plots Level III reflectivity data at four scan elevations (this software is available at Open Channel Software, ). By using spatial and temporal interpolation/extrapolation based on hydrometeor fall dynamics, we can merge the hail disdrometer array data coupled with local Weather Surveillance Radar-1988, Doppler (WSR-88D) radial velocity and reflectivity data into a 4-D (3-D space and time) picture of hail size distributions. Hail flux maps can then be generated and used for damage prediction and assessment over specific surfaces corresponding to structures within the disdrometer array volume. Immediately following a hail storm, specific damage areas and degree of damage can be identified for inspection crews.

Monitoring Method of Cow Anthrax Based on Gis and Spatial Statistical Analysis

NASA Astrophysics Data System (ADS)

Li, Lin; Yang, Yong; Wang, Hongbin; Dong, Jing; Zhao, Yujun; He, Jianbin; Fan, Honggang

Geographic information system (GIS) is a computer application system, which possesses the ability of manipulating spatial information and has been used in many fields related with the spatial information management. Many methods and models have been established for analyzing animal diseases distribution models and temporal-spatial transmission models. Great benefits have been gained from the application of GIS in animal disease epidemiology. GIS is now a very important tool in animal disease epidemiological research. Spatial analysis function of GIS can be widened and strengthened by using spatial statistical analysis, allowing for the deeper exploration, analysis, manipulation and interpretation of spatial pattern and spatial correlation of the animal disease. In this paper, we analyzed the cow anthrax spatial distribution characteristics in the target district A (due to the secret of epidemic data we call it district A) based on the established GIS of the cow anthrax in this district in combination of spatial statistical analysis and GIS. The Cow anthrax is biogeochemical disease, and its geographical distribution is related closely to the environmental factors of habitats and has some spatial characteristics, and therefore the correct analysis of the spatial distribution of anthrax cow for monitoring and the prevention and control of anthrax has a very important role. However, the application of classic statistical methods in some areas is very difficult because of the pastoral nomadic context. The high mobility of livestock and the lack of enough suitable sampling for the some of the difficulties in monitoring currently make it nearly impossible to apply rigorous random sampling methods. It is thus necessary to develop an alternative sampling method, which could overcome the lack of sampling and meet the requirements for randomness. The GIS computer application software ArcGIS9.1 was used to overcome the lack of data of sampling sites.Using ArcGIS 9.1 and GEODA to analyze the cow anthrax spatial distribution of district A. we gained some conclusions about cow anthrax' density: (1) there is a spatial clustering model. (2) there is an intensely spatial autocorrelation. We established a prediction model to estimate the anthrax distribution based on the spatial characteristic of the density of cow anthrax. Comparing with the true distribution, the prediction model has a well coincidence and is feasible to the application. The method using a GIS tool facilitates can be implemented significantly in the cow anthrax monitoring and investigation, and the space statistics - related prediction model provides a fundamental use for other study on space-related animal diseases.

Geographic Information Systems and Web Page Development

NASA Technical Reports Server (NTRS)

Reynolds, Justin

2004-01-01

The Facilities Engineering and Architectural Branch is responsible for the design and maintenance of buildings, laboratories, and civil structures. In order to improve efficiency and quality, the FEAB has dedicated itself to establishing a data infrastructure based on Geographic Information Systems, GIS. The value of GIS was explained in an article dating back to 1980 entitled "Need for a Multipurpose Cadastre" which stated, "There is a critical need for a better land-information system in the United States to improve land-conveyance procedures, furnish a basis for equitable taxation, and provide much-needed information for resource management and environmental planning." Scientists and engineers both point to GIS as the solution. What is GIS? According to most text books, Geographic Information Systems is a class of software that stores, manages, and analyzes mapable features on, above, or below the surface of the earth. GIS software is basically database management software to the management of spatial data and information. Simply put, Geographic Information Systems manage, analyze, chart, graph, and map spatial information. GIS can be broken down into two main categories, urban GIS and natural resource GIS. Further still, natural resource GIS can be broken down into six sub-categories, agriculture, forestry, wildlife, catchment management, archaeology, and geology/mining. Agriculture GIS has several applications, such as agricultural capability analysis, land conservation, market analysis, or whole farming planning. Forestry GIs can be used for timber assessment and management, harvest scheduling and planning, environmental impact assessment, and pest management. GIS when used in wildlife applications enables the user to assess and manage habitats, identify and track endangered and rare species, and monitor impact assessment.

Applying spatial analysis tools in public health: an example using SaTScan to detect geographic targets for colorectal cancer screening interventions.

PubMed

Sherman, Recinda L; Henry, Kevin A; Tannenbaum, Stacey L; Feaster, Daniel J; Kobetz, Erin; Lee, David J

2014-03-20

Epidemiologists are gradually incorporating spatial analysis into health-related research as geocoded cases of disease become widely available and health-focused geospatial computer applications are developed. One health-focused application of spatial analysis is cluster detection. Using cluster detection to identify geographic areas with high-risk populations and then screening those populations for disease can improve cancer control. SaTScan is a free cluster-detection software application used by epidemiologists around the world to describe spatial clusters of infectious and chronic disease, as well as disease vectors and risk factors. The objectives of this article are to describe how spatial analysis can be used in cancer control to detect geographic areas in need of colorectal cancer screening intervention, identify issues commonly encountered by SaTScan users, detail how to select the appropriate methods for using SaTScan, and explain how method selection can affect results. As an example, we used various methods to detect areas in Florida where the population is at high risk for late-stage diagnosis of colorectal cancer. We found that much of our analysis was underpowered and that no single method detected all clusters of statistical or public health significance. However, all methods detected 1 area as high risk; this area is potentially a priority area for a screening intervention. Cluster detection can be incorporated into routine public health operations, but the challenge is to identify areas in which the burden of disease can be alleviated through public health intervention. Reliance on SaTScan's default settings does not always produce pertinent results.

A new spatial multi-criteria decision support tool for site selection for implementation of managed aquifer recharge.

PubMed

Rahman, M Azizur; Rusteberg, Bernd; Gogu, R C; Lobo Ferreira, J P; Sauter, Martin

2012-05-30

This study reports the development of a new spatial multi-criteria decision analysis (SMCDA) software tool for selecting suitable sites for Managed Aquifer Recharge (MAR) systems. The new SMCDA software tool functions based on the combination of existing multi-criteria evaluation methods with modern decision analysis techniques. More specifically, non-compensatory screening, criteria standardization and weighting, and Analytical Hierarchy Process (AHP) have been combined with Weighted Linear Combination (WLC) and Ordered Weighted Averaging (OWA). This SMCDA tool may be implemented with a wide range of decision maker's preferences. The tool's user-friendly interface helps guide the decision maker through the sequential steps for site selection, those steps namely being constraint mapping, criteria hierarchy, criteria standardization and weighting, and criteria overlay. The tool offers some predetermined default criteria and standard methods to increase the trade-off between ease-of-use and efficiency. Integrated into ArcGIS, the tool has the advantage of using GIS tools for spatial analysis, and herein data may be processed and displayed. The tool is non-site specific, adaptive, and comprehensive, and may be applied to any type of site-selection problem. For demonstrating the robustness of the new tool, a case study was planned and executed at Algarve Region, Portugal. The efficiency of the SMCDA tool in the decision making process for selecting suitable sites for MAR was also demonstrated. Specific aspects of the tool such as built-in default criteria, explicit decision steps, and flexibility in choosing different options were key features, which benefited the study. The new SMCDA tool can be augmented by groundwater flow and transport modeling so as to achieve a more comprehensive approach to the selection process for the best locations of the MAR infiltration basins, as well as the locations of recovery wells and areas of groundwater protection. The new spatial multicriteria analysis tool has already been implemented within the GIS based Gabardine decision support system as an innovative MAR planning tool. Copyright © 2012 Elsevier Ltd. All rights reserved.

Segment fusion of ToF-SIMS images.

PubMed

Milillo, Tammy M; Miller, Mary E; Fischione, Remo; Montes, Angelina; Gardella, Joseph A

2016-06-08

The imaging capabilities of time-of-flight secondary ion mass spectrometry (ToF-SIMS) have not been used to their full potential in the analysis of polymer and biological samples. Imaging has been limited by the size of the dataset and the chemical complexity of the sample being imaged. Pixel and segment based image fusion algorithms commonly used in remote sensing, ecology, geography, and geology provide a way to improve spatial resolution and classification of biological images. In this study, a sample of Arabidopsis thaliana was treated with silver nanoparticles and imaged with ToF-SIMS. These images provide insight into the uptake mechanism for the silver nanoparticles into the plant tissue, giving new understanding to the mechanism of uptake of heavy metals in the environment. The Munechika algorithm was programmed in-house and applied to achieve pixel based fusion, which improved the spatial resolution of the image obtained. Multispectral and quadtree segment or region based fusion algorithms were performed using ecognition software, a commercially available remote sensing software suite, and used to classify the images. The Munechika fusion improved the spatial resolution for the images containing silver nanoparticles, while the segment fusion allowed classification and fusion based on the tissue types in the sample, suggesting potential pathways for the uptake of the silver nanoparticles.

Simulation of Hyperspectral Images

NASA Technical Reports Server (NTRS)

Richsmeier, Steven C.; Singer-Berk, Alexander; Bernstein, Lawrence S.

2004-01-01

A software package generates simulated hyperspectral imagery for use in validating algorithms that generate estimates of Earth-surface spectral reflectance from hyperspectral images acquired by airborne and spaceborne instruments. This software is based on a direct simulation Monte Carlo approach for modeling three-dimensional atmospheric radiative transport, as well as reflections from surfaces characterized by spatially inhomogeneous bidirectional reflectance distribution functions. In this approach, "ground truth" is accurately known through input specification of surface and atmospheric properties, and it is practical to consider wide variations of these properties. The software can treat both land and ocean surfaces, as well as the effects of finite clouds with surface shadowing. The spectral/spatial data cubes computed by use of this software can serve both as a substitute for, and a supplement to, field validation data.

WaveAR: A software tool for calculating parameters for water waves with incident and reflected components

NASA Astrophysics Data System (ADS)

Landry, Blake J.; Hancock, Matthew J.; Mei, Chiang C.; García, Marcelo H.

2012-09-01

The ability to determine wave heights and phases along a spatial domain is vital to understanding a wide range of littoral processes. The software tool presented here employs established Stokes wave theory and sampling methods to calculate parameters for the incident and reflected components of a field of weakly nonlinear waves, monochromatic at first order in wave slope and propagating in one horizontal dimension. The software calculates wave parameters over an entire wave tank and accounts for reflection, weak nonlinearity, and a free second harmonic. Currently, no publicly available program has such functionality. The included MATLAB®-based open source code has also been compiled for Windows®, Mac® and Linux® operating systems. An additional companion program, VirtualWave, is included to generate virtual wave fields for WaveAR. Together, the programs serve as ideal analysis and teaching tools for laboratory water wave systems.

The analysis of the accuracy of spatial models using photogrammetric software: Agisoft Photoscan and Pix4D

NASA Astrophysics Data System (ADS)

Barbasiewicz, Adrianna; Widerski, Tadeusz; Daliga, Karol

2018-01-01

This article was created as a result of research conducted within the master thesis. The purpose of the measurements was to analyze the accuracy of the positioning of points by computer programs. Selected software was a specialized computer software dedicated to photogrammetric work. For comparative purposes it was decided to use tools with similar functionality. As the basic parameters that affect the results selected the resolution of the photos on which the key points were searched. In order to determine the location of the determined points, it was decided to follow the photogrammetric resection rule. In order to automate the measurement, the measurement session planning was omitted. The coordinates of the points collected by the tachymetric measure were used as a reference system. The resulting deviations and linear displacements oscillate in millimeters. The visual aspects of the cloud points have also been briefly analyzed.

Spatial regression analysis of traffic crashes in Seoul.

PubMed

Rhee, Kyoung-Ah; Kim, Joon-Ki; Lee, Young-ihn; Ulfarsson, Gudmundur F

2016-06-01

Traffic crashes can be spatially correlated events and the analysis of the distribution of traffic crash frequency requires evaluation of parameters that reflect spatial properties and correlation. Typically this spatial aspect of crash data is not used in everyday practice by planning agencies and this contributes to a gap between research and practice. A database of traffic crashes in Seoul, Korea, in 2010 was developed at the traffic analysis zone (TAZ) level with a number of GIS developed spatial variables. Practical spatial models using available software were estimated. The spatial error model was determined to be better than the spatial lag model and an ordinary least squares baseline regression. A geographically weighted regression model provided useful insights about localization of effects. The results found that an increased length of roads with speed limit below 30 km/h and a higher ratio of residents below age of 15 were correlated with lower traffic crash frequency, while a higher ratio of residents who moved to the TAZ, more vehicle-kilometers traveled, and a greater number of access points with speed limit difference between side roads and mainline above 30 km/h all increased the number of traffic crashes. This suggests, for example, that better control or design for merging lower speed roads with higher speed roads is important. A key result is that the length of bus-only center lanes had the largest effect on increasing traffic crashes. This is important as bus-only center lanes with bus stop islands have been increasingly used to improve transit times. Hence the potential negative safety impacts of such systems need to be studied further and mitigated through improved design of pedestrian access to center bus stop islands. Copyright © 2016 Elsevier Ltd. All rights reserved.

Automated Video-Based Analysis of Contractility and Calcium Flux in Human-Induced Pluripotent Stem Cell-Derived Cardiomyocytes Cultured over Different Spatial Scales.

PubMed

Huebsch, Nathaniel; Loskill, Peter; Mandegar, Mohammad A; Marks, Natalie C; Sheehan, Alice S; Ma, Zhen; Mathur, Anurag; Nguyen, Trieu N; Yoo, Jennie C; Judge, Luke M; Spencer, C Ian; Chukka, Anand C; Russell, Caitlin R; So, Po-Lin; Conklin, Bruce R; Healy, Kevin E

2015-05-01

Contractile motion is the simplest metric of cardiomyocyte health in vitro, but unbiased quantification is challenging. We describe a rapid automated method, requiring only standard video microscopy, to analyze the contractility of human-induced pluripotent stem cell-derived cardiomyocytes (iPS-CM). New algorithms for generating and filtering motion vectors combined with a newly developed isogenic iPSC line harboring genetically encoded calcium indicator, GCaMP6f, allow simultaneous user-independent measurement and analysis of the coupling between calcium flux and contractility. The relative performance of these algorithms, in terms of improving signal to noise, was tested. Applying these algorithms allowed analysis of contractility in iPS-CM cultured over multiple spatial scales from single cells to three-dimensional constructs. This open source software was validated with analysis of isoproterenol response in these cells, and can be applied in future studies comparing the drug responsiveness of iPS-CM cultured in different microenvironments in the context of tissue engineering.

USING THE ECLPSS SOFTWARE ENVIRONMENT TO BUILD A SPATIALLY EXPLICIT COMPONENT-BASED MODEL OF OZONE EFFECTS ON FOREST ECOSYSTEMS. (R827958)

EPA Science Inventory

We have developed a modeling framework to support grid-based simulation of ecosystems at multiple spatial scales, the Ecological Component Library for Parallel Spatial Simulation (ECLPSS). ECLPSS helps ecologists to build robust spatially explicit simulations of ...

[Analysis of epidemic features of scrub typhus between year 2006 and 2010 in Shandong province, China].

PubMed

Ding, Lei; Li, Zhong; Wang, Xian-jun; Ding, Shu-jun; Zhang, Meng; Zhao, Zhong-tang

2012-04-01

To explore the epidemic features of scrub typhus between year 2006 and 2010 in Shandong Province. Based on the data collected through Diseases Reporting Information System between year 2006 and 2010 in Shandong province, 1291 cases of scrub typhus were selected. The study described the population distribution features of the scrub typhus patients, and explored the temporal and spatial distribution features of the disease by applying the methods of spatial thematic mapping, inverse distance weighted, spatial autocorrelation analysis, spatial clustering analysis, temporal clustering analysis and spatial variation analysis in temporal trends based on Geographic Information software (ArcGIS 9.3) and Spatial Clustering Software (SatScan 7.0). The onset age of the 1291 patients ranged between 1 and 92 years old.639 out of 1291 patients were over 55 years old, accounting for 49.5%.640 patients were male and the other 651 patients were female, occupying 49.6% and 50.4% respectively. The gender ratio was 1:1.02. Patients were found in farmers, workers, students and preschool children. However, most of the cases were farmers, up to 84.8% (1095/1291). Global Moran's I index was 0.324 (P < 0.01). The local Moran's I index in 8 locations were proved to have statistical significance (P < 0.01); all of which were H-H clustering areas. Gangcheng (38 cases), Laicheng (154 cases), Xintai (160 cases) and Donggang (105 cases) were important locations, whose local Moran's I index were 2.111, 1.642, 1.277 and 0.775 respectively. The clustering period of scrub typhus in respective year were as follows: 2006.09.23 - 2006.11.20 (202 cases), 2007.10.02 - 2007.11.11 (197 cases), 2008.09.30 - 2008.11.07 (302 cases), 2009.09.25 - 2009.11.10 (204 cases), and 2010.10.05 - 2010.11.13 (226 cases), whose RR values were separately 45.55, 34.60, 50.64, 53.09 and 79.84 (P < 0.01). Two spatial clustering area were found in the study, one was the area centered Taian and Xintai with radiation radius at 58.28 km (542 cases) and the other one was the area centered Rizhao and Donggang with radiation radius at 22.68 km (134 cases), whose RR values were 4.52 and 3.96 (P < 0.01). The spatial features of the two clustering areas were inland low hills area and coastal hills area. The highest annual growth rate of the disease was 45.04%, found in the area centered Linyi and Mengyin counties, with the radiation radius at 45.82 km. The RR value was 3.68 (P < 0.01). The majority of the scrub typhus patients were middle-aged and elderly farmers. The epidemic peak was between the last 10 days of September and the first 10 days of November. A positive spatial correlation of the disease was found; and most cases clustered in inland low hills area and costal hills area; especially the area around Linyi and Mengyin, with the highest annual growth rates of the disease.

A Study on Environmental Research Trends Using Text-Mining Method - Focus on Spatial information and ICT -

NASA Astrophysics Data System (ADS)

Lee, M. J.; Oh, K. Y.; Joung-ho, L.

2016-12-01

Recently there are many research about analysing the interaction between entities by text-mining analysis in various fields. In this paper, we aimed to quantitatively analyse research-trends in the area of environmental research relating either spatial information or ICT (Information and Communications Technology) by Text-mining analysis. To do this, we applied low-dimensional embedding method, clustering analysis, and association rule to find meaningful associative patterns of key words frequently appeared in the articles. As the authors suppose that KCI (Korea Citation Index) articles reflect academic demands, total 1228 KCI articles that have been published from 1996 to 2015 were reviewed and analysed by Text-mining method. First, we derived KCI articles from NDSL(National Discovery for Science Leaders) site. And then we pre-processed their key-words elected from abstract and then classified those in separable sectors. We investigated the appearance rates and association rule of key-words for articles in the two fields: spatial-information and ICT. In order to detect historic trends, analysis was conducted separately for the four periods: 1996-2000, 2001-2005, 2006-2010, 2011-2015. These analysis were conducted with the usage of R-software. As a result, we conformed that environmental research relating spatial information mainly focused upon such fields as `GIS(35%)', `Remote-Sensing(25%)', `environmental theme map(15.7%)'. Next, `ICT technology(23.6%)', `ICT service(5.4%)', `mobile(24%)', `big data(10%)', `AI(7%)' are primarily emerging from environmental research relating ICT. Thus, from the analysis results, this paper asserts that research trends and academic progresses are well-structured to review recent spatial information and ICT technology and the outcomes of the analysis can be an adequate guidelines to establish environment policies and strategies. KEY WORDS: Big data, Test-mining, Environmental research, Spatial-information, ICT Acknowledgements: The authors appreciate the support that this study has received from `Building application frame of environmental issues, to respond to the latest ICT trends'.

Spatiotemporal analysis of dengue fever in Nepal from 2010 to 2014.

PubMed

Acharya, Bipin Kumar; Cao, ChunXiang; Lakes, Tobia; Chen, Wei; Naeem, Shahid

2016-08-22

Due to recent emergence, dengue is becoming one of the major public health problems in Nepal. The numbers of reported dengue cases in general and the area with reported dengue cases are both continuously increasing in recent years. However, spatiotemporal patterns and clusters of dengue have not been investigated yet. This study aims to fill this gap by analyzing spatiotemporal patterns based on monthly surveillance data aggregated at district. Dengue cases from 2010 to 2014 at district level were collected from the Nepal government's health and mapping agencies respectively. GeoDa software was used to map crude incidence, excess hazard and spatially smoothed incidence. Cluster analysis was performed in SaTScan software to explore spatiotemporal clusters of dengue during the above-mentioned time period. Spatiotemporal distribution of dengue fever in Nepal from 2010 to 2014 was mapped at district level in terms of crude incidence, excess risk and spatially smoothed incidence. Results show that the distribution of dengue fever was not random but clustered in space and time. Chitwan district was identified as the most likely cluster and Jhapa district was the first secondary cluster in both spatial and spatiotemporal scan. July to September of 2010 was identified as a significant temporal cluster. This study assessed and mapped for the first time the spatiotemporal pattern of dengue fever in Nepal. Two districts namely Chitwan and Jhapa were found highly affected by dengue fever. The current study also demonstrated the importance of geospatial approach in epidemiological research. The initial result on dengue patterns and risk of this study may assist institutions and policy makers to develop better preventive strategies.

iGlobe Interactive Visualization and Analysis of Spatial Data

NASA Technical Reports Server (NTRS)

Hogan, Patrick

2012-01-01

iGlobe is open-source software built on NASA World Wind virtual globe technology. iGlobe provides a growing set of tools for weather science, climate research, and agricultural analysis. Up until now, these types of sophisticated tools have been developed in isolation by national agencies, academic institutions, and research organizations. By providing an open-source solution to analyze and visualize weather, climate, and agricultural data, the scientific and research communities can more readily advance solutions needed to understand better the dynamics of our home planet, Earth

Spatial 3D infrastructure: display-independent software framework, high-speed rendering electronics, and several new displays

NASA Astrophysics Data System (ADS)

Chun, Won-Suk; Napoli, Joshua; Cossairt, Oliver S.; Dorval, Rick K.; Hall, Deirdre M.; Purtell, Thomas J., II; Schooler, James F.; Banker, Yigal; Favalora, Gregg E.

2005-03-01

We present a software and hardware foundation to enable the rapid adoption of 3-D displays. Different 3-D displays - such as multiplanar, multiview, and electroholographic displays - naturally require different rendering methods. The adoption of these displays in the marketplace will be accelerated by a common software framework. The authors designed the SpatialGL API, a new rendering framework that unifies these display methods under one interface. SpatialGL enables complementary visualization assets to coexist through a uniform infrastructure. Also, SpatialGL supports legacy interfaces such as the OpenGL API. The authors" first implementation of SpatialGL uses multiview and multislice rendering algorithms to exploit the performance of modern graphics processing units (GPUs) to enable real-time visualization of 3-D graphics from medical imaging, oil & gas exploration, and homeland security. At the time of writing, SpatialGL runs on COTS workstations (both Windows and Linux) and on Actuality"s high-performance embedded computational engine that couples an NVIDIA GeForce 6800 Ultra GPU, an AMD Athlon 64 processor, and a proprietary, high-speed, programmable volumetric frame buffer that interfaces to a 1024 x 768 x 3 digital projector. Progress is illustrated using an off-the-shelf multiview display, Actuality"s multiplanar Perspecta Spatial 3D System, and an experimental multiview display. The experimental display is a quasi-holographic view-sequential system that generates aerial imagery measuring 30 mm x 25 mm x 25 mm, providing 198 horizontal views.

Integrating a geographic information system, a scientific visualization system and an orographic precipitation model

USGS Publications Warehouse

Hay, L.; Knapp, L.

1996-01-01

Investigating natural, potential, and man-induced impacts on hydrological systems commonly requires complex modelling with overlapping data requirements, and massive amounts of one- to four-dimensional data at multiple scales and formats. Given the complexity of most hydrological studies, the requisite software infrastructure must incorporate many components including simulation modelling, spatial analysis and flexible, intuitive displays. There is a general requirement for a set of capabilities to support scientific analysis which, at this time, can only come from an integration of several software components. Integration of geographic information systems (GISs) and scientific visualization systems (SVSs) is a powerful technique for developing and analysing complex models. This paper describes the integration of an orographic precipitation model, a GIS and a SVS. The combination of these individual components provides a robust infrastructure which allows the scientist to work with the full dimensionality of the data and to examine the data in a more intuitive manner.

An enhanced droplet-based liquid microjunction surface sampling system coupled with HPLC-ESI-MS/MS for spatially resolved analysis

DOE PAGES

Van Berkel, Gary J.; Weiskittel, Taylor M.; Kertesz, Vilmos

2014-11-07

Droplet-based liquid microjunction surface sampling coupled with high-performance liquid chromatography (HPLC)-electrospray ionization (ESI)-tandem mass spectrometry (MS/MS) for spatially resolved analysis provides the possibility of effective analysis of complex matrix samples and can provide a greater degree of chemical information from a single spot sample than is typically possible with a direct analysis of an extract. Described here is the setup and enhanced capabilities of a discrete droplet liquid microjunction surface sampling system employing a commercially available CTC PAL autosampler. The system enhancements include incorporation of a laser distance sensor enabling unattended analysis of samples and sample locations of dramatically disparatemore » height as well as reliably dispensing just 0.5 μL of extraction solvent to make the liquid junction to the surface, wherein the extraction spot size was confined to an area about 0.7 mm in diameter; software modifications improving the spatial resolution of sampling spot selection from 1.0 to 0.1 mm; use of an open bed tray system to accommodate samples as large as whole-body rat thin tissue sections; and custom sample/solvent holders that shorten sampling time to approximately 1 min per sample. Lastly, the merit of these new features was demonstrated by spatially resolved sampling, HPLC separation, and mass spectral detection of pharmaceuticals and metabolites from whole-body rat thin tissue sections and razor blade (“crude”) cut mouse tissue.« less

An enhanced droplet-based liquid microjunction surface sampling system coupled with HPLC-ESI-MS/MS for spatially resolved analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Berkel, Gary J.; Weiskittel, Taylor M.; Kertesz, Vilmos

Droplet-based liquid microjunction surface sampling coupled with high-performance liquid chromatography (HPLC)-electrospray ionization (ESI)-tandem mass spectrometry (MS/MS) for spatially resolved analysis provides the possibility of effective analysis of complex matrix samples and can provide a greater degree of chemical information from a single spot sample than is typically possible with a direct analysis of an extract. Described here is the setup and enhanced capabilities of a discrete droplet liquid microjunction surface sampling system employing a commercially available CTC PAL autosampler. The system enhancements include incorporation of a laser distance sensor enabling unattended analysis of samples and sample locations of dramatically disparatemore » height as well as reliably dispensing just 0.5 μL of extraction solvent to make the liquid junction to the surface, wherein the extraction spot size was confined to an area about 0.7 mm in diameter; software modifications improving the spatial resolution of sampling spot selection from 1.0 to 0.1 mm; use of an open bed tray system to accommodate samples as large as whole-body rat thin tissue sections; and custom sample/solvent holders that shorten sampling time to approximately 1 min per sample. Lastly, the merit of these new features was demonstrated by spatially resolved sampling, HPLC separation, and mass spectral detection of pharmaceuticals and metabolites from whole-body rat thin tissue sections and razor blade (“crude”) cut mouse tissue.« less

Generating Mosaics of Astronomical Images

NASA Technical Reports Server (NTRS)

Bergou, Attila; Berriman, Bruce; Good, John; Jacob, Joseph; Katz, Daniel; Laity, Anastasia; Prince, Thomas; Williams, Roy

2005-01-01

"Montage" is the name of a service of the National Virtual Observatory (NVO), and of software being developed to implement the service via the World Wide Web. Montage generates science-grade custom mosaics of astronomical images on demand from input files that comply with the Flexible Image Transport System (FITS) standard and contain image data registered on projections that comply with the World Coordinate System (WCS) standards. "Science-grade" in this context signifies that terrestrial and instrumental features are removed from images in a way that can be described quantitatively. "Custom" refers to user-specified parameters of projection, coordinates, size, rotation, and spatial sampling. The greatest value of Montage is expected to lie in its ability to analyze images at multiple wavelengths, delivering them on a common projection, coordinate system, and spatial sampling, and thereby enabling further analysis as though they were part of a single, multi-wavelength image. Montage will be deployed as a computation-intensive service through existing astronomy portals and other Web sites. It will be integrated into the emerging NVO architecture and will be executed on the TeraGrid. The Montage software will also be portable and publicly available.

GeolOkit 1.0: a new Open Source, Cross-Platform software for geological data visualization in Google Earth environment

NASA Astrophysics Data System (ADS)

Triantafyllou, Antoine; Bastin, Christophe; Watlet, Arnaud

2016-04-01

GIS software suites are today's essential tools to gather and visualise geological data, to apply spatial and temporal analysis and in fine, to create and share interactive maps for further geosciences' investigations. For these purposes, we developed GeolOkit: an open-source, freeware and lightweight software, written in Python, a high-level, cross-platform programming language. GeolOkit software is accessible through a graphical user interface, designed to run in parallel with Google Earth. It is a super user-friendly toolbox that allows 'geo-users' to import their raw data (e.g. GPS, sample locations, structural data, field pictures, maps), to use fast data analysis tools and to plot these one into Google Earth environment using KML code. This workflow requires no need of any third party software, except Google Earth itself. GeolOkit comes with large number of geosciences' labels, symbols, colours and placemarks and may process : (i) multi-points data, (ii) contours via several interpolations methods, (iii) discrete planar and linear structural data in 2D or 3D supporting large range of structures input format, (iv) clustered stereonets and rose diagram, (v) drawn cross-sections as vertical sections, (vi) georeferenced maps and vectors, (vii) field pictures using either geo-tracking metadata from a camera built-in GPS module, or the same-day track of an external GPS. We are looking for you to discover all the functionalities of GeolOkit software. As this project is under development, we are definitely looking to discussions regarding your proper needs, your ideas and contributions to GeolOkit project.

Computerized stratified random site-selection approaches for design of a ground-water-quality sampling network

USGS Publications Warehouse

Scott, J.C.

1990-01-01

Computer software was written to randomly select sites for a ground-water-quality sampling network. The software uses digital cartographic techniques and subroutines from a proprietary geographic information system. The report presents the approaches, computer software, and sample applications. It is often desirable to collect ground-water-quality samples from various areas in a study region that have different values of a spatial characteristic, such as land-use or hydrogeologic setting. A stratified network can be used for testing hypotheses about relations between spatial characteristics and water quality, or for calculating statistical descriptions of water-quality data that account for variations that correspond to the spatial characteristic. In the software described, a study region is subdivided into areal subsets that have a common spatial characteristic to stratify the population into several categories from which sampling sites are selected. Different numbers of sites may be selected from each category of areal subsets. A population of potential sampling sites may be defined by either specifying a fixed population of existing sites, or by preparing an equally spaced population of potential sites. In either case, each site is identified with a single category, depending on the value of the spatial characteristic of the areal subset in which the site is located. Sites are selected from one category at a time. One of two approaches may be used to select sites. Sites may be selected randomly, or the areal subsets in the category can be grouped into cells and sites selected randomly from each cell.

GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update.

PubMed

Peakall, Rod; Smouse, Peter E

2012-10-01

GenAlEx: Genetic Analysis in Excel is a cross-platform package for population genetic analyses that runs within Microsoft Excel. GenAlEx offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences. Both frequency-based (F-statistics, heterozygosity, HWE, population assignment, relatedness) and distance-based (AMOVA, PCoA, Mantel tests, multivariate spatial autocorrelation) analyses are provided. New features include calculation of new estimators of population structure: G'(ST), G''(ST), Jost's D(est) and F'(ST) through AMOVA, Shannon Information analysis, linkage disequilibrium analysis for biallelic data and novel heterogeneity tests for spatial autocorrelation analysis. Export to more than 30 other data formats is provided. Teaching tutorials and expanded step-by-step output options are included. The comprehensive guide has been fully revised. GenAlEx is written in VBA and provided as a Microsoft Excel Add-in (compatible with Excel 2003, 2007, 2010 on PC; Excel 2004, 2011 on Macintosh). GenAlEx, and supporting documentation and tutorials are freely available at: http://biology.anu.edu.au/GenAlEx. rod.peakall@anu.edu.au.

Study the effect of reservoir spatial heterogeneity on CO2 sequestration under an uncertainty quantification (UQ) software framework

NASA Astrophysics Data System (ADS)

Fang, Y.; Hou, J.; Engel, D.; Lin, G.; Yin, J.; Han, B.; Fang, Z.; Fountoulakis, V.

2011-12-01

In this study, we introduce an uncertainty quantification (UQ) software framework for carbon sequestration, with the focus of studying being the effect of spatial heterogeneity of reservoir properties on CO2 migration. We use a sequential Gaussian method (SGSIM) to generate realizations of permeability fields with various spatial statistical attributes. To deal with the computational difficulties, we integrate the following ideas/approaches: 1) firstly, we use three different sampling approaches (probabilistic collocation, quasi-Monte Carlo, and adaptive sampling approaches) to reduce the required forward calculations while trying to explore the parameter space and quantify the input uncertainty; 2) secondly, we use eSTOMP as the forward modeling simulator. eSTOMP is implemented using the Global Arrays toolkit (GA) that is based on one-sided inter-processor communication and supports a shared memory programming style on distributed memory platforms. It provides highly-scalable performance. It uses a data model to partition most of the large scale data structures into a relatively small number of distinct classes. The lower level simulator infrastructure (e.g. meshing support, associated data structures, and data mapping to processors) is separated from the higher level physics and chemistry algorithmic routines using a grid component interface; and 3) besides the faster model and more efficient algorithms to speed up the forward calculation, we built an adaptive system infrastructure to select the best possible data transfer mechanisms, to optimally allocate system resources to improve performance, and to integrate software packages and data for composing carbon sequestration simulation, computation, analysis, estimation and visualization. We will demonstrate the framework with a given CO2 injection scenario in a heterogeneous sandstone reservoir.

Parameters assessment of the inductively-coupled circuit for wireless power transfer

NASA Astrophysics Data System (ADS)

Isaev, Yu N.; Vasileva, O. V.; Budko, A. A.; Lefebvre, S.

2017-02-01

In this paper, a wireless power transfer model through the example of inductively-coupled coils of irregular shape in software package COMSOL Multiphysics is studied. Circuit parameters, such as inductance, coil resistance and self-capacitance were defined through electromagnetic energy by the finite-element method. The study was carried out according to Helmholtz equation. Spatial distribution of current per unit depending on frequency and the coupling coefficient for analysis of resonant frequency and spatial distribution of the vector magnetic potential at different distances between coils were presented. The resulting algorithm allows simulating the wireless power transfer between the inductively coupled coils of irregular shape with the assessment of the optimal parameters.

Spatial Dmbs Architecture for a Free and Open Source Bim

NASA Astrophysics Data System (ADS)

Logothetis, S.; Valari, E.; Karachaliou, E.; Stylianidis, E.

2017-08-01

Recent research on the field of Building Information Modelling (BIM) technology, revealed that except of a few, accessible and free BIM viewers there is a lack of Free & Open Source Software (FOSS) BIM software for the complete BIM process. With this in mind and considering BIM as the technological advancement of Computer-Aided Design (CAD) systems, the current work proposes the use of a FOSS CAD software in order to extend its capabilities and transform it gradually into a FOSS BIM platform. Towards this undertaking, a first approach on developing a spatial Database Management System (DBMS) able to store, organize and manage the overall amount of information within a single application, is presented.

DoE Phase II SBIR: Spectrally-Assisted Vehicle Tracking

DOE Office of Scientific and Technical Information (OSTI.GOV)

Villeneuve, Pierre V.

2013-02-28

The goal of this Phase II SBIR is to develop a prototype software package to demonstrate spectrally-aided vehicle tracking performance. The primary application is to demonstrate improved target vehicle tracking performance in complex environments where traditional spatial tracker systems may show reduced performance. Example scenarios in Figure 1 include a) the target vehicle obscured by a large structure for an extended period of time, or b), the target engaging in extreme maneuvers amongst other civilian vehicles. The target information derived from spatial processing is unable to differentiate between the green versus the red vehicle. Spectral signature exploitation enables comparison ofmore » new candidate targets with existing track signatures. The ambiguity in this confusing scenario is resolved by folding spectral analysis results into each target nomination and association processes. Figure 3 shows a number of example spectral signatures from a variety of natural and man-made materials. The work performed over the two-year effort was divided into three general areas: algorithm refinement, software prototype development, and prototype performance demonstration. The tasks performed under this Phase II to accomplish the program goals were as follows: 1. Acquire relevant vehicle target datasets to support prototype. 2. Refine algorithms for target spectral feature exploitation. 3. Implement a prototype multi-hypothesis target tracking software package. 4. Demonstrate and quantify tracking performance using relevant data.« less

A 'user friendly' geographic information system in a color interactive digital image processing system environment

NASA Technical Reports Server (NTRS)

Campbell, W. J.; Goldberg, M.

1982-01-01

NASA's Eastern Regional Remote Sensing Applications Center (ERRSAC) has recognized the need to accommodate spatial analysis techniques in its remote sensing technology transfer program. A computerized Geographic Information System to incorporate remotely sensed data, specifically Landsat, with other relevant data was considered a realistic approach to address a given resource problem. Questions arose concerning the selection of a suitable available software system to demonstrate, train, and undertake demonstration projects with ERRSAC's user community. The very specific requirements for such a system are discussed. The solution found involved the addition of geographic information processing functions to the Interactive Digital Image Manipulation System (IDIMS). Details regarding the functions of the new integrated system are examined along with the characteristics of the software.

Integrated thermal disturbance analysis of optical system of astronomical telescope

NASA Astrophysics Data System (ADS)

Yang, Dehua; Jiang, Zibo; Li, Xinnan

2008-07-01

During operation, astronomical telescope will undergo thermal disturbance, especially more serious in solar telescope, which may cause degradation of image quality. As drives careful thermal load investigation and measure applied to assess its effect on final image quality during design phase. Integrated modeling analysis is boosting the process to find comprehensive optimum design scheme by software simulation. In this paper, we focus on the Finite Element Analysis (FEA) software-ANSYS-for thermal disturbance analysis and the optical design software-ZEMAX-for optical system design. The integrated model based on ANSYS and ZEMAX is briefed in the first from an overview of point. Afterwards, we discuss the establishment of thermal model. Complete power series polynomial with spatial coordinates is introduced to present temperature field analytically. We also borrow linear interpolation technique derived from shape function in finite element theory to interface the thermal model and structural model and further to apply the temperatures onto structural model nodes. Thereby, the thermal loads are transferred with as high fidelity as possible. Data interface and communication between the two softwares are discussed mainly on mirror surfaces and hence on the optical figure representation and transformation. We compare and comment the two different methods, Zernike polynomials and power series expansion, for representing and transforming deformed optical surface to ZEMAX. Additionally, these methods applied to surface with non-circular aperture are discussed. At the end, an optical telescope with parabolic primary mirror of 900 mm in diameter is analyzed to illustrate the above discussion. Finite Element Model with most interested parts of the telescope is generated in ANSYS with necessary structural simplification and equivalence. Thermal analysis is performed and the resulted positions and figures of the optics are to be retrieved and transferred to ZEMAX, and thus final image quality is evaluated with thermal disturbance.

Comparison of performance of object-based image analysis techniques available in open source software (Spring and Orfeo Toolbox/Monteverdi) considering very high spatial resolution data

NASA Astrophysics Data System (ADS)

Teodoro, Ana C.; Araujo, Ricardo

2016-01-01

The use of unmanned aerial vehicles (UAVs) for remote sensing applications is becoming more frequent. However, this type of information can result in several software problems related to the huge amount of data available. Object-based image analysis (OBIA) has proven to be superior to pixel-based analysis for very high-resolution images. The main objective of this work was to explore the potentialities of the OBIA methods available in two different open source software applications, Spring and OTB/Monteverdi, in order to generate an urban land cover map. An orthomosaic derived from UAVs was considered, 10 different regions of interest were selected, and two different approaches were followed. The first one (Spring) uses the region growing segmentation algorithm followed by the Bhattacharya classifier. The second approach (OTB/Monteverdi) uses the mean shift segmentation algorithm followed by the support vector machine (SVM) classifier. Two strategies were followed: four classes were considered using Spring and thereafter seven classes were considered for OTB/Monteverdi. The SVM classifier produces slightly better results and presents a shorter processing time. However, the poor spectral resolution of the data (only RGB bands) is an important factor that limits the performance of the classifiers applied.

Geospatial Data Stream Processing in Python Using FOSS4G Components

NASA Astrophysics Data System (ADS)

McFerren, G.; van Zyl, T.

2016-06-01

One viewpoint of current and future IT systems holds that there is an increase in the scale and velocity at which data are acquired and analysed from heterogeneous, dynamic sources. In the earth observation and geoinformatics domains, this process is driven by the increase in number and types of devices that report location and the proliferation of assorted sensors, from satellite constellations to oceanic buoy arrays. Much of these data will be encountered as self-contained messages on data streams - continuous, infinite flows of data. Spatial analytics over data streams concerns the search for spatial and spatio-temporal relationships within and amongst data "on the move". In spatial databases, queries can assess a store of data to unpack spatial relationships; this is not the case on streams, where spatial relationships need to be established with the incomplete data available. Methods for spatially-based indexing, filtering, joining and transforming of streaming data need to be established and implemented in software components. This article describes the usage patterns and performance metrics of a number of well known FOSS4G Python software libraries within the data stream processing paradigm. In particular, we consider the RTree library for spatial indexing, the Shapely library for geometric processing and transformation and the PyProj library for projection and geodesic calculations over streams of geospatial data. We introduce a message oriented Python-based geospatial data streaming framework called Swordfish, which provides data stream processing primitives, functions, transports and a common data model for describing messages, based on the Open Geospatial Consortium Observations and Measurements (O&M) and Unidata Common Data Model (CDM) standards. We illustrate how the geospatial software components are integrated with the Swordfish framework. Furthermore, we describe the tight temporal constraints under which geospatial functionality can be invoked when processing high velocity, potentially infinite geospatial data streams. The article discusses the performance of these libraries under simulated streaming loads (size, complexity and volume of messages) and how they can be deployed and utilised with Swordfish under real load scenarios, illustrated by a set of Vessel Automatic Identification System (AIS) use cases. We conclude that the described software libraries are able to perform adequately under geospatial data stream processing scenarios - many real application use cases will be handled sufficiently by the software.

The MIND PALACE: A Multi-Spectral Imaging and Spectroscopy Database for Planetary Science

NASA Astrophysics Data System (ADS)

Eshelman, E.; Doloboff, I.; Hara, E. K.; Uckert, K.; Sapers, H. M.; Abbey, W.; Beegle, L. W.; Bhartia, R.

2017-12-01

The Multi-Instrument Database (MIND) is the web-based home to a well-characterized set of analytical data collected by a suite of deep-UV fluorescence/Raman instruments built at the Jet Propulsion Laboratory (JPL). Samples derive from a growing body of planetary surface analogs, mineral and microbial standards, meteorites, spacecraft materials, and other astrobiologically relevant materials. In addition to deep-UV spectroscopy, datasets stored in MIND are obtained from a variety of analytical techniques obtained over multiple spatial and spectral scales including electron microscopy, optical microscopy, infrared spectroscopy, X-ray fluorescence, and direct fluorescence imaging. Multivariate statistical analysis techniques, primarily Principal Component Analysis (PCA), are used to guide interpretation of these large multi-analytical spectral datasets. Spatial co-referencing of integrated spectral/visual maps is performed using QGIS (geographic information system software). Georeferencing techniques transform individual instrument data maps into a layered co-registered data cube for analysis across spectral and spatial scales. The body of data in MIND is intended to serve as a permanent, reliable, and expanding database of deep-UV spectroscopy datasets generated by this unique suite of JPL-based instruments on samples of broad planetary science interest.

Spatio-temporal analysis of prodelta dynamics by means of new satellite generation: the case of Po river by Landsat-8 data

NASA Astrophysics Data System (ADS)

Manzo, Ciro; Braga, Federica; Zaggia, Luca; Brando, Vittorio Ernesto; Giardino, Claudia; Bresciani, Mariano; Bassani, Cristiana

2018-04-01

This paper describes a procedure to perform spatio-temporal analysis of river plume dispersion in prodelta areas by multi-temporal Landsat-8-derived products for identifying zones sensitive to water discharge and for providing geostatistical patterns of turbidity linked to different meteo-marine forcings. In particular, we characterized the temporal and spatial variability of turbidity and sea surface temperature (SST) in the Po River prodelta (Northern Adriatic Sea, Italy) during the period 2013-2016. To perform this analysis, a two-pronged processing methodology was implemented and the resulting outputs were analysed through a series of statistical tools. A pixel-based spatial correlation analysis was carried out by comparing temporal curves of turbidity and SST hypercubes with in situ time series of wind speed and water discharge, providing correlation coefficient maps. A geostatistical analysis was performed to determine the spatial dependency of the turbidity datasets per each satellite image, providing maps of correlation and variograms. The results show a linear correlation between water discharge and turbidity variations in the points more affected by the buoyant plumes and along the southern coast of Po River delta. Better inverse correlation was found between turbidity and SST during floods rather than other periods. The correlation maps of wind speed with turbidity show different spatial patterns depending on local or basin-scale wind effects. Variogram maps identify different spatial anisotropy structures of turbidity in response to ambient conditions (i.e. strong Bora or Scirocco winds, floods). Since the implemented processing methodology is based on open source software and free satellite data, it represents a promising tool for the monitoring of maritime ecosystems and to address water quality analyses and the investigations of sediment dynamics in estuarine and coastal waters.

Methodological approach in determination of small spatial units in a highly complex terrain in atmospheric pollution research: the case of Zasavje region in Slovenia.

PubMed

Kukec, Andreja; Boznar, Marija Z; Mlakar, Primoz; Grasic, Bostjan; Herakovic, Andrej; Zadnik, Vesna; Zaletel-Kragelj, Lijana; Farkas, Jerneja; Erzen, Ivan

2014-05-01

The study of atmospheric air pollution research in complex terrains is challenged by the lack of appropriate methodology supporting the analysis of the spatial relationship between phenomena affected by a multitude of factors. The key is optimal design of a meaningful approach based on small spatial units of observation. The Zasavje region, Slovenia, was chosen as study area with the main objective to investigate in practice the role of such units in a test environment. The process consisted of three steps: modelling of pollution in the atmosphere with dispersion models, transfer of the results to geographical information system software, and then moving on to final determination of the function of small spatial units. A methodology capable of designing useful units for atmospheric air pollution research in highly complex terrains was created, and the results were deemed useful in offering starting points for further research in the field of geospatial health.

MOLNs: A CLOUD PLATFORM FOR INTERACTIVE, REPRODUCIBLE, AND SCALABLE SPATIAL STOCHASTIC COMPUTATIONAL EXPERIMENTS IN SYSTEMS BIOLOGY USING PyURDME

PubMed Central

Drawert, Brian; Trogdon, Michael; Toor, Salman; Petzold, Linda; Hellander, Andreas

2017-01-01

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools and a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments. PMID:28190948

Software Framework for Development of Web-GIS Systems for Analysis of Georeferenced Geophysical Data

NASA Astrophysics Data System (ADS)

Okladnikov, I.; Gordov, E. P.; Titov, A. G.

2011-12-01

Georeferenced datasets (meteorological databases, modeling and reanalysis results, remote sensing products, etc.) are currently actively used in numerous applications including modeling, interpretation and forecast of climatic and ecosystem changes for various spatial and temporal scales. Due to inherent heterogeneity of environmental datasets as well as their size which might constitute up to tens terabytes for a single dataset at present studies in the area of climate and environmental change require a special software support. A dedicated software framework for rapid development of providing such support information-computational systems based on Web-GIS technologies has been created. The software framework consists of 3 basic parts: computational kernel developed using ITTVIS Interactive Data Language (IDL), a set of PHP-controllers run within specialized web portal, and JavaScript class library for development of typical components of web mapping application graphical user interface (GUI) based on AJAX technology. Computational kernel comprise of number of modules for datasets access, mathematical and statistical data analysis and visualization of results. Specialized web-portal consists of web-server Apache, complying OGC standards Geoserver software which is used as a base for presenting cartographical information over the Web, and a set of PHP-controllers implementing web-mapping application logic and governing computational kernel. JavaScript library aiming at graphical user interface development is based on GeoExt library combining ExtJS Framework and OpenLayers software. Based on the software framework an information-computational system for complex analysis of large georeferenced data archives was developed. Structured environmental datasets available for processing now include two editions of NCEP/NCAR Reanalysis, JMA/CRIEPI JRA-25 Reanalysis, ECMWF ERA-40 Reanalysis, ECMWF ERA Interim Reanalysis, MRI/JMA APHRODITE's Water Resources Project Reanalysis, meteorological observational data for the territory of the former USSR for the 20th century, and others. Current version of the system is already involved into a scientific research process. Particularly, recently the system was successfully used for analysis of Siberia climate changes and its impact in the region. The software framework presented allows rapid development of Web-GIS systems for geophysical data analysis thus providing specialists involved into multidisciplinary research projects with reliable and practical instruments for complex analysis of climate and ecosystems changes on global and regional scales. This work is partially supported by RFBR grants #10-07-00547, #11-05-01190, and SB RAS projects 4.31.1.5, 4.31.2.7, 4, 8, 9, 50 and 66.

Integrating environmental gap analysis with spatial conservation prioritization: a case study from Victoria, Australia.

PubMed

Sharafi, Seyedeh Mahdieh; Moilanen, Atte; White, Matt; Burgman, Mark

2012-12-15

Gap analysis is used to analyse reserve networks and their coverage of biodiversity, thus identifying gaps in biodiversity representation that may be filled by additional conservation measures. Gap analysis has been used to identify priorities for species and habitat types. When it is applied to identify gaps in the coverage of environmental variables, it embodies the assumption that combinations of environmental variables are effective surrogates for biodiversity attributes. The question remains of how to fill gaps in conservation systems efficiently. Conservation prioritization software can identify those areas outside existing conservation areas that contribute to the efficient covering of gaps in biodiversity features. We show how environmental gap analysis can be implemented using high-resolution information about environmental variables and ecosystem condition with the publicly available conservation prioritization software, Zonation. Our method is based on the conversion of combinations of environmental variables into biodiversity features. We also replicated the analysis by using Species Distribution Models (SDMs) as biodiversity features to evaluate the robustness and utility of our environment-based analysis. We apply the technique to a planning case study of the state of Victoria, Australia. Copyright © 2012 Elsevier Ltd. All rights reserved.

Graphics Software Packages as Instructional Tools.

ERIC Educational Resources Information Center

Chiavaroli, Julius J.; Till, Ronald J.

1985-01-01

Graphics software can assist hearing-impaired students in visualizing and comparing ideas and can also demonstrate spatial relations and encourage creativity. Teachers and students can create and present data, diagrams, drawings, or charts quickly and accurately. (Author/CL)

Enhancing User Customization through Novel Software Architecture for Utility Scale Solar Siting Software

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brant Peery; Sam Alessi; Randy Lee

2014-06-01

There is a need for a spatial decision support application that allows users to create customized metrics for comparing proposed locations of a new solar installation. This document discusses how PVMapper was designed to overcome the customization problem through the development of loosely coupled spatial and decision components in a JavaScript plugin architecture. This allows the user to easily add functionality and data to the system. The paper also explains how PVMapper provides the user with a dynamic and customizable decision tool that enables them to visually modify the formulas that are used in the decision algorithms that convert datamore » to comparable metrics. The technologies that make up the presentation and calculation software stack are outlined. This document also explains the architecture that allows the tool to grow through custom plugins created by the software users. Some discussion is given on the difficulties encountered while designing the system.« less

Making Temporal Search More Central in Spatial Data Infrastructures

NASA Astrophysics Data System (ADS)

Corti, P.; Lewis, B.

2017-10-01

A temporally enabled Spatial Data Infrastructure (SDI) is a framework of geospatial data, metadata, users, and tools intended to provide an efficient and flexible way to use spatial information which includes the historical dimension. One of the key software components of an SDI is the catalogue service which is needed to discover, query, and manage the metadata. A search engine is a software system capable of supporting fast and reliable search, which may use any means necessary to get users to the resources they need quickly and efficiently. These techniques may include features such as full text search, natural language processing, weighted results, temporal search based on enrichment, visualization of patterns in distributions of results in time and space using temporal and spatial faceting, and many others. In this paper we will focus on the temporal aspects of search which include temporal enrichment using a time miner - a software engine able to search for date components within a larger block of text, the storage of time ranges in the search engine, handling historical dates, and the use of temporal histograms in the user interface to display the temporal distribution of search results.

OpenMSI Arrayed Analysis Toolkit: Analyzing Spatially Defined Samples Using Mass Spectrometry Imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

de Raad, Markus; de Rond, Tristan; Rübel, Oliver

Mass spectrometry imaging (MSI) has primarily been applied in localizing biomolecules within biological matrices. Although well-suited, the application of MSI for comparing thousands of spatially defined spotted samples has been limited. One reason for this is a lack of suitable and accessible data processing tools for the analysis of large arrayed MSI sample sets. In this paper, the OpenMSI Arrayed Analysis Toolkit (OMAAT) is a software package that addresses the challenges of analyzing spatially defined samples in MSI data sets. OMAAT is written in Python and is integrated with OpenMSI (http://openmsi.nersc.gov), a platform for storing, sharing, and analyzing MSI data.more » By using a web-based python notebook (Jupyter), OMAAT is accessible to anyone without programming experience yet allows experienced users to leverage all features. OMAAT was evaluated by analyzing an MSI data set of a high-throughput glycoside hydrolase activity screen comprising 384 samples arrayed onto a NIMS surface at a 450 μm spacing, decreasing analysis time >100-fold while maintaining robust spot-finding. The utility of OMAAT was demonstrated for screening metabolic activities of different sized soil particles, including hydrolysis of sugars, revealing a pattern of size dependent activities. Finally, these results introduce OMAAT as an effective toolkit for analyzing spatially defined samples in MSI. OMAAT runs on all major operating systems, and the source code can be obtained from the following GitHub repository: https://github.com/biorack/omaat.« less

Bulk tank milk prevalence and production losses, spatial analysis, and predictive risk mapping of Ostertagia ostertagi infections in Mexican cattle herds.

PubMed

Villa-Mancera, Abel; Pastelín-Rojas, César; Olivares-Pérez, Jaime; Córdova-Izquierdo, Alejandro; Reynoso-Palomar, Alejandro

2018-05-01

This study investigated the prevalence, production losses, spatial clustering, and predictive risk mapping in different climate zones in five states of Mexico. The bulk tank milk samples obtained between January and April 2015 were analyzed for antibodies against Ostertagia ostertagi using the Svanovir ELISA. A total of 1204 farm owners or managers answered the questionnaire. The overall herd prevalence and mean optical density ratio (ODR) of parasite were 61.96% and 0.55, respectively. Overall, the production loss was approximately 0.542 kg of milk per parasited cow per day (mean ODR = 0.92, 142 farms, 11.79%). The spatial disease cluster analysis using SatScan software indicated that two high-risk clusters were observed. In the multivariable analysis, three models were tested for potential association with the ELISA results supported by climatic, environmental, and management factors. The final logistic regression model based on both climatic/environmental and management variables included the factors rainfall, elevation, land surface temperature (LST) day, and parasite control program that were significantly associated with an increased risk of infection. Geostatistical kriging was applied to generate a risk map for the presence of parasite in dairy cattle herds in Mexico. The results indicate that climatic and meteorological factors had a higher potential impact on the spatial distribution of O. ostertagi than the management factors.

Your Personal Analysis Toolkit - An Open Source Solution

NASA Astrophysics Data System (ADS)

Mitchell, T.

2009-12-01

Open source software is commonly known for its web browsers, word processors and programming languages. However, there is a vast array of open source software focused on geographic information management and geospatial application building in general. As geo-professionals, having easy access to tools for our jobs is crucial. Open source software provides the opportunity to add a tool to your tool belt and carry it with you for your entire career - with no license fees, a supportive community and the opportunity to test, adopt and upgrade at your own pace. OSGeo is a US registered non-profit representing more than a dozen mature geospatial data management applications and programming resources. Tools cover areas such as desktop GIS, web-based mapping frameworks, metadata cataloging, spatial database analysis, image processing and more. Learn about some of these tools as they apply to AGU members, as well as how you can join OSGeo and its members in getting the job done with powerful open source tools. If you haven't heard of OSSIM, MapServer, OpenLayers, PostGIS, GRASS GIS or the many other projects under our umbrella - then you need to hear this talk. Invest in yourself - use open source!

Real time quantitative imaging for semiconductor crystal growth, control and characterization

NASA Technical Reports Server (NTRS)

Wargo, Michael J.

1991-01-01

A quantitative real time image processing system has been developed which can be software-reconfigured for semiconductor processing and characterization tasks. In thermal imager mode, 2D temperature distributions of semiconductor melt surfaces (900-1600 C) can be obtained with temperature and spatial resolutions better than 0.5 C and 0.5 mm, respectively, as demonstrated by analysis of melt surface thermal distributions. Temporal and spatial image processing techniques and multitasking computational capabilities convert such thermal imaging into a multimode sensor for crystal growth control. A second configuration of the image processing engine in conjunction with bright and dark field transmission optics is used to nonintrusively determine the microdistribution of free charge carriers and submicron sized crystalline defects in semiconductors. The IR absorption characteristics of wafers are determined with 10-micron spatial resolution and, after calibration, are converted into charge carrier density.

DENSITY: software for analysing capture-recapture data from passive detector arrays

USGS Publications Warehouse

Efford, M.G.; Dawson, D.K.; Robbins, C.S.

2004-01-01

A general computer-intensive method is described for fitting spatial detection functions to capture-recapture data from arrays of passive detectors such as live traps and mist nets. The method is used to estimate the population density of 10 species of breeding birds sampled by mist-netting in deciduous forest at Patuxent Research Refuge, Laurel, Maryland, U.S.A., from 1961 to 1972. Total density (9.9 ? 0.6 ha-1 mean ? SE) appeared to decline over time (slope -0.41 ? 0.15 ha-1y-1). The mean precision of annual estimates for all 10 species pooled was acceptable (CV(D) = 14%). Spatial analysis of closed-population capture-recapture data highlighted deficiencies in non-spatial methodologies. For example, effective trapping area cannot be assumed constant when detection probability is variable. Simulation may be used to evaluate alternative designs for mist net arrays where density estimation is a study goal.

SDMtoolbox 2.0: the next generation Python-based GIS toolkit for landscape genetic, biogeographic and species distribution model analyses.

PubMed

Brown, Jason L; Bennett, Joseph R; French, Connor M

2017-01-01

SDMtoolbox 2.0 is a software package for spatial studies of ecology, evolution, and genetics. The release of SDMtoolbox 2.0 allows researchers to use the most current ArcGIS software and MaxEnt software, and reduces the amount of time that would be spent developing common solutions. The central aim of this software is to automate complicated and repetitive spatial analyses in an intuitive graphical user interface. One core tenant facilitates careful parameterization of species distribution models (SDMs) to maximize each model's discriminatory ability and minimize overfitting. This includes carefully processing of occurrence data, environmental data, and model parameterization. This program directly interfaces with MaxEnt, one of the most powerful and widely used species distribution modeling software programs, although SDMtoolbox 2.0 is not limited to species distribution modeling or restricted to modeling in MaxEnt. Many of the SDM pre- and post-processing tools have 'universal' analogs for use with any modeling software. The current version contains a total of 79 scripts that harness the power of ArcGIS for macroecology, landscape genetics, and evolutionary studies. For example, these tools allow for biodiversity quantification (such as species richness or corrected weighted endemism), generation of least-cost paths and corridors among shared haplotypes, assessment of the significance of spatial randomizations, and enforcement of dispersal limitations of SDMs projected into future climates-to only name a few functions contained in SDMtoolbox 2.0. Lastly, dozens of generalized tools exists for batch processing and conversion of GIS data types or formats, which are broadly useful to any ArcMap user.

Characterization of Disease-Related Covariance Topographies with SSMPCA Toolbox: Effects of Spatial Normalization and PET Scanners

PubMed Central

Peng, Shichun; Ma, Yilong; Spetsieris, Phoebe G; Mattis, Paul; Feigin, Andrew; Dhawan, Vijay; Eidelberg, David

2013-01-01

In order to generate imaging biomarkers from disease-specific brain networks, we have implemented a general toolbox to rapidly perform scaled subprofile modeling (SSM) based on principal component analysis (PCA) on brain images of patients and normals. This SSMPCA toolbox can define spatial covariance patterns whose expression in individual subjects can discriminate patients from controls or predict behavioral measures. The technique may depend on differences in spatial normalization algorithms and brain imaging systems. We have evaluated the reproducibility of characteristic metabolic patterns generated by SSMPCA in patients with Parkinson's disease (PD). We used [18F]fluorodeoxyglucose PET scans from PD patients and normal controls. Motor-related (PDRP) and cognition-related (PDCP) metabolic patterns were derived from images spatially normalized using four versions of SPM software (spm99, spm2, spm5 and spm8). Differences between these patterns and subject scores were compared across multiple independent groups of patients and control subjects. These patterns and subject scores were highly reproducible with different normalization programs in terms of disease discrimination and cognitive correlation. Subject scores were also comparable in PD patients imaged across multiple PET scanners. Our findings confirm a very high degree of consistency among brain networks and their clinical correlates in PD using images normalized in four different SPM platforms. SSMPCA toolbox can be used reliably for generating disease-specific imaging biomarkers despite the continued evolution of image preprocessing software in the neuroimaging community. Network expressions can be quantified in individual patients independent of different physical characteristics of PET cameras. PMID:23671030

Characterization of disease-related covariance topographies with SSMPCA toolbox: effects of spatial normalization and PET scanners.

PubMed

Peng, Shichun; Ma, Yilong; Spetsieris, Phoebe G; Mattis, Paul; Feigin, Andrew; Dhawan, Vijay; Eidelberg, David

2014-05-01

To generate imaging biomarkers from disease-specific brain networks, we have implemented a general toolbox to rapidly perform scaled subprofile modeling (SSM) based on principal component analysis (PCA) on brain images of patients and normals. This SSMPCA toolbox can define spatial covariance patterns whose expression in individual subjects can discriminate patients from controls or predict behavioral measures. The technique may depend on differences in spatial normalization algorithms and brain imaging systems. We have evaluated the reproducibility of characteristic metabolic patterns generated by SSMPCA in patients with Parkinson's disease (PD). We used [(18) F]fluorodeoxyglucose PET scans from patients with PD and normal controls. Motor-related (PDRP) and cognition-related (PDCP) metabolic patterns were derived from images spatially normalized using four versions of SPM software (spm99, spm2, spm5, and spm8). Differences between these patterns and subject scores were compared across multiple independent groups of patients and control subjects. These patterns and subject scores were highly reproducible with different normalization programs in terms of disease discrimination and cognitive correlation. Subject scores were also comparable in patients with PD imaged across multiple PET scanners. Our findings confirm a very high degree of consistency among brain networks and their clinical correlates in PD using images normalized in four different SPM platforms. SSMPCA toolbox can be used reliably for generating disease-specific imaging biomarkers despite the continued evolution of image preprocessing software in the neuroimaging community. Network expressions can be quantified in individual patients independent of different physical characteristics of PET cameras. Copyright © 2013 Wiley Periodicals, Inc.

Ontology Based Quality Evaluation for Spatial Data

NASA Astrophysics Data System (ADS)

Yılmaz, C.; Cömert, Ç.

2015-08-01

Many institutions will be providing data to the National Spatial Data Infrastructure (NSDI). Current technical background of the NSDI is based on syntactic web services. It is expected that this will be replaced by semantic web services. The quality of the data provided is important in terms of the decision-making process and the accuracy of transactions. Therefore, the data quality needs to be tested. This topic has been neglected in Turkey. Data quality control for NSDI may be done by private or public "data accreditation" institutions. A methodology is required for data quality evaluation. There are studies for data quality including ISO standards, academic studies and software to evaluate spatial data quality. ISO 19157 standard defines the data quality elements. Proprietary software such as, 1Spatial's 1Validate and ESRI's Data Reviewer offers quality evaluation based on their own classification of rules. Commonly, rule based approaches are used for geospatial data quality check. In this study, we look for the technical components to devise and implement a rule based approach with ontologies using free and open source software in semantic web context. Semantic web uses ontologies to deliver well-defined web resources and make them accessible to end-users and processes. We have created an ontology conforming to the geospatial data and defined some sample rules to show how to test data with respect to data quality elements including; attribute, topo-semantic and geometrical consistency using free and open source software. To test data against rules, sample GeoSPARQL queries are created, associated with specifications.

Producing genome structure populations with the dynamic and automated PGS software.

PubMed

Hua, Nan; Tjong, Harianto; Shin, Hanjun; Gong, Ke; Zhou, Xianghong Jasmine; Alber, Frank

2018-05-01

Chromosome conformation capture technologies such as Hi-C are widely used to investigate the spatial organization of genomes. Because genome structures can vary considerably between individual cells of a population, interpreting ensemble-averaged Hi-C data can be challenging, in particular for long-range and interchromosomal interactions. We pioneered a probabilistic approach for the generation of a population of distinct diploid 3D genome structures consistent with all the chromatin-chromatin interaction probabilities from Hi-C experiments. Each structure in the population is a physical model of the genome in 3D. Analysis of these models yields new insights into the causes and the functional properties of the genome's organization in space and time. We provide a user-friendly software package, called PGS, which runs on local machines (for practice runs) and high-performance computing platforms. PGS takes a genome-wide Hi-C contact frequency matrix, along with information about genome segmentation, and produces an ensemble of 3D genome structures entirely consistent with the input. The software automatically generates an analysis report, and provides tools to extract and analyze the 3D coordinates of specific domains. Basic Linux command-line knowledge is sufficient for using this software. A typical running time of the pipeline is ∼3 d with 300 cores on a computer cluster to generate a population of 1,000 diploid genome structures at topological-associated domain (TAD)-level resolution.

Scene Analysis: Non-Linear Spatial Filtering for Automatic Target Detection.

DTIC Science & Technology

1982-12-01

In this thesis, a method for two-dimensional pattern recognition was developed and tested. The method included a global search scheme for candidate...test global switch TYPEO Creating negative video file only.W 11=0 12=256 13=512 14=768 GO 70 2 1 TYPE" Creating negative and horizontally flipped video...purpose was to develop a base of image processing software for the AFIT Digital Signal Processing Laboratory NOVA- ECLIPSE minicomputer system, for

Highlights: US Commercial Remote Sensing Industry Analysis

NASA Technical Reports Server (NTRS)

Rabin, Ron

2002-01-01

This viewgraph presentation profiles the US remote sensing industry based on responses to a survey by 1450 industry professionals. The presentation divides the industry into three sectors: academic, commercial, and government; the survey results from each are covered in a section of the presentation. The presentation also divides survey results on user needs into the following sectors: spatial resolution, geolocation accuracy; elevation accuracy, area coverage, imagery types, and timeliness. Data, information, and software characteristics are also covered in the presentation.

CAMECA IMS 1300-HR3: The New Generation Ion Microprobe

NASA Astrophysics Data System (ADS)

Peres, P.; Choi, S. Y.; Renaud, L.; Saliot, P.; Larson, D. J.

2016-12-01

The success of secondary ion mass spectrometry (SIMS) in Geo- and Cosmo-chemistry relies on its performance in terms of: 1) very high sensitivity (mandatory for high precision measurements or to achieve low detection limits); 2) a broad mass range of elemental and isotopic species, from low mass (H) to high mass (U and above); 3) in-situ analysis of any solid flat polished surface; and 4) high spatial resolution from tens of microns down to sub-micron scale. The IMS 1300-HR3 (High Reproducibility, High spatial Resolution, High mass Resolution) is the latest generation of CAMECA's large geometry magnetic sector SIMS (or ion microprobe), successor to the internationally recognized IMS 1280-HR. The 1300-HR3delivers unmatched analytical performance for a wide range of applications (stable isotopes, geochronology, trace elements, nuclear safeguards and environmental studies…) due to: • High brightness RF-plasma oxygen ion source with enhanced beam density and current stability, dramatically improving spatial resolution, data reproducibility, and throughput • Automated sample loading system with motorized sample height (Z) adjustment, significantly increasing analysis precision, ease-of-use, and productivity • UV-light microscope for enhanced optical image resolution, together with dedicated software for easy sample navigation (developed by University of Wisconsin, USA) • Low noise 1012Ω resistor Faraday cup preamplifier boards for measuring low signal intensities In addition, improvements in electronics and software have been integrated into the new instrument. In order to meet a growing demand from geochronologists, CAMECA also introduces the KLEORA, which is a fully optimized ion microprobe for advanced mineral dating derived from the IMS 1300-HR3. Instrumental developments as well as data obtained for stable isotope and U-Pb dating applications will be presented in detail.

DigiFract: A software and data model implementation for flexible acquisition and processing of fracture data from outcrops

NASA Astrophysics Data System (ADS)

Hardebol, N. J.; Bertotti, G.

2013-04-01

This paper presents the development and use of our new DigiFract software designed for acquiring fracture data from outcrops more efficiently and more completely than done with other methods. Fracture surveys often aim at measuring spatial information (such as spacing) directly in the field. Instead, DigiFract focuses on collecting geometries and attributes and derives spatial information through subsequent analyses. Our primary development goal was to support field acquisition in a systematic digital format and optimized for a varied range of (spatial) analyses. DigiFract is developed using the programming interface of the Quantum Geographic Information System (GIS) with versatile functionality for spatial raster and vector data handling. Among other features, this includes spatial referencing of outcrop photos, and tools for digitizing geometries and assigning attribute information through a graphical user interface. While a GIS typically operates in map-view, DigiFract collects features on a surface of arbitrary orientation in 3D space. This surface is overlain with an outcrop photo and serves as reference frame for digitizing geologic features. Data is managed through a data model and stored in shapefiles or in a spatial database system. Fracture attributes, such as spacing or length, is intrinsic information of the digitized geometry and becomes explicit through follow-up data processing. Orientation statistics, scan-line or scan-window analyses can be performed from the graphical user interface or can be obtained through flexible Python scripts that directly access the fractdatamodel and analysisLib core modules of DigiFract. This workflow has been applied in various studies and enabled a faster collection of larger and more accurate fracture datasets. The studies delivered a better characterization of fractured reservoirs analogues in terms of fracture orientation and intensity distributions. Furthermore, the data organisation and analyses provided more independent constraints on the bed-confined or through-going nature of fractures relative to the stratigraphic layering.

Assessing SaTScan ability to detect space-time clusters in wildfires

NASA Astrophysics Data System (ADS)

Costa, Ricardo; Pereira, Mário; Caramelo, Liliana; Vega Orozco, Carmen; Kanevski, Mikhail

2013-04-01

Besides classical cluster analysis techniques which are able to analyse spatial and temporal data, SaTScan software analyses space-time data using the spatial, temporal or space-time scan statistics. This software requires the spatial coordinates of the fire, but since in the Rural Fire Portuguese Database (PRFD) (Pereira et al, 2011) the location of each fire is the parish where the ignition occurs, the fire spatial coordinates were considered as coordinates of the centroid of the parishes. Moreover, in general, the northern region is characterized by a large number of small parishes while the southern comprises parish much larger. The objectives of this study are: (i) to test the ability of SaTScan to detect the correct space-time clusters, in what respects to spatial and temporal location and size; and, (ii) to evaluate the effect of the dimensions of the parishes and of aggregating all fires occurred in a parish in a single point. Results obtained with a synthetic database where clusters were artificially created with different densities, in different regions of the country and with different sizes and durations, allow to conclude: the ability of SaTScan to correctly identify the clusters (location, shape and spatial and temporal dimension); and objectively assess the influence of the size of the parishes and windows used in space-time detection. Pereira, M. G., Malamud, B. D., Trigo, R. M., and Alves, P. I.: The history and characteristics of the 1980-2005 Portuguese rural fire database, Nat. Hazards Earth Syst. Sci., 11, 3343-3358, doi:10.5194/nhess-11-3343-2011, 2011 This work is supported by European Union Funds (FEDER/COMPETE - Operational Competitiveness Programme) and by national funds (FCT - Portuguese Foundation for Science and Technology) under the project FCOMP-01-0124-FEDER-022692, the project FLAIR (PTDC/AAC-AMB/104702/2008) and the EU 7th Framework Program through FUME (contract number 243888).

Spatial landscape model to characterize biological diversity using R statistical computing environment.

PubMed

Singh, Hariom; Garg, R D; Karnatak, Harish C; Roy, Arijit

2018-01-15

Due to urbanization and population growth, the degradation of natural forests and associated biodiversity are now widely recognized as a global environmental concern. Hence, there is an urgent need for rapid assessment and monitoring of biodiversity on priority using state-of-art tools and technologies. The main purpose of this research article is to develop and implement a new methodological approach to characterize biological diversity using spatial model developed during the study viz. Spatial Biodiversity Model (SBM). The developed model is scale, resolution and location independent solution for spatial biodiversity richness modelling. The platform-independent computation model is based on parallel computation. The biodiversity model based on open-source software has been implemented on R statistical computing platform. It provides information on high disturbance and high biological richness areas through different landscape indices and site specific information (e.g. forest fragmentation (FR), disturbance index (DI) etc.). The model has been developed based on the case study of Indian landscape; however it can be implemented in any part of the world. As a case study, SBM has been tested for Uttarakhand state in India. Inputs for landscape ecology are derived through multi-criteria decision making (MCDM) techniques in an interactive command line environment. MCDM with sensitivity analysis in spatial domain has been carried out to illustrate the model stability and robustness. Furthermore, spatial regression analysis has been made for the validation of the output. Copyright © 2017 Elsevier Ltd. All rights reserved.

Educational utility of advanced three-dimensional virtual imaging in evaluating the anatomical configuration of the frontal recess.

PubMed

Agbetoba, Abib; Luong, Amber; Siow, Jin Keat; Senior, Brent; Callejas, Claudio; Szczygielski, Kornel; Citardi, Martin J

2017-02-01

Endoscopic sinus surgery represents a cornerstone in the professional development of otorhinolaryngology trainees. Mastery of these surgical skills requires an understanding of paranasal sinus and skull-base anatomy. The frontal sinus is associated with a wide range of variation and complex anatomical configuration, and thus represents an important challenge for all trainees performing endoscopic sinus surgery. Forty-five otorhinolaryngology trainees and 20 medical school students from 5 academic institutions were enrolled and randomized into 1 of 2 groups. Each subject underwent learning of frontal recess anatomy with both traditional 2-dimensional (2D) learning methods using a standard Digital Imaging and Communications in Medicine (DICOM) viewing software (RadiAnt Dicom Viewer Version 1.9.16) and 3-dimensional (3D) learning utilizing a novel preoperative virtual planning software (Scopis Building Blocks), with one half learning with the 2D method first and the other half learning with the 3D method first. Four questionnaires that included a total of 20 items were scored for subjects' self-assessment on knowledge of frontal recess and frontal sinus drainage pathway anatomy following each learned modality. A 2-sample Wilcoxon rank-sum test was used in the statistical analysis comparing the 2 groups. Most trainees (89%) believed that the virtual 3D planning software significantly improved their understanding of the spatial orientation of the frontal sinus drainage pathway. Incorporation of virtual 3D planning surgical software may help augment trainees' understanding and spatial orientation of the frontal recess and sinus anatomy. The potential increase in trainee proficiency and comprehension theoretically may translate to improved surgical skill and patient outcomes and in reduced surgical time. © 2016 ARS-AAOA, LLC.

The effects of computer-aided design software on engineering students' spatial visualisation skills

NASA Astrophysics Data System (ADS)

Kösa, Temel; Karakuş, Fatih

2018-03-01

The purpose of this study was to determine the influence of computer-aided design (CAD) software-based instruction on the spatial visualisation skills of freshman engineering students in a computer-aided engineering drawing course. A quasi-experimental design was applied, using the Purdue Spatial Visualization Test-Visualization of Rotations (PSVT:R) for both the pre- and the post-test. The participants were 116 freshman students in the first year of their undergraduate programme in the Department of Mechanical Engineering at a university in Turkey. A total of 72 students comprised the experimental group; they were instructed with CAD-based activities in an engineering drawing course. The control group consisted of 44 students who did not attend this course. The results of the study showed that a CAD-based engineering drawing course had a positive effect on developing engineering students' spatial visualisation skills. Additionally, the results of the study showed that spatial visualisation skills can be a predictor for success in a computer-aided engineering drawing course.

A working environment for digital planetary data processing and mapping using ISIS and GRASS GIS

USGS Publications Warehouse

Frigeri, A.; Hare, T.; Neteler, M.; Coradini, A.; Federico, C.; Orosei, R.

2011-01-01

Since the beginning of planetary exploration, mapping has been fundamental to summarize observations returned by scientific missions. Sensor-based mapping has been used to highlight specific features from the planetary surfaces by means of processing. Interpretative mapping makes use of instrumental observations to produce thematic maps that summarize observations of actual data into a specific theme. Geologic maps, for example, are thematic interpretative maps that focus on the representation of materials and processes and their relative timing. The advancements in technology of the last 30 years have allowed us to develop specialized systems where the mapping process can be made entirely in the digital domain. The spread of networked computers on a global scale allowed the rapid propagation of software and digital data such that every researcher can now access digital mapping facilities on his desktop. The efforts to maintain planetary missions data accessible to the scientific community have led to the creation of standardized digital archives that facilitate the access to different datasets by software capable of processing these data from the raw level to the map projected one. Geographic Information Systems (GIS) have been developed to optimize the storage, the analysis, and the retrieval of spatially referenced Earth based environmental geodata; since the last decade these computer programs have become popular among the planetary science community, and recent mission data start to be distributed in formats compatible with these systems. Among all the systems developed for the analysis of planetary and spatially referenced data, we have created a working environment combining two software suites that have similar characteristics in their modular design, their development history, their policy of distribution and their support system. The first, the Integrated Software for Imagers and Spectrometers (ISIS) developed by the United States Geological Survey, represents the state of the art for processing planetary remote sensing data, from the raw unprocessed state to the map projected product. The second, the Geographic Resources Analysis Support System (GRASS) is a Geographic Information System developed by an international team of developers, and one of the core projects promoted by the Open Source Geospatial Foundation (OSGeo). We have worked on enabling the combined use of these software systems throughout the set-up of a common user interface, the unification of the cartographic reference system nomenclature and the minimization of data conversion. Both software packages are distributed with free open source licenses, as well as the source code, scripts and configuration files hereafter presented. In this paper we describe our work done to merge these working environments into a common one, where the user benefits from functionalities of both systems without the need to switch or transfer data from one software suite to the other one. Thereafter we provide an example of its usage in the handling of planetary data and the crafting of a digital geologic map. ?? 2010 Elsevier Ltd. All rights reserved.

Automated Video-Based Analysis of Contractility and Calcium Flux in Human-Induced Pluripotent Stem Cell-Derived Cardiomyocytes Cultured over Different Spatial Scales

PubMed Central

Huebsch, Nathaniel; Loskill, Peter; Mandegar, Mohammad A.; Marks, Natalie C.; Sheehan, Alice S.; Ma, Zhen; Mathur, Anurag; Nguyen, Trieu N.; Yoo, Jennie C.; Judge, Luke M.; Spencer, C. Ian; Chukka, Anand C.; Russell, Caitlin R.; So, Po-Lin

2015-01-01

Contractile motion is the simplest metric of cardiomyocyte health in vitro, but unbiased quantification is challenging. We describe a rapid automated method, requiring only standard video microscopy, to analyze the contractility of human-induced pluripotent stem cell-derived cardiomyocytes (iPS-CM). New algorithms for generating and filtering motion vectors combined with a newly developed isogenic iPSC line harboring genetically encoded calcium indicator, GCaMP6f, allow simultaneous user-independent measurement and analysis of the coupling between calcium flux and contractility. The relative performance of these algorithms, in terms of improving signal to noise, was tested. Applying these algorithms allowed analysis of contractility in iPS-CM cultured over multiple spatial scales from single cells to three-dimensional constructs. This open source software was validated with analysis of isoproterenol response in these cells, and can be applied in future studies comparing the drug responsiveness of iPS-CM cultured in different microenvironments in the context of tissue engineering. PMID:25333967

A Spatial Analysis and Modeling System (SAMS) for environment management

NASA Technical Reports Server (NTRS)

Stetina, Fran; Hill, John; Chan, Paul; Jaske, Robert; Rochon, Gilbert

1993-01-01

This is a proposal to develop a uniform global environmental data gathering and distribution system to support the calibration and validation of remotely sensed data. SAMS is based on an enhanced version of FEMA's Integrated Emergency Management Information Systems and the Department of Defense's Air land Battlefield Environment Software Systems. This system consists of state-of-the-art graphics and visualization techniques, simulation models, database management and expert systems for conducting environmental and disaster preparedness studies. This software package will be integrated into various Landsat and UNEP-GRID stations which are planned to become direct readout stations during the EOS (Earth Observing System) timeframe. This system would be implemented as a pilot program to support the Tropical Rainfall Measuring Mission (TRMM). This will be a joint NASA-FEMA-University-Industry project.

A Spatial Analysis and Modeling System (SAMS) for environment management

NASA Technical Reports Server (NTRS)

Vermillion, Charles H.; Stetina, Fran; Hill, John; Chan, Paul; Jaske, Robert; Rochon, Gilbert

1992-01-01

This is a proposal to develop a uniform global environmental data gathering and distribution system to support the calibration and validation of remotely sensed data. SAMS is based on an enhanced version of FE MA's Integrated Emergency Management Information Systems and the Department of Defense's Air Land Battlefield Environment Software Systems. This system consists of state-of-the-art graphics and visualization techniques, simulation models, database management and expert systems for conducting environmental and disaster preparedness studies. This software package will be integrated into various Landsat and UNEP-GRID stations which are planned to become direct readout stations during the EOS timeframe. This system would be implemented as a pilot program to support the Tropical Rainfall Measuring Mission (TRMM). This will be a joint NASA-FEMA-University-Industry project.

Study on Earthquake Emergency Evacuation Drill Trainer Development

NASA Astrophysics Data System (ADS)

ChangJiang, L.

2016-12-01

With the improvement of China's urbanization, to ensure people survive the earthquake needs scientific routine emergency evacuation drills. Drawing on cellular automaton, shortest path algorithm and collision avoidance, we designed a model of earthquake emergency evacuation drill for school scenes. Based on this model, we made simulation software for earthquake emergency evacuation drill. The software is able to perform the simulation of earthquake emergency evacuation drill by building spatial structural model and selecting the information of people's location grounds on actual conditions of constructions. Based on the data of simulation, we can operate drilling in the same building. RFID technology could be used here for drill data collection which read personal information and send it to the evacuation simulation software via WIFI. Then the simulation software would contrast simulative data with the information of actual evacuation process, such as evacuation time, evacuation path, congestion nodes and so on. In the end, it would provide a contrastive analysis report to report assessment result and optimum proposal. We hope the earthquake emergency evacuation drill software and trainer can provide overall process disposal concept for earthquake emergency evacuation drill in assembly occupancies. The trainer can make the earthquake emergency evacuation more orderly, efficient, reasonable and scientific to fulfill the increase in coping capacity of urban hazard.

GABBs: Cyberinfrastructure for Self-Service Geospatial Data Exploration, Computation, and Sharing

NASA Astrophysics Data System (ADS)

Song, C. X.; Zhao, L.; Biehl, L. L.; Merwade, V.; Villoria, N.

2016-12-01

Geospatial data are present everywhere today with the proliferation of location-aware computing devices. This is especially true in the scientific community where large amounts of data are driving research and education activities in many domains. Collaboration over geospatial data, for example, in modeling, data analysis and visualization, must still overcome the barriers of specialized software and expertise among other challenges. In addressing these needs, the Geospatial data Analysis Building Blocks (GABBs) project aims at building geospatial modeling, data analysis and visualization capabilities in an open source web platform, HUBzero. Funded by NSF's Data Infrastructure Building Blocks initiative, GABBs is creating a geospatial data architecture that integrates spatial data management, mapping and visualization, and interfaces in the HUBzero platform for scientific collaborations. The geo-rendering enabled Rappture toolkit, a generic Python mapping library, geospatial data exploration and publication tools, and an integrated online geospatial data management solution are among the software building blocks from the project. The GABBS software will be available through Amazon's AWS Marketplace VM images and open source. Hosting services are also available to the user community. The outcome of the project will enable researchers and educators to self-manage their scientific data, rapidly create GIS-enable tools, share geospatial data and tools on the web, and build dynamic workflows connecting data and tools, all without requiring significant software development skills, GIS expertise or IT administrative privileges. This presentation will describe the GABBs architecture, toolkits and libraries, and showcase the scientific use cases that utilize GABBs capabilities, as well as the challenges and solutions for GABBs to interoperate with other cyberinfrastructure platforms.

Spatial epidemiological techniques in cholera mapping and analysis towards a local scale predictive modelling

NASA Astrophysics Data System (ADS)

Rasam, A. R. A.; Ghazali, R.; Noor, A. M. M.; Mohd, W. M. N. W.; Hamid, J. R. A.; Bazlan, M. J.; Ahmad, N.

2014-02-01

Cholera spatial epidemiology is the study of the spread and control of the disease spatial pattern and epidemics. Previous studies have shown that multi-factorial causation such as human behaviour, ecology and other infectious risk factors influence the disease outbreaks. Thus, understanding spatial pattern and possible interrelationship factors of the outbreaks are crucial to be explored an in-depth study. This study focuses on the integration of geographical information system (GIS) and epidemiological techniques in exploratory analyzing the cholera spatial pattern and distribution in the selected district of Sabah. Spatial Statistic and Pattern tools in ArcGIS and Microsoft Excel software were utilized to map and analyze the reported cholera cases and other data used. Meanwhile, cohort study in epidemiological technique was applied to investigate multiple outcomes of the disease exposure. The general spatial pattern of cholera was highly clustered showed the disease spread easily at a place or person to others especially 1500 meters from the infected person and locations. Although the cholera outbreaks in the districts are not critical, it could be endemic at the crowded areas, unhygienic environment, and close to contaminated water. It was also strongly believed that the coastal water of the study areas has possible relationship with the cholera transmission and phytoplankton bloom since the areas recorded higher cases. GIS demonstrates a vital spatial epidemiological technique in determining the distribution pattern and elucidating the hypotheses generating of the disease. The next research would be applying some advanced geo-analysis methods and other disease risk factors for producing a significant a local scale predictive risk model of the disease in Malaysia.

Novel probabilistic models of spatial genetic ancestry with applications to stratification correction in genome-wide association studies.

PubMed

Bhaskar, Anand; Javanmard, Adel; Courtade, Thomas A; Tse, David

2017-03-15

Genetic variation in human populations is influenced by geographic ancestry due to spatial locality in historical mating and migration patterns. Spatial population structure in genetic datasets has been traditionally analyzed using either model-free algorithms, such as principal components analysis (PCA) and multidimensional scaling, or using explicit spatial probabilistic models of allele frequency evolution. We develop a general probabilistic model and an associated inference algorithm that unify the model-based and data-driven approaches to visualizing and inferring population structure. Our spatial inference algorithm can also be effectively applied to the problem of population stratification in genome-wide association studies (GWAS), where hidden population structure can create fictitious associations when population ancestry is correlated with both the genotype and the trait. Our algorithm Geographic Ancestry Positioning (GAP) relates local genetic distances between samples to their spatial distances, and can be used for visually discerning population structure as well as accurately inferring the spatial origin of individuals on a two-dimensional continuum. On both simulated and several real datasets from diverse human populations, GAP exhibits substantially lower error in reconstructing spatial ancestry coordinates compared to PCA. We also develop an association test that uses the ancestry coordinates inferred by GAP to accurately account for ancestry-induced correlations in GWAS. Based on simulations and analysis of a dataset of 10 metabolic traits measured in a Northern Finland cohort, which is known to exhibit significant population structure, we find that our method has superior power to current approaches. Our software is available at https://github.com/anand-bhaskar/gap . abhaskar@stanford.edu or ajavanma@usc.edu. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update

PubMed Central

Peakall, Rod; Smouse, Peter E.

2012-01-01

Summary: GenAlEx: Genetic Analysis in Excel is a cross-platform package for population genetic analyses that runs within Microsoft Excel. GenAlEx offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences. Both frequency-based (F-statistics, heterozygosity, HWE, population assignment, relatedness) and distance-based (AMOVA, PCoA, Mantel tests, multivariate spatial autocorrelation) analyses are provided. New features include calculation of new estimators of population structure: G′ST, G′′ST, Jost’s Dest and F′ST through AMOVA, Shannon Information analysis, linkage disequilibrium analysis for biallelic data and novel heterogeneity tests for spatial autocorrelation analysis. Export to more than 30 other data formats is provided. Teaching tutorials and expanded step-by-step output options are included. The comprehensive guide has been fully revised. Availability and implementation: GenAlEx is written in VBA and provided as a Microsoft Excel Add-in (compatible with Excel 2003, 2007, 2010 on PC; Excel 2004, 2011 on Macintosh). GenAlEx, and supporting documentation and tutorials are freely available at: http://biology.anu.edu.au/GenAlEx. Contact: rod.peakall@anu.edu.au PMID:22820204

High-throughput mathematical analysis identifies Turing networks for patterning with equally diffusing signals.

PubMed

Marcon, Luciano; Diego, Xavier; Sharpe, James; Müller, Patrick

2016-04-08

The Turing reaction-diffusion model explains how identical cells can self-organize to form spatial patterns. It has been suggested that extracellular signaling molecules with different diffusion coefficients underlie this model, but the contribution of cell-autonomous signaling components is largely unknown. We developed an automated mathematical analysis to derive a catalog of realistic Turing networks. This analysis reveals that in the presence of cell-autonomous factors, networks can form a pattern with equally diffusing signals and even for any combination of diffusion coefficients. We provide a software (available at http://www.RDNets.com) to explore these networks and to constrain topologies with qualitative and quantitative experimental data. We use the software to examine the self-organizing networks that control embryonic axis specification and digit patterning. Finally, we demonstrate how existing synthetic circuits can be extended with additional feedbacks to form Turing reaction-diffusion systems. Our study offers a new theoretical framework to understand multicellular pattern formation and enables the wide-spread use of mathematical biology to engineer synthetic patterning systems.

High-throughput mathematical analysis identifies Turing networks for patterning with equally diffusing signals

PubMed Central

Marcon, Luciano; Diego, Xavier; Sharpe, James; Müller, Patrick

2016-01-01

The Turing reaction-diffusion model explains how identical cells can self-organize to form spatial patterns. It has been suggested that extracellular signaling molecules with different diffusion coefficients underlie this model, but the contribution of cell-autonomous signaling components is largely unknown. We developed an automated mathematical analysis to derive a catalog of realistic Turing networks. This analysis reveals that in the presence of cell-autonomous factors, networks can form a pattern with equally diffusing signals and even for any combination of diffusion coefficients. We provide a software (available at http://www.RDNets.com) to explore these networks and to constrain topologies with qualitative and quantitative experimental data. We use the software to examine the self-organizing networks that control embryonic axis specification and digit patterning. Finally, we demonstrate how existing synthetic circuits can be extended with additional feedbacks to form Turing reaction-diffusion systems. Our study offers a new theoretical framework to understand multicellular pattern formation and enables the wide-spread use of mathematical biology to engineer synthetic patterning systems. DOI: http://dx.doi.org/10.7554/eLife.14022.001 PMID:27058171

The use of GIS tools in determining the intensity of meandering of rivers based on the example of Noteć River (Poland)

NASA Astrophysics Data System (ADS)

Szatten, Dawid; Rabant, Hubert; Nadolny, Grzegorz

2017-11-01

The study used the tools of Geographic Information System (GIS) in the analysis of the intensity of meandering of Noteć River, calculated using indicators proposed by Brice [16], Leopold et al. [17], Rust [15] and Rosgen [18]. In this work the emphasis is placed on showing the suitability of using modelling software and spatial data. The study was based on archival cartographic materials and orthophotomap presenting the current course of the river channel. The software of geographic information system used for analysis was ArcMap v.10.0. The rate of meandering of the river in a multiyear period 1876-2013 and four typical scenarios of the development of river channel were determined. Comparing them with the types of human intervention in the fluvial system, the dynamics of transformation channel in the analysed period of time was specified. These types are characteristic for all the meandering rivers. These scenarios can determine the amount of anthropopressure and to evaluate the usefulness of GIS in the analysis of transformations of the fluvial system.

Integrated Web-Based Immersive Exploration of the Coordinated Canyon Experiment Data using Open Source STOQS Software

NASA Astrophysics Data System (ADS)

McCann, M. P.; Gwiazda, R.; O'Reilly, T. C.; Maier, K. L.; Lundsten, E. M.; Parsons, D. R.; Paull, C. K.

2017-12-01

The Coordinated Canyon Experiment (CCE) in Monterey Submarine Canyon has produced a wealth of oceanographic measurements whose analysis will improve understanding of turbidity current processes. Exploration of this data set, consisting of over 60 parameters from 15 platforms, is facilitated by using the open source Spatial Temporal Oceanographic Query System (STOQS) software (https://github.com/stoqs/stoqs). The Monterey Bay Aquarium Research Institute (MBARI) originally developed STOQS to help manage and visualize upper water column oceanographic measurements, but the generality of its data model permits effective use for any kind of spatial/temporal measurement data. STOQS consists of a PostgreSQL database and server-side Python/Django software; the client-side is jQuery JavaScript supporting AJAX requests to update a single page web application. The User Interface (UI) is optimized to provide a quick overview of data in spatial and temporal dimensions, as well as in parameter, platform, and data value space. A user may zoom into any feature of interest and select it, initiating a filter operation that updates the UI with an overview of all the data in the new filtered selection. When details are desired, radio buttons and checkboxes are selected to generate a number of different types of visualizations. These include color-filled temporal section and line plots, parameter-parameter plots, 2D map plots, and interactive 3D spatial visualizations. The Extensible 3D (X3D) standard and X3DOM JavaScript library provide the technology for presenting animated 3D data directly within the web browser. Most of the oceanographic measurements from the CCE (e.g. mooring mounted ADCP and CTD data) are easily visualized using established methods. However, unified integration and multiparameter display of several concurrently deployed sensors across a network of platforms is a challenge we hope to solve. Moreover, STOQS also allows display of data from a new instrument - the Benthic Event Detector (BED). The BED records 50Hz samples of orientation and acceleration when it moves. These data are converted to the CF-NetCDF format and then loaded into a STOQS database. Using the Spatial-3D view a user may interact with a virtual playback of BED motions, giving new insight into submarine canyon sediment density flows.

Wildlife tracking data management: a new vision.

PubMed

Urbano, Ferdinando; Cagnacci, Francesca; Calenge, Clément; Dettki, Holger; Cameron, Alison; Neteler, Markus

2010-07-27

To date, the processing of wildlife location data has relied on a diversity of software and file formats. Data management and the following spatial and statistical analyses were undertaken in multiple steps, involving many time-consuming importing/exporting phases. Recent technological advancements in tracking systems have made large, continuous, high-frequency datasets of wildlife behavioural data available, such as those derived from the global positioning system (GPS) and other animal-attached sensor devices. These data can be further complemented by a wide range of other information about the animals' environment. Management of these large and diverse datasets for modelling animal behaviour and ecology can prove challenging, slowing down analysis and increasing the probability of mistakes in data handling. We address these issues by critically evaluating the requirements for good management of GPS data for wildlife biology. We highlight that dedicated data management tools and expertise are needed. We explore current research in wildlife data management. We suggest a general direction of development, based on a modular software architecture with a spatial database at its core, where interoperability, data model design and integration with remote-sensing data sources play an important role in successful GPS data handling.

Principles and Best Practices Emerging from Data Basin: A Data Platform Supporting Scientific Research and Landscape Conservation Planning

NASA Astrophysics Data System (ADS)

Comendant, T.; Strittholt, J. R.; Ward, B. C.; Bachelet, D. M.; Grossman, D.; Stevenson-Molnar, N.; Henifin, K.; Lundin, M.; Marvin, T. S.; Peterman, W. L.; Corrigan, G. N.; O'Connor, K.

2013-12-01

A multi-disciplinary team of scientists, software engineers, and outreach staff at the Conservation Biology Institute launched an open-access, web-based spatial data platform called Data Basin (www.databasin.org) in 2010. Primarily built to support research and environmental resource planning, Data Basin provides the capability for individuals and organizations to explore, create, interpret, and collaborate around their priority topics and geographies. We used a stakeholder analysis to assess the needs of data consumers/produces and help prioritize primary and secondary audiences. Data Basin's simple and user-friendly interface makes mapping and geo-processing tools more accessible to less technical audiences. Input from users is considered in system planning, testing, and implementation. The team continually develops using an agile software development approach, which allows new features, improvements, and bug fixes to be deployed to the live system on a frequent basis. The data import process is handled through administrative approval and Data Basin requires spatial data (biological, physical, and socio-economic) to be well-documented. Outreach and training is used to convey the scope and appropriate use of the scientific information and available resources.

Wildlife tracking data management: a new vision

PubMed Central

Urbano, Ferdinando; Cagnacci, Francesca; Calenge, Clément; Dettki, Holger; Cameron, Alison; Neteler, Markus

2010-01-01

To date, the processing of wildlife location data has relied on a diversity of software and file formats. Data management and the following spatial and statistical analyses were undertaken in multiple steps, involving many time-consuming importing/exporting phases. Recent technological advancements in tracking systems have made large, continuous, high-frequency datasets of wildlife behavioural data available, such as those derived from the global positioning system (GPS) and other animal-attached sensor devices. These data can be further complemented by a wide range of other information about the animals' environment. Management of these large and diverse datasets for modelling animal behaviour and ecology can prove challenging, slowing down analysis and increasing the probability of mistakes in data handling. We address these issues by critically evaluating the requirements for good management of GPS data for wildlife biology. We highlight that dedicated data management tools and expertise are needed. We explore current research in wildlife data management. We suggest a general direction of development, based on a modular software architecture with a spatial database at its core, where interoperability, data model design and integration with remote-sensing data sources play an important role in successful GPS data handling. PMID:20566495

Assessment and prediction of urban air pollution caused by motor transport exhaust gases using computer simulation methods

NASA Astrophysics Data System (ADS)

Boyarshinov, Michael G.; Vaismana, Yakov I.

2016-10-01

The following methods were used in order to identify the pollution fields of urban air caused by the motor transport exhaust gases: the mathematical model, which enables to consider the influence of the main factors that determine pollution fields formation in the complex spatial domain; the authoring software designed for computational modeling of the gas flow, generated by numerous mobile point sources; the results of computing experiments on pollutant spread analysis and evolution of their concentration fields. The computational model of exhaust gas distribution and dispersion in a spatial domain, which includes urban buildings, structures and main traffic arteries, takes into account a stochastic character of cars apparition on the borders of the examined territory and uses a Poisson process. The model also considers the traffic lights switching and permits to define the fields of velocity, pressure and temperature of the discharge gases in urban air. The verification of mathematical model and software used confirmed their satisfactory fit to the in-situ measurements data and the possibility to use the obtained computing results for assessment and prediction of urban air pollution caused by motor transport exhaust gases.

HydroDesktop: An Open Source GIS-Based Platform for Hydrologic Data Discovery, Visualization, and Analysis

NASA Astrophysics Data System (ADS)

Ames, D. P.; Kadlec, J.; Cao, Y.; Grover, D.; Horsburgh, J. S.; Whiteaker, T.; Goodall, J. L.; Valentine, D. W.

2010-12-01

A growing number of hydrologic information servers are being deployed by government agencies, university networks, and individual researchers using the Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI) Hydrologic Information System (HIS). The CUAHSI HIS Project has developed a standard software stack, called HydroServer, for publishing hydrologic observations data. It includes the Observations Data Model (ODM) database and Water Data Service web services, which together enable publication of data on the Internet in a standard format called Water Markup Language (WaterML). Metadata describing available datasets hosted on these servers is compiled within a central metadata catalog called HIS Central at the San Diego Supercomputer Center and is searchable through a set of predefined web services based queries. Together, these servers and central catalog service comprise a federated HIS of a scale and comprehensiveness never previously available. This presentation will briefly review/introduce the CUAHSI HIS system with special focus on a new HIS software tool called "HydroDesktop" and the open source software development web portal, www.HydroDesktop.org, which supports community development and maintenance of the software. HydroDesktop is a client-side, desktop software application that acts as a search and discovery tool for exploring the distributed network of HydroServers, downloading specific data series, visualizing and summarizing data series and exporting these to formats needed for analysis by external software. HydroDesktop is based on the open source DotSpatial GIS developer toolkit which provides it with map-based data interaction and visualization, and a plug-in interface that can be used by third party developers and researchers to easily extend the software using Microsoft .NET programming languages. HydroDesktop plug-ins that are presently available or currently under development within the project and by third party collaborators include functions for data search and discovery, extensive graphing, data editing and export, HydroServer exploration, integration with the OpenMI workflow and modeling system, and an interface for data analysis through the R statistical package.

SDMtoolbox 2.0: the next generation Python-based GIS toolkit for landscape genetic, biogeographic and species distribution model analyses

PubMed Central

Bennett, Joseph R.; French, Connor M.

2017-01-01

SDMtoolbox 2.0 is a software package for spatial studies of ecology, evolution, and genetics. The release of SDMtoolbox 2.0 allows researchers to use the most current ArcGIS software and MaxEnt software, and reduces the amount of time that would be spent developing common solutions. The central aim of this software is to automate complicated and repetitive spatial analyses in an intuitive graphical user interface. One core tenant facilitates careful parameterization of species distribution models (SDMs) to maximize each model’s discriminatory ability and minimize overfitting. This includes carefully processing of occurrence data, environmental data, and model parameterization. This program directly interfaces with MaxEnt, one of the most powerful and widely used species distribution modeling software programs, although SDMtoolbox 2.0 is not limited to species distribution modeling or restricted to modeling in MaxEnt. Many of the SDM pre- and post-processing tools have ‘universal’ analogs for use with any modeling software. The current version contains a total of 79 scripts that harness the power of ArcGIS for macroecology, landscape genetics, and evolutionary studies. For example, these tools allow for biodiversity quantification (such as species richness or corrected weighted endemism), generation of least-cost paths and corridors among shared haplotypes, assessment of the significance of spatial randomizations, and enforcement of dispersal limitations of SDMs projected into future climates—to only name a few functions contained in SDMtoolbox 2.0. Lastly, dozens of generalized tools exists for batch processing and conversion of GIS data types or formats, which are broadly useful to any ArcMap user. PMID:29230356

Rule-based topology system for spatial databases to validate complex geographic datasets

NASA Astrophysics Data System (ADS)

Martinez-Llario, J.; Coll, E.; Núñez-Andrés, M.; Femenia-Ribera, C.

2017-06-01

A rule-based topology software system providing a highly flexible and fast procedure to enforce integrity in spatial relationships among datasets is presented. This improved topology rule system is built over the spatial extension Jaspa. Both projects are open source, freely available software developed by the corresponding author of this paper. Currently, there is no spatial DBMS that implements a rule-based topology engine (considering that the topology rules are designed and performed in the spatial backend). If the topology rules are applied in the frontend (as in many GIS desktop programs), ArcGIS is the most advanced solution. The system presented in this paper has several major advantages over the ArcGIS approach: it can be extended with new topology rules, it has a much wider set of rules, and it can mix feature attributes with topology rules as filters. In addition, the topology rule system can work with various DBMSs, including PostgreSQL, H2 or Oracle, and the logic is performed in the spatial backend. The proposed topology system allows users to check the complex spatial relationships among features (from one or several spatial layers) that require some complex cartographic datasets, such as the data specifications proposed by INSPIRE in Europe and the Land Administration Domain Model (LADM) for Cadastral data.

Snow cover monitoring by machine processing of multitemporal LANDSAT MSS data

NASA Technical Reports Server (NTRS)

Luther, S. G.; Bartolucci, L. A.; Hoffer, R. M.

1975-01-01

LANDSAT frames were geometrically corrected and data sets from six different dates were overlaid to produce a 24 channel (six dates and four wavelength bands) data tape. Changes in the extent of the snowpack could be accurately and easily determined using a change detection technique on data which had previously been classified by the LARSYS software system. A second phase of the analysis involved determination of the relationship between spatial resolution or data sampling frequency and accuracy of measuring the area of the snowpack.

Spherical Panoramas for Astrophysical Data Visualization

NASA Astrophysics Data System (ADS)

Kent, Brian R.

2017-05-01

Data immersion has advantages in astrophysical visualization. Complex multi-dimensional data and phase spaces can be explored in a seamless and interactive viewing environment. Putting the user in the data is a first step toward immersive data analysis. We present a technique for creating 360° spherical panoramas with astrophysical data. The three-dimensional software package Blender and the Google Spatial Media module are used together to immerse users in data exploration. Several examples employing these methods exhibit how the technique works using different types of astronomical data.

AirMISR WISCONSIN

Atmospheric Science Data Center

2014-04-25

AirMISR WISCONSIN 2000 Project Title:  AirMISR Discipline:  ... Platform:  ER-2 Spatial Coverage:  Wisconsin (35.92, 43.79)(-97.94, -90.23) Spatial Resolution:  ... Order Data Readme Files:  Readme Wisconsin Read Software Files :  IDL Code ...

Parallel Computing for the Computed-Tomography Imaging Spectrometer

NASA Technical Reports Server (NTRS)

Lee, Seungwon

2008-01-01

This software computes the tomographic reconstruction of spatial-spectral data from raw detector images of the Computed-Tomography Imaging Spectrometer (CTIS), which enables transient-level, multi-spectral imaging by capturing spatial and spectral information in a single snapshot.

A Powerful, Cost Effective, Web Based Engineering Solution Supporting Conjunction Detection and Visual Analysis

NASA Astrophysics Data System (ADS)

Novak, Daniel M.; Biamonti, Davide; Gross, Jeremy; Milnes, Martin

2013-08-01

An innovative and visually appealing tool is presented for efficient all-vs-all conjunction analysis on a large catalogue of objects. The conjunction detection uses a nearest neighbour search algorithm, based on spatial binning and identification of pairs of objects in adjacent bins. This results in the fastest all vs all filtering the authors are aware of. The tool is constructed on a server-client architecture, where the server broadcasts to the client the conjunction data and ephemerides, while the client supports the user interface through a modern browser, without plug-in. In order to make the tool flexible and maintainable, Java software technologies were used on the server side, including Spring, Camel, ActiveMQ and CometD. The user interface and visualisation are based on the latest web technologies: HTML5, WebGL, THREE.js. Importance has been given on the ergonomics and visual appeal of the software. In fact certain design concepts have been borrowed from the gaming industry.

TXM-Wizard: a program for advanced data collection and evaluation in full-field transmission X-ray microscopy

PubMed Central

Liu, Yijin; Meirer, Florian; Williams, Phillip A.; Wang, Junyue; Andrews, Joy C.; Pianetta, Piero

2012-01-01

Transmission X-ray microscopy (TXM) has been well recognized as a powerful tool for non-destructive investigation of the three-dimensional inner structure of a sample with spatial resolution down to a few tens of nanometers, especially when combined with synchrotron radiation sources. Recent developments of this technique have presented a need for new tools for both system control and data analysis. Here a software package developed in MATLAB for script command generation and analysis of TXM data is presented. The first toolkit, the script generator, allows automating complex experimental tasks which involve up to several thousand motor movements. The second package was designed to accomplish computationally intense tasks such as data processing of mosaic and mosaic tomography datasets; dual-energy contrast imaging, where data are recorded above and below a specific X-ray absorption edge; and TXM X-ray absorption near-edge structure imaging datasets. Furthermore, analytical and iterative tomography reconstruction algorithms were implemented. The compiled software package is freely available. PMID:22338691

Water Quality Analysis Tool (WQAT) | Science Inventory | US ...

EPA Pesticide Factsheets

The purpose of the Water Quality Analysis Tool (WQAT) software is to provide a means for analyzing and producing useful remotely sensed data products for an entire estuary, a particular point or area of interest (AOI or POI) in estuaries, or water bodies of interest where pre-processed and geographically gridded remotely sensed images are available. A graphical user interface (GUI), was created to enable the user to select and display imagery from a variety of remote sensing data sources. The user can select a date (or date range) and location to extract pixels from the remotely sensed imagery. The GUI is used to obtain all available pixel values (i.e. pixel from all available bands of all available satellites) for a given location on a given date and time. The resultant data set can be analyzed or saved to a file for future use. The WQAT software provides users with a way to establish algorithms between remote sensing reflectance (Rrs) and any available in situ parameters, as well as statistical and regression analysis. The combined data sets can be used to improve water quality research and studies. Satellites provide spatially synoptic data at high frequency (daily to weekly). These characteristics are desirable for supplementing existing water quality observations and for providing information for large aquatic ecosystems that are historically under-sampled by field programs. Thus, the Water Quality Assessment Tool (WQAT) software tool was developed to suppo

TransFit: Finite element analysis data fitting software

NASA Technical Reports Server (NTRS)

Freeman, Mark

1993-01-01

The Advanced X-Ray Astrophysics Facility (AXAF) mission support team has made extensive use of geometric ray tracing to analyze the performance of AXAF developmental and flight optics. One important aspect of this performance modeling is the incorporation of finite element analysis (FEA) data into the surface deformations of the optical elements. TransFit is software designed for the fitting of FEA data of Wolter I optical surface distortions with a continuous surface description which can then be used by SAO's analytic ray tracing software, currently OSAC (Optical Surface Analysis Code). The improved capabilities of Transfit over previous methods include bicubic spline fitting of FEA data to accommodate higher spatial frequency distortions, fitted data visualization for assessing the quality of fit, the ability to accommodate input data from three FEA codes plus other standard formats, and options for alignment of the model coordinate system with the ray trace coordinate system. TransFit uses the AnswerGarden graphical user interface (GUI) to edit input parameters and then access routines written in PV-WAVE, C, and FORTRAN to allow the user to interactively create, evaluate, and modify the fit. The topics covered include an introduction to TransFit: requirements, designs philosophy, and implementation; design specifics: modules, parameters, fitting algorithms, and data displays; a procedural example; verification of performance; future work; and appendices on online help and ray trace results of the verification section.

The Effect of Dynamic Geometry Software on Student Mathematics Teachers' Spatial Visualization Skills

ERIC Educational Resources Information Center

Güven, Bülent; Kosa, Temel

2008-01-01

Geometry is the study of shape and space. Without spatial ability, students cannot fully appreciate the natural world. Spatial ability is also very important for work in various fields such as computer graphics, engineering, architecture, and cartography. A number of studies have demonstrated that technology has an important potential to develop…

WESTPA: An interoperable, highly scalable software package for weighted ensemble simulation and analysis

PubMed Central

Zwier, Matthew C.; Adelman, Joshua L.; Kaus, Joseph W.; Pratt, Adam J.; Wong, Kim F.; Rego, Nicholas B.; Suárez, Ernesto; Lettieri, Steven; Wang, David W.; Grabe, Michael; Zuckerman, Daniel M.; Chong, Lillian T.

2015-01-01

The weighted ensemble (WE) path sampling approach orchestrates an ensemble of parallel calculations with intermittent communication to enhance the sampling of rare events, such as molecular associations or conformational changes in proteins or peptides. Trajectories are replicated and pruned in a way that focuses computational effort on under-explored regions of configuration space while maintaining rigorous kinetics. To enable the simulation of rare events at any scale (e.g. atomistic, cellular), we have developed an open-source, interoperable, and highly scalable software package for the execution and analysis of WE simulations: WESTPA (The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis). WESTPA scales to thousands of CPU cores and includes a suite of analysis tools that have been implemented in a massively parallel fashion. The software has been designed to interface conveniently with any dynamics engine and has already been used with a variety of molecular dynamics (e.g. GROMACS, NAMD, OpenMM, AMBER) and cell-modeling packages (e.g. BioNetGen, MCell). WESTPA has been in production use for over a year, and its utility has been demonstrated for a broad set of problems, ranging from atomically detailed host-guest associations to non-spatial chemical kinetics of cellular signaling networks. The following describes the design and features of WESTPA, including the facilities it provides for running WE simulations, storing and analyzing WE simulation data, as well as examples of input and output. PMID:26392815

Visualization techniques to aid in the analysis of multi-spectral astrophysical data sets

NASA Technical Reports Server (NTRS)

Brugel, Edward W.; Domik, Gitta O.; Ayres, Thomas R.

1993-01-01

The goal of this project was to support the scientific analysis of multi-spectral astrophysical data by means of scientific visualization. Scientific visualization offers its greatest value if it is not used as a method separate or alternative to other data analysis methods but rather in addition to these methods. Together with quantitative analysis of data, such as offered by statistical analysis, image or signal processing, visualization attempts to explore all information inherent in astrophysical data in the most effective way. Data visualization is one aspect of data analysis. Our taxonomy as developed in Section 2 includes identification and access to existing information, preprocessing and quantitative analysis of data, visual representation and the user interface as major components to the software environment of astrophysical data analysis. In pursuing our goal to provide methods and tools for scientific visualization of multi-spectral astrophysical data, we therefore looked at scientific data analysis as one whole process, adding visualization tools to an already existing environment and integrating the various components that define a scientific data analysis environment. As long as the software development process of each component is separate from all other components, users of data analysis software are constantly interrupted in their scientific work in order to convert from one data format to another, or to move from one storage medium to another, or to switch from one user interface to another. We also took an in-depth look at scientific visualization and its underlying concepts, current visualization systems, their contributions, and their shortcomings. The role of data visualization is to stimulate mental processes different from quantitative data analysis, such as the perception of spatial relationships or the discovery of patterns or anomalies while browsing through large data sets. Visualization often leads to an intuitive understanding of the meaning of data values and their relationships by sacrificing accuracy in interpreting the data values. In order to be accurate in the interpretation, data values need to be measured, computed on, and compared to theoretical or empirical models (quantitative analysis). If visualization software hampers quantitative analysis (which happens with some commercial visualization products), its use is greatly diminished for astrophysical data analysis. The software system STAR (Scientific Toolkit for Astrophysical Research) was developed as a prototype during the course of the project to better understand the pragmatic concerns raised in the project. STAR led to a better understanding on the importance of collaboration between astrophysicists and computer scientists.

A computer software system for integration and analysis of grid-based remote sensing data with other natural resource data. Remote Sensing Project

NASA Technical Reports Server (NTRS)

Tilmann, S. E.; Enslin, W. R.; Hill-Rowley, R.

1977-01-01

A computer-based information system is described designed to assist in the integration of commonly available spatial data for regional planning and resource analysis. The Resource Analysis Program (RAP) provides a variety of analytical and mapping phases for single factor or multi-factor analyses. The unique analytical and graphic capabilities of RAP are demonstrated with a study conducted in Windsor Township, Eaton County, Michigan. Soil, land cover/use, topographic and geological maps were used as a data base to develope an eleven map portfolio. The major themes of the portfolio are land cover/use, non-point water pollution, waste disposal, and ground water recharge.

PP-SWAT: A phython-based computing software for efficient multiobjective callibration of SWAT

USDA-ARS?s Scientific Manuscript database

With enhanced data availability, distributed watershed models for large areas with high spatial and temporal resolution are increasingly used to understand water budgets and examine effects of human activities and climate change/variability on water resources. Developing parallel computing software...

A methodology for investigating interdependencies between measured throughfall, meteorological variables and canopy structure on a small catchment.

NASA Astrophysics Data System (ADS)

Maurer, Thomas; Gustavos Trujillo Siliézar, Carlos; Oeser, Anne; Pohle, Ina; Hinz, Christoph

2016-04-01

In evolving initial landscapes, vegetation development depends on a variety of feedback effects. One of the less understood feedback loops is the interaction between throughfall and plant canopy development. The amount of throughfall is governed by the characteristics of the vegetation canopy, whereas vegetation pattern evolution may in turn depend on the spatio-temporal distribution of throughfall. Meteorological factors that may influence throughfall, while at the same time interacting with the canopy, are e.g. wind speed, wind direction and rainfall intensity. Our objective is to investigate how throughfall, vegetation canopy and meteorological variables interact in an exemplary eco-hydrological system in its initial development phase, in which the canopy is very heterogeneous and rapidly changing. For that purpose, we developed a methodological approach combining field methods, raster image analysis and multivariate statistics. The research area for this study is the Hühnerwasser ('Chicken Creek') catchment in Lower Lusatia, Brandenburg, Germany, where after eight years of succession, the spatial distribution of plant species is highly heterogeneous, leading to increasingly differentiated throughfall patterns. The constructed 6-ha catchment offers ideal conditions for our study due to the rapidly changing vegetation structure and the availability of complementary monitoring data. Throughfall data were obtained by 50 tipping bucket rain gauges arranged in two transects and connected via a wireless sensor network that cover the predominant vegetation types on the catchment (locust copses, dense sallow thorn bushes and reeds, base herbaceous and medium-rise small-reed vegetation, and open areas covered by moss and lichens). The spatial configuration of the vegetation canopy for each measurement site was described via digital image analysis of hemispheric photographs of the canopy using the ArcGIS Spatial Analyst, GapLight and ImageJ software. Meteorological data from two on-site weather stations (wind direction, wind speed, air temperature, air humidity, insolation, soil temperature, precipitation) were provided by the 'Research Platform Chicken Creek' (https://www.tu-cottbus.de/projekte/en/oekosysteme/startseite.html). Data were combined and multivariate statistical analysis (PCA, cluster analysis, regression trees) were conducted using the R-software to i) obtain statistical indices describing the relevant characteristics of the data and ii) to identify the determining factors for throughfall intensity. The methodology is currently tested and results will be presented. Preliminary evaluation of the image analysis approach showed only marginal, systematic deviation of results for the different software tools applied, which makes the developed workflow a viable tool for canopy characterization. Results from this study will have a broad spectrum of possible applications, for instance the development / calibration of rainfall interception models, the incorporation into eco-hydrological models, or to test the fault tolerance of wireless rainfall sensor networks.

Statistical Approaches Used to Assess the Equity of Access to Food Outlets: A Systematic Review

PubMed Central

Lamb, Karen E.; Thornton, Lukar E.; Cerin, Ester; Ball, Kylie

2015-01-01

Background Inequalities in eating behaviours are often linked to the types of food retailers accessible in neighbourhood environments. Numerous studies have aimed to identify if access to healthy and unhealthy food retailers is socioeconomically patterned across neighbourhoods, and thus a potential risk factor for dietary inequalities. Existing reviews have examined differences between methodologies, particularly focussing on neighbourhood and food outlet access measure definitions. However, no review has informatively discussed the suitability of the statistical methodologies employed; a key issue determining the validity of study findings. Our aim was to examine the suitability of statistical approaches adopted in these analyses. Methods Searches were conducted for articles published from 2000–2014. Eligible studies included objective measures of the neighbourhood food environment and neighbourhood-level socio-economic status, with a statistical analysis of the association between food outlet access and socio-economic status. Results Fifty-four papers were included. Outlet accessibility was typically defined as the distance to the nearest outlet from the neighbourhood centroid, or as the number of food outlets within a neighbourhood (or buffer). To assess if these measures were linked to neighbourhood disadvantage, common statistical methods included ANOVA, correlation, and Poisson or negative binomial regression. Although all studies involved spatial data, few considered spatial analysis techniques or spatial autocorrelation. Conclusions With advances in GIS software, sophisticated measures of neighbourhood outlet accessibility can be considered. However, approaches to statistical analysis often appear less sophisticated. Care should be taken to consider assumptions underlying the analysis and the possibility of spatially correlated residuals which could affect the results. PMID:29546115

Spatial Data Transfer Standard (SDTS), part 3 : ISO 8211 encoding

DOT National Transportation Integrated Search

1997-11-20

The ISO 8211 encoding provides a representation of a Spatial Data Transfer Standard (SDTS) file set in a standardized method enabling the file set to be exported to or imported from different media by general purpose ISO 8211 software.

A Permutation-Randomization Approach to Test the Spatial Distribution of Plant Diseases.

PubMed

Lione, G; Gonthier, P

2016-01-01

The analysis of the spatial distribution of plant diseases requires the availability of trustworthy geostatistical methods. The mean distance tests (MDT) are here proposed as a series of permutation and randomization tests to assess the spatial distribution of plant diseases when the variable of phytopathological interest is categorical. A user-friendly software to perform the tests is provided. Estimates of power and type I error, obtained with Monte Carlo simulations, showed the reliability of the MDT (power > 0.80; type I error < 0.05). A biological validation on the spatial distribution of spores of two fungal pathogens causing root rot on conifers was successfully performed by verifying the consistency between the MDT responses and previously published data. An application of the MDT was carried out to analyze the relation between the plantation density and the distribution of the infection of Gnomoniopsis castanea, an emerging fungal pathogen causing nut rot on sweet chestnut. Trees carrying nuts infected by the pathogen were randomly distributed in areas with different plantation densities, suggesting that the distribution of G. castanea was not related to the plantation density. The MDT could be used to analyze the spatial distribution of plant diseases both in agricultural and natural ecosystems.

Open source tools for fluorescent imaging.

PubMed

Hamilton, Nicholas A

2012-01-01

As microscopy becomes increasingly automated and imaging expands in the spatial and time dimensions, quantitative analysis tools for fluorescent imaging are becoming critical to remove both bottlenecks in throughput as well as fully extract and exploit the information contained in the imaging. In recent years there has been a flurry of activity in the development of bio-image analysis tools and methods with the result that there are now many high-quality, well-documented, and well-supported open source bio-image analysis projects with large user bases that cover essentially every aspect from image capture to publication. These open source solutions are now providing a viable alternative to commercial solutions. More importantly, they are forming an interoperable and interconnected network of tools that allow data and analysis methods to be shared between many of the major projects. Just as researchers build on, transmit, and verify knowledge through publication, open source analysis methods and software are creating a foundation that can be built upon, transmitted, and verified. Here we describe many of the major projects, their capabilities, and features. We also give an overview of the current state of open source software for fluorescent microscopy analysis and the many reasons to use and develop open source methods. Copyright © 2012 Elsevier Inc. All rights reserved.

An open source platform for multi-scale spatially distributed simulations of microbial ecosystems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Segre, Daniel

2014-08-14

The goal of this project was to develop a tool for facilitating simulation, validation and discovery of multiscale dynamical processes in microbial ecosystems. This led to the development of an open-source software platform for Computation Of Microbial Ecosystems in Time and Space (COMETS). COMETS performs spatially distributed time-dependent flux balance based simulations of microbial metabolism. Our plan involved building the software platform itself, calibrating and testing it through comparison with experimental data, and integrating simulations and experiments to address important open questions on the evolution and dynamics of cross-feeding interactions between microbial species.

Application of the automated spatial surveillance program to birth defects surveillance data.

PubMed

Gardner, Bennett R; Strickland, Matthew J; Correa, Adolfo

2007-07-01

Although many birth defects surveillance programs incorporate georeferenced records into their databases, practical methods for routine spatial surveillance are lacking. We present a macroprogram written for the software package R designed for routine exploratory spatial analysis of birth defects data, the Automated Spatial Surveillance Program (ASSP), and present an application of this program using spina bifida prevalence data for metropolitan Atlanta. Birth defects surveillance data were collected by the Metropolitan Atlanta Congenital Defects Program. We generated ASSP maps for two groups of years that correspond roughly to the periods before (1994-1998) and after (1999-2002) folic acid fortification of flour. ASSP maps display census tract-specific spina bifida prevalence, smoothed prevalence contours, and locations of statistically elevated prevalence. We used these maps to identify areas of elevated prevalence for spina bifida. We identified a large area of potential concern in the years following fortification of grains and cereals with folic acid. This area overlapped census tracts containing large numbers of Hispanic residents. The potential utility of ASSP for spatial disease monitoring was demonstrated by the identification of areas of high prevalence of spina bifida and may warrant further study and monitoring. We intend to further develop ASSP so that it becomes practical for routine spatial monitoring of birth defects. (c) 2007 Wiley-Liss, Inc.

Applicability of Various Interpolation Approaches for High Resolution Spatial Mapping of Climate Data in Korea

NASA Astrophysics Data System (ADS)

Jo, A.; Ryu, J.; Chung, H.; Choi, Y.; Jeon, S.

2018-04-01

The purpose of this study is to create a new dataset of spatially interpolated monthly climate data for South Korea at high spatial resolution (approximately 30m) by performing various spatio-statistical interpolation and comparing with forecast LDAPS gridded climate data provided from Korea Meterological Administration (KMA). Automatic Weather System (AWS) and Automated Synoptic Observing System (ASOS) data in 2017 obtained from KMA were included for the spatial mapping of temperature and rainfall; instantaneous temperature and 1-hour accumulated precipitation at 09:00 am on 31th March, 21th June, 23th September, and 24th December. Among observation data, 80 percent of the total point (478) and remaining 120 points were used for interpolations and for quantification, respectively. With the training data and digital elevation model (DEM) with 30 m resolution, inverse distance weighting (IDW), co-kriging, and kriging were performed by using ArcGIS10.3.1 software and Python 3.6.4. Bias and root mean square were computed to compare prediction performance quantitatively. When statistical analysis was performed for each cluster using 20 % validation data, co kriging was more suitable for spatialization of instantaneous temperature than other interpolation method. On the other hand, IDW technique was appropriate for spatialization of precipitation.

Nasendoscopy: an analysis of measurement uncertainties.

PubMed

Gilleard, Onur; Sommerlad, Brian; Sell, Debbie; Ghanem, Ali; Birch, Malcolm

2013-05-01

Objective : The purpose of this study was to analyze the optical characteristics of two different nasendoscopes used to assess velopharyngeal insufficiency and to quantify the measurement uncertainties that will occur in a typical set of clinical data. Design : The magnification and barrel distortion associated with nasendoscopy was estimated by using computer software to analyze the apparent dimensions of a spatially calibrated test object at varying object-lens distances. In addition, a method of semiquantitative analysis of velopharyngeal closure using nasendoscopy and computer software is described. To calculate the reliability of this method, 10 nasendoscopy examinations were analyzed two times by three separate operators. The measure of intraoperator and interoperator agreement was evaluated using Pearson's r correlation coefficient. Results : Over an object lens distance of 9 mm, magnification caused the visualized dimensions of the test object to increase by 80%. In addition, dimensions of objects visualized in the far-peripheral field of the nasendoscopic examinations appeared approximately 40% smaller than those visualized in the central field. Using computer software to analyze velopharyngeal closure, the mean correlation coefficient for intrarater reliability was .94 and for interrater reliability was .90. Conclusion : Using a custom-designed apparatus, the effect object-lens distance has on the magnification of nasendoscopic images has been quantified. Barrel distortion has also been quantified and was found to be independent of object-lens distance. Using computer software to analyze clinical images, the intraoperator and interoperator correlation appears to show that ratio-metric measurements are reliable.

Pattern detection in stream networks: Quantifying spatialvariability in fish distribution

USGS Publications Warehouse

Torgersen, Christian E.; Gresswell, Robert E.; Bateman, Douglas S.

2004-01-01

Biological and physical properties of rivers and streams are inherently difficult to sample and visualize at the resolution and extent necessary to detect fine-scale distributional patterns over large areas. Satellite imagery and broad-scale fish survey methods are effective for quantifying spatial variability in biological and physical variables over a range of scales in marine environments but are often too coarse in resolution to address conservation needs in inland fisheries management. We present methods for sampling and analyzing multiscale, spatially continuous patterns of stream fishes and physical habitat in small- to medium-size watersheds (500–1000 hectares). Geospatial tools, including geographic information system (GIS) software such as ArcInfo dynamic segmentation and ArcScene 3D analyst modules, were used to display complex biological and physical datasets. These tools also provided spatial referencing information (e.g. Cartesian and route-measure coordinates) necessary for conducting geostatistical analyses of spatial patterns (empirical semivariograms and wavelet analysis) in linear stream networks. Graphical depiction of fish distribution along a one-dimensional longitudinal profile and throughout the stream network (superimposed on a 10-metre digital elevation model) provided the spatial context necessary for describing and interpreting the relationship between landscape pattern and the distribution of coastal cutthroat trout (Oncorhynchus clarki clarki) in western Oregon, U.S.A. The distribution of coastal cutthroat trout was highly autocorrelated and exhibited a spherical semivariogram with a defined nugget, sill, and range. Wavelet analysis of the main-stem longitudinal profile revealed periodicity in trout distribution at three nested spatial scales corresponding ostensibly to landscape disturbances and the spacing of tributary junctions.

Correlation analysis of fracture arrangement in space

NASA Astrophysics Data System (ADS)

Marrett, Randall; Gale, Julia F. W.; Gómez, Leonel A.; Laubach, Stephen E.

2018-03-01

We present new techniques that overcome limitations of standard approaches to documenting spatial arrangement. The new techniques directly quantify spatial arrangement by normalizing to expected values for randomly arranged fractures. The techniques differ in terms of computational intensity, robustness of results, ability to detect anti-correlation, and use of fracture size data. Variation of spatial arrangement across a broad range of length scales facilitates distinguishing clustered and periodic arrangements-opposite forms of organization-from random arrangements. Moreover, self-organized arrangements can be distinguished from arrangements due to extrinsic organization. Traditional techniques for analysis of fracture spacing are hamstrung because they account neither for the sequence of fracture spacings nor for possible coordination between fracture size and position, attributes accounted for by our methods. All of the new techniques reveal fractal clustering in a test case of veins, or cement-filled opening-mode fractures, in Pennsylvanian Marble Falls Limestone. The observed arrangement is readily distinguishable from random and periodic arrangements. Comparison of results that account for fracture size with results that ignore fracture size demonstrates that spatial arrangement is dominated by the sequence of fracture spacings, rather than coordination of fracture size with position. Fracture size and position are not completely independent in this example, however, because large fractures are more clustered than small fractures. Both spatial and size organization of veins here probably emerged from fracture interaction during growth. The new approaches described here, along with freely available software to implement the techniques, can be applied with effect to a wide range of structures, or indeed many other phenomena such as drilling response, where spatial heterogeneity is an issue.

Influence of Spatial Resolution in Three-dimensional Cine Phase Contrast Magnetic Resonance Imaging on the Accuracy of Hemodynamic Analysis

PubMed Central

Fukuyama, Atsushi; Isoda, Haruo; Morita, Kento; Mori, Marika; Watanabe, Tomoya; Ishiguro, Kenta; Komori, Yoshiaki; Kosugi, Takafumi

2017-01-01

Introduction: We aim to elucidate the effect of spatial resolution of three-dimensional cine phase contrast magnetic resonance (3D cine PC MR) imaging on the accuracy of the blood flow analysis, and examine the optimal setting for spatial resolution using flow phantoms. Materials and Methods: The flow phantom has five types of acrylic pipes that represent human blood vessels (inner diameters: 15, 12, 9, 6, and 3 mm). The pipes were fixed with 1% agarose containing 0.025 mol/L gadolinium contrast agent. A blood-mimicking fluid with human blood property values was circulated through the pipes at a steady flow. Magnetic resonance (MR) images (three-directional phase images with speed information and magnitude images for information of shape) were acquired using the 3-Tesla MR system and receiving coil. Temporal changes in spatially-averaged velocity and maximum velocity were calculated using hemodynamic analysis software. We calculated the error rates of the flow velocities based on the volume flow rates measured with a flowmeter and examined measurement accuracy. Results: When the acrylic pipe was the size of the thoracicoabdominal or cervical artery and the ratio of pixel size for the pipe was set at 30% or lower, spatially-averaged velocity measurements were highly accurate. When the pixel size ratio was set at 10% or lower, maximum velocity could be measured with high accuracy. It was difficult to accurately measure maximum velocity of the 3-mm pipe, which was the size of an intracranial major artery, but the error for spatially-averaged velocity was 20% or less. Conclusions: Flow velocity measurement accuracy of 3D cine PC MR imaging for pipes with inner sizes equivalent to vessels in the cervical and thoracicoabdominal arteries is good. The flow velocity accuracy for the pipe with a 3-mm-diameter that is equivalent to major intracranial arteries is poor for maximum velocity, but it is relatively good for spatially-averaged velocity. PMID:28132996

Evaluation of comprehensive environmental effect about coastal zone development activities in Liaoning Province and management advice.

PubMed

Wang, Wei-Wei; Cai, Yue-Yin; Sun, Yong-Guang; Ma, Hong-Wei

2015-07-01

Using spatial analysis function of Arcgis software, the present study investigated the building environment impact evaluation index system of coastal development in Liaoning Province. The factors of it included of current state of environmental quality, environmental impact of marine development and marine environmental disaster. Weighted factor analysis and comprehensive index method were utilized. At the end, comprehensive environment effect of coastal development in Liaoning Province were evaluated successfully. The result showed that the environmental effect of development activity were most serious, along the Zhao Jiatun coast in north of Zhimao bay and coast of Mianhua island in Dalian bay.

Research on electromechanical resonance of two-axis tracking system

NASA Astrophysics Data System (ADS)

Zhao, Zhi-ming; Xue, Ying-jie; Zeng, Shu-qin; Li, Zhi-guo

2017-02-01

The multi-axes synchronous system about the spatial two-axis turntable is the key equipment for semi-physical simulation and test in aerospace. In this paper, the whole structure design of the turntable is created by using Solidworks, then putting the three-dimensional solid model into ANSYS to build the finite element model. The software ANSYS is used to do the simulation about the static and dynamic analysis of two-axis turntable. Based on the modal analysis, we can forecast the inherent frequencies and the mode of vibration during the launch conditions which is very important to the design and safety of the structure.

Place-Based Education and Geographic Information Systems: Enhancing the Spatial Awareness of Middle School Students in Maine

ERIC Educational Resources Information Center

Perkins, Nancy; Hazelton, Eric; Erickson, Jeryl; Allan, Walter

2010-01-01

Spatial literacy is a new frontier in K-12 education. This article describes a place-based introductory GIS/GPS middle school curriculum unit in which students used measuring tools, GPS units, and My World GIS software to collect physical and spatial data of trees to create a schoolyard tree inventory. Maine students completed "memory…

JAMS - a software platform for modular hydrological modelling

NASA Astrophysics Data System (ADS)

Kralisch, Sven; Fischer, Christian

2015-04-01

Current challenges of understanding and assessing the impacts of climate and land use changes on environmental systems demand for an ever-increasing integration of data and process knowledge in corresponding simulation models. Software frameworks that allow for a seamless creation of integrated models based on less complex components (domain models, process simulation routines) have therefore gained increasing attention during the last decade. JAMS is an Open-Source software framework that has been especially designed to cope with the challenges of eco-hydrological modelling. This is reflected by (i) its flexible approach for representing time and space, (ii) a strong separation of process simulation components from the declarative description of more complex models using domain specific XML, (iii) powerful analysis and visualization functions for spatial and temporal input and output data, and (iv) parameter optimization and uncertainty analysis functions commonly used in environmental modelling. Based on JAMS, different hydrological and nutrient-transport simulation models were implemented and successfully applied during the last years. We will present the JAMS core concepts and give an overview of models, simulation components and support tools available for that framework. Sample applications will be used to underline the advantages of component-based model designs and to show how JAMS can be used to address the challenges of integrated hydrological modelling.

Using 3D Geometric Models to Teach Spatial Geometry Concepts.

ERIC Educational Resources Information Center

Bertoline, Gary R.

1991-01-01

An explanation of 3-D Computer Aided Design (CAD) usage to teach spatial geometry concepts using nontraditional techniques is presented. The software packages CADKEY and AutoCAD are described as well as their usefulness in solving space geometry problems. (KR)

UAV-based detection and spatial analyses of periglacial landforms on Demay Point (King George Island, South Shetland Islands, Antarctica)

NASA Astrophysics Data System (ADS)

Dąbski, Maciej; Zmarz, Anna; Pabjanek, Piotr; Korczak-Abshire, Małgorzata; Karsznia, Izabela; Chwedorzewska, Katarzyna J.

2017-08-01

High-resolution aerial images allow detailed analyses of periglacial landforms, which is of particular importance in light of climate change and resulting changes in active layer thickness. The aim of this study is to show possibilities of using UAV-based photography to perform spatial analysis of periglacial landforms on the Demay Point peninsula, King George Island, and hence to supplement previous geomorphological studies of the South Shetland Islands. Photogrammetric flights were performed using a PW-ZOOM fixed-winged unmanned aircraft vehicle. Digital elevation models (DEM) and maps of slope and contour lines were prepared in ESRI ArcGIS 10.3 with the Spatial Analyst extension, and three-dimensional visualizations in ESRI ArcScene 10.3 software. Careful interpretation of orthophoto and DEM, allowed us to vectorize polygons of landforms, such as (i) solifluction landforms (solifluction sheets, tongues, and lobes); (ii) scarps, taluses, and a protalus rampart; (iii) patterned ground (hummocks, sorted circles, stripes, nets and labyrinths, and nonsorted nets and stripes); (iv) coastal landforms (cliffs and beaches); (v) landslides and mud flows; and (vi) stone fields and bedrock outcrops. We conclude that geomorphological studies based on commonly accessible aerial and satellite images can underestimate the spatial extent of periglacial landforms and result in incomplete inventories. The PW-ZOOM UAV is well suited to gather detailed geomorphological data and can be used in spatial analysis of periglacial landforms in the Western Antarctic Peninsula region.

Stray Light Analysis

NASA Technical Reports Server (NTRS)

1997-01-01

Based on a Small Business Innovation Research contract from the Jet Propulsion Laboratory, TracePro is state-of-the-art interactive software created by Lambda Research Corporation to detect stray light in optical systems. An image can be ruined by incidental light in an optical system. To maintain image excellence from an optical system, stray light must be detected and eliminated. TracePro accounts for absorption, specular reflection and refraction, scattering and aperture diffraction of light. Output from the software consists of spatial irradiance plots and angular radiance plots. Results can be viewed as contour maps or as ray histories in tabular form. TracePro is adept at modeling solids such as lenses, baffles, light pipes, integrating spheres, non-imaging concentrators, and complete illumination systems. The firm's customer base includes Lockheed Martin, Samsung Electronics and other manufacturing, optical, aerospace, and educational companies worldwide.

Efficient multi-objective calibration of a computationally intensive hydrologic model with parallel computing software in Python

USDA-ARS?s Scientific Manuscript database

With enhanced data availability, distributed watershed models for large areas with high spatial and temporal resolution are increasingly used to understand water budgets and examine effects of human activities and climate change/variability on water resources. Developing parallel computing software...

qSR: a quantitative super-resolution analysis tool reveals the cell-cycle dependent organization of RNA Polymerase I in live human cells.

PubMed

Andrews, J O; Conway, W; Cho, W -K; Narayanan, A; Spille, J -H; Jayanth, N; Inoue, T; Mullen, S; Thaler, J; Cissé, I I

2018-05-09

We present qSR, an analytical tool for the quantitative analysis of single molecule based super-resolution data. The software is created as an open-source platform integrating multiple algorithms for rigorous spatial and temporal characterizations of protein clusters in super-resolution data of living cells. First, we illustrate qSR using a sample live cell data of RNA Polymerase II (Pol II) as an example of highly dynamic sub-diffractive clusters. Then we utilize qSR to investigate the organization and dynamics of endogenous RNA Polymerase I (Pol I) in live human cells, throughout the cell cycle. Our analysis reveals a previously uncharacterized transient clustering of Pol I. Both stable and transient populations of Pol I clusters co-exist in individual living cells, and their relative fraction vary during cell cycle, in a manner correlating with global gene expression. Thus, qSR serves to facilitate the study of protein organization and dynamics with very high spatial and temporal resolutions directly in live cell.

Comparison of Object-Based Image Analysis Approaches to Mapping New Buildings in Accra, Ghana Using Multi-Temporal QuickBird Satellite Imagery

PubMed Central

Tsai, Yu Hsin; Stow, Douglas; Weeks, John

2013-01-01

The goal of this study was to map and quantify the number of newly constructed buildings in Accra, Ghana between 2002 and 2010 based on high spatial resolution satellite image data. Two semi-automated feature detection approaches for detecting and mapping newly constructed buildings based on QuickBird very high spatial resolution satellite imagery were analyzed: (1) post-classification comparison; and (2) bi-temporal layerstack classification. Feature Analyst software based on a spatial contextual classifier and ENVI Feature Extraction that uses a true object-based image analysis approach of image segmentation and segment classification were evaluated. Final map products representing new building objects were compared and assessed for accuracy using two object-based accuracy measures, completeness and correctness. The bi-temporal layerstack method generated more accurate results compared to the post-classification comparison method due to less confusion with background objects. The spectral/spatial contextual approach (Feature Analyst) outperformed the true object-based feature delineation approach (ENVI Feature Extraction) due to its ability to more reliably delineate individual buildings of various sizes. Semi-automated, object-based detection followed by manual editing appears to be a reliable and efficient approach for detecting and enumerating new building objects. A bivariate regression analysis was performed using neighborhood-level estimates of new building density regressed on a census-derived measure of socio-economic status, yielding an inverse relationship with R2 = 0.31 (n = 27; p = 0.00). The primary utility of the new building delineation results is to support spatial analyses of land cover and land use and demographic change. PMID:24415810

Thinking Egyptian: Active Models for Understanding Spatial Representation.

ERIC Educational Resources Information Center

Schiferl, Ellen

This paper highlights how introductory textbooks on Egyptian art inhibit understanding by reinforcing student preconceptions, and demonstrates another approach to discussing space with a classroom exercise and software. The alternative approach, an active model for spatial representation, introduced here was developed by adapting classroom…

SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes.

PubMed

Bielejec, Filip; Baele, Guy; Vrancken, Bram; Suchard, Marc A; Rambaut, Andrew; Lemey, Philippe

2016-08-01

Model-based phylogenetic reconstructions increasingly consider spatial or phenotypic traits in conjunction with sequence data to study evolutionary processes. Alongside parameter estimation, visualization of ancestral reconstructions represents an integral part of these analyses. Here, we present a complete overhaul of the spatial phylogenetic reconstruction of evolutionary dynamics software, now called SpreaD3 to emphasize the use of data-driven documents, as an analysis and visualization package that primarily complements Bayesian inference in BEAST (http://beast.bio.ed.ac.uk, last accessed 9 May 2016). The integration of JavaScript D3 libraries (www.d3.org, last accessed 9 May 2016) offers novel interactive web-based visualization capacities that are not restricted to spatial traits and extend to any discrete or continuously valued trait for any organism of interest. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Spatial distribution pattern of termite in Endau Rompin Plantation

NASA Astrophysics Data System (ADS)

Jalaludin, Nur-Atiqah; Rahim, Faszly

2015-09-01

We censused 18 field blocks approximately 190 ha with total of 28,604 palms in a grid of 2×4 palms from July 2011 to March 2013. The field blocks comprise of rows of palm trees, harvesting paths, field drains and stacking rows with maximum of 30 palms per row, planted about 9 m apart, alternately in maximum of 80 rows. SADIE analysis generating index of aggregation, Ia, local clustering value, Vi and local gap value, Vj is adopted to estimate spatial pattern. The patterns were then presented in contour map using Surfer 12 software. The patterns produced associated with factors i.e. habitat disturbance, habitat fragmentation and resources affecting nesting and foraging activities. Result shows that field blocks with great habitat disturbance recorded highest dead palms and termites hits. Blocks located far from the main access road recorded less than 2% palms with termite hits. This research may provide ecological data on termite spatial pattern in oil palm ecosystem.

Development of a prototype spatial information processing system for hydrologic research

NASA Technical Reports Server (NTRS)

Sircar, Jayanta K.

1991-01-01

Significant advances have been made in the last decade in the areas of Geographic Information Systems (GIS) and spatial analysis technology, both in hardware and software. Science user requirements are so problem specific that currently no single system can satisfy all of the needs. The work presented here forms part of a conceptual framework for an all-encompassing science-user workstation system. While definition and development of the system as a whole will take several years, it is intended that small scale projects such as the current work will address some of the more short term needs. Such projects can provide a quick mechanism to integrate tools into the workstation environment forming a larger, more complete hydrologic analysis platform. Described here are two components that are very important to the practical use of remote sensing and digital map data in hydrology. Described here is a graph-theoretic technique to rasterize elevation contour maps. Also described is a system to manipulate synthetic aperture radar (SAR) data files and extract soil moisture data.

Estimation of skeletal movement of human locomotion from body surface shapes using dynamic spatial video camera (DSVC) and 4D human model.

PubMed

Saito, Toshikuni; Suzuki, Naoki; Hattori, Asaki; Suzuki, Shigeyuki; Hayashibe, Mitsuhiro; Otake, Yoshito

2006-01-01

We have been developing a DSVC (Dynamic Spatial Video Camera) system to measure and observe human locomotion quantitatively and freely. A 4D (four-dimensional) human model with detailed skeletal structure, joint, muscle, and motor functionality has been built. The purpose of our research was to estimate skeletal movements from body surface shapes using DSVC and the 4D human model. For this purpose, we constructed a body surface model of a subject and resized the standard 4D human model to match with geometrical features of the subject's body surface model. Software that integrates the DSVC system and the 4D human model, and allows dynamic skeletal state analysis from body surface movement data was also developed. We practically applied the developed system in dynamic skeletal state analysis of a lower limb in motion and were able to visualize the motion using geometrically resized standard 4D human model.

Automated Ontology Generation Using Spatial Reasoning

NASA Astrophysics Data System (ADS)

Coalter, Alton; Leopold, Jennifer L.

Recently there has been much interest in using ontologies to facilitate knowledge representation, integration, and reasoning. Correspondingly, the extent of the information embodied by an ontology is increasing beyond the conventional is_a and part_of relationships. To address these requirements, a vast amount of digitally available information may need to be considered when building ontologies, prompting a desire for software tools to automate at least part of the process. The main efforts in this direction have involved textual information retrieval and extraction methods. For some domains extension of the basic relationships could be enhanced further by the analysis of 2D and/or 3D images. For this type of media, image processing algorithms are more appropriate than textual analysis methods. Herein we present an algorithm that, given a collection of 3D image files, utilizes Qualitative Spatial Reasoning (QSR) to automate the creation of an ontology for the objects represented by the images, relating the objects in terms of is_a and part_of relationships and also through unambiguous Relational Connection Calculus (RCC) relations.

Digital Transplantation Pathology: Combining Whole Slide Imaging, Multiplex Staining, and Automated Image Analysis

PubMed Central

Isse, Kumiko; Lesniak, Andrew; Grama, Kedar; Roysam, Badrinath; Minervini, Martha I.; Demetris, Anthony J

2013-01-01

Conventional histopathology is the gold standard for allograft monitoring, but its value proposition is increasingly questioned. “-Omics” analysis of tissues, peripheral blood and fluids and targeted serologic studies provide mechanistic insights into allograft injury not currently provided by conventional histology. Microscopic biopsy analysis, however, provides valuable and unique information: a) spatial-temporal relationships; b) rare events/cells; c) complex structural context; and d) integration into a “systems” model. Nevertheless, except for immunostaining, no transformative advancements have “modernized” routine microscopy in over 100 years. Pathologists now team with hardware and software engineers to exploit remarkable developments in digital imaging, nanoparticle multiplex staining, and computational image analysis software to bridge the traditional histology - global “–omic” analyses gap. Included are side-by-side comparisons, objective biopsy finding quantification, multiplexing, automated image analysis, and electronic data and resource sharing. Current utilization for teaching, quality assurance, conferencing, consultations, research and clinical trials is evolving toward implementation for low-volume, high-complexity clinical services like transplantation pathology. Cost, complexities of implementation, fluid/evolving standards, and unsettled medical/legal and regulatory issues remain as challenges. Regardless, challenges will be overcome and these technologies will enable transplant pathologists to increase information extraction from tissue specimens and contribute to cross-platform biomarker discovery for improved outcomes. PMID:22053785

Software analysis handbook: Software complexity analysis and software reliability estimation and prediction

NASA Technical Reports Server (NTRS)

Lee, Alice T.; Gunn, Todd; Pham, Tuan; Ricaldi, Ron

1994-01-01

This handbook documents the three software analysis processes the Space Station Software Analysis team uses to assess space station software, including their backgrounds, theories, tools, and analysis procedures. Potential applications of these analysis results are also presented. The first section describes how software complexity analysis provides quantitative information on code, such as code structure and risk areas, throughout the software life cycle. Software complexity analysis allows an analyst to understand the software structure, identify critical software components, assess risk areas within a software system, identify testing deficiencies, and recommend program improvements. Performing this type of analysis during the early design phases of software development can positively affect the process, and may prevent later, much larger, difficulties. The second section describes how software reliability estimation and prediction analysis, or software reliability, provides a quantitative means to measure the probability of failure-free operation of a computer program, and describes the two tools used by JSC to determine failure rates and design tradeoffs between reliability, costs, performance, and schedule.

Spatial Query for Planetary Data

NASA Technical Reports Server (NTRS)

Shams, Khawaja S.; Crockett, Thomas M.; Powell, Mark W.; Joswig, Joseph C.; Fox, Jason M.

2011-01-01

Science investigators need to quickly and effectively assess past observations of specific locations on a planetary surface. This innovation involves a location-based search technology that was adapted and applied to planetary science data to support a spatial query capability for mission operations software. High-performance location-based searching requires the use of spatial data structures for database organization. Spatial data structures are designed to organize datasets based on their coordinates in a way that is optimized for location-based retrieval. The particular spatial data structure that was adapted for planetary data search is the R+ tree.

GLOBIL: WWF's Global Observation and Biodiversity Information Portal

NASA Astrophysics Data System (ADS)

Shapiro, A. C.; Nijsten, L.; Schmitt, S.; Tibaldeschi, P.

2015-04-01

Despite ever increasing availability of satellite imagery and spatial data, conservation managers, decision makers and planners are often unable to analyze data without special knowledge or software. WWF is bridging this gap by putting extensive spatial data into an easy to use online mapping environment, to allow visualization, manipulation and analysis of large data sets by any user. Consistent, reliable and repeatable ecosystem monitoring information for priority eco-regions is needed to increase transparency in WWF's global conservation work, to measure conservation impact, and to provide communications with the general public and organization members. Currently, much of this monitoring and evaluation data is isolated, incompatible, or inaccessible and not readily usable or available for those without specialized software or knowledge. Launched in 2013 by WWF Netherlands and WWF Germany, the Global Observation and Biodiversity Information Portal (GLOBIL) is WWF's new platform to unite, centralize, standardize and visualize geo-spatial data and information from more than 150 active GIS users worldwide via cloud-based ArcGIS Online. GLOBIL is increasing transparency, providing baseline data for monitoring and evaluation while communicating impacts and conservation successes to the public. GLOBIL is currently being used in the worldwide marine campaign as an advocacy tool for establishing more marine protected areas, and a monitoring interface to track the progress towards ocean protection goals. In the Kavango-Zambezi (KAZA) Transfrontier Conservation area, local partners are using the platform to monitor land cover changes, barriers to species migrations, potential human-wildlife conflict and local conservation impacts in vast wildlife corridor. In East Africa, an early warning system is providing conservation practitioners with real-time alerts of threats particularly to protected areas and World Heritage Sites by industrial extractive activities. And for globally consistent baseline ecosystem monitoring, MODIS-derived data are being combined with local information to provide visible advocacy for conservation. As GLOBIL is built up through the WWF network, the worldwide organization is able to provide open access to its data on biodiversity and remote sensing, spatial analysis and projects to support goal setting, monitoring and evaluation, and fundraising activities.

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

PubMed Central

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

2010-01-01

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. PMID:21344013

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.

Evaluation of SLAR and thematic mapper MSS data for forest cover mapping using computer-aided analysis techniques

NASA Technical Reports Server (NTRS)

Hoffer, R. M. (Principal Investigator)

1980-01-01

The column normalizing technique was used to adjust the data for variations in the amplitude of the signal due to look angle effects with respect to solar zenith angle along the scan lines (i.e., across columns). Evaluation of the data set containing the geometric and radiometric adjustments, indicates that the data set should be satisfactory for further processing and analysis. Software was developed for degrading the spatial resolution of the aircraft data to produce a total of four data sets for further analysis. The quality of LANDSAT 2 CCT data for the test site is good for channels four, five, and six. Channel seven was not present on the tape. The data received were reformatted and analysis of the test site area was initiated.

Digital-image processing and image analysis of glacier ice

USGS Publications Warehouse

Fitzpatrick, Joan J.

2013-01-01

This document provides a methodology for extracting grain statistics from 8-bit color and grayscale images of thin sections of glacier ice—a subset of physical properties measurements typically performed on ice cores. This type of analysis is most commonly used to characterize the evolution of ice-crystal size, shape, and intercrystalline spatial relations within a large body of ice sampled by deep ice-coring projects from which paleoclimate records will be developed. However, such information is equally useful for investigating the stress state and physical responses of ice to stresses within a glacier. The methods of analysis presented here go hand-in-hand with the analysis of ice fabrics (aggregate crystal orientations) and, when combined with fabric analysis, provide a powerful method for investigating the dynamic recrystallization and deformation behaviors of bodies of ice in motion. The procedures described in this document compose a step-by-step handbook for a specific image acquisition and data reduction system built in support of U.S. Geological Survey ice analysis projects, but the general methodology can be used with any combination of image processing and analysis software. The specific approaches in this document use the FoveaPro 4 plug-in toolset to Adobe Photoshop CS5 Extended but it can be carried out equally well, though somewhat less conveniently, with software such as the image processing toolbox in MATLAB, Image-Pro Plus, or ImageJ.

Prostate-specific membrane antigen PET/MRI validation of MR textural analysis for detection of transition zone prostate cancer.

PubMed

Bates, Anthony; Miles, Kenneth

2017-12-01

To validate MR textural analysis (MRTA) for detection of transition zone (TZ) prostate cancer through comparison with co-registered prostate-specific membrane antigen (PSMA) PET-MR. Retrospective analysis was performed for 30 men who underwent simultaneous PSMA PET-MR imaging for staging of prostate cancer. Thirty texture features were derived from each manually contoured T2-weighted, transaxial, prostatic TZ using texture analysis software that applies a spatial band-pass filter and quantifies texture through histogram analysis. Texture features of the TZ were compared to PSMA expression on the corresponding PET images. The Benjamini-Hochberg correction controlled the false discovery rate at <5%. Eighty-eight T2-weighted images in 18 patients demonstrated abnormal PSMA expression within the TZ on PET-MR. 123 images were PSMA negative. Based on the corrected p-value of 0.005, significant differences between PSMA positive and negative slices were found for 16 texture parameters: Standard deviation and mean of positive pixels for all spatial filters (p = <0.0001 for both at all spatial scaling factor (SSF) values) and mean intensity following filtration for SSF 3-6 mm (p = 0.0002-0.0018). Abnormal expression of PSMA within the TZ is associated with altered texture on T2-weighted MR, providing validation of MRTA for the detection of TZ prostate cancer. • Prostate transition zone (TZ) MR texture analysis may assist in prostate cancer detection. • Abnormal transition zone PSMA expression correlates with altered texture on T2-weighted MR. • TZ with abnormal PSMA expression demonstrates significantly reduced MI, SD and MPP.

[Temporal-spatial analysis of bacillary dysentery in the Three Gorges Area of China, 2005-2016].

PubMed

Zhang, P; Zhang, J; Chang, Z R; Li, Z J

2018-01-10

Objective: To analyze the spatial and temporal distributions of bacillary dysentery in Chongqing, Yichang and Enshi (the Three Gorges Area) from 2005 to 2016, and provide evidence for the disease prevention and control. Methods: The incidence data of bacillary dysentery in the Three Gorges Area during this period were collected from National Notifiable Infectious Disease Reporting System. The spatial-temporal scan statistic was conducted with software SaTScan 9.4 and bacillary dysentery clusters were visualized with software ArcGIS 10.3. Results: A total of 126 196 cases were reported in the Three Gorges Area during 2005-2016, with an average incidence rate of 29.67/100 000. The overall incidence was in a downward trend, with an average annual decline rate of 4.74%. Cases occurred all the year round but with an obvious seasonal increase between May and October. Among the reported cases, 44.71% (56 421/126 196) were children under 5-year-old, the cases in children outside child care settings accounted for 41.93% (52 918/126 196) of the total. The incidence rates in districts of Yuzhong, Dadukou, Jiangbei, Shapingba, Jiulongpo, Nanan, Yubei, Chengkou of Chongqing and districts of Xiling and Wujiagang of Yichang city of Hubei province were high, ranging from 60.20/100 000 to 114.81/100 000. Spatial-temporal scan statistic for the spatial and temporal distributions of bacillary dysentery during this period revealed that the temporal distribution was during May-October, and there were 12 class Ⅰ clusters, 35 class Ⅱ clusters, and 9 clusters without statistical significance in counties with high incidence. All the class Ⅰ clusters were in urban area of Chongqing (Yuzhong, Dadukou, Jiangbei, Shapingba, Jiulongpo, Nanan, Beibei, Yubei, Banan) and surrounding counties, and the class Ⅱ clusters transformed from concentrated distribution to scattered distribution. Conclusions: Temporal and spatial cluster of bacillary dysentery incidence existed in the three gorges area during 2005-2016. It is necessary to strengthen the bacillary dysentery prevention and control in urban areas of Chongqing and Yichang.

The Role of NASA's Planetary Data System in the Planetary Spatial Data Infrastructure Initiative

NASA Astrophysics Data System (ADS)

Arvidson, R. E.; Gaddis, L. R.

2017-12-01

An effort underway in NASA's planetary science community is the Mapping and Planetary Spatial Infrastructure Team (MAPSIT, http://www.lpi.usra.edu/mapsit/). MAPSIT is a community assessment group organized to address a lack of strategic spatial data planning for space science and exploration. Working with MAPSIT, a new initiative of NASA and USGS is the development of a Planetary Spatial Data Infrastructure (PSDI) that builds on extensive knowledge on storing, accessing, and working with terrestrial spatial data. PSDI is a knowledge and technology framework that enables the efficient discovery, access, and exploitation of planetary spatial data to facilitate data analysis, knowledge synthesis, and decision-making. NASA's Planetary Data System (PDS) archives >1.2 petabytes of digital data resulting from decades of planetary exploration and research. The PDS charter focuses on the efficient collection, archiving, and accessibility of these data. The PDS emphasis on data preservation and archiving is complementary to that of the PSDI initiative because the latter utilizes and extends available data to address user needs in the areas of emerging technologies, rapid development of tailored delivery systems, and development of online collaborative research environments. The PDS plays an essential PSDI role because it provides expertise to help NASA missions and other data providers to organize and document their planetary data, to collect and maintain the archives with complete, well-documented and peer-reviewed planetary data, to make planetary data accessible by providing online data delivery tools and search services, and ultimately to ensure the long-term preservation and usability of planetary data. The current PDS4 information model extends and expands PDS metadata and relationships between and among elements of the collections. The PDS supports data delivery through several node services, including the Planetary Image Atlas (https://pds-imaging.jpl.nasa.gov/search/), the Orbital Data Explorers (http://ode.rsl.wustl.edu/), and the Planetary Image Locator Tool (PILOT, https://pilot.wr.usgs.gov/); the latter offers ties to the Integrated Software for Imagers and Spectrometers (ISIS), the premier planetary cartographic software package from USGS's Astrogeology Science Team.

An Overview of the GIS Weasel

USGS Publications Warehouse

Viger, Roland J.

2008-01-01

This fact sheet provides a high-level description of the GIS Weasel, a software system designed to aid users in preparing spatial information as input to lumped and distributed parameter environmental simulation models (ESMs). The GIS Weasel provides geographic information system (GIS) tools to help create maps of geographic features relevant to the application of a user?s ESM and to generate parameters from those maps. The operation of the GIS Weasel does not require a user to be a GIS expert, only that a user has an understanding of the spatial information requirements of the model. The GIS Weasel software system provides a GIS-based graphical user interface (GUI), C programming language executables, and general utility scripts. The software will run on any computing platform where ArcInfo Workstation (version 8.1 or later) and the GRID extension are accessible. The user controls the GIS Weasel by interacting with menus, maps, and tables.

Enhancement of Spatial Thinking with Virtual Spaces 1.0

ERIC Educational Resources Information Center

Hauptman, Hanoch

2010-01-01

Developing a software environment to enhance 3D geometric proficiency demands the consideration of theoretical views of the learning process. Simultaneously, this effort requires taking into account the range of tools that technology offers, as well as their limitations. In this paper, we report on the design of Virtual Spaces 1.0 software, a…

Section 4. The GIS Weasel User's Manual

USGS Publications Warehouse

Viger, Roland J.; Leavesley, George H.

2007-01-01

INTRODUCTION The GIS Weasel was designed to aid in the preparation of spatial information for input to lumped and distributed parameter hydrologic or other environmental models. The GIS Weasel provides geographic information system (GIS) tools to help create maps of geographic features relevant to a user's model and to generate parameters from those maps. The operation of the GIS Weasel does not require the user to be a GIS expert, only that the user have an understanding of the spatial information requirements of the environmental simulation model being used. The GIS Weasel software system uses a GIS-based graphical user interface (GUI), the C programming language, and external scripting languages. The software will run on any computing platform where ArcInfo Workstation (version 8.0.2 or later) and the GRID extension are accessible. The user controls the processing of the GIS Weasel by interacting with menus, maps, and tables. The purpose of this document is to describe the operation of the software. This document is not intended to describe the usage of this software in support of any particular environmental simulation model. Such guides are published separately.

Spatial Data Management System (SDMS)

NASA Technical Reports Server (NTRS)

Hutchison, Mark W.

1994-01-01

The Spatial Data Management System (SDMS) is a testbed for retrieval and display of spatially related material. SDMS permits the linkage of large graphical display objects with detail displays and explanations of its smaller components. SDMS combines UNIX workstations, MIT's X Window system, TCP/IP and WAIS information retrieval technology to prototype a means of associating aggregate data linked via spatial orientation. SDMS capitalizes upon and extends previous accomplishments of the Software Technology Branch in the area of Virtual Reality and Automated Library Systems.

ASKI: A modular toolbox for scattering-integral-based seismic full waveform inversion and sensitivity analysis utilizing external forward codes

NASA Astrophysics Data System (ADS)

Schumacher, Florian; Friederich, Wolfgang

Due to increasing computational resources, the development of new numerically demanding methods and software for imaging Earth's interior remains of high interest in Earth sciences. Here, we give a description from a user's and programmer's perspective of the highly modular, flexible and extendable software package ASKI-Analysis of Sensitivity and Kernel Inversion-recently developed for iterative scattering-integral-based seismic full waveform inversion. In ASKI, the three fundamental steps of solving the seismic forward problem, computing waveform sensitivity kernels and deriving a model update are solved by independent software programs that interact via file output/input only. Furthermore, the spatial discretizations of the model space used for solving the seismic forward problem and for deriving model updates, respectively, are kept completely independent. For this reason, ASKI does not contain a specific forward solver but instead provides a general interface to established community wave propagation codes. Moreover, the third fundamental step of deriving a model update can be repeated at relatively low costs applying different kinds of model regularization or re-selecting/weighting the inverted dataset without need to re-solve the forward problem or re-compute the kernels. Additionally, ASKI offers the user sensitivity and resolution analysis tools based on the full sensitivity matrix and allows to compose customized workflows in a consistent computational environment. ASKI is written in modern Fortran and Python, it is well documented and freely available under terms of the GNU General Public License (http://www.rub.de/aski).

Simulated single molecule microscopy with SMeagol.

PubMed

Lindén, Martin; Ćurić, Vladimir; Boucharin, Alexis; Fange, David; Elf, Johan

2016-08-01

SMeagol is a software tool to simulate highly realistic microscopy data based on spatial systems biology models, in order to facilitate development, validation and optimization of advanced analysis methods for live cell single molecule microscopy data. SMeagol runs on Matlab R2014 and later, and uses compiled binaries in C for reaction-diffusion simulations. Documentation, source code and binaries for Mac OS, Windows and Ubuntu Linux can be downloaded from http://smeagol.sourceforge.net johan.elf@icm.uu.se Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

TESS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dmitriy Morozov, Tom Peterka

2014-07-29

Computing a Voronoi or Delaunay tessellation from a set of points is a core part of the analysis of many simulated and measured datasets. As the scale of simulations and observations surpasses billions of particles, a distributed-memory scalable parallel algorithm is the only feasible approach. The primary contribution of this software is a distributed-memory parallel Delaunay and Voronoi tessellation algorithm based on existing serial computational geometry libraries that automatically determines which neighbor points need to be exchanged among the subdomains of a spatial decomposition. Other contributions include the addition of periodic and wall boundary conditions.

Edge directed image interpolation with Bamberger pyramids

NASA Astrophysics Data System (ADS)

Rosiles, Jose Gerardo

2005-08-01

Image interpolation is a standard feature in digital image editing software, digital camera systems and printers. Classical methods for resizing produce blurred images with unacceptable quality. Bamberger Pyramids and filter banks have been successfully used for texture and image analysis. They provide excellent multiresolution and directional selectivity. In this paper we present an edge-directed image interpolation algorithm which takes advantage of the simultaneous spatial-directional edge localization at the subband level. The proposed algorithm outperform classical schemes like bilinear and bicubic schemes from the visual and numerical point of views.

LA-iMageS: a software for elemental distribution bioimaging using LA-ICP-MS data.

PubMed

López-Fernández, Hugo; de S Pessôa, Gustavo; Arruda, Marco A Z; Capelo-Martínez, José L; Fdez-Riverola, Florentino; Glez-Peña, Daniel; Reboiro-Jato, Miguel

2016-01-01

The spatial distribution of chemical elements in different types of samples is an important field in several research areas such as biology, paleontology or biomedicine, among others. Elemental distribution imaging by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) is an effective technique for qualitative and quantitative imaging due to its high spatial resolution and sensitivity. By applying this technique, vast amounts of raw data are generated to obtain high-quality images, essentially making the use of specific LA-ICP-MS imaging software that can process such data absolutely mandatory. Since existing solutions are usually commercial or hard-to-use for average users, this work introduces LA-iMageS, an open-source, free-to-use multiplatform application for fast and automatic generation of high-quality elemental distribution bioimages from LA-ICP-MS data in the PerkinElmer Elan XL format, whose results can be directly exported to external applications for further analysis. A key strength of LA-iMageS is its substantial added value for users, with particular regard to the customization of the elemental distribution bioimages, which allows, among other features, the ability to change color maps, increase image resolution or toggle between 2D and 3D visualizations.

Using Space Syntax to Assess Safety in Public Areas - Case Study of Tarbiat Pedestrian Area, Tabriz-Iran

NASA Astrophysics Data System (ADS)

Cihangir Çamur, Kübra; Roshani, Mehdi; Pirouzi, Sania

2017-10-01

In studying the urban complex issues, simulation and modelling of public space use considerably helps in determining and measuring factors such as urban safety. Depth map software for determining parameters of the spatial layout techniques; and Statistical Package for Social Sciences (SPSS) software for analysing and evaluating the views of the pedestrians on public safety were used in this study. Connectivity, integration, and depth of the area in the Tarbiat city blocks were measured using the Space Syntax Method, and these parameters are presented as graphical and mathematical data. The combination of the results obtained from the questionnaire and statistical analysis with the results of spatial arrangement technique represents the appropriate and inappropriate spaces for pedestrians. This method provides a useful and effective instrument for decision makers, planners, urban designers and programmers in order to evaluate public spaces in the city. Prior to physical modification of urban public spaces, space syntax simulates the pedestrian safety to be used as an analytical tool by the city management. Finally, regarding the modelled parameters and identification of different characteristics of the case, this study represents the strategies and policies in order to increase the safety of the pedestrians of Tarbiat in Tabriz.

[Scale effect of Nanjing urban green infrastructure network pattern and connectivity analysis.

PubMed

Yu, Ya Ping; Yin, Hai Wei; Kong, Fan Hua; Wang, Jing Jing; Xu, Wen Bin

2016-07-01

Based on ArcGIS, Erdas, GuidosToolbox, Conefor and other software platforms, using morphological spatial pattern analysis (MSPA) and landscape connectivity analysis methods, this paper quantitatively analysed the scale effect, edge effect and distance effect of the Nanjing urban green infrastructure network pattern in 2013 by setting different pixel sizes (P) and edge widths in MSPA analysis, and setting different dispersal distance thresholds in landscape connectivity analysis. The results showed that the type of landscape acquired based on the MSPA had a clear scale effect and edge effect, and scale effects only slightly affected landscape types, whereas edge effects were more obvious. Different dispersal distances had a great impact on the landscape connectivity, 2 km or 2.5 km dispersal distance was a critical threshold for Nanjing. When selecting the pixel size 30 m of the input data and the edge wide 30 m used in the morphological model, we could get more detailed landscape information of Nanjing UGI network. Based on MSPA and landscape connectivity, analysis of the scale effect, edge effect, and distance effect on the landscape types of the urban green infrastructure (UGI) network was helpful for selecting the appropriate size, edge width, and dispersal distance when developing these networks, and for better understanding the spatial pattern of UGI networks and the effects of scale and distance on the ecology of a UGI network. This would facilitate a more scientifically valid set of design parameters for UGI network spatiotemporal pattern analysis. The results of this study provided an important reference for Nanjing UGI networks and a basis for the analysis of the spatial and temporal patterns of medium-scale UGI landscape networks in other regions.

microMS: A Python Platform for Image-Guided Mass Spectrometry Profiling

NASA Astrophysics Data System (ADS)

Comi, Troy J.; Neumann, Elizabeth K.; Do, Thanh D.; Sweedler, Jonathan V.

2017-09-01

Image-guided mass spectrometry (MS) profiling provides a facile framework for analyzing samples ranging from single cells to tissue sections. The fundamental workflow utilizes a whole-slide microscopy image to select targets of interest, determine their spatial locations, and subsequently perform MS analysis at those locations. Improving upon prior reported methodology, a software package was developed for working with microscopy images. microMS, for microscopy-guided mass spectrometry, allows the user to select and profile diverse samples using a variety of target patterns and mass analyzers. Written in Python, the program provides an intuitive graphical user interface to simplify image-guided MS for novice users. The class hierarchy of instrument interactions permits integration of new MS systems while retaining the feature-rich image analysis framework. microMS is a versatile platform for performing targeted profiling experiments using a series of mass spectrometers. The flexibility in mass analyzers greatly simplifies serial analyses of the same targets by different instruments. The current capabilities of microMS are presented, and its application for off-line analysis of single cells on three distinct instruments is demonstrated. The software has been made freely available for research purposes. [Figure not available: see fulltext.

microMS: A Python Platform for Image-Guided Mass Spectrometry Profiling.

PubMed

Comi, Troy J; Neumann, Elizabeth K; Do, Thanh D; Sweedler, Jonathan V

2017-09-01

Image-guided mass spectrometry (MS) profiling provides a facile framework for analyzing samples ranging from single cells to tissue sections. The fundamental workflow utilizes a whole-slide microscopy image to select targets of interest, determine their spatial locations, and subsequently perform MS analysis at those locations. Improving upon prior reported methodology, a software package was developed for working with microscopy images. microMS, for microscopy-guided mass spectrometry, allows the user to select and profile diverse samples using a variety of target patterns and mass analyzers. Written in Python, the program provides an intuitive graphical user interface to simplify image-guided MS for novice users. The class hierarchy of instrument interactions permits integration of new MS systems while retaining the feature-rich image analysis framework. microMS is a versatile platform for performing targeted profiling experiments using a series of mass spectrometers. The flexibility in mass analyzers greatly simplifies serial analyses of the same targets by different instruments. The current capabilities of microMS are presented, and its application for off-line analysis of single cells on three distinct instruments is demonstrated. The software has been made freely available for research purposes. Graphical Abstract ᅟ.

Enhancing GIS Capabilities for High Resolution Earth Science Grids

NASA Astrophysics Data System (ADS)

Koziol, B. W.; Oehmke, R.; Li, P.; O'Kuinghttons, R.; Theurich, G.; DeLuca, C.

2017-12-01

Applications for high performance GIS will continue to increase as Earth system models pursue more realistic representations of Earth system processes. Finer spatial resolution model input and output, unstructured or irregular modeling grids, data assimilation, and regional coordinate systems present novel challenges for GIS frameworks operating in the Earth system modeling domain. This presentation provides an overview of two GIS-driven applications that combine high performance software with big geospatial datasets to produce value-added tools for the modeling and geoscientific community. First, a large-scale interpolation experiment using National Hydrography Dataset (NHD) catchments, a high resolution rectilinear CONUS grid, and the Earth System Modeling Framework's (ESMF) conservative interpolation capability will be described. ESMF is a parallel, high-performance software toolkit that provides capabilities (e.g. interpolation) for building and coupling Earth science applications. ESMF is developed primarily by the NOAA Environmental Software Infrastructure and Interoperability (NESII) group. The purpose of this experiment was to test and demonstrate the utility of high performance scientific software in traditional GIS domains. Special attention will be paid to the nuanced requirements for dealing with high resolution, unstructured grids in scientific data formats. Second, a chunked interpolation application using ESMF and OpenClimateGIS (OCGIS) will demonstrate how spatial subsetting can virtually remove computing resource ceilings for very high spatial resolution interpolation operations. OCGIS is a NESII-developed Python software package designed for the geospatial manipulation of high-dimensional scientific datasets. An overview of the data processing workflow, why a chunked approach is required, and how the application could be adapted to meet operational requirements will be discussed here. In addition, we'll provide a general overview of OCGIS's parallel subsetting capabilities including challenges in the design and implementation of a scientific data subsetter.

Spatial occupancy models for large data sets

USGS Publications Warehouse

Johnson, Devin S.; Conn, Paul B.; Hooten, Mevin B.; Ray, Justina C.; Pond, Bruce A.

2013-01-01

Since its development, occupancy modeling has become a popular and useful tool for ecologists wishing to learn about the dynamics of species occurrence over time and space. Such models require presence–absence data to be collected at spatially indexed survey units. However, only recently have researchers recognized the need to correct for spatially induced overdisperison by explicitly accounting for spatial autocorrelation in occupancy probability. Previous efforts to incorporate such autocorrelation have largely focused on logit-normal formulations for occupancy, with spatial autocorrelation induced by a random effect within a hierarchical modeling framework. Although useful, computational time generally limits such an approach to relatively small data sets, and there are often problems with algorithm instability, yielding unsatisfactory results. Further, recent research has revealed a hidden form of multicollinearity in such applications, which may lead to parameter bias if not explicitly addressed. Combining several techniques, we present a unifying hierarchical spatial occupancy model specification that is particularly effective over large spatial extents. This approach employs a probit mixture framework for occupancy and can easily accommodate a reduced-dimensional spatial process to resolve issues with multicollinearity and spatial confounding while improving algorithm convergence. Using open-source software, we demonstrate this new model specification using a case study involving occupancy of caribou (Rangifer tarandus) over a set of 1080 survey units spanning a large contiguous region (108 000 km2) in northern Ontario, Canada. Overall, the combination of a more efficient specification and open-source software allows for a facile and stable implementation of spatial occupancy models for large data sets.

Visualization techniques to aid in the analysis of multispectral astrophysical data sets

NASA Technical Reports Server (NTRS)

Brugel, E. W.; Domik, Gitta O.; Ayres, T. R.

1993-01-01

The goal of this project was to support the scientific analysis of multi-spectral astrophysical data by means of scientific visualization. Scientific visualization offers its greatest value if it is not used as a method separate or alternative to other data analysis methods but rather in addition to these methods. Together with quantitative analysis of data, such as offered by statistical analysis, image or signal processing, visualization attempts to explore all information inherent in astrophysical data in the most effective way. Data visualization is one aspect of data analysis. Our taxonomy as developed in Section 2 includes identification and access to existing information, preprocessing and quantitative analysis of data, visual representation and the user interface as major components to the software environment of astrophysical data analysis. In pursuing our goal to provide methods and tools for scientific visualization of multi-spectral astrophysical data, we therefore looked at scientific data analysis as one whole process, adding visualization tools to an already existing environment and integrating the various components that define a scientific data analysis environment. As long as the software development process of each component is separate from all other components, users of data analysis software are constantly interrupted in their scientific work in order to convert from one data format to another, or to move from one storage medium to another, or to switch from one user interface to another. We also took an in-depth look at scientific visualization and its underlying concepts, current visualization systems, their contributions and their shortcomings. The role of data visualization is to stimulate mental processes different from quantitative data analysis, such as the perception of spatial relationships or the discovery of patterns or anomalies while browsing through large data sets. Visualization often leads to an intuitive understanding of the meaning of data values and their relationships by sacrificing accuracy in interpreting the data values. In order to be accurate in the interpretation, data values need to be measured, computed on, and compared to theoretical or empirical models (quantitative analysis). If visualization software hampers quantitative analysis (which happens with some commercial visualization products), its use is greatly diminished for astrophysical data analysis. The software system STAR (Scientific Toolkit for Astrophysical Research) was developed as a prototype during the course of the project to better understand the pragmatic concerns raised in the project. STAR led to a better understanding on the importance of collaboration between astrophysicists and computer scientists. Twenty-one examples of the use of visualization for astrophysical data are included with this report. Sixteen publications related to efforts performed during or initiated through work on this project are listed at the end of this report.

Visual Data Analysis for Satellites

NASA Technical Reports Server (NTRS)

Lau, Yee; Bhate, Sachin; Fitzpatrick, Patrick

2008-01-01

The Visual Data Analysis Package is a collection of programs and scripts that facilitate visual analysis of data available from NASA and NOAA satellites, as well as dropsonde, buoy, and conventional in-situ observations. The package features utilities for data extraction, data quality control, statistical analysis, and data visualization. The Hierarchical Data Format (HDF) satellite data extraction routines from NASA's Jet Propulsion Laboratory were customized for specific spatial coverage and file input/output. Statistical analysis includes the calculation of the relative error, the absolute error, and the root mean square error. Other capabilities include curve fitting through the data points to fill in missing data points between satellite passes or where clouds obscure satellite data. For data visualization, the software provides customizable Generic Mapping Tool (GMT) scripts to generate difference maps, scatter plots, line plots, vector plots, histograms, timeseries, and color fill images.

Distance education course on spatial multi-hazard risk assessment, using Open Source software

NASA Astrophysics Data System (ADS)

van Westen, C. J.; Frigerio, S.

2009-04-01

As part of the capacity building activities of the United Nations University - ITC School on Disaster Geo-Information Management (UNU-ITC DGIM) the International Institute for Geoinformation Science and Earth Observation (ITC) has developed a distance education course on the application of Geographic Information Systems for multi-hazard risk assessment. This course is designed for academic staff, as well as for professionals working in (non-) governmental organizations where knowledge of disaster risk management is essential. The course guides the participants through the entire process of risk assessment, on the basis of a case study of a city exposed to multiple hazards, in a developing country. The courses consists of eight modules, each with a guide book explaining the theoretical background, and guiding the participants through spatial data requirements for risk assessment, hazard assessment procedures, generation of elements at risk databases, vulnerability assessment, qualitative and quantitative risk assessment methods, risk evaluation and risk reduction. Linked to the theory is a large set of exercises, with exercise descriptions, answer sheets, demos and GIS data. The exercises deal with four different types of hazards: earthquakes, flooding, technological hazards, and landslides. One important consideration in designing the course is that people from developing countries should not be restricted in using it due to financial burdens for software acquisition. Therefore the aim was to use Open Source software as a basis. The GIS exercises are written for the ILWIS software. All exercises have also been integrated into a WebGIS, using the Open source software CartoWeb (based on GNU License). It is modular and customizable thanks to its object-oriented architecture and based on a hierarchical structure (to manage and organize every package of information of every step required in risk assessment). Different switches for every component of the risk assessment course have been defined and through various menus the user can define the options for every exercise. For every layer of information tools for querying, printing, searching and surface analysis are implemented, allowing the option to compare maps at different scale and for on-line interpretations.

Incorporating Spatial Data into Enterprise Applications

NASA Astrophysics Data System (ADS)

Akiki, Pierre; Maalouf, Hoda

The main goal of this chapter is to discuss the usage of spatial data within enterprise as well as smaller line-of-business applications. In particular, this chapter proposes new methodologies for storing and manipulating vague spatial data and provides methods for visualizing both crisp and vague spatial data. It also provides a comparison between different types of spatial data, mainly 2D crisp and vague spatial data, and their respective fields of application. Additionally, it compares existing commercial relational database management systems, which are the most widely used with enterprise applications, and discusses their deficiencies in terms of spatial data support. A new spatial extension package called Spatial Extensions (SPEX) is provided in this chapter and is tested on a software prototype.

Optical high-resolution analysis of rotational movement: testing circular spatial filter velocimetry (CSFV) with rotating biological cells

NASA Astrophysics Data System (ADS)

Schaeper, M.; Schmidt, R.; Kostbade, R.; Damaschke, N.; Gimsa, J.

2016-07-01

Circular spatial filtering velocimetry (CSFV) was tested during the microscopic registration of the individual rotations of baker’s yeast cells. Their frequency-dependent rotation (electrorotation; ER) was induced in rotating electric fields, which were generated in a glass chip chamber with four electrodes (600 μm tip-to-tip distance). The electrodes were driven with sinusoidal quadrature signals of 5 or 8 V PP with frequencies up to 3 MHz. The observed cell rotation was of the order of 1-100 s per revolution. At each measuring frequency, the independent rotations of up to 20 cells were simultaneously recorded with a high-speed camera. CSFV was software-implemented using circular spatial filters with harmonic gratings. ER was proportional to the phase shift between the values of the spatial filtering signal of consecutive frames. ER spectra obtained by CSFV from the rotation velocities at different ER-field frequencies agreed well with manual measurements and theoretical spectra. Oscillations in the rotation velocity of a single cell in the elliptically polarized field near an electrode, which were resolved by CSFV, could not be visually discerned. ER step responses after field-on were recorded at 2500 frames per second. Analysis proved the high temporal resolution of CSFV and revealed a largely linear torque-friction relation during the acceleration phase of ER. Future applications of CSFV will allow for the simple and cheap automated high-resolution analysis of rotational movements where mechanical detection has too low a resolution or is not possible, e.g. in polluted environments or for gas and fluid vortices, microscopic objects, etc.

A geomatic methodology for spatio-temporal analysis of climatologic variables and water related diseases

NASA Astrophysics Data System (ADS)

Quentin, E.; Gómez Albores, M. A.; Díaz Delgado, C.

2009-04-01

The main objective of this research is to propose, by the way of geomatic developments, an integrated tool to analyze and model the spatio-temporal pattern of human diseases related to environmental conditions, in particular the ones that are linked to water resources. The geomatic developments follows four generic steps : requirement analysis, conceptual modeling, geomatic modeling and implementation (in Idrisi GIS software). A first development consists of the preprocessing of water, population and health data in order to facilitate the conversion and validation of tabular data into the required structure for spatio-temporal analysis. Three parallel developments follow : water balance, demographic state and evolution, epidemiological measures (morbidity and mortality rates, diseases burden). The new geomatic modules in their actual state have been tested on various regions of Mexico Republic (Lerma watershed, Chiapas state) focusing on diarrhea and vector borne diseases (dengue and malaria) and considering records over the last decade : a yearly as well as seasonal spreading trend can be observed in correlation with precipitation and temperature data. In an ecohealth perspective, the geomatic approach results particularly appropriate since one of its purposes is the integration of the various spatial themes implied in the study problem, environmental as anthropogenic. By the use of powerful spatial analysis functions, it permits the detection of spatial trends which, combined to the temporal evolution, can be of particularly use for example in climate change context, if sufficiently valid historical data can be obtain.

Integration agent-based models and GIS as a virtual urban dynamic laboratory

NASA Astrophysics Data System (ADS)

Chen, Peng; Liu, Miaolong

2007-06-01

Based on the Agent-based Model and spatial data model, a tight-coupling integrating method of GIS and Agent-based Model (ABM) is to be discussed in this paper. The use of object-orientation for both spatial data and spatial process models facilitates their integration, which can allow exploration and explanation of spatial-temporal phenomena such as urban dynamic. In order to better understand how tight coupling might proceed and to evaluate the possible functional and efficiency gains from such a tight coupling, the agent-based model and spatial data model are discussed, and then the relationships affecting spatial data model and agent-based process models interaction. After that, a realistic crowd flow simulation experiment is presented. Using some tools provided by general GIS systems and a few specific programming languages, a new software system integrating GIS and MAS as a virtual laboratory applicable for simulating pedestrian flows in a crowd activity centre has been developed successfully. Under the environment supported by the software system, as an applicable case, a dynamic evolution process of the pedestrian's flows (dispersed process for the spectators) in a crowds' activity center - The Shanghai Stadium has been simulated successfully. At the end of the paper, some new research problems have been pointed out for the future.

Surface Temperature Data Analysis

NASA Technical Reports Server (NTRS)

Hansen, James; Ruedy, Reto

2012-01-01

Small global mean temperature changes may have significant to disastrous consequences for the Earth's climate if they persist for an extended period. Obtaining global means from local weather reports is hampered by the uneven spatial distribution of the reliably reporting weather stations. Methods had to be developed that minimize as far as possible the impact of that situation. This software is a method of combining temperature data of individual stations to obtain a global mean trend, overcoming/estimating the uncertainty introduced by the spatial and temporal gaps in the available data. Useful estimates were obtained by the introduction of a special grid, subdividing the Earth's surface into 8,000 equal-area boxes, using the existing data to create virtual stations at the center of each of these boxes, and combining temperature anomalies (after assessing the radius of high correlation) rather than temperatures.

Dataset on spatial distribution and location of universities in Nigeria.

PubMed

Adeyemi, G A; Edeki, S O

2018-06-01

Access to quality educational system, and the location of educational institutions are of great importance for future prospect of youth in any nation. These in return, have great effects on the economy growth and development of any country. Thus, the dataset contained in this article examines and explains the spatial distribution of universities in the Nigeria system of education. Data from the university commission, Nigeria, as at December 2017 are used. These include all the 40 federal universities, 44 states universities, and 69 private universities making a total of 153 universities in the Nigerian system of education. The data analysis is via the Geographic Information System (GIS) software. The dataset contained in this article will be of immense assistance to the national educational policy makers, parents, and potential students as regards smart and reliable decision making academically.

High spatial resolution mapping of folds and fractures using Unmanned Aerial Vehicle (UAV) photogrammetry

NASA Astrophysics Data System (ADS)

Cruden, A. R.; Vollgger, S.

2016-12-01

The emerging capability of UAV photogrammetry combines a simple and cost-effective method to acquire digital aerial images with advanced computer vision algorithms that compute spatial datasets from a sequence of overlapping digital photographs from various viewpoints. Depending on flight altitude and camera setup, sub-centimeter spatial resolution orthophotographs and textured dense point clouds can be achieved. Orientation data can be collected for detailed structural analysis by digitally mapping such high-resolution spatial datasets in a fraction of time and with higher fidelity compared to traditional mapping techniques. Here we describe a photogrammetric workflow applied to a structural study of folds and fractures within alternating layers of sandstone and mudstone at a coastal outcrop in SE Australia. We surveyed this location using a downward looking digital camera mounted on commercially available multi-rotor UAV that autonomously followed waypoints at a set altitude and speed to ensure sufficient image overlap, minimum motion blur and an appropriate resolution. The use of surveyed ground control points allowed us to produce a geo-referenced 3D point cloud and an orthophotograph from hundreds of digital images at a spatial resolution < 10 mm per pixel, and cm-scale location accuracy. Orientation data of brittle and ductile structures were semi-automatically extracted from these high-resolution datasets using open-source software. This resulted in an extensive and statistically relevant orientation dataset that was used to 1) interpret the progressive development of folds and faults in the region, and 2) to generate a 3D structural model that underlines the complex internal structure of the outcrop and quantifies spatial variations in fold geometries. Overall, our work highlights how UAV photogrammetry can contribute to new insights in structural analysis.

Spatial Distribution of Megacopta cribraria (Hemiptera: Plataspidae) Adults, Eggs and Parasitism by Paratelenomus saccharalis (Hymenoptera: Platygastridae) in Soybean.

PubMed

Knight, Ian A; Roberts, Phillip M; Gardner, Wayne A; Oliver, Kerry M; Reay-Jones, Francis P F; Reisig, Dominic D; Toews, Michael D

2017-12-08

Since 2014, populations of the kudzu bug, Megacopta cribraria (F.) (Hemiptera: Plataspidae), have declined in the southeastern United States and seldom require treatment. This decline follows the discovery of Paratelenomus saccharalis (Dodd; Hymenoptera: Platygastridae), a non-native egg parasitoid. The objective of this project was to observe the temporal and spatial dynamics of P. saccharalis parasitism of kudzu bug egg masses in commercial soybean fields. Four fields were sampled weekly for kudzu bugs and egg masses at a density of one sample per 0.6 ha. Sampling commenced when soybean reached the R2 maturity stage and continued until no more egg masses were present. Responses including kudzu bugs, egg masses, and parasitism rates were analyzed using ANOVA, Spatial Analysis by Distance Indices (SADIE), and SaTScan spatial analysis software. Egg masses were collected from the field, held in the lab and monitored for emergence of kudzu bug nymphs or P. saccharalis. Kudzu bug populations were generally lower than previously reported in the literature and spatial aggregation was not consistently observed. Egg parasitism was first detected in early July and increased to nearly 40% in mid-August. Significant spatial patterns in parasitism were observed with spatio-temporal clusters being loosely associated with clusters of egg masses. There were no significant differences in parasitism rates between field margins and interiors, suggesting that P. saccharalis is an effective parasitoid of kudzu bug egg masses on a whole-field scale. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The Modularized Software Package ASKI - Full Waveform Inversion Based on Waveform Sensitivity Kernels Utilizing External Seismic Wave Propagation Codes

NASA Astrophysics Data System (ADS)

Schumacher, F.; Friederich, W.

2015-12-01

We present the modularized software package ASKI which is a flexible and extendable toolbox for seismic full waveform inversion (FWI) as well as sensitivity or resolution analysis operating on the sensitivity matrix. It utilizes established wave propagation codes for solving the forward problem and offers an alternative to the monolithic, unflexible and hard-to-modify codes that have typically been written for solving inverse problems. It is available under the GPL at www.rub.de/aski. The Gauss-Newton FWI method for 3D-heterogeneous elastic earth models is based on waveform sensitivity kernels and can be applied to inverse problems at various spatial scales in both Cartesian and spherical geometries. The kernels are derived in the frequency domain from Born scattering theory as the Fréchet derivatives of linearized full waveform data functionals, quantifying the influence of elastic earth model parameters on the particular waveform data values. As an important innovation, we keep two independent spatial descriptions of the earth model - one for solving the forward problem and one representing the inverted model updates. Thereby we account for the independent needs of spatial model resolution of forward and inverse problem, respectively. Due to pre-integration of the kernels over the (in general much coarser) inversion grid, storage requirements for the sensitivity kernels are dramatically reduced.ASKI can be flexibly extended to other forward codes by providing it with specific interface routines that contain knowledge about forward code-specific file formats and auxiliary information provided by the new forward code. In order to sustain flexibility, the ASKI tools must communicate via file output/input, thus large storage capacities need to be accessible in a convenient way. Storing the complete sensitivity matrix to file, however, permits the scientist full manual control over each step in a customized procedure of sensitivity/resolution analysis and full waveform inversion.

Photogrammetry and remote sensing for visualization of spatial data in a virtual reality environment

NASA Astrophysics Data System (ADS)

Bhagawati, Dwipen

2001-07-01

Researchers in many disciplines have started using the tool of Virtual Reality (VR) to gain new insights into problems in their respective disciplines. Recent advances in computer graphics, software and hardware technologies have created many opportunities for VR systems, advanced scientific and engineering applications being among them. In Geometronics, generally photogrammetry and remote sensing are used for management of spatial data inventory. VR technology can be suitably used for management of spatial data inventory. This research demonstrates usefulness of VR technology for inventory management by taking the roadside features as a case study. Management of roadside feature inventory involves positioning and visualization of the features. This research has developed a methodology to demonstrate how photogrammetric principles can be used to position the features using the video-logging images and GPS camera positioning and how image analysis can help produce appropriate texture for building the VR, which then can be visualized in a Cave Augmented Virtual Environment (CAVE). VR modeling was implemented in two stages to demonstrate the different approaches for modeling the VR scene. A simulated highway scene was implemented with the brute force approach, while modeling software was used to model the real world scene using feature positions produced in this research. The first approach demonstrates an implementation of the scene by writing C++ codes to include a multi-level wand menu for interaction with the scene that enables the user to interact with the scene. The interactions include editing the features inside the CAVE display, navigating inside the scene, and performing limited geographic analysis. The second approach demonstrates creation of a VR scene for a real roadway environment using feature positions determined in this research. The scene looks realistic with textures from the real site mapped on to the geometry of the scene. Remote sensing and digital image processing techniques were used for texturing the roadway features in this scene.

Localization-based super-resolution imaging meets high-content screening.

PubMed

Beghin, Anne; Kechkar, Adel; Butler, Corey; Levet, Florian; Cabillic, Marine; Rossier, Olivier; Giannone, Gregory; Galland, Rémi; Choquet, Daniel; Sibarita, Jean-Baptiste

2017-12-01

Single-molecule localization microscopy techniques have proven to be essential tools for quantitatively monitoring biological processes at unprecedented spatial resolution. However, these techniques are very low throughput and are not yet compatible with fully automated, multiparametric cellular assays. This shortcoming is primarily due to the huge amount of data generated during imaging and the lack of software for automation and dedicated data mining. We describe an automated quantitative single-molecule-based super-resolution methodology that operates in standard multiwell plates and uses analysis based on high-content screening and data-mining software. The workflow is compatible with fixed- and live-cell imaging and allows extraction of quantitative data like fluorophore photophysics, protein clustering or dynamic behavior of biomolecules. We demonstrate that the method is compatible with high-content screening using 3D dSTORM and DNA-PAINT based super-resolution microscopy as well as single-particle tracking.

Cerebral aneurysms: relations between geometry, hemodynamics and aneurysm location in the cerebral vasculature

NASA Astrophysics Data System (ADS)

Passerini, Tiziano; Veneziani, Alessandro; Sangalli, Laura; Secchi, Piercesare; Vantini, Simone

2010-11-01

In cerebral blood circulation, the interplay of arterial geometrical features and flow dynamics is thought to play a significant role in the development of aneurysms. In the framework of the Aneurisk project, patient-specific morphology reconstructions were conducted with the open-source software VMTK (www.vmtk.org) on a set of computational angiography images provided by Ospedale Niguarda (Milano, Italy). Computational fluid dynamics (CFD) simulations were performed with a software based on the library LifeV (www.lifev.org). The joint statistical analysis of geometries and simulations highlights the possible association of certain spatial patterns of radius, curvature and shear load along the Internal Carotid Artery (ICA) with the presence, position and previous event of rupture of an aneurysm in the entire cerebral vasculature. Moreover, some possible landmarks are identified to be monitored for the assessment of a Potential Rupture Risk Index.

Airborne single particle mass spectrometers (SPLAT II & miniSPLAT) and new software for data visualization and analysis in a geo-spatial context.

PubMed

Zelenyuk, Alla; Imre, Dan; Wilson, Jacqueline; Zhang, Zhiyuan; Wang, Jun; Mueller, Klaus

2015-02-01

Understanding the effect of aerosols on climate requires knowledge of the size and chemical composition of individual aerosol particles-two fundamental properties that determine an aerosol's optical properties and ability to serve as cloud condensation or ice nuclei. Here we present our aircraft-compatible single particle mass spectrometers, SPLAT II and its new, miniaturized version, miniSPLAT that measure in-situ and in real-time the size and chemical composition of individual aerosol particles with extremely high sensitivity, temporal resolution, and sizing precision on the order of a monolayer. Although miniSPLAT's size, weight, and power consumption are significantly smaller, its performance is on par with SPLAT II. Both instruments operate in dual data acquisition mode to measure, in addition to single particle size and composition, particle number concentrations, size distributions, density, and asphericity with high temporal resolution. We also present ND-Scope, our newly developed interactive visual analytics software package. ND-Scope is designed to explore and visualize the vast amount of complex, multidimensional data acquired by our single particle mass spectrometers, along with other aerosol and cloud characterization instruments on-board aircraft. We demonstrate that ND-Scope makes it possible to visualize the relationships between different observables and to view the data in a geo-spatial context, using the interactive and fully coupled Google Earth and Parallel Coordinates displays. Here we illustrate the utility of ND-Scope to visualize the spatial distribution of atmospheric particles of different compositions, and explore the relationship between individual particle compositions and their activity as cloud condensation nuclei.

Constructing Benchmark Databases and Protocols for Medical Image Analysis: Diabetic Retinopathy

PubMed Central

Kauppi, Tomi; Kämäräinen, Joni-Kristian; Kalesnykiene, Valentina; Sorri, Iiris; Uusitalo, Hannu; Kälviäinen, Heikki

2013-01-01

We address the performance evaluation practices for developing medical image analysis methods, in particular, how to establish and share databases of medical images with verified ground truth and solid evaluation protocols. Such databases support the development of better algorithms, execution of profound method comparisons, and, consequently, technology transfer from research laboratories to clinical practice. For this purpose, we propose a framework consisting of reusable methods and tools for the laborious task of constructing a benchmark database. We provide a software tool for medical image annotation helping to collect class label, spatial span, and expert's confidence on lesions and a method to appropriately combine the manual segmentations from multiple experts. The tool and all necessary functionality for method evaluation are provided as public software packages. As a case study, we utilized the framework and tools to establish the DiaRetDB1 V2.1 database for benchmarking diabetic retinopathy detection algorithms. The database contains a set of retinal images, ground truth based on information from multiple experts, and a baseline algorithm for the detection of retinopathy lesions. PMID:23956787

Validation of luminescent source reconstruction using spectrally resolved bioluminescence images

NASA Astrophysics Data System (ADS)

Virostko, John M.; Powers, Alvin C.; Jansen, E. D.

2008-02-01

This study examines the accuracy of the Living Image® Software 3D Analysis Package (Xenogen, Alameda, CA) in reconstruction of light source depth and intensity. Constant intensity light sources were placed in an optically homogeneous medium (chicken breast). Spectrally filtered images were taken at 560, 580, 600, 620, 640, and 660 nanometers. The Living Image® Software 3D Analysis Package was employed to reconstruct source depth and intensity using these spectrally filtered images. For sources shallower than the mean free path of light there was proportionally higher inaccuracy in reconstruction. For sources deeper than the mean free path, the average error in depth and intensity reconstruction was less than 4% and 12%, respectively. The ability to distinguish multiple sources decreased with increasing source depth and typically required a spatial separation of twice the depth. The constant intensity light sources were also implanted in mice to examine the effect of optical inhomogeneity. The reconstruction accuracy suffered in inhomogeneous tissue with accuracy influenced by the choice of optical properties used in reconstruction.

Analyzing spatial clustering and the spatiotemporal nature and trends of HIV/AIDS prevalence using GIS: the case of Malawi, 1994-2010.

PubMed

Zulu, Leo C; Kalipeni, Ezekiel; Johannes, Eliza

2014-05-23

Although local spatiotemporal analysis can improve understanding of geographic variation of the HIV epidemic, its drivers, and the search for targeted interventions, it is limited in sub-Saharan Africa. Despite recent declines, Malawi's estimated 10.0% HIV prevalence (2011) remained among the highest globally. Using data on pregnant women in Malawi, this study 1) examines spatiotemporal trends in HIV prevalence 1994-2010, and 2) for 2010, identifies and maps the spatial variation/clustering of factors associated with HIV prevalence at district level. Inverse distance weighting was used within ArcGIS Geographic Information Systems (GIS) software to generate continuous surfaces of HIV prevalence from point data (1994, 1996, 1999, 2001, 2003, 2005, 2007, and 2010) obtained from surveillance antenatal clinics. From the surfaces prevalence estimates were extracted at district level and the results mapped nationally. Spatial dependency (autocorrelation) and clustering of HIV prevalence were also analyzed. Correlation and multiple regression analyses were used to identify factors associated with HIV prevalence for 2010 and their spatial variation/clustering mapped and compared to HIV clustering. Analysis revealed wide spatial variation in HIV prevalence at regional, urban/rural, district and sub-district levels. However, prevalence was spatially leveling out within and across 'sub-epidemics' while declining significantly after 1999. Prevalence exhibited statistically significant spatial dependence nationally following initial (1995-1999) localized, patchy low/high patterns as the epidemic spread rapidly. Locally, HIV "hotspots" clustered among eleven southern districts/cities while a "coldspot" captured configurations of six central region districts. Preliminary multiple regression of 2010 HIV prevalence produced a model with four significant explanatory factors (adjusted R2 = 0.688): mean distance to main roads, mean travel time to nearest transport, percentage that had taken an HIV test ever, and percentage attaining a senior primary education. Spatial clustering linked some factors to particular subsets of high HIV-prevalence districts. Spatial analysis enhanced understanding of local spatiotemporal variation in HIV prevalence, possible underlying factors, and potential for differentiated spatial targeting of interventions. Findings suggest that intervention strategies should also emphasize improved access to health/HIV services, basic education, and syphilis management, particularly in rural hotspot districts, as further research is done on drivers at finer scale.

Analyzing spatial clustering and the spatiotemporal nature and trends of HIV/AIDS prevalence using GIS: the case of Malawi, 1994-2010

PubMed Central

2014-01-01

Background Although local spatiotemporal analysis can improve understanding of geographic variation of the HIV epidemic, its drivers, and the search for targeted interventions, it is limited in sub-Saharan Africa. Despite recent declines, Malawi’s estimated 10.0% HIV prevalence (2011) remained among the highest globally. Using data on pregnant women in Malawi, this study 1) examines spatiotemporal trends in HIV prevalence 1994-2010, and 2) for 2010, identifies and maps the spatial variation/clustering of factors associated with HIV prevalence at district level. Methods Inverse distance weighting was used within ArcGIS Geographic Information Systems (GIS) software to generate continuous surfaces of HIV prevalence from point data (1994, 1996, 1999, 2001, 2003, 2005, 2007, and 2010) obtained from surveillance antenatal clinics. From the surfaces prevalence estimates were extracted at district level and the results mapped nationally. Spatial dependency (autocorrelation) and clustering of HIV prevalence were also analyzed. Correlation and multiple regression analyses were used to identify factors associated with HIV prevalence for 2010 and their spatial variation/clustering mapped and compared to HIV clustering. Results Analysis revealed wide spatial variation in HIV prevalence at regional, urban/rural, district and sub-district levels. However, prevalence was spatially leveling out within and across ‘sub-epidemics’ while declining significantly after 1999. Prevalence exhibited statistically significant spatial dependence nationally following initial (1995-1999) localized, patchy low/high patterns as the epidemic spread rapidly. Locally, HIV “hotspots” clustered among eleven southern districts/cities while a “coldspot” captured configurations of six central region districts. Preliminary multiple regression of 2010 HIV prevalence produced a model with four significant explanatory factors (adjusted R2 = 0.688): mean distance to main roads, mean travel time to nearest transport, percentage that had taken an HIV test ever, and percentage attaining a senior primary education. Spatial clustering linked some factors to particular subsets of high HIV-prevalence districts. Conclusions Spatial analysis enhanced understanding of local spatiotemporal variation in HIV prevalence, possible underlying factors, and potential for differentiated spatial targeting of interventions. Findings suggest that intervention strategies should also emphasize improved access to health/HIV services, basic education, and syphilis management, particularly in rural hotspot districts, as further research is done on drivers at finer scale. PMID:24886573

Multiscale analysis of river networks using the R package linbin

USGS Publications Warehouse

Welty, Ethan Z.; Torgersen, Christian E.; Brenkman, Samuel J.; Duda, Jeffrey J.; Armstrong, Jonathan B.

2015-01-01

Analytical tools are needed in riverine science and management to bridge the gap between GIS and statistical packages that were not designed for the directional and dendritic structure of streams. We introduce linbin, an R package developed for the analysis of riverscapes at multiple scales. With this software, riverine data on aquatic habitat and species distribution can be scaled and plotted automatically with respect to their position in the stream network or—in the case of temporal data—their position in time. The linbin package aggregates data into bins of different sizes as specified by the user. We provide case studies illustrating the use of the software for (1) exploring patterns at different scales by aggregating variables at a range of bin sizes, (2) comparing repeat observations by aggregating surveys into bins of common coverage, and (3) tailoring analysis to data with custom bin designs. Furthermore, we demonstrate the utility of linbin for summarizing patterns throughout an entire stream network, and we analyze the diel and seasonal movements of tagged fish past a stationary receiver to illustrate how linbin can be used with temporal data. In short, linbin enables more rapid analysis of complex data sets by fisheries managers and stream ecologists and can reveal underlying spatial and temporal patterns of fish distribution and habitat throughout a riverscape.

A GIS-based spatial correlation analysis for ambient air pollution and AECOPD hospitalizations in Jinan, China.

PubMed

Wang, Wenqiao; Ying, Yangyang; Wu, Quanyuan; Zhang, Haiping; Ma, Dedong; Xiao, Wei

2015-03-01

Acute exacerbations of COPD (AECOPD) are important events during disease procedure. AECOPD have negative effect on patients' quality of life, symptoms and lung function, and result in high socioeconomic costs. Though previous studies have demonstrated the significant association between outdoor air pollution and AECOPD hospitalizations, little is known about the spatial relationship utilized a spatial analyzing technique- Geographical Information System (GIS). Using GIS to investigate the spatial association between ambient air pollution and AECOPD hospitalizations in Jinan City, 2009. 414 AECOPD hospitalization cases in Jinan, 2009 were enrolled in our analysis. Monthly concentrations of five monitored air pollutants (NO2, SO2, PM10, O3, CO) during January 2009-December 2009 were provided by Environmental Protection Agency of Shandong Province. Each individual was geocoded in ArcGIS10.0 software. The spatial distribution of five pollutants and the temporal-spatial specific air pollutants exposure level for each individual was estimated by ordinary Kriging model. Spatial autocorrelation (Global Moran's I) was employed to explore the spatial association between ambient air pollutants and AECOPD hospitalizations. A generalized linear model (GLM) using a Poisson distribution with log-link function was used to construct a core model. At residence, concentrations of SO2, PM10, NO2, CO, O3 and AECOPD hospitalization cases showed statistical significant spatially clustered. The Z-score of SO2, PM10, CO, O3, NO2 at residence is 15.88, 13.93, 12.60, 4.02, 2.44 respectively, while at workplace, concentrations of PM10, SO2, O3, CO and AECOPD hospitalization cases showed statistical significant spatially clustered. The Z-score of PM10, SO2, O3, CO at workplace is 11.39, 8.07, 6.10, and 5.08 respectively. After adjusting for potential confounders in the model, only the PM10 concentrations at workplace showed statistical significance, with a 10 μg/m(3) increase of PM10 at workplace associated with a 7% (95%CI: [3.3%, 10%]) increase of hospitalizations due to AECOPD. Ambient air pollution is correlated with AECOPD hospitalizations spatially. A 10 μg/m(3) increase of PM10 at workplace was associated with a 7% (95%CI: [3.3%, 10%]) increase of hospitalizations due to AECOPD in Jinan, 2009. As a spatial data processing tool, GIS has novel and great potential on air pollutants exposure assessment and spatial analysis in AECOPD research. Copyright © 2015 Elsevier Ltd. All rights reserved.

Click-On-Diagram Questions: a New Tool to Study Conceptions Using Classroom Response Systems

NASA Astrophysics Data System (ADS)

LaDue, Nicole D.; Shipley, Thomas F.

2018-06-01

Geoscience instructors depend upon photos, diagrams, and other visualizations to depict geologic structures and processes that occur over a wide range of temporal and spatial scales. This proof-of-concept study tests click-on-diagram (COD) questions, administered using a classroom response system (CRS), as a research tool for identifying spatial misconceptions. First, we propose a categorization of spatial conceptions associated with geoscience concepts. Second, we implemented the COD questions in an undergraduate introductory geology course. Each question was implemented three times: pre-instruction, post-instruction, and at the end of the course to evaluate the stability of students' conceptual understanding. We classified each instance as (1) a false belief that was easily remediated, (2) a flawed mental model that was not fully transformed, or (3) a robust misconception that persisted despite targeted instruction. Geographic Information System (GIS) software facilitated spatial analysis of students' answers. The COD data confirmed known misconceptions about Earth's structure, geologic time, and base level and revealed a novel robust misconception about hot spot formation. Questions with complex spatial attributes were less likely to change following instruction and more likely to be classified as a robust misconception. COD questions provided efficient access to students' conceptual understanding. CRS-administered COD questions present an opportunity to gather spatial conceptions with large groups of students, immediately, building the knowledge base about students' misconceptions and providing feedback to guide instruction.

Air Pollution Measurements by Citizen Scientists and NASA Satellites: Data Integration and Analysis

NASA Astrophysics Data System (ADS)

Gupta, P.; Maibach, J.; Levy, R. C.; Doraiswamy, P.; Pikelnaya, O.; Feenstra, B.; Polidori, A.

2017-12-01

PM2.5, or fine particulate matter, is a category of air pollutant consisting of solid particles with effective aerodynamic diameter of less than 2.5 microns. These particles are hazardous to human health, as their small size allows them to penetrate deep into the lungs. Since the late 1990's, the US Environmental Protection Agency has been monitoring PM2.5 using a network of ground-level sensors. Due to cost and space restrictions, the EPA monitoring network remains spatially sparse. That is, while the network spans the extent of the US, the distance between sensors is large enough that significant spatial variation in PM concentration can go undetected. To increase the spatial resolution of monitoring, previous studies have used satellite data to estimate ground-level PM concentrations. From imagery, one can create a measure of haziness due to aerosols, called aerosol optical depth (AOD), which then can be used to estimate PM concentrations using statistical and physical modeling. Additionally, previous research has identified a number of meteorological variables, such as relative humidity and mixing height, which aide in estimating PM concentrations from AOD. Although the high spatial resolution of satellite data is valuable alone for forecasting air quality, higher resolution ground-level data is needed to effectively study the relationship between PM2.5 concentrations and AOD. To this end, we discuss a citizen-science PM monitoring network deployed in California. Using low-cost PM sensors, this network achieves higher spatial resolution. We additionally discuss a software pipeline for integrating resulting PM measurements with satellite data, as well as initial data analysis.

J-Earth: An Essential Resource for Terrestrial Remote Sensing and Data Analysis

NASA Astrophysics Data System (ADS)

Dunn, S.; Rupp, J.; Cheeseman, S.; Christensen, P. R.; Prashad, L. C.; Dickenshied, S.; Anwar, S.; Noss, D.; Murray, K.

2011-12-01

There is a need for a software tool that has the ability to display and analyze various types of earth science and social data through a simple, user-friendly interface. The J-Earth software tool has been designed to be easily accessible for download and intuitive use, regardless of the technical background of the user base. This tool does not require courses or text books to learn to use, yet is powerful enough to allow a more general community of users to perform complex data analysis. Professions that will benefit from this tool range from geologists, geographers, and climatologists to sociologists, economists, and ecologists as well as policy makers. J-Earth was developed by the Arizona State University Mars Space Flight Facility as part of the JMARS (Java Mission-planning and Analysis for Remote Sensing) suite of open-source tools. The program is a Geographic Information Systems (GIS) application used for viewing and processing satellite and airborne remote sensing data. While the functionality of JMARS has historically focused on the research needs of the planetary science community, J-Earth has been designed for a much broader Earth-based user audience. NASA instrument products accessible within J-Earth include data from ASTER, GOES, Landsat, MODIS, and TIMS. While J-Earth contains exceptionally comprehensive and high resolution satellite-derived data and imagery, this tool also includes many socioeconomic data products from projects lead by international organizations and universities. Datasets used in J-Earth take the form of grids, rasters, remote sensor "stamps", maps, and shapefiles. Some highly demanded global datasets available within J-Earth include five levels of administrative/political boundaries, climate data for current conditions as well as models for future climates, population counts and densities, land cover/land use, and poverty indicators. While this application does share the same powerful functionality of JMARS, J-Earth's apperance is enhanced for much easier data analysis. J-Earth utilizes a layering system to view data from different sources which can then be exported, scaled, colored and superimposed for quick comparisons. Users may now perform spatial analysis over several diverse datasets with respect to a defined geographic area or the entire globe. In addition, several newly acquired global datasets contain a temporal dimension which when accessed through J-Earth, make this a unique and powerful tool for spatial analysis over time. The functionality and ease of use set J-Earth apart from all other terrestrial GIS software packages and enable endless social, political, and scientific possibilities

Retrieving and Indexing Spatial Data in the Cloud Computing Environment

NASA Astrophysics Data System (ADS)

Wang, Yonggang; Wang, Sheng; Zhou, Daliang

In order to solve the drawbacks of spatial data storage in common Cloud Computing platform, we design and present a framework for retrieving, indexing, accessing and managing spatial data in the Cloud environment. An interoperable spatial data object model is provided based on the Simple Feature Coding Rules from the OGC such as Well Known Binary (WKB) and Well Known Text (WKT). And the classic spatial indexing algorithms like Quad-Tree and R-Tree are re-designed in the Cloud Computing environment. In the last we develop a prototype software based on Google App Engine to implement the proposed model.

An Integrated GIS-Expert System Framework for Live Hazard Monitoring and Detection.

PubMed

McCarthy, James D; Graniero, Phil A; Rozic, Steven M

2008-02-08

In the context of hazard monitoring, using sensor web technology to monitor anddetect hazardous conditions in near-real-time can result in large amounts of spatial data thatcan be used to drive analysis at an instrumented site. These data can be used for decisionmaking and problem solving, however as with any analysis problem the success ofanalyzing hazard potential is governed by many factors such as: the quality of the sensordata used as input; the meaning that can be derived from those data; the reliability of themodel used to describe the problem; the strength of the analysis methods; and the ability toeffectively communicate the end results of the analysis. For decision makers to make use ofsensor web data these issues must be dealt with to some degree. The work described in thispaper addresses all of these areas by showing how raw sensor data can be automaticallytransformed into a representation which matches a predefined model of the problem context.This model can be understood by analysis software that leverages rule-based logic andinference techniques to reason with, and draw conclusions about, spatial data. These toolsare integrated with a well known Geographic Information System (GIS) and existinggeospatial and sensor web infrastructure standards, providing expert users with the toolsneeded to thoroughly explore a problem site and investigate hazards in any domain.

An open-source, FireWire camera-based, Labview-controlled image acquisition system for automated, dynamic pupillometry and blink detection.

PubMed

de Souza, John Kennedy Schettino; Pinto, Marcos Antonio da Silva; Vieira, Pedro Gabrielle; Baron, Jerome; Tierra-Criollo, Carlos Julio

2013-12-01

The dynamic, accurate measurement of pupil size is extremely valuable for studying a large number of neuronal functions and dysfunctions. Despite tremendous and well-documented progress in image processing techniques for estimating pupil parameters, comparatively little work has been reported on practical hardware issues involved in designing image acquisition systems for pupil analysis. Here, we describe and validate the basic features of such a system which is based on a relatively compact, off-the-shelf, low-cost FireWire digital camera. We successfully implemented two configurable modes of video record: a continuous mode and an event-triggered mode. The interoperability of the whole system is guaranteed by a set of modular software components hosted on a personal computer and written in Labview. An offline analysis suite of image processing algorithms for automatically estimating pupillary and eyelid parameters were assessed using data obtained in human subjects. Our benchmark results show that such measurements can be done in a temporally precise way at a sampling frequency of up to 120 Hz and with an estimated maximum spatial resolution of 0.03 mm. Our software is made available free of charge to the scientific community, allowing end users to either use the software as is or modify it to suit their own needs. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Free and simple GIS as appropriate for health mapping in a low resource setting: a case study in eastern Indonesia.

PubMed

Fisher, Rohan P; Myers, Bronwyn A

2011-02-25

Despite the demonstrated utility of GIS for health applications, there are perceived problems in low resource settings: GIS software can be expensive and complex; input data are often of low quality. This study aimed to test the appropriateness of new, inexpensive and simple GIS tools in poorly resourced areas of a developing country. GIS applications were trialled in pilot studies based on mapping of health resources and health indicators at the clinic and district level in the predominantly rural province of Nusa Tenggara Timur in eastern Indonesia. The pilot applications were (i) rapid field collection of health infrastructure data using a GPS enabled PDA, (ii) mapping health indicator data using open source GIS software, and (iii) service availability mapping using a free modelling tool. Through contextualised training, district and clinic staff acquired skills in spatial analysis and visualisation and, six months after the pilot studies, they were using these skills for advocacy in the planning process, to inform the allocation of some health resources, and to evaluate some public health initiatives. We demonstrated that GIS can be a useful and inexpensive tool for the decentralisation of health data analysis to low resource settings through the use of free and simple software, locally relevant training materials and by providing data collection tools to ensure data reliability.

Free and simple GIS as appropriate for health mapping in a low resource setting: a case study in eastern Indonesia

PubMed Central

2011-01-01

Background Despite the demonstrated utility of GIS for health applications, there are perceived problems in low resource settings: GIS software can be expensive and complex; input data are often of low quality. This study aimed to test the appropriateness of new, inexpensive and simple GIS tools in poorly resourced areas of a developing country. GIS applications were trialled in pilot studies based on mapping of health resources and health indicators at the clinic and district level in the predominantly rural province of Nusa Tenggara Timur in eastern Indonesia. The pilot applications were (i) rapid field collection of health infrastructure data using a GPS enabled PDA, (ii) mapping health indicator data using open source GIS software, and (iii) service availability mapping using a free modelling tool. Results Through contextualised training, district and clinic staff acquired skills in spatial analysis and visualisation and, six months after the pilot studies, they were using these skills for advocacy in the planning process, to inform the allocation of some health resources, and to evaluate some public health initiatives. Conclusions We demonstrated that GIS can be a useful and inexpensive tool for the decentralisation of health data analysis to low resource settings through the use of free and simple software, locally relevant training materials and by providing data collection tools to ensure data reliability. PMID:21352553

Distributed and Collaborative Software Analysis

NASA Astrophysics Data System (ADS)

Ghezzi, Giacomo; Gall, Harald C.

Throughout the years software engineers have come up with a myriad of specialized tools and techniques that focus on a certain type of software analysissoftware analysis such as source code analysis, co-change analysis or bug prediction. However, easy and straight forward synergies between these analyses and tools rarely exist because of their stand-alone nature, their platform dependence, their different input and output formats and the variety of data to analyze. As a consequence, distributed and collaborative software analysiscollaborative software analysis scenarios and in particular interoperability are severely limited. We describe a distributed and collaborative software analysis platform that allows for a seamless interoperability of software analysis tools across platform, geographical and organizational boundaries. We realize software analysis tools as services that can be accessed and composed over the Internet. These distributed analysis services shall be widely accessible in our incrementally augmented Software Analysis Broker software analysis broker where organizations and tool providers can register and share their tools. To allow (semi-) automatic use and composition of these tools, they are classified and mapped into a software analysis taxonomy and adhere to specific meta-models and ontologiesontologies for their category of analysis.

Visualizer: 3D Gridded Data Visualization Software for Geoscience Education and Research

NASA Astrophysics Data System (ADS)

Harwood, C.; Billen, M. I.; Kreylos, O.; Jadamec, M.; Sumner, D. Y.; Kellogg, L. H.; Hamann, B.

2008-12-01

In both research and education learning is an interactive and iterative process of exploring and analyzing data or model results. However, visualization software often presents challenges on the path to learning because it assumes the user already knows the locations and types of features of interest, instead of enabling flexible and intuitive examination of results. We present examples of research and teaching using the software, Visualizer, specifically designed to create an effective and intuitive environment for interactive, scientific analysis of 3D gridded data. Visualizer runs in a range of 3D virtual reality environments (e.g., GeoWall, ImmersaDesk, or CAVE), but also provides a similar level of real-time interactivity on a desktop computer. When using Visualizer in a 3D-enabled environment, the software allows the user to interact with the data images as real objects, grabbing, rotating or walking around the data to gain insight and perspective. On the desktop, simple features, such as a set of cross-bars marking the plane of the screen, provide extra 3D spatial cues that allow the user to more quickly understand geometric relationships within the data. This platform portability allows the user to more easily integrate research results into classroom demonstrations and exercises, while the interactivity provides an engaging environment for self-directed and inquiry-based learning by students. Visualizer software is freely available for download (www.keckcaves.org) and runs on Mac OSX and Linux platforms.

Algorithms and software for U-Pb geochronology by LA-ICPMS

NASA Astrophysics Data System (ADS)

McLean, Noah M.; Bowring, James F.; Gehrels, George

2016-07-01

The past 15 years have produced numerous innovations in geochronology, including experimental methods, instrumentation, and software that are revolutionizing the acquisition and application of geochronological data. For example, exciting advances are being driven by Laser-Ablation ICP Mass Spectrometry (LA-ICPMS), which allows for rapid determination of U-Th-Pb ages with 10s of micrometer-scale spatial resolution. This method has become the most commonly applied tool for dating zircons, constraining a host of geological problems. The LA-ICPMS community is now faced with archiving these data with associated analytical results and, more importantly, ensuring that data meet the highest standards for precision and accuracy and that interlaboratory biases are minimized. However, there is little consensus with regard to analytical strategies and data reduction protocols for LA-ICPMS geochronology. The result is systematic interlaboratory bias and both underestimation and overestimation of uncertainties on calculated dates that, in turn, decrease the value of data in repositories such as EarthChem, which archives data and analytical results from participating laboratories. We present free open-source software that implements new algorithms for evaluating and resolving many of these discrepancies. This solution is the result of a collaborative effort to extend the U-Pb_Redux software for the ID-TIMS community to the LA-ICPMS community. Now named ET_Redux, our new software automates the analytical and scientific workflows of data acquisition, statistical filtering, data analysis and interpretation, publication, community-based archiving, and the compilation and comparison of data from different laboratories to support collaborative science.

Design and realization of tourism spatial decision support system based on GIS

NASA Astrophysics Data System (ADS)

Ma, Zhangbao; Qi, Qingwen; Xu, Li

2008-10-01

In this paper, the existing problems of current tourism management information system are analyzed. GIS, tourism as well as spatial decision support system are introduced, and the application of geographic information system technology and spatial decision support system to tourism management and the establishment of tourism spatial decision support system based on GIS are proposed. System total structure, system hardware and software environment, database design and structure module design of this system are introduced. Finally, realization methods of this systemic core functions are elaborated.

Applications of the Coastal Zone Color Scanner in oceanography

NASA Technical Reports Server (NTRS)

Mcclain, C. R.

1988-01-01

Research activity has continued to be focused on the applications of the Coastal Zone Color Scanner (CZCS) imagery in oceanography. A number of regional studies were completed including investigations of temporal and spatial variability of phytoplankton populations in the South Atlantic Bight, Northwest Spain, Weddell Sea, Bering Sea, Caribbean Sea and in tropical Atlantic Ocean. In addition to the regional studies, much work was dedicated to developing ancillary global scale meteorological and hydrographic data sets to complement the global CZCS processing products. To accomplish this, SEAPAK's image analysis capability was complemented with an interface to GEMPAK (Severe Storm Branch's meteorological analysis software package) for the analysis and graphical display of gridded data fields. Plans are being made to develop a similar interface to SEAPAK for hydrographic data using EPIC (a hydrographic data analysis package developed by NOAA/PMEL).

Digital transplantation pathology: combining whole slide imaging, multiplex staining and automated image analysis.

PubMed

Isse, K; Lesniak, A; Grama, K; Roysam, B; Minervini, M I; Demetris, A J

2012-01-01

Conventional histopathology is the gold standard for allograft monitoring, but its value proposition is increasingly questioned. "-Omics" analysis of tissues, peripheral blood and fluids and targeted serologic studies provide mechanistic insights into allograft injury not currently provided by conventional histology. Microscopic biopsy analysis, however, provides valuable and unique information: (a) spatial-temporal relationships; (b) rare events/cells; (c) complex structural context; and (d) integration into a "systems" model. Nevertheless, except for immunostaining, no transformative advancements have "modernized" routine microscopy in over 100 years. Pathologists now team with hardware and software engineers to exploit remarkable developments in digital imaging, nanoparticle multiplex staining, and computational image analysis software to bridge the traditional histology-global "-omic" analyses gap. Included are side-by-side comparisons, objective biopsy finding quantification, multiplexing, automated image analysis, and electronic data and resource sharing. Current utilization for teaching, quality assurance, conferencing, consultations, research and clinical trials is evolving toward implementation for low-volume, high-complexity clinical services like transplantation pathology. Cost, complexities of implementation, fluid/evolving standards, and unsettled medical/legal and regulatory issues remain as challenges. Regardless, challenges will be overcome and these technologies will enable transplant pathologists to increase information extraction from tissue specimens and contribute to cross-platform biomarker discovery for improved outcomes. ©Copyright 2011 The American Society of Transplantation and the American Society of Transplant Surgeons.

FracPaQ: a MATLAB™ Toolbox for the Quantification of Fracture Patterns

NASA Astrophysics Data System (ADS)

Healy, D.; Rizzo, R. E.; Cornwell, D. G.; Timms, N.; Farrell, N. J.; Watkins, H.; Gomez-Rivas, E.; Smith, M.

2016-12-01

The patterns of fractures in deformed rocks are rarely uniform or random. Fracture orientations, sizes, shapes and spatial distributions often exhibit some kind of order. In detail, there may be relationships among the different fracture attributes e.g. small fractures dominated by one orientation, larger fractures by another. These relationships are important because the mechanical (e.g. strength, anisotropy) and transport (e.g. fluids, heat) properties of rock depend on these fracture patterns and fracture attributes. This presentation describes an open source toolbox to quantify fracture patterns, including distributions in fracture attributes and their spatial variation. Software has been developed to quantify fracture patterns from 2-D digital images, such as thin section micrographs, geological maps, outcrop or aerial photographs or satellite images. The toolbox comprises a suite of MATLAB™ scripts based on published quantitative methods for the analysis of fracture attributes: orientations, lengths, intensity, density and connectivity. An estimate of permeability in 2-D is made using a parallel plate model. The software provides an objective and consistent methodology for quantifying fracture patterns and their variations in 2-D across a wide range of length scales. Our current focus for the application of the software is on quantifying the fracture patterns in and around fault zones. There is a large body of published work on the quantification of relatively simple joint patterns, but fault zones present a bigger, and arguably more important, challenge. The method presented is inherently scale independent, and a key task will be to analyse and integrate quantitative fracture pattern data from micro- to macro-scales. Planned future releases will incorporate multi-scale analyses based on a wavelet method to look for scale transitions, and combining fracture traces from multiple 2-D images to derive the statistically equivalent 3-D fracture pattern.

Image Segmentation Analysis for NASA Earth Science Applications

NASA Technical Reports Server (NTRS)

Tilton, James C.

2010-01-01

NASA collects large volumes of imagery data from satellite-based Earth remote sensing sensors. Nearly all of the computerized image analysis of this data is performed pixel-by-pixel, in which an algorithm is applied directly to individual image pixels. While this analysis approach is satisfactory in many cases, it is usually not fully effective in extracting the full information content from the high spatial resolution image data that s now becoming increasingly available from these sensors. The field of object-based image analysis (OBIA) has arisen in recent years to address the need to move beyond pixel-based analysis. The Recursive Hierarchical Segmentation (RHSEG) software developed by the author is being used to facilitate moving from pixel-based image analysis to OBIA. The key unique aspect of RHSEG is that it tightly intertwines region growing segmentation, which produces spatially connected region objects, with region object classification, which groups sets of region objects together into region classes. No other practical, operational image segmentation approach has this tight integration of region growing object finding with region classification This integration is made possible by the recursive, divide-and-conquer implementation utilized by RHSEG, in which the input image data is recursively subdivided until the image data sections are small enough to successfully mitigat the combinatorial explosion caused by the need to compute the dissimilarity between each pair of image pixels. RHSEG's tight integration of region growing object finding and region classification is what enables the high spatial fidelity of the image segmentations produced by RHSEG. This presentation will provide an overview of the RHSEG algorithm and describe how it is currently being used to support OBIA or Earth Science applications such as snow/ice mapping and finding archaeological sites from remotely sensed data.

Remote sensing and GIS integration: Towards intelligent imagery within a spatial data infrastructure

NASA Astrophysics Data System (ADS)

Abdelrahim, Mohamed Mahmoud Hosny

2001-11-01

In this research, an "Intelligent Imagery System Prototype" (IISP) was developed. IISP is an integration tool that facilitates the environment for active, direct, and on-the-fly usage of high resolution imagery, internally linked to hidden GIS vector layers, to query the real world phenomena and, consequently, to perform exploratory types of spatial analysis based on a clear/undisturbed image scene. The IISP was designed and implemented using the software components approach to verify the hypothesis that a fully rectified, partially rectified, or even unrectified digital image can be internally linked to a variety of different hidden vector databases/layers covering the end user area of interest, and consequently may be reliably used directly as a base for "on-the-fly" querying of real-world phenomena and for performing exploratory types of spatial analysis. Within IISP, differentially rectified, partially rectified (namely, IKONOS GEOCARTERRA(TM)), and unrectified imagery (namely, scanned aerial photographs and captured video frames) were investigated. The system was designed to handle four types of spatial functions, namely, pointing query, polygon/line-based image query, database query, and buffering. The system was developed using ESRI MapObjects 2.0a as the core spatial component within Visual Basic 6.0. When used to perform the pre-defined spatial queries using different combinations of image and vector data, the IISP provided the same results as those obtained by querying pre-processed vector layers even when the image used was not orthorectified and the vector layers had different parameters. In addition, the real-time pixel location orthorectification technique developed and presented within the IKONOS GEOCARTERRA(TM) case provided a horizontal accuracy (RMSE) of +/- 2.75 metres. This accuracy is very close to the accuracy level obtained when purchasing the orthorectified IKONOS PRECISION products (RMSE of +/- 1.9 metre). The latter cost approximately four times as much as the IKONOS GEOCARTERRA(TM) products. The developed IISP is a step closer towards the direct and active involvement of high-resolution remote sensing imagery in querying the real world and performing exploratory types of spatial analysis. (Abstract shortened by UMI.)

[Spatial and temporal analysis of the coverage for neonatal hearing screening in Brazil (2008-2015)].

PubMed

Paschoal, Monique Ramos; Cavalcanti, Hannalice Gottschalck; Ferreira, Maria Ângela Fernandes

2017-11-01

This article seeks to establish the coverage of neonatal hearing screening in Brazil between January 2008 and June 2015. It is an ecological study that uses the country, through the Urban Articulation Regions, as a base. To calculate the screening coverage percentage, the Live Births Information System, the Outpatient Information System and the Beneficiaries of the National Supplementary Health Agency Information System were used. An exploratory analysis of maps and spatial statistical analysis was conducted using TerraView 4.2.2 software. The coverage of neonatal hearing screening saw an increase of 9.3% to 37.2% during the study period. In 2008-2009 it was observed that the percentage of coverage ranged from 0% to 79.92%, but most areas received coverage from 0% to 20%, though in 2014-2015 coverage ranged from 0% to 171.77%, and there was a visible increase in the percentage of coverage in the country, mainly in the Southern Region. The screening coverage has increased over time, but is still low with an uneven distribution in the territory, which may be explained by local laws and policies and by the existence of different types of auditory health service in the country.

MEG/EEG Source Reconstruction, Statistical Evaluation, and Visualization with NUTMEG

PubMed Central

Dalal, Sarang S.; Zumer, Johanna M.; Guggisberg, Adrian G.; Trumpis, Michael; Wong, Daniel D. E.; Sekihara, Kensuke; Nagarajan, Srikantan S.

2011-01-01

NUTMEG is a source analysis toolbox geared towards cognitive neuroscience researchers using MEG and EEG, including intracranial recordings. Evoked and unaveraged data can be imported to the toolbox for source analysis in either the time or time-frequency domains. NUTMEG offers several variants of adaptive beamformers, probabilistic reconstruction algorithms, as well as minimum-norm techniques to generate functional maps of spatiotemporal neural source activity. Lead fields can be calculated from single and overlapping sphere head models or imported from other software. Group averages and statistics can be calculated as well. In addition to data analysis tools, NUTMEG provides a unique and intuitive graphical interface for visualization of results. Source analyses can be superimposed onto a structural MRI or headshape to provide a convenient visual correspondence to anatomy. These results can also be navigated interactively, with the spatial maps and source time series or spectrogram linked accordingly. Animations can be generated to view the evolution of neural activity over time. NUTMEG can also display brain renderings and perform spatial normalization of functional maps using SPM's engine. As a MATLAB package, the end user may easily link with other toolboxes or add customized functions. PMID:21437174

MEG/EEG source reconstruction, statistical evaluation, and visualization with NUTMEG.

PubMed

Dalal, Sarang S; Zumer, Johanna M; Guggisberg, Adrian G; Trumpis, Michael; Wong, Daniel D E; Sekihara, Kensuke; Nagarajan, Srikantan S

2011-01-01

NUTMEG is a source analysis toolbox geared towards cognitive neuroscience researchers using MEG and EEG, including intracranial recordings. Evoked and unaveraged data can be imported to the toolbox for source analysis in either the time or time-frequency domains. NUTMEG offers several variants of adaptive beamformers, probabilistic reconstruction algorithms, as well as minimum-norm techniques to generate functional maps of spatiotemporal neural source activity. Lead fields can be calculated from single and overlapping sphere head models or imported from other software. Group averages and statistics can be calculated as well. In addition to data analysis tools, NUTMEG provides a unique and intuitive graphical interface for visualization of results. Source analyses can be superimposed onto a structural MRI or headshape to provide a convenient visual correspondence to anatomy. These results can also be navigated interactively, with the spatial maps and source time series or spectrogram linked accordingly. Animations can be generated to view the evolution of neural activity over time. NUTMEG can also display brain renderings and perform spatial normalization of functional maps using SPM's engine. As a MATLAB package, the end user may easily link with other toolboxes or add customized functions.

The Use of Virtual Globes as a Spatial Teaching Tool with Suggestions for Metadata Standards

ERIC Educational Resources Information Center

Schultz, Richard B.; Kerski, Joseph J.; Patterson, Todd C.

2008-01-01

Virtual Globe software has become extremely popular both inside and outside of educational settings. This software allows users to explore the Earth in three dimensions while streaming satellite imagery, elevation, and other data from the Internet. Virtual Globes, such as Google Earth, NASA World Wind, and ESRI's ArcGIS Explorer can be effectively…

The Effect of Using Dynamic Mathematics Software: Cross Section and Visualization

ERIC Educational Resources Information Center

Kösa, Temel

2016-01-01

The main purpose of this study is to determine the effects of using dynamic mathematics software on pre-service mathematics teachers' ability to infer the shape of a cross section of a three-dimensional solid, as well as on their spatial visualization skills. The study employed a quasi-experimental design with a control group; the Purdue Spatial…

Objected-oriented remote sensing image classification method based on geographic ontology model

NASA Astrophysics Data System (ADS)

Chu, Z.; Liu, Z. J.; Gu, H. Y.

2016-11-01

Nowadays, with the development of high resolution remote sensing image and the wide application of laser point cloud data, proceeding objected-oriented remote sensing classification based on the characteristic knowledge of multi-source spatial data has been an important trend on the field of remote sensing image classification, which gradually replaced the traditional method through improving algorithm to optimize image classification results. For this purpose, the paper puts forward a remote sensing image classification method that uses the he characteristic knowledge of multi-source spatial data to build the geographic ontology semantic network model, and carries out the objected-oriented classification experiment to implement urban features classification, the experiment uses protégé software which is developed by Stanford University in the United States, and intelligent image analysis software—eCognition software as the experiment platform, uses hyperspectral image and Lidar data that is obtained through flight in DaFeng City of JiangSu as the main data source, first of all, the experiment uses hyperspectral image to obtain feature knowledge of remote sensing image and related special index, the second, the experiment uses Lidar data to generate nDSM(Normalized DSM, Normalized Digital Surface Model),obtaining elevation information, the last, the experiment bases image feature knowledge, special index and elevation information to build the geographic ontology semantic network model that implement urban features classification, the experiment results show that, this method is significantly higher than the traditional classification algorithm on classification accuracy, especially it performs more evidently on the respect of building classification. The method not only considers the advantage of multi-source spatial data, for example, remote sensing image, Lidar data and so on, but also realizes multi-source spatial data knowledge integration and application of the knowledge to the field of remote sensing image classification, which provides an effective way for objected-oriented remote sensing image classification in the future.

Trends and spatial distribution of deaths of children aged 12-60 months in São Paulo, Brazil, 1980-98.

PubMed Central

Antunes, José Leopoldo Ferreira; Waldman, Eliseu Alves

2002-01-01

OBJECTIVE: To describe trends in the mortality of children aged 12-60 months and to perform spatial data analysis of its distribution at the inner city district level in São Paulo from 1980 to 1998. METHODS: Official mortality data were analysed in relation to the underlying causes of death. The population of children aged 12-60 months, disaggregated by sex and age, was estimated for each year. Educational levels, income, employment status, and other socioeconomic indices were also assessed. Statistical Package for Social Sciences software was used for the statistical processing of time series. The Cochrane-Orcutt procedure of generalized least squares regression analysis was used to estimate the regression parameters with control of first-order autocorrelation. Spatial data analysis employed the discrimination of death rates and socioeconomic indices at the inner city district level. For classifying area-level death rates the method of K-means cluster analysis was used. Spatial correlation between variables was analysed by the simultaneous autoregressive regression method. FINDINGS: There was a steady decline in death rates during the 1980s at an average rate of 3.08% per year, followed by a levelling off. Infectious diseases remained the major cause of mortality, accounting for 43.1% of deaths during the last three years of the study. Injuries accounted for 16.5% of deaths. Mortality rates at the area level clearly demonstrated inequity in the city's health profile: there was an increasing difference between the rich and the underprivileged social strata in this respect. CONCLUSION: The overall mortality rate among children aged 12-60 months dropped by almost 30% during the study period. Most of the decline happened during the 1980s. Many people still live in a state of deprivation in underserved areas. Time-series and spatial data analysis provided indications of potential value in the planning of social policies promoting well-being, through the identification of factors affecting child survival and the regions with the worst health profiles, to which programmes and resources should be preferentially directed. PMID:12077615

Timescape: a simple space-time interpolation geostatistical Algorithm

NASA Astrophysics Data System (ADS)

Ciolfi, Marco; Chiocchini, Francesca; Gravichkova, Olga; Pisanelli, Andrea; Portarena, Silvia; Scartazza, Andrea; Brugnoli, Enrico; Lauteri, Marco

2016-04-01

Environmental sciences include both time and space variability in their datasets. Some established tools exist for both spatial interpolation and time series analysis alone, but mixing space and time variability calls for compromise: Researchers are often forced to choose which is the main source of variation, neglecting the other. We propose a simple algorithm, which can be used in many fields of Earth and environmental sciences when both time and space variability must be considered on equal grounds. The algorithm has already been implemented in Java language and the software is currently available at https://sourceforge.net/projects/timescapeglobal/ (it is published under GNU-GPL v3.0 Free Software License). The published version of the software, Timescape Global, is focused on continent- to Earth-wide spatial domains, using global longitude-latitude coordinates for samples localization. The companion Timescape Local software is currently under development ad will be published with an open license as well; it will use projected coordinates for a local to regional space scale. The basic idea of the Timescape Algorithm consists in converting time into a sort of third spatial dimension, with the addition of some causal constraints, which drive the interpolation including or excluding observations according to some user-defined rules. The algorithm is applicable, as a matter of principle, to anything that can be represented with a continuous variable (a scalar field, technically speaking). The input dataset should contain position, time and observed value of all samples. Ancillary data can be included in the interpolation as well. After the time-space conversion, Timescape follows basically the old-fashioned IDW (Inverse Distance Weighted) interpolation Algorithm, although users have a wide choice of customization options that, at least partially, overcome some of the known issues of IDW. The three-dimensional model produced by the Timescape Algorithm can be explored in many ways, including the extraction of time series at fixed locations and GIS layers at constant times, allowing for the inclusion of the model in the users' established workflow. The software requirements are relatively modest since it has been purposely designed for potential users in various research field with a limited computing power at their disposal. Any respectful modern PC or laptop can run it. Users however need a separate database for sample data and models storage because these can be quite bulky in terms of data output: a single model can be composed of several billions of voxels (three-dimensional discrete cells, a sort of 3D pixels). Running times range from a few minutes for sketch models to some days of evaluation for a full-size model, depending on the users' hardware and model size.

Near-field radiative heat transfer in scanning thermal microscopy computed with the boundary element method

NASA Astrophysics Data System (ADS)

Nguyen, K. L.; Merchiers, O.; Chapuis, P.-O.

2017-11-01

We compute the near-field radiative heat transfer between a hot AFM tip and a cold substrate. This contribution to the tip-sample heat transfer in Scanning Thermal Microscopy is often overlooked, despite its leading role when the tip is out of contact. For dielectrics, we provide power levels exchanged as a function of the tip-sample distance in vacuum and spatial maps of the heat flux deposited into the sample which indicate the near-contact spatial resolution. The results are compared to analytical expressions of the Proximity Flux Approximation. The numerical results are obtained by means of the Boundary Element Method (BEM) implemented in the SCUFF-EM software, and require first a thorough convergence analysis of the progressive implementation of this method to the thermal emission by a sphere, the radiative transfer between two spheres, and the radiative exchange between a sphere and a finite substrate.

Studying groundwater and surface water interactions using airborne remote sensing in Heihe River basin, northwest China

NASA Astrophysics Data System (ADS)

Liu, C.; Liu, J.; Hu, Y.; Zheng, C.

2015-05-01

Managing surface water and groundwater as a unified system is important for water resource exploitation and aquatic ecosystem conservation. The unified approach to water management needs accurate characterization of surface water and groundwater interactions. Temperature is a natural tracer for identifying surface water and groundwater interactions, and the use of remote sensing techniques facilitates basin-scale temperature measurement. This study focuses on the Heihe River basin, the second largest inland river basin in the arid and semi-arid northwest of China where surface water and groundwater undergoes dynamic exchanges. The spatially continuous river-surface temperature of the midstream section of the Heihe River was obtained by using an airborne pushbroom hyperspectral thermal sensor system. By using the hot spot analysis toolkit in the ArcGIS software, abnormally cold water zones were identified as indicators of the spatial pattern of groundwater discharge to the river.

Computer-Aided-Design of the Hydraulic System of Three-Dimensional Cartridge Valve Blocks (Selected Articles)

DTIC Science & Technology

1991-03-21

sectional representation of the spatial figure can be correctly determined. 6 The AutoLisp language system in the AutoCAD software provides the most...softwares are developed on the 32-bit machines and little progress has been reported for the 16-bit machines. Even the AutoCAD is a two-ard-a-half... AutoCAD software as the basis, developed the design package of 3-D cartridge valve blocks on IM PC/AT. To realize the 3-D displaying of cartridge valves

Spatial data software integration - Merging CAD/CAM/mapping with GIS and image processing

NASA Technical Reports Server (NTRS)

Logan, Thomas L.; Bryant, Nevin A.

1987-01-01

The integration of CAD/CAM/mapping with image processing using geographic information systems (GISs) as the interface is examined. Particular emphasis is given to the development of software interfaces between JPL's Video Image Communication and Retrieval (VICAR)/Imaged Based Information System (IBIS) raster-based GIS and the CAD/CAM/mapping system. The design and functions of the VICAR and IBIS are described. Vector data capture and editing are studied. Various software programs for interfacing between the VICAR/IBIS and CAD/CAM/mapping are presented and analyzed.

LIMAO: Cross-platform software for simulating laser-induced alignment and orientation dynamics of linear-, symmetric- and asymmetric tops

NASA Astrophysics Data System (ADS)

Szidarovszky, Tamás; Jono, Maho; Yamanouchi, Kaoru

2018-07-01

A user-friendly and cross-platform software called Laser-Induced Molecular Alignment and Orientation simulator (LIMAO) has been developed. The program can be used to simulate within the rigid rotor approximation the rotational dynamics of gas phase molecules induced by linearly polarized intense laser fields at a given temperature. The software is implemented in the Java and Mathematica programming languages. The primary aim of LIMAO is to aid experimental scientists in predicting and analyzing experimental data representing laser-induced spatial alignment and orientation of molecules.

Spatial-temporal analysis of dengue deaths: identifying social vulnerabilities.

PubMed

Silva, Maria do Socorro da; Branco, Maria Dos Remédios Freitas Carvalho; Aquino, José; Queiroz, Rejane Christine de Sousa; Bani, Emanuele; Moreira, Emnielle Pinto Borges; Medeiros, Maria Nilza Lima; Rodrigues, Zulimar Márita Ribeiro

2017-01-01

Currently, dengue fever, chikungunya fever, and zika virus represent serious public health issues in Brazil, despite efforts to control the vector, the Aedes aegypti mosquito. This was a descriptive and ecological study of dengue deaths occurring from 2002 to 2013 in São Luis, Maranhão, Brazil. Geoprocessing software was used to draw maps, linking the geo-referenced deaths with urban/social data at census tract level. There were 74 deaths, concentrated in areas of social vulnerability. The use of geo-technology tools pointed to a concentration of dengue deaths in specific intra-urban areas.

Freely-available, true-color volume rendering software and cryohistology data sets for virtual exploration of the temporal bone anatomy.

PubMed

Kahrs, Lüder Alexander; Labadie, Robert Frederick

2013-01-01

Cadaveric dissection of temporal bone anatomy is not always possible or feasible in certain educational environments. Volume rendering using CT and/or MRI helps understanding spatial relationships, but they suffer in nonrealistic depictions especially regarding color of anatomical structures. Freely available, nonstained histological data sets and software which are able to render such data sets in realistic color could overcome this limitation and be a very effective teaching tool. With recent availability of specialized public-domain software, volume rendering of true-color, histological data sets is now possible. We present both feasibility as well as step-by-step instructions to allow processing of publicly available data sets (Visible Female Human and Visible Ear) into easily navigable 3-dimensional models using free software. Example renderings are shown to demonstrate the utility of these free methods in virtual exploration of the complex anatomy of the temporal bone. After exploring the data sets, the Visible Ear appears more natural than the Visible Human. We provide directions for an easy-to-use, open-source software in conjunction with freely available histological data sets. This work facilitates self-education of spatial relationships of anatomical structures inside the human temporal bone as well as it allows exploration of surgical approaches prior to cadaveric testing and/or clinical implementation. Copyright © 2013 S. Karger AG, Basel.

Spatial Temporal Mathematics at Scale: An Innovative and Fully Developed Paradigm to Boost Math Achievement among All Learners

ERIC Educational Resources Information Center

Rutherford, Teomara; Kibrick, Melissa; Burchinal, Margaret; Richland, Lindsey; Conley, AnneMarie; Osborne, Keara; Schneider, Stephanie; Duran, Lauren; Coulson, Andrew; Antenore, Fran; Daniels, Abby; Martinez, Michael E.

2010-01-01

This paper describes the background, methodology, preliminary findings, and anticipated future directions of a large-scale multi-year randomized field experiment addressing the efficacy of ST Math [Spatial-Temporal Math], a fully-developed math curriculum that uses interactive animated software. ST Math's unique approach minimizes the use of…

Evaluation of the MIND Research Institute's Spatial-Temporal Math (ST Math) Program in California

ERIC Educational Resources Information Center

Wendt, Staci; Rice, John; Nakamoto, Jonathan

2014-01-01

The MIND Research Institute contracted with the Evaluation Research Program at WestEd to conduct an independent assessment of mathematics outcomes in elementary school grades across California that were provided with the ST Math program. Spatial-Temporal (ST) Math is a game-based instructional software designed to boost K-5 and secondary-level…

Spatial Visualization by Realistic 3D Views

ERIC Educational Resources Information Center

Yue, Jianping

2008-01-01

In this study, the popular Purdue Spatial Visualization Test-Visualization by Rotations (PSVT-R) in isometric drawings was recreated with CAD software that allows 3D solid modeling and rendering to provide more realistic pictorial views. Both the original and the modified PSVT-R tests were given to students and their scores on the two tests were…

Modelling the Effects of Land-Use Changes on Climate: a Case Study on Yamula DAM

NASA Astrophysics Data System (ADS)

Köylü, Ü.; Geymen, A.

2016-10-01

Dams block flow of rivers and cause artificial water reservoirs which affect the climate and the land use characteristics of the river basin. In this research, the effect of the huge water body obtained by Yamula Dam in Kızılırmak Basin is analysed over surrounding spatial's land use and climate change. Mann Kendal non-parametrical statistical test, Theil&Sen Slope method, Inverse Distance Weighting (IDW), Soil Conservation Service-Curve Number (SCS-CN) methods are integrated for spatial and temporal analysis of the research area. For this research humidity, temperature, wind speed, precipitation observations which are collected in 16 weather stations nearby Kızılırmak Basin are analyzed. After that these statistical information is combined by GIS data over years. An application is developed for GIS analysis in Python Programming Language and integrated with ArcGIS software. Statistical analysis calculated in the R Project for Statistical Computing and integrated with developed application. According to the statistical analysis of extracted time series of meteorological parameters, statistical significant spatiotemporal trends are observed for climate change and land use characteristics. In this study, we indicated the effect of big dams in local climate on semi-arid Yamula Dam.

Integration of modern statistical tools for the analysis of climate extremes into the web-GIS “CLIMATE”

NASA Astrophysics Data System (ADS)

Ryazanova, A. A.; Okladnikov, I. G.; Gordov, E. P.

2017-11-01

The frequency of occurrence and magnitude of precipitation and temperature extreme events show positive trends in several geographical regions. These events must be analyzed and studied in order to better understand their impact on the environment, predict their occurrences, and mitigate their effects. For this purpose, we augmented web-GIS called “CLIMATE” to include a dedicated statistical package developed in the R language. The web-GIS “CLIMATE” is a software platform for cloud storage processing and visualization of distributed archives of spatial datasets. It is based on a combined use of web and GIS technologies with reliable procedures for searching, extracting, processing, and visualizing the spatial data archives. The system provides a set of thematic online tools for the complex analysis of current and future climate changes and their effects on the environment. The package includes new powerful methods of time-dependent statistics of extremes, quantile regression and copula approach for the detailed analysis of various climate extreme events. Specifically, the very promising copula approach allows obtaining the structural connections between the extremes and the various environmental characteristics. The new statistical methods integrated into the web-GIS “CLIMATE” can significantly facilitate and accelerate the complex analysis of climate extremes using only a desktop PC connected to the Internet.

ZWD time series analysis derived from NRT data processing. A regional study of PW in Greece.

NASA Astrophysics Data System (ADS)

Pikridas, Christos; Balidakis, Kyriakos; Katsougiannopoulos, Symeon

2015-04-01

ZWD (Zenith Wet/non-hydrostatic Delay) estimates are routinely derived Near Real Time from the new established Analysis Center in the Department of Geodesy and Surveying of Aristotle University of Thessaloniki (DGS/AUT-AC), in the framework of E-GVAP (EUMETNET GNSS water vapour project) since October 2014. This process takes place on an hourly basis and yields, among else, station coordinates and tropospheric parameter estimates for a network of 90+ permanent GNSS (Global Navigation Satellite System) stations. These are distributed at the wider part of Hellenic region. In this study, temporal and spatial variability of ZWD estimates were examined, as well as their relation with coordinate series extracted from both float and fixed solution of the initial phase ambiguities. For this investigation, Bernese GNSS Software v5.2 was used for the acquisition of the 6 month dataset from the aforementioned network. For time series analysis we employed techniques such as the Generalized Lomb-Scargle periodogram and Burg's maximum entropy method due to inefficiencies of the Discrete Fourier Transform application in the test dataset. Through the analysis, interesting results for further geophysical interpretation were drawn. In addition, the spatial and temporal distributions of Precipitable Water vapour (PW) obtained from both ZWD estimates and ERA-Interim reanalysis grids were investigated.

Hierarchical spatial capture-recapture models: Modeling population density from stratified populations

USGS Publications Warehouse

Royle, J. Andrew; Converse, Sarah J.

2014-01-01

Capture–recapture studies are often conducted on populations that are stratified by space, time or other factors. In this paper, we develop a Bayesian spatial capture–recapture (SCR) modelling framework for stratified populations – when sampling occurs within multiple distinct spatial and temporal strata.We describe a hierarchical model that integrates distinct models for both the spatial encounter history data from capture–recapture sampling, and also for modelling variation in density among strata. We use an implementation of data augmentation to parameterize the model in terms of a latent categorical stratum or group membership variable, which provides a convenient implementation in popular BUGS software packages.We provide an example application to an experimental study involving small-mammal sampling on multiple trapping grids over multiple years, where the main interest is in modelling a treatment effect on population density among the trapping grids.Many capture–recapture studies involve some aspect of spatial or temporal replication that requires some attention to modelling variation among groups or strata. We propose a hierarchical model that allows explicit modelling of group or strata effects. Because the model is formulated for individual encounter histories and is easily implemented in the BUGS language and other free software, it also provides a general framework for modelling individual effects, such as are present in SCR models.

Exploring the relationship between food access and foodborne illness by using spatial analysis.

PubMed

Newbold, Bruce; Watson, Susannah; Mackay, Kevin; Isaacs, Sandy

2013-09-01

There is some evidence that neighborhood deprivation increases residents' risk of foodborne illnesses. Because urban areas with the least available access to adequate amounts of nutritious or affordable food options (or "food deserts") also tend to be the most deprived areas within a city, it is hypothesized that food access and foodborne illness risk are linked. However, the complexity of tracking numbers and sources of gastrointestinal (GI) illnesses often leads researchers to speculate about reasons for disproportionate rates of pathogen outbreaks among demographic groups. This study explores the suitability of existing data to examine associations between food deserts and the spatial distribution of GI illnesses in Hamilton, Ontario, Canada. A spatial analysis by using GIS software methodology was used to identify and map food retail outlets and accessibility, as well as GI illness outbreaks and sales of antidiarrhea, antinausea, and rehydration products (used as a proxy for GI cases) within the city, based on available data. Statistical analysis of the maps shows no statistical relationship between location, access to food outlets, and rates of GI illness. The analysis points to shortfalls and gaps in the existing data, which leaves us unable to draw conclusions either supporting or refuting our hypothesis. This article includes recommendations to improve the current system of illness reporting and to continue to refine the definition and process of mapping food access issues. A more comprehensive set of data would enable municipalities to more easily identify groups most at risk, depending on exposures and the type of pathogen, and reduce the occurrence of foodborne disease.

Spatial Distribution of Phlebotomine Sand Fly Species (Diptera: Psychodidae) in Qom Province, Central Iran.

PubMed

Saghafipour, Abedin; Vatandoost, Hassan; Zahraei-Ramazani, Ali Reza; Yaghoobi-Ershadi, Mohammad Reza; Rassi, Yavar; Shirzadi, Mohammad Reza; Akhavan, Amir Ahmad

2017-01-01

Zoonotic cutaneous leishmaniasis (ZCL) is transmitted to humans by phlebotomine sand fly bites. ZCL is a major health problem in Iran, where basic knowledge gaps about sand fly species diversity persist in some ZCL-endemic areas. This paper describes the richness and spatial distribution of sand fly species, collected with sticky traps, in Qom province, a ZCL-endemic area in central Iran, where sand fly fauna has been poorly studied. Collected species were mapped on urban and rural digital maps based on a scale of 1/50,000. All analyses were undertaken with rural- and urban-level precision, i.e., rural and urban levels were our basic units of analysis. After identifying the sand flies, high-risk foci were determined. For spatial analysis of vector species population, the entomological sampling sites were geo-referenced using GPS. Arc GIS 9.3 software was used to determine the foci with leishmaniasis vector species. Following the analyses, two genera (Phlebotomus and Sergentomyia) and 14 species were identified. Based on the mapping and sand fly dispersion analysis, the rural districts were categorized into three groups-infection reported, without infection, and no report. Based on Geographical Information System analyses, Kahak and Markazi districts were identified as high-risk foci with leishmaniasis vector species. These findings can act as a help guide to direct active control measures to the identified high-risk foci and, eventually, lead to reduction in incidence of the disease. © Crown copyright 2016.

Spatial analysis and health risk assessment of heavy metals concentration in drinking water resources.

PubMed

Fallahzadeh, Reza Ali; Ghaneian, Mohammad Taghi; Miri, Mohammad; Dashti, Mohamad Mehdi

2017-11-01

The heavy metals available in drinking water can be considered as a threat to human health. Oncogenic risk of such metals is proven in several studies. Present study aimed to investigate concentration of the heavy metals including As, Cd, Cr, Cu, Fe, Hg, Mn, Ni, Pb, and Zn in 39 water supply wells and 5 water reservoirs within the cities Ardakan, Meibod, Abarkouh, Bafgh, and Bahabad. The spatial distribution of the concentration was carried out by the software ArcGIS. Such simulations as non-carcinogenic hazard and lifetime cancer risk were conducted for lead and nickel using Monte Carlo technique. The sensitivity analysis was carried out to find the most important and effective parameters on risk assessment. The results indicated that concentration of all metals in 39 wells (except iron in 3 cases) reached the levels mentioned in EPA, World Health Organization, and Pollution Control Department standards. Based on the spatial distribution results at all studied regions, the highest concentrations of metals were derived, respectively, for iron and zinc. Calculated HQ values for non-carcinogenic hazard indicated a reasonable risk. Average lifetime cancer risks for the lead in Ardakan and nickel in Meibod and Bahabad were shown to be 1.09 × 10 -3 , 1.67 × 10 -1 , and 2 × 10 -1 , respectively, demonstrating high carcinogenic risk compared to similar standards and studies. The sensitivity analysis suggests high impact of concentration and BW in carcinogenic risk.

Novel scanning procedure enabling the vectorization of entire rhizotron-grown root systems

PubMed Central

2013-01-01

This paper presents an original spit-and-combine imaging procedure that enables the complete vectorization of complex root systems grown in rhizotrons. The general principle of the method is to (1) separate the root system into a small number of large pieces to reduce root overlap, (2) scan these pieces one by one, (3) analyze separate images with a root tracing software and (4) combine all tracings into a single vectorized root system. This method generates a rich dataset containing morphological, topological and geometrical information of entire root systems grown in rhizotrons. The utility of the method is illustrated with a detailed architectural analysis of a 20-day old maize root system, coupled with a spatial analysis of water uptake patterns. PMID:23286457

Novel scanning procedure enabling the vectorization of entire rhizotron-grown root systems.

PubMed

Lobet, Guillaume; Draye, Xavier

2013-01-04

: This paper presents an original spit-and-combine imaging procedure that enables the complete vectorization of complex root systems grown in rhizotrons. The general principle of the method is to (1) separate the root system into a small number of large pieces to reduce root overlap, (2) scan these pieces one by one, (3) analyze separate images with a root tracing software and (4) combine all tracings into a single vectorized root system. This method generates a rich dataset containing morphological, topological and geometrical information of entire root systems grown in rhizotrons. The utility of the method is illustrated with a detailed architectural analysis of a 20-day old maize root system, coupled with a spatial analysis of water uptake patterns.

ForceAtlas2, a continuous graph layout algorithm for handy network visualization designed for the Gephi software.

PubMed

Jacomy, Mathieu; Venturini, Tommaso; Heymann, Sebastien; Bastian, Mathieu

2014-01-01

Gephi is a network visualization software used in various disciplines (social network analysis, biology, genomics...). One of its key features is the ability to display the spatialization process, aiming at transforming the network into a map, and ForceAtlas2 is its default layout algorithm. The latter is developed by the Gephi team as an all-around solution to Gephi users' typical networks (scale-free, 10 to 10,000 nodes). We present here for the first time its functioning and settings. ForceAtlas2 is a force-directed layout close to other algorithms used for network spatialization. We do not claim a theoretical advance but an attempt to integrate different techniques such as the Barnes Hut simulation, degree-dependent repulsive force, and local and global adaptive temperatures. It is designed for the Gephi user experience (it is a continuous algorithm), and we explain which constraints it implies. The algorithm benefits from much feedback and is developed in order to provide many possibilities through its settings. We lay out its complete functioning for the users who need a precise understanding of its behaviour, from the formulas to graphic illustration of the result. We propose a benchmark for our compromise between performance and quality. We also explain why we integrated its various features and discuss our design choices.

ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software

PubMed Central

Jacomy, Mathieu; Venturini, Tommaso; Heymann, Sebastien; Bastian, Mathieu

2014-01-01

Gephi is a network visualization software used in various disciplines (social network analysis, biology, genomics…). One of its key features is the ability to display the spatialization process, aiming at transforming the network into a map, and ForceAtlas2 is its default layout algorithm. The latter is developed by the Gephi team as an all-around solution to Gephi users’ typical networks (scale-free, 10 to 10,000 nodes). We present here for the first time its functioning and settings. ForceAtlas2 is a force-directed layout close to other algorithms used for network spatialization. We do not claim a theoretical advance but an attempt to integrate different techniques such as the Barnes Hut simulation, degree-dependent repulsive force, and local and global adaptive temperatures. It is designed for the Gephi user experience (it is a continuous algorithm), and we explain which constraints it implies. The algorithm benefits from much feedback and is developed in order to provide many possibilities through its settings. We lay out its complete functioning for the users who need a precise understanding of its behaviour, from the formulas to graphic illustration of the result. We propose a benchmark for our compromise between performance and quality. We also explain why we integrated its various features and discuss our design choices. PMID:24914678

LIME: 3D visualisation and interpretation of virtual geoscience models

NASA Astrophysics Data System (ADS)

Buckley, Simon; Ringdal, Kari; Dolva, Benjamin; Naumann, Nicole; Kurz, Tobias

2017-04-01

Three-dimensional and photorealistic acquisition of surface topography, using methods such as laser scanning and photogrammetry, has become widespread across the geosciences over the last decade. With recent innovations in photogrammetric processing software, robust and automated data capture hardware, and novel sensor platforms, including unmanned aerial vehicles, obtaining 3D representations of exposed topography has never been easier. In addition to 3D datasets, fusion of surface geometry with imaging sensors, such as multi/hyperspectral, thermal and ground-based InSAR, and geophysical methods, create novel and highly visual datasets that provide a fundamental spatial framework to address open geoscience research questions. Although data capture and processing routines are becoming well-established and widely reported in the scientific literature, challenges remain related to the analysis, co-visualisation and presentation of 3D photorealistic models, especially for new users (e.g. students and scientists new to geomatics methods). Interpretation and measurement is essential for quantitative analysis of 3D datasets, and qualitative methods are valuable for presentation purposes, for planning and in education. Motivated by this background, the current contribution presents LIME, a lightweight and high performance 3D software for interpreting and co-visualising 3D models and related image data in geoscience applications. The software focuses on novel data integration and visualisation of 3D topography with image sources such as hyperspectral imagery, logs and interpretation panels, geophysical datasets and georeferenced maps and images. High quality visual output can be generated for dissemination purposes, to aid researchers with communication of their research results. The background of the software is described and case studies from outcrop geology, in hyperspectral mineral mapping and geophysical-geospatial data integration are used to showcase the novel methods developed.

Airborne Single Particle Mass Spectrometers (SPLAT II & miniSPLAT) and New Software for Data Visualization and Analysis in a Geo-Spatial Context

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zelenyuk, Alla; Imre, D.; Wilson, Jacqueline M.

2015-02-01

Understanding the effect of aerosols on climate requires knowledge of the size and chemical composition of individual aerosol particles - two fundamental properties that determine an aerosol’s optical properties and ability to serve as cloud condensation or ice nuclei. Here we present miniSPLAT, our new aircraft compatible single particle mass spectrometer, that measures in-situ and in real-time size and chemical composition of individual aerosol particles with extremely high sensitivity, temporal resolution, and sizing precision on the order of a monolayer. miniSPLAT operates in dual data acquisition mode to measure, in addition to single particle size and composition, particle number concentrations,more » size distributions, density, and asphericity with high temporal resolution. When compared to our previous instrument, SPLAT II, miniSPLAT has been significantly reduced in size, weight, and power consumption without loss in performance. We also present ND-Scope, our newly developed interactive visual analytics software package. ND-Scope is designed to explore and visualize the vast amount of complex, multidimensional data acquired by our single particle mass spectrometers, along with other aerosol and cloud characterization instruments on-board aircraft. We demonstrate that ND-Scope makes it possible to visualize the relationships between different observables and to view the data in a geo-spatial context, using the interactive and fully coupled Google Earth and Parallel Coordinates displays. Here we illustrate the utility of ND-Scope to visualize the spatial distribution of atmospheric particles of different compositions, and explore the relationship between individual particle composition and their activity as cloud condensation nuclei.« less

Spatial distribution and cluster analysis of risky sexual behaviours and STDs reported by Chinese adults in Guangzhou, China: a representative population-based study

PubMed Central

Chen, Wen; Zhou, Fangjing; Hall, Brian J; Wang, Yu; Latkin, Carl; Ling, Li; Tucker, Joseph D

2016-01-01

Objectives To assess associations between residences location, risky sexual behaviours and sexually transmitted diseases (STDs) among adults living in Guangzhou, China. Methods Data were obtained from 751 Chinese adults aged 18–59 years in Guangzhou, China, using stratified random sampling by using spatial epidemiological methods. Face-to-face household interviews were conducted to collect self-report data on risky sexual behaviours and diagnosed STDs. Kulldorff’s spatial scan statistic was implemented to identify and detect spatial distribution and clusters of risky sexual behaviours and STDs. The presence and location of statistically significant clusters were mapped in the study areas using ArcGIS software. Results The prevalence of self-reported risky sexual behaviours was between 5.1% and 50.0%. The self-reported lifetime prevalence of diagnosed STDs was 7.06%. Anal intercourse clustered in an area located along the border within the rural–urban continuum (p=0.001). High rate clusters for alcohol or other drugs using before sex (p=0.008) and migrants who lived in Guangzhou <1 year (p=0.007) overlapped this cluster. Excess cases for unprotected sex (p=0.031) overlapped the cluster for college students (p<0.001). Five of nine (55.6%) students who had sexual experience during the last 12 months located in the cluster of unprotected sex. Conclusions Short-term migrants and college students reported greater risky sexual behaviours. Programmes to increase safer sex within these communities to reduce the risk of STDs are warranted in Guangzhou. Spatial analysis identified geographical clusters of risky sexual behaviours, which is critical for optimising surveillance and targeting control measures for these locations in the future. PMID:26843400

Parallel Multiscale Algorithms for Astrophysical Fluid Dynamics Simulations

NASA Technical Reports Server (NTRS)

Norman, Michael L.

1997-01-01

Our goal is to develop software libraries and applications for astrophysical fluid dynamics simulations in multidimensions that will enable us to resolve the large spatial and temporal variations that inevitably arise due to gravity, fronts and microphysical phenomena. The software must run efficiently on parallel computers and be general enough to allow the incorporation of a wide variety of physics. Cosmological structure formation with realistic gas physics is the primary application driver in this work. Accurate simulations of e.g. galaxy formation require a spatial dynamic range (i.e., ratio of system scale to smallest resolved feature) of 104 or more in three dimensions in arbitrary topologies. We take this as our technical requirement. We have achieved, and in fact, surpassed these goals.

General Mode Scanning Probe Microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Somnath, Suhas; Jesse, Stephen

A critical part of SPM measurements is the information transfer from the probe-sample junction to the measurement system. Current information transfer methods heavily compress the information-rich data stream by averaging the data over a time interval, or via heterodyne detection approaches such as lock-in amplifiers and phase-locked loops. As a consequence, highly valuable information at the sub-microsecond time scales or information from frequencies outside the measurement band is lost. We have developed a fundamentally new approach called General Mode (G-mode), where we can capture the complete information stream from the detectors in the microscope. The availability of the complete informationmore » allows the microscope operator to analyze the data via information-theory analysis or comprehensive physical models. Furthermore, the complete data stream enables advanced data-driven filtering algorithms, multi-resolution imaging, ultrafast spectroscropic imaging, spatial mapping of multidimensional variability in material properties, etc. Though we applied this approach to scanning probe microscopy, the general philosophy of G-mode can be applied to many other modes of microscopy. G-mode data is captured by completely custom software written in LabVIEW and Matlab. The software generates the waveforms to electrically, thermally, or mechanically excite the SPM probe. It handles real-time communications with the microscope software for operations such as moving the SPM probe position and also controls other instrumentation hardware. The software also controls multiple variants of high-speed data acquisition cards to excite the SPM probe with the excitation waveform and simultaneously measure multiple channels of information from the microscope detectors at sampling rates of 1-100 MHz. The software also saves the raw data to the computer and allows the microscope operator to visualize processed or filtered data during the experiment. The software performs all these features while offering a user-friendly interface.« less

Development and implementation of software systems for imaging spectroscopy

USGS Publications Warehouse

Boardman, J.W.; Clark, R.N.; Mazer, A.S.; Biehl, L.L.; Kruse, F.A.; Torson, J.; Staenz, K.

2006-01-01

Specialized software systems have played a crucial role throughout the twenty-five year course of the development of the new technology of imaging spectroscopy, or hyperspectral remote sensing. By their very nature, hyperspectral data place unique and demanding requirements on the computer software used to visualize, analyze, process and interpret them. Often described as a marriage of the two technologies of reflectance spectroscopy and airborne/spaceborne remote sensing, imaging spectroscopy, in fact, produces data sets with unique qualities, unlike previous remote sensing or spectrometer data. Because of these unique spatial and spectral properties hyperspectral data are not readily processed or exploited with legacy software systems inherited from either of the two parent fields of study. This paper provides brief reviews of seven important software systems developed specifically for imaging spectroscopy.

Computer-based classification of bacteria species by analysis of their colonies Fresnel diffraction patterns

NASA Astrophysics Data System (ADS)

Suchwalko, Agnieszka; Buzalewicz, Igor; Podbielska, Halina

2012-01-01

In the presented paper the optical system with converging spherical wave illumination for classification of bacteria species, is proposed. It allows for compression of the observation space, observation of Fresnel patterns, diffraction pattern scaling and low level of optical aberrations, which are not possessed by other optical configurations. Obtained experimental results have shown that colonies of specific bacteria species generate unique diffraction signatures. Analysis of Fresnel diffraction patterns of bacteria colonies can be fast and reliable method for classification and recognition of bacteria species. To determine the unique features of bacteria colonies diffraction patterns the image processing analysis was proposed. Classification can be performed by analyzing the spatial structure of diffraction patterns, which can be characterized by set of concentric rings. The characteristics of such rings depends on the bacteria species. In the paper, the influence of basic features and ring partitioning number on the bacteria classification, is analyzed. It is demonstrated that Fresnel patterns can be used for classification of following species: Salmonella enteritidis, Staplyococcus aureus, Proteus mirabilis and Citrobacter freundii. Image processing is performed by free ImageJ software, for which a special macro with human interaction, was written. LDA classification, CV method, ANOVA and PCA visualizations preceded by image data extraction were conducted using the free software R.

A conceptual holding model for veterinary applications.

PubMed

Ferrè, Nicola; Kuhn, Werner; Rumor, Massimo; Marangon, Stefano

2014-05-01

Spatial references are required when geographical information systems (GIS) are used for the collection, storage and management of data. In the veterinary domain, the spatial component of a holding (of animals) is usually defined by coordinates, and no other relevant information needs to be interpreted or used for manipulation of the data in the GIS environment provided. Users trying to integrate or reuse spatial data organised in such a way, frequently face the problem of data incompatibility and inconsistency. The root of the problem lies in differences with respect to syntax as well as variations in the semantic, spatial and temporal representations of the geographic features. To overcome these problems and to facilitate the inter-operability of different GIS, spatial data must be defined according to a \\"schema\\" that includes the definition, acquisition, analysis, access, presentation and transfer of such data between different users and systems. We propose an application \\"schema\\" of holdings for GIS applications in the veterinary domain according to the European directive framework (directive 2007/2/EC--INSPIRE). The conceptual model put forward has been developed at two specific levels to produce the essential and the abstract model, respectively. The former establishes the conceptual linkage of the system design to the real world, while the latter describes how the system or software works. The result is an application \\"schema\\" that formalises and unifies the information-theoretic foundations of how to spatially represent a holding in order to ensure straightforward information-sharing within the veterinary community.

Spatial-temporal modeling of malware propagation in networks.

PubMed

Chen, Zesheng; Ji, Chuanyi

2005-09-01

Network security is an important task of network management. One threat to network security is malware (malicious software) propagation. One type of malware is called topological scanning that spreads based on topology information. The focus of this work is on modeling the spread of topological malwares, which is important for understanding their potential damages, and for developing countermeasures to protect the network infrastructure. Our model is motivated by probabilistic graphs, which have been widely investigated in machine learning. We first use a graphical representation to abstract the propagation of malwares that employ different scanning methods. We then use a spatial-temporal random process to describe the statistical dependence of malware propagation in arbitrary topologies. As the spatial dependence is particularly difficult to characterize, the problem becomes how to use simple (i.e., biased) models to approximate the spatially dependent process. In particular, we propose the independent model and the Markov model as simple approximations. We conduct both theoretical analysis and extensive simulations on large networks using both real measurements and synthesized topologies to test the performance of the proposed models. Our results show that the independent model can capture temporal dependence and detailed topology information and, thus, outperforms the previous models, whereas the Markov model incorporates a certain spatial dependence and, thus, achieves a greater accuracy in characterizing both transient and equilibrium behaviors of malware propagation.

Towards real-time non contact spatial resolved oxygenation monitoring using a multi spectral filter array camera in various light conditions

NASA Astrophysics Data System (ADS)

Bauer, Jacob R.; van Beekum, Karlijn; Klaessens, John; Noordmans, Herke Jan; Boer, Christa; Hardeberg, Jon Y.; Verdaasdonk, Rudolf M.

2018-02-01

Non contact spatial resolved oxygenation measurements remain an open challenge in the biomedical field and non contact patient monitoring. Although point measurements are the clinical standard till this day, regional differences in the oxygenation will improve the quality and safety of care. Recent developments in spectral imaging resulted in spectral filter array cameras (SFA). These provide the means to acquire spatial spectral videos in real-time and allow a spatial approach to spectroscopy. In this study, the performance of a 25 channel near infrared SFA camera was studied to obtain spatial oxygenation maps of hands during an occlusion of the left upper arm in 7 healthy volunteers. For comparison a clinical oxygenation monitoring system, INVOS, was used as a reference. In case of the NIRS SFA camera, oxygenation curves were derived from 2-3 wavelength bands with a custom made fast analysis software using a basic algorithm. Dynamic oxygenation changes were determined with the NIR SFA camera and INVOS system at different regional locations of the occluded versus non-occluded hands and showed to be in good agreement. To increase the signal to noise ratio, algorithm and image acquisition were optimised. The measurement were robust to different illumination conditions with NIR light sources. This study shows that imaging of relative oxygenation changes over larger body areas is potentially possible in real time.

[Ecological suitability assessment and optimization of urban land expansion space in Guiyang City].

PubMed

Qiu, Cong-hao; Li, Yang-bing; Feng, Yuan-song

2015-09-01

Based on the case study of Guiyang City, the minimum cumulative resistance model integrating construction land source, ecological rigid constraints and ecological function type resistance factor, was built by use of cost-distance analysis of urban spatial expansion resistance value through ArcGIS 9.3 software in this paper. Then, the ecological resistance of city spatial expansion of Guiyang from 2010 was simulated dynamically and the ecological suitability classification of city spatial expansion was assessed. According to the conflict between the newly increased city construction land in 2014 and its ecological suitability, the unreasonable city land spatial allocation was discussed also. The results showed that the ecological suitability zonation and the city expansion in the study area were basically consistent during 2010-2014, but the conflict between the new city construction and its land ecological suitability was more serious. The ecological conflict area accounted for 58.2% of the new city construction sites, 35.4% of which happened in the ecological control area, 13.9% in the limited development area and 8.9% in the prohibition development area. The intensification of ecological land use conflict would impair the ecological service function and ecological safety, so this paper put forward the city spatial expansion optimal path to preserve the ecological land and improve the construction land space pattern of Guiyang City so as to ensure its ecological safety.

[Kriging analysis of vegetation index depression in peak cluster karst area].

PubMed

Yang, Qi-Yong; Jiang, Zhong-Cheng; Ma, Zu-Lu; Cao, Jian-Hua; Luo, Wei-Qun; Li, Wen-Jun; Duan, Xiao-Fang

2012-04-01

In order to master the spatial variability of the normal different vegetation index (NDVI) of the peak cluster karst area, taking into account the problem of the mountain shadow "missing" information of remote sensing images existing in the karst area, NDVI of the non-shaded area were extracted in Guohua Ecological Experimental Area, in Pingguo County, Guangxi applying image processing software, ENVI. The spatial variability of NDVI was analyzed applying geostatistical method, and the NDVI of the mountain shadow areas was predicted and validated. The results indicated that the NDVI of the study area showed strong spatial variability and spatial autocorrelation resulting from the impact of intrinsic factors, and the range was 300 m. The spatial distribution maps of the NDVI interpolated by Kriging interpolation method showed that the mean of NDVI was 0.196, apparently strip and block. The higher NDVI values distributed in the area where the slope was greater than 25 degrees of the peak cluster area, while the lower values distributed in the area such as foot of the peak cluster and depression, where slope was less than 25 degrees. Kriging method validation results show that interpolation has a very high prediction accuracy and could predict the NDVI of the shadow area, which provides a new idea and method for monitoring and evaluation of the karst rocky desertification.

Construction and comparative evaluation of different activity detection methods in brain FDG-PET.

PubMed

Buchholz, Hans-Georg; Wenzel, Fabian; Gartenschläger, Martin; Thiele, Frank; Young, Stewart; Reuss, Stefan; Schreckenberger, Mathias

2015-08-18

We constructed and evaluated reference brain FDG-PET databases for usage by three software programs (Computer-aided diagnosis for dementia (CAD4D), Statistical Parametric Mapping (SPM) and NEUROSTAT), which allow a user-independent detection of dementia-related hypometabolism in patients' brain FDG-PET. Thirty-seven healthy volunteers were scanned in order to construct brain FDG reference databases, which reflect the normal, age-dependent glucose consumption in human brain, using either software. Databases were compared to each other to assess the impact of different stereotactic normalization algorithms used by either software package. In addition, performance of the new reference databases in the detection of altered glucose consumption in the brains of patients was evaluated by calculating statistical maps of regional hypometabolism in FDG-PET of 20 patients with confirmed Alzheimer's dementia (AD) and of 10 non-AD patients. Extent (hypometabolic volume referred to as cluster size) and magnitude (peak z-score) of detected hypometabolism was statistically analyzed. Differences between the reference databases built by CAD4D, SPM or NEUROSTAT were observed. Due to the different normalization methods, altered spatial FDG patterns were found. When analyzing patient data with the reference databases created using CAD4D, SPM or NEUROSTAT, similar characteristic clusters of hypometabolism in the same brain regions were found in the AD group with either software. However, larger z-scores were observed with CAD4D and NEUROSTAT than those reported by SPM. Better concordance with CAD4D and NEUROSTAT was achieved using the spatially normalized images of SPM and an independent z-score calculation. The three software packages identified the peak z-scores in the same brain region in 11 of 20 AD cases, and there was concordance between CAD4D and SPM in 16 AD subjects. The clinical evaluation of brain FDG-PET of 20 AD patients with either CAD4D-, SPM- or NEUROSTAT-generated databases from an identical reference dataset showed similar patterns of hypometabolism in the brain regions known to be involved in AD. The extent of hypometabolism and peak z-score appeared to be influenced by the calculation method used in each software package rather than by different spatial normalization parameters.

'spup' - an R package for uncertainty propagation analysis in spatial environmental modelling

NASA Astrophysics Data System (ADS)

Sawicka, Kasia; Heuvelink, Gerard

2017-04-01

Computer models have become a crucial tool in engineering and environmental sciences for simulating the behaviour of complex static and dynamic systems. However, while many models are deterministic, the uncertainty in their predictions needs to be estimated before they are used for decision support. Currently, advances in uncertainty propagation and assessment have been paralleled by a growing number of software tools for uncertainty analysis, but none has gained recognition for a universal applicability and being able to deal with case studies with spatial models and spatial model inputs. Due to the growing popularity and applicability of the open source R programming language we undertook a project to develop an R package that facilitates uncertainty propagation analysis in spatial environmental modelling. In particular, the 'spup' package provides functions for examining the uncertainty propagation starting from input data and model parameters, via the environmental model onto model predictions. The functions include uncertainty model specification, stochastic simulation and propagation of uncertainty using Monte Carlo (MC) techniques, as well as several uncertainty visualization functions. Uncertain environmental variables are represented in the package as objects whose attribute values may be uncertain and described by probability distributions. Both numerical and categorical data types are handled. Spatial auto-correlation within an attribute and cross-correlation between attributes is also accommodated for. For uncertainty propagation the package has implemented the MC approach with efficient sampling algorithms, i.e. stratified random sampling and Latin hypercube sampling. The design includes facilitation of parallel computing to speed up MC computation. The MC realizations may be used as an input to the environmental models called from R, or externally. Selected visualization methods that are understandable by non-experts with limited background in statistics can be used to summarize and visualize uncertainty about the measured input, model parameters and output of the uncertainty propagation. We demonstrate that the 'spup' package is an effective and easy tool to apply and can be used in multi-disciplinary research and model-based decision support.

The Development of GIS Educational Resources Sharing among Central Taiwan Universities

NASA Astrophysics Data System (ADS)

Chou, T.-Y.; Yeh, M.-L.; Lai, Y.-C.

2011-09-01

Using GIS in the classroom enhance students' computer skills and explore the range of knowledge. The paper highlights GIS integration on e-learning platform and introduces a variety of abundant educational resources. This research project will demonstrate tools for e-learning environment and delivers some case studies for learning interaction from Central Taiwan Universities. Feng Chia University (FCU) obtained a remarkable academic project subsidized by Ministry of Education and developed e-learning platform for excellence in teaching/learning programs among Central Taiwan's universities. The aim of the project is to integrate the educational resources of 13 universities in central Taiwan. FCU is serving as the hub of Center University. To overcome the problem of distance, e-platforms have been established to create experiences with collaboration enhanced learning. The e-platforms provide coordination of web service access among the educational community and deliver GIS educational resources. Most of GIS related courses cover the development of GIS, principles of cartography, spatial data analysis and overlaying, terrain analysis, buffer analysis, 3D GIS application, Remote Sensing, GPS technology, and WebGIS, MobileGIS, ArcGIS manipulation. In each GIS case study, students have been taught to know geographic meaning, collect spatial data and then use ArcGIS software to analyze spatial data. On one of e-Learning platforms provide lesson plans and presentation slides. Students can learn Arc GIS online. As they analyze spatial data, they can connect to GIS hub to get data they need including satellite images, aerial photos, and vector data. Moreover, e-learning platforms provide solutions and resources. Different levels of image scales have been integrated into the systems. Multi-scale spatial development and analyses in Central Taiwan integrate academic research resources among CTTLRC partners. Thus, establish decision-making support mechanism in teaching and learning. Accelerate communication, cooperation and sharing among academic units

WE-D-204-06: An Open Source ImageJ CatPhan Analysis Tool

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nelson, G

2015-06-15

Purpose: The CatPhan is a popular QA device for assessing CT image quality. There are a number of software options which perform analysis of the CatPhan. However, there is often little ability for the user to adjust the analysis if it isn’t running properly, and these are all expensive options. An open source tool is an effective solution. Methods: To use the software, the user imports the CT as an image sequence in ImageJ. The user then scrolls to the slice with the lateral dots. The user then runs the plugin. If tolerance constraints are not already created, the usermore » is prompted to enter them or to use generic tolerances. Upon completion of the analysis, the plugin calls pdfLaTex to compile the pdf report. There is a csv version of the report as well. A log of the results from all CatPhan scans is kept as a csv file. The user can use this to baseline the machine. Results: The tool is capable of detecting the orientation of the phantom. If the CatPhan was scanned backwards, one can simply flip the stack of images horizontally and proceed with the analysis. The analysis includes Sensitometry (estimating the effective beam energy), HU values and linearity, Low Contrast Visibility (using LDPE & Polystyrene), Contrast Scale, Geometric Accuracy, Slice Thickness Accuracy, Spatial resolution (giving the MTF using the line pairs as well as the point spread function), CNR, Low Contrast Detectability (including the raw data), Uniformity (including the Cupping Effect). Conclusion: This is a robust tool that analyzes more components of the CatPhan than other software options (with the exception of ImageOwl). It produces an elegant pdf and keeps a log of analyses for long-term tracking of the system. Because it is open source, users are able to customize any component of it.« less

[Spatial pattern of forest biomass and its influencing factors in the Great Xing'an Mountains, Heilongjiang Province, China].

PubMed

Wang, Xiao-Li; Chang, Yu; Chen, Hong-Wei; Hu, Yuan-Man; Jiao, Lin-Lin; Feng, Yu-Ting; Wu, Wen; Wu, Hai-Feng

2014-04-01

Based on field inventory data and vegetation index EVI (enhanced vegetation index), the spatial pattern of the forest biomass in the Great Xing'an Mountains, Heilongjiang Province was quantitatively analyzed. Using the spatial analysis and statistics tools in ArcGIS software, the impacts of climatic zone, elevation, slope, aspect and vegetation type on the spatial pattern of forest biomass were explored. The results showed that the forest biomass in the Great Xing'an Mountains was 350 Tg and spatially aggregated with great increasing potentials. Forest biomass density in the cold temperate humid zone (64.02 t x hm(-2)) was higher than that in the temperate humid zone (60.26 t x hm(-2)). The biomass density of each vegetation type was in the order of mixed coniferous forest (65.13 t x hm(-2)) > spruce-fir forest (63.92 t x hm(-2)) > Pinus pumila-Larix gmelinii forest (63.79 t x hm(-2)) > Pinus sylvestris var. mongolica forest (61.97 t x hm(-2)) > Larix gmelinii forest (61.40 t x hm(-2)) > deciduous broadleaf forest (58.96 t x hm(-2)). With the increasing elevation and slope, the forest biomass density first decreased and then increased. The forest biomass density in the shady slopes was greater than that in the sunny slopes. The spatial pattern of forest biomass in the Great Xing' an Mountains exhibited a heterogeneous pattern due to the variation of climatic zone, vegetation type and topographical factor. This spatial heterogeneity needs to be accounted when evaluating forest biomass at regional scales.

Geomatics for Maritime Parks and Preserved Areas

NASA Astrophysics Data System (ADS)

Lo Tauro, Agata

2009-11-01

The aim of this research is to use hyperspectral MIVIS data for protection of sensitive cultural, natural resources, Nature Reserves and maritime parks. A knowledge of the distribution of submerged vegetation is useful to monitor the health of ecosystems in coastal areas. The objective of this project was to develop a new methodology within geomatic environment to facilitate the analysis and application of Local Institutions who are not familiar with Spatial Analysis softwares in order to implement new research activities in this field of study. Field controls may be carried out with the support of accurate and novel in situ analysis in order to determine the training sites for the novel tested classification. The methodology applied demonstrates that the combination of hyperspectral sensors and ESA Remote Sensing (RS) data can be used to analyse thematic cartography of submerged vegetation and land use analysis for Sustainable Development. This project will be implemented for Innovative Educational and Research Programmes.

Selecting landing sites for lunar lander missions using spatial analysis

NASA Astrophysics Data System (ADS)

Djachkova, Maia; Lazarev, Evgeniy

Russian Federal Space Agency (Roscosmos) is planning to launch two spacecrafts to the Moon with lander missions in 2015 and 2017. [1] Here, we present an approach to create a method of landing sites selection. We researched the physical features of the Moon using spatial analysis techniques presented in ArcGIS Desktop Software in accordance with its suitability for automatic landing. Hence we analyzed Russian lunar program and received the technical characteristics of the spacecrafts and scientific goals that they should meet [1]. Thus we identified the criteria of surface suitability for landing. We divided them into two groups: scientific criteria (the hydrogen content of the regolith [2] and day and night sur-face temperature [3]) and safety criteria (surface slopes and roughness, sky view factor, the Earth altitude, presence of polar permanently shadowed regions). In conformity with some investigations it is believed that the south polar region of the Moon is the most promising territory where water ice can be found (finding water ice is the main goal for Russian lunar missions [1]). According to the selected criteria and selected area of research we used remote sensing data from LRO (Lunar Reconnaissance Orbiter) [4] as basic data, because it is the most actual and easily available. The data was processed and analyzed using spatial analysis techniques of ArcGIS Desktop Software, so we created a number of maps depicting the criteria and then combined and overlaid them. As a result of overlay process we received five territories where the landing will be safe and the scientific goals will have being met. It should be noted that our analysis is only the first order assessment and the results cannot be used as actual landing sites for the lunar missions in 2015 and 2017, since a number of factors, which can only be analyzed in a very large scale, was not taken into account. However, an area of researching is narrowed to five territories, what can make the future research much easier. The analysis of these five areas in a large scale will be the subject of further research. References: [1] Mitrofanov I. G. et al. (2011) LPS XLII, Abstract #1798 [2] Mitrofanov I. G., et al. Hydrogen Mapping of the Lunar South Pole Using the LRO Neutron Detector Experiment LEND // Science vol. 330 2010, pp. 483-486 [3] Paige D.A. et al. (2011) LPS XLII, Abstract #2544 [4] Zuber M.T. et al. (2010) Space Sci. Rev., 150, 63-80

Investigating social cognition in infants and adults using dense array electroencephalography ((d)EEG).

PubMed

Akano, Adekemi J; Haley, David W; Dudek, Joanna

2011-06-27

Dense array electroencephalography ((d)EEG), which provides a non-invasive window for measuring brain activity and a temporal resolution unsurpassed by any other current brain imaging technology¹, ² is being used increasingly in the study of social cognitive functioning in infants and adults. While (d)EEG is enabling researchers to examine brain activity patterns with unprecedented levels of sensitivity, conventional EEG recording systems continue to face certain limitations, including 1) poor spatial resolution and source localization³,⁴2) the physical discomfort for test subjects of enduring the individual application of numerous electrodes to the surface of the scalp, and 3) the complexity for researchers of learning to use multiple software packages to collect and process data. Here we present an overview of an established methodology that represents a significant improvement on conventional methodologies for studying EEG in infants and adults. Although several analytical software techniques can be used to establish indirect indices of source localization to improve the spatial resolution of (d)EEG, the HydroCel Geodesic Sensor Net (HCGSN) by Electrical Geodesics, Inc. (EGI), a dense sensory array that maintains equal distances among adjacent recording electrodes on all surfaces of the scalp, further enhances spatial resolution⁴,⁵(,)⁶ compared to standard (d)EEG systems. The sponge-based HCGSN can be applied rapidly and without scalp abrasion, making it ideal for use with adults⁷,⁸ children⁹,¹⁰, ¹¹,¹² and infants¹², in both research and clinical ⁴,⁵,⁶,¹³,¹⁴,¹⁵settings. This feature allows for considerable cost and time savings by decreasing the average net application time compared to other (d)EEG systems. Moreover, the HCGSN includes unified, seamless software applications for all phases of data, greatly simplifying the collection, processing, and analysis of (d)EEG data. The HCGSN features a low-profile electrode pedestal, which, when filled with electrolyte solution, creates a sealed microenvironment and an electrode-scalp interface. In all Geodesic (d;)EEG systems, EEG sensors detect changes in voltage originating from the participant's scalp, along with a small amount of electrical noise originating from the room environment. Electrical signals from all sensors of the Geodesic sensor net are received simultaneously by the amplifier, where they are automatically processed, packaged, and sent to the data-acquisition computer (DAC). Once received by the DAC, scalp electrical activity can be isolated from artifacts for analysis using the filtering and artifact detection tools included in the EGI software. Typically, the HCGSN can be used continuously for only up to two hours because the electrolyte solution dries out over time, gradually decreasing the quality of the scalp-electrode interface. In the Parent-Infant Research Lab at the University of Toronto, we are using (d)EEG to study social cognitive processes including memory, emotion, goals, intentionality, anticipation, and executive functioning in both adult and infant participants.

Designing a Software for Flood Risk Assessment Based on Multi Criteria Desicion Analysis and Information Diffusion Methods

NASA Astrophysics Data System (ADS)

Musaoglu, N.; Saral, A.; Seker, D. Z.

2012-12-01

Flooding is one of the major natural disasters not only in Turkey but also in all over the world and it causes serious damage and harm. It is estimated that of the total economic loss caused by all kinds of disasters, 40% was due to floods. In July 1995, the Ayamama Creek in Istanbul was flooded, the insurance sector received around 1,200 claims notices during that period, insurance companies had to pay a total of $40 million for claims. In 2009, the same creek was flooded again and killed 31 people over two days and insurance firms paid for damages around cost €150 million for claims. To solve these kinds of problems modern tools such as GIS and Remote Sensing should be utilized. In this study, a software was designed for the flood risk analysis with Analytic Hierarchy Process (AHP) and Information Diffusion( InfoDif) methods.In the developed sofware, five evaluation criterias were taken into account, which were slope, aspect, elevation, geology and land use which were extracted from the satellite sensor data. The Digital Elevation Model (DEM) of the Ayamama River Basin was acquired from the SPOT 5 satellite image with 2.5 meter spatial resolution. Slope and aspect values of the study basin were extracted from this DEM. The land use of the Ayamama Creek was obtained by performing object-oriented nearest neighbor classification method by image segmentation on SPOT 5 image dated 2010. All produced data were used as an input for the part of Multi Criteria Desicion Analysis (MCDA) method of this software. Criterias and their each sub criteras were weighted and flood vulnerability was determined with MCDA-AHP. Also, daily flood data was collected from Florya Meteorological Station, between 1975 to 2009 years and the daily flood peak discharge was calculated with the method of Soil Conservation Service-Curve Number (SCS-CN) and were used as an input in the software for the part of InfoDif.Obtained results were verified using ground truth data and it has been clearly seen that the developed (TRA) software which uses two different methods for flood risk analysis, can be more effective for achieving different decision problems, from conventional techniques and produce more reliable results in a short time.; Study Area

Assessing Visual-Spatial Creativity in Youth on the Autism Spectrum

ERIC Educational Resources Information Center

Diener, Marissa L.; Wright, Cheryl A.; Smith, Katherine N.; Wright, Scott D.

2014-01-01

The goal of this study was to develop a measure of creativity that builds on the strengths of youth with autism spectrum disorders (ASD). The assessment of creativity focused on the visual-spatial abilities of these youth using 3D modeling software. One of the objectives of the research was to develop a measure of creativity in an authentic…

Regression methods for spatially correlated data: an example using beetle attacks in a seed orchard

Treesearch

Preisler Haiganoush; Nancy G. Rappaport; David L. Wood

1997-01-01

We present a statistical procedure for studying the simultaneous effects of observed covariates and unmeasured spatial variables on responses of interest. The procedure uses regression type analyses that can be used with existing statistical software packages. An example using the rate of twig beetle attacks on Douglas-fir trees in a seed orchard illustrates the...

Teaching the blind to find their way by playing video games.

PubMed

Merabet, Lotfi B; Connors, Erin C; Halko, Mark A; Sánchez, Jaime

2012-01-01

Computer based video games are receiving great interest as a means to learn and acquire new skills. As a novel approach to teaching navigation skills in the blind, we have developed Audio-based Environment Simulator (AbES); a virtual reality environment set within the context of a video game metaphor. Despite the fact that participants were naïve to the overall purpose of the software, we found that early blind users were able to acquire relevant information regarding the spatial layout of a previously unfamiliar building using audio based cues alone. This was confirmed by a series of behavioral performance tests designed to assess the transfer of acquired spatial information to a large-scale, real-world indoor navigation task. Furthermore, learning the spatial layout through a goal directed gaming strategy allowed for the mental manipulation of spatial information as evidenced by enhanced navigation performance when compared to an explicit route learning strategy. We conclude that the immersive and highly interactive nature of the software greatly engages the blind user to actively explore the virtual environment. This in turn generates an accurate sense of a large-scale three-dimensional space and facilitates the learning and transfer of navigation skills to the physical world.

MicroCT analysis of a retrieved root restored with a bonded fiber-reinforced composite dowel: a pilot study.

PubMed

Lorenzoni, Fabio Cesar; Bonfante, Estevam A; Bonfante, Gerson; Martins, Leandro M; Witek, Lukasz; Silva, Nelson R F A

2013-08-01

This evaluation aimed to (1) validate micro-computed tomography (microCT) findings using scanning electron microscopy (SEM) imaging, and (2) quantify the volume of voids and the bonded surface area resulting from fiber-reinforced composite (FRC) dowel cementation technique using microCT scanning technology/3D reconstructing software. A fiberglass dowel was cemented in a condemned maxillary lateral incisor prior to its extraction. A microCT scan was performed of the extracted tooth creating a large volume of data in DICOM format. This set of images was imported to image-processing software to inspect the internal architecture of structures. The outer surface and the spatial relationship of dentin, FRC dowel, cement layer, and voids were reconstructed. Three-dimensional spatial architecture of structures and volumetric analysis revealed that 9.89% of the resin cement was composed of voids and that the bonded area between root dentin and cement was 60.63% larger than that between cement and FRC dowel. SEM imaging demonstrated the presence of voids similarly observed using microCT technology (aim 1). MicroCT technology was able to nondestructively measure the volume of voids within the cement layer and the bonded surface area at the root/cement/FRC interfaces (aim 2). The interfaces at the root dentin/cement/dowel represent a timely and relevant topic where several efforts have been conducted in the past few years to understand their inherent features. MicroCT technology combined with 3D reconstruction allows for not only inspecting the internal arrangement rendered by fiberglass adhesively bonded to root dentin, but also estimating the volume of voids and contacted bond area between the dentin and cement layer. © 2013 by the American College of Prosthodontists.

Preparing the Next Generation of Environmental Scientists to Work at the Frontier of Data-Intensive Research

NASA Astrophysics Data System (ADS)

Hampton, S. E.

2015-12-01

The science necessary to unravel complex environmental problems confronts severe computational challenges - coping with huge volumes of heterogeneous data, spanning vast spatial scales at high resolution, and requiring integration of disparate measurements from multiple disciplines. But as cyberinfrastructure advances to support such work, scientists in many fields lack sufficient computational skills to participate in interdisciplinary, data-intensive research. In response, we developed innovative training workshops for early-career scientists, in order to explore both the needs and solutions for training next-generation scientists in skills for data-intensive environmental research. In 2013 and 2014 we ran intensive 3-week training workshops for early-career researchers. One of the workshops was run concurrently in California and North Carolina, connected by virtual technologies and coordinated schedules. We attracted applicants to the workshop with the opportunity to pursue data-intensive small-group research projects that they proposed. This approach presented a realistic possibility that publishable products could result from 3 weeks of focused hands-on classroom instruction combined with self-directed group research in which instructors were present to assist trainees. Instruction addressed 1) collaboration modes and technologies, 2) data management, preservation, and sharing, 3) preparing data for analysis using scripting, 4) reproducible research, 5) sustainable software practices, 6) data analysis and modeling, and 7) communicating results to broad communities. The most dramatic improvements in technical skills were in data management, version control, and working with spatial data outside of proprietary software. In addition, participants built strong networks and collaborative skills that later resulted in a successful student-led grant proposal, published manuscripts, and participants reported that the training was a highly influential experience.

Analysis of land suitability for urban development in Ahwaz County in southwestern Iran using fuzzy logic and analytic network process (ANP).

PubMed

Malmir, Maryam; Zarkesh, Mir Masoud Kheirkhah; Monavari, Seyed Masoud; Jozi, Seyed Ali; Sharifi, Esmail

2016-08-01

The ever-increasing development of cities due to population growth and migration has led to unplanned constructions and great changes in urban spatial structure, especially the physical development of cities in unsuitable places, which requires conscious guidance and fundamental organization. It is therefore necessary to identify suitable sites for future development of cities and prevent urban sprawl as one of the main concerns of urban managers and planners. In this study, to determine the suitable sites for urban development in the county of Ahwaz, the effective biophysical and socioeconomic criteria (including 27 sub-criteria) were initially determined based on literature review and interviews with certified experts. In the next step, a database of criteria and sub-criteria was prepared. Standardization of values and unification of scales in map layers were done using fuzzy logic. The criteria and sub-criteria were weighted by analytic network process (ANP) in the Super Decision software. Next, the map layers were overlaid using weighted linear combination (WLC) in the GIS software. According to the research findings, the final land suitability map was prepared with five suitability classes of very high (5.86 %), high (31.93 %), medium (38.61 %), low (17.65 %), and very low (5.95 %). Also, in terms of spatial distribution, suitable lands for urban development are mainly located in the central and southern parts of the Ahwaz County. It is expected that integration of fuzzy logic and ANP model will provide a better decision support tool compared with other models. The developed model can also be used in the land suitability analysis of other cities.

Geographic information systems (GIS): an emerging method to assess demand and provision for rehabilitation services.

PubMed

Passalent, Laura; Borsy, Emily; Landry, Michel D; Cott, Cheryl

2013-09-01

To illustrate the application of geographic information systems (GIS) as a tool to assess rehabilitation service delivery by presenting results from research recently conducted to assess demand and provision for community rehabilitation service delivery in Ontario, Canada. Secondary analysis of data obtained from existing sources was used to establish demand and provision profiles for community rehabilitation services. These data were integrated using GIS software. A number of descriptive maps were produced that show the geographical distribution of service provision variables (location of individual rehabilitation health care providers and location of private and publicly funded community rehabilitation clinics) in relation to the distribution of demand variables (location of the general population; location of specific populations (i.e., residents age 65 and older) and distribution of household income). GIS provides a set of tools for describing and understanding the spatial organization of the health of populations and the distribution of health services that can aid the development of health policy and answer key research questions with respect to rehabilitation health services delivery. Implications for Rehabilitation It is important to seek out alternative and innovative methods to examine rehabilitation service delivery. GIS is a computer-based program that takes any data linked to a geographically referenced location and processes it through a software system that manages, analyses and displays the data in the form of a map, allowing for an alternative level of analysis. GIS provides a set of tools for describing and understanding the spatial organization of population health and health services that can aid the development of health policy and answer key research questions with respect to rehabilitation health services delivery.

A portable platform to collect and review behavioral data simultaneously with neurophysiological signals.

PubMed

Tianxiao Jiang; Siddiqui, Hasan; Ray, Shruti; Asman, Priscella; Ozturk, Musa; Ince, Nuri F

2017-07-01

This paper presents a portable platform to collect and review behavioral data simultaneously with neurophysiological signals. The whole system is comprised of four parts: a sensor data acquisition interface, a socket server for real-time data streaming, a Simulink system for real-time processing and an offline data review and analysis toolbox. A low-cost microcontroller is used to acquire data from external sensors such as accelerometer and hand dynamometer. The micro-controller transfers the data either directly through USB or wirelessly through a bluetooth module to a data server written in C++ for MS Windows OS. The data server also interfaces with the digital glove and captures HD video from webcam. The acquired sensor data are streamed under User Datagram Protocol (UDP) to other applications such as Simulink/Matlab for real-time analysis and recording. Neurophysiological signals such as electroencephalography (EEG), electrocorticography (ECoG) and local field potential (LFP) recordings can be collected simultaneously in Simulink and fused with behavioral data. In addition, we developed a customized Matlab Graphical User Interface (GUI) software to review, annotate and analyze the data offline. The software provides a fast, user-friendly data visualization environment with synchronized video playback feature. The software is also capable of reviewing long-term neural recordings. Other featured functions such as fast preprocessing with multithreaded filters, annotation, montage selection, power-spectral density (PSD) estimate, time-frequency map and spatial spectral map are also implemented.

Orbiter subsystem hardware/software interaction analysis. Volume 8: AFT reaction control system, part 2

NASA Technical Reports Server (NTRS)

Becker, D. D.

1980-01-01

The orbiter subsystems and interfacing program elements which interact with the orbiter computer flight software are analyzed. The failure modes identified in the subsystem/element failure mode and effects analysis are examined. Potential interaction with the software is examined through an evaluation of the software requirements. The analysis is restricted to flight software requirements and excludes utility/checkout software. The results of the hardware/software interaction analysis for the forward reaction control system are presented.

The EpiCanvas infectious disease weather map: an interactive visual exploration of temporal and spatial correlations

PubMed Central

Livnat, Yarden; Galli, Nathan; Samore, Matthew H; Gundlapalli, Adi V

2012-01-01

Advances in surveillance science have supported public health agencies in tracking and responding to disease outbreaks. Increasingly, epidemiologists have been tasked with interpreting multiple streams of heterogeneous data arising from varied surveillance systems. As a result public health personnel have experienced an overload of plots and charts as information visualization techniques have not kept pace with the rapid expansion in data availability. This study sought to advance the science of public health surveillance data visualization by conceptualizing a visual paradigm that provides an ‘epidemiological canvas’ for detection, monitoring, exploration and discovery of regional infectious disease activity and developing a software prototype of an ‘infectious disease weather map'. Design objectives were elucidated and the conceptual model was developed using cognitive task analysis with public health epidemiologists. The software prototype was pilot tested using retrospective data from a large, regional pediatric hospital, and gastrointestinal and respiratory disease outbreaks were re-created as a proof of concept. PMID:22358039

The Adoption of the Arcgis System to Support the Analyses of the Influence of the Mining Tremors on the Building Objects

NASA Astrophysics Data System (ADS)

Sokoła-Szewioła, Violetta; Żogała, Monika

2016-12-01

Nowadays the mining companies use the Spatial Information System in order to facilitate data management, gathered during the mining activity. For these purposes various kinds of applications and software information are used. They allow for faster and easier data processing. In the paper there are presented the possibilities of using the ArcGIS system to support the tasks performed in the mining industry in the scope of the analysis of the influence of the mining tremors, induced by the longwall exploitation on the facilities construction sited on the surface area. These possibilities are presented by the example of the database developed for the coal mine KWK "Rydułtowy-Anna." The developed database was created using ArcGIS software for Desktop 10. 1. It contains the values of parameters, specified for its implementation relevant to the analyses of the influence of the mining tremors on the surface structures.

Assessing morphology and function of the semicircular duct system: introducing new in-situ visualization and software toolbox

PubMed Central

David, R.; Stoessel, A.; Berthoz, A.; Spoor, F.; Bennequin, D.

2016-01-01

The semicircular duct system is part of the sensory organ of balance and essential for navigation and spatial awareness in vertebrates. Its function in detecting head rotations has been modelled with increasing sophistication, but the biomechanics of actual semicircular duct systems has rarely been analyzed, foremost because the fragile membranous structures in the inner ear are hard to visualize undistorted and in full. Here we present a new, easy-to-apply and non-invasive method for three-dimensional in-situ visualization and quantification of the semicircular duct system, using X-ray micro tomography and tissue staining with phosphotungstic acid. Moreover, we introduce Ariadne, a software toolbox which provides comprehensive and improved morphological and functional analysis of any visualized duct system. We demonstrate the potential of these methods by presenting results for the duct system of humans, the squirrel monkey and the rhesus macaque, making comparisons with past results from neurophysiological, oculometric and biomechanical studies. Ariadne is freely available at http://www.earbank.org. PMID:27604473

Spatial distribution of low birthweight infants in Taubaté, São Paulo, Brazil

PubMed Central

Nascimento, Luiz Fernando C.; Costa, Thais Moreira; Zöllner, Maria Stella A. da C.

2013-01-01

OBJECTIVE: To identify the spatial pattern of low birth weight infants in the city of Taubaté, São Paulo, Southeast Brazil. METHODS: Ecological and exploratory study, developed with the data acquired from the Health Department of Taubaté, regarding the period from January 1st 2006 and December 31st 2010. Birth certificates were used to obtain the data from infants weighing less than 2500g. A digital basis of census tracts was applied and the Global Moran index (IM) was estimated. Thematic maps were built for the distribution of low birth weight, health centers and tracts, according to the priority care (Moran map). The adopted statistical significance was α=5% and TerraView software conducted the spatial analysis. RESULTS: There were 18,915 live births during the study period, with 1,817 low birth weight infants (9.6%). The low birth weight infants' prevalence during the period ranged from 9.3 to 9.8%. A total of 1,185 infants with known addresses, compatible with the digital base (65.2% of low birth weight infants), were included. The IM for low birth weight was 0.12, with p<0.01; regarding the health centers distribution, IM was -0.07, with p=0.01. The Moran map identified 11 census tracts with high priority for intervention by health managers, located in the outskirts of the city. CONCLUSIONS: The spatial analysis identified the low birth weight distribution by census tracts and the sectors with a high priority for intervention. PMID:24473951

Spatial variation of pneumonia hospitalization risk in Twin Cities metro area, Minnesota.

PubMed

Iroh Tam, P Y; Krzyzanowski, B; Oakes, J M; Kne, L; Manson, S

2017-11-01

Fine resolution spatial variability in pneumonia hospitalization may identify correlates with socioeconomic, demographic and environmental factors. We performed a retrospective study within the Fairview Health System network of Minnesota. Patients 2 months of age and older hospitalized with pneumonia between 2011 and 2015 were geocoded to their census block group, and pneumonia hospitalization risk was analyzed in relation to socioeconomic, demographic and environmental factors. Spatial analyses were performed using Esri's ArcGIS software, and multivariate Poisson regression was used. Hospital encounters of 17 840 patients were included in the analysis. Multivariate Poisson regression identified several significant associations, including a 40% increased risk of pneumonia hospitalization among census block groups with large, compared with small, populations of ⩾65 years, a 56% increased risk among census block groups in the bottom (first) quartile of median household income compared to the top (fourth) quartile, a 44% higher risk in the fourth quartile of average nitrogen dioxide emissions compared with the first quartile, and a 47% higher risk in the fourth quartile of average annual solar insolation compared to the first quartile. After adjusting for income, moving from the first to the second quartile of the race/ethnic diversity index resulted in a 21% significantly increased risk of pneumonia hospitalization. In conclusion, the risk of pneumonia hospitalization at the census-block level is associated with age, income, race/ethnic diversity index, air quality, and solar insolation, and varies by region-specific factors. Identifying correlates using fine spatial analysis provides opportunities for targeted prevention and control.

Four applications of a software data collection and analysis methodology

NASA Technical Reports Server (NTRS)

Basili, Victor R.; Selby, Richard W., Jr.

1985-01-01

The evaluation of software technologies suffers because of the lack of quantitative assessment of their effect on software development and modification. A seven-step data collection and analysis methodology couples software technology evaluation with software measurement. Four in-depth applications of the methodology are presented. The four studies represent each of the general categories of analyses on the software product and development process: blocked subject-project studies, replicated project studies, multi-project variation studies, and single project strategies. The four applications are in the areas of, respectively, software testing, cleanroom software development, characteristic software metric sets, and software error analysis.

Ibmdbpy-spatial : An Open-source implementation of in-database geospatial analytics in Python

NASA Astrophysics Data System (ADS)

Roy, Avipsa; Fouché, Edouard; Rodriguez Morales, Rafael; Moehler, Gregor

2017-04-01

As the amount of spatial data acquired from several geodetic sources has grown over the years and as data infrastructure has become more powerful, the need for adoption of in-database analytic technology within geosciences has grown rapidly. In-database analytics on spatial data stored in a traditional enterprise data warehouse enables much faster retrieval and analysis for making better predictions about risks and opportunities, identifying trends and spot anomalies. Although there are a number of open-source spatial analysis libraries like geopandas and shapely available today, most of them have been restricted to manipulation and analysis of geometric objects with a dependency on GEOS and similar libraries. We present an open-source software package, written in Python, to fill the gap between spatial analysis and in-database analytics. Ibmdbpy-spatial provides a geospatial extension to the ibmdbpy package, implemented in 2015. It provides an interface for spatial data manipulation and access to in-database algorithms in IBM dashDB, a data warehouse platform with a spatial extender that runs as a service on IBM's cloud platform called Bluemix. Working in-database reduces the network overload, as the complete data need not be replicated into the user's local system altogether and only a subset of the entire dataset can be fetched into memory in a single instance. Ibmdbpy-spatial accelerates Python analytics by seamlessly pushing operations written in Python into the underlying database for execution using the dashDB spatial extender, thereby benefiting from in-database performance-enhancing features, such as columnar storage and parallel processing. The package is currently supported on Python versions from 2.7 up to 3.4. The basic architecture of the package consists of three main components - 1) a connection to the dashDB represented by the instance IdaDataBase, which uses a middleware API namely - pypyodbc or jaydebeapi to establish the database connection via ODBC or JDBC respectively, 2) an instance to represent the spatial data stored in the database as a dataframe in Python, called the IdaGeoDataFrame, with a specific geometry attribute which recognises a planar geometry column in dashDB and 3) Python wrappers for spatial functions like within, distance, area, buffer} and more which dashDB currently supports to make the querying process from Python much simpler for the users. The spatial functions translate well-known geopandas-like syntax into SQL queries utilising the database connection to perform spatial operations in-database and can operate on single geometries as well two different geometries from different IdaGeoDataFrames. The in-database queries strictly follow the standards of OpenGIS Implementation Specification for Geographic information - Simple feature access for SQL. The results of the operations obtained can thereby be accessed dynamically via interactive Jupyter notebooks from any system which supports Python, without any additional dependencies and can also be combined with other open source libraries such as matplotlib and folium in-built within Jupyter notebooks for visualization purposes. We built a use case to analyse crime hotspots in New York city to validate our implementation and visualized the results as a choropleth map for each borough.

An open-source solution for advanced imaging flow cytometry data analysis using machine learning.

PubMed

Hennig, Holger; Rees, Paul; Blasi, Thomas; Kamentsky, Lee; Hung, Jane; Dao, David; Carpenter, Anne E; Filby, Andrew

2017-01-01

Imaging flow cytometry (IFC) enables the high throughput collection of morphological and spatial information from hundreds of thousands of single cells. This high content, information rich image data can in theory resolve important biological differences among complex, often heterogeneous biological samples. However, data analysis is often performed in a highly manual and subjective manner using very limited image analysis techniques in combination with conventional flow cytometry gating strategies. This approach is not scalable to the hundreds of available image-based features per cell and thus makes use of only a fraction of the spatial and morphometric information. As a result, the quality, reproducibility and rigour of results are limited by the skill, experience and ingenuity of the data analyst. Here, we describe a pipeline using open-source software that leverages the rich information in digital imagery using machine learning algorithms. Compensated and corrected raw image files (.rif) data files from an imaging flow cytometer (the proprietary .cif file format) are imported into the open-source software CellProfiler, where an image processing pipeline identifies cells and subcellular compartments allowing hundreds of morphological features to be measured. This high-dimensional data can then be analysed using cutting-edge machine learning and clustering approaches using "user-friendly" platforms such as CellProfiler Analyst. Researchers can train an automated cell classifier to recognize different cell types, cell cycle phases, drug treatment/control conditions, etc., using supervised machine learning. This workflow should enable the scientific community to leverage the full analytical power of IFC-derived data sets. It will help to reveal otherwise unappreciated populations of cells based on features that may be hidden to the human eye that include subtle measured differences in label free detection channels such as bright-field and dark-field imagery. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Open Data, Open Specifications and Free and Open Source Software: A powerful mix to create distributed Web-based water information systems

NASA Astrophysics Data System (ADS)

Arias, Carolina; Brovelli, Maria Antonia; Moreno, Rafael

2015-04-01

We are in an age when water resources are increasingly scarce and the impacts of human activities on them are ubiquitous. These problems don't respect administrative or political boundaries and they must be addressed integrating information from multiple sources at multiple spatial and temporal scales. Communication, coordination and data sharing are critical for addressing the water conservation and management issues of the 21st century. However, different countries, provinces, local authorities and agencies dealing with water resources have diverse organizational, socio-cultural, economic, environmental and information technology (IT) contexts that raise challenges to the creation of information systems capable of integrating and distributing information across their areas of responsibility in an efficient and timely manner. Tight and disparate financial resources, and dissimilar IT infrastructures (data, hardware, software and personnel expertise) further complicate the creation of these systems. There is a pressing need for distributed interoperable water information systems that are user friendly, easily accessible and capable of managing and sharing large volumes of spatial and non-spatial data. In a distributed system, data and processes are created and maintained in different locations each with competitive advantages to carry out specific activities. Open Data (data that can be freely distributed) is available in the water domain, and it should be further promoted across countries and organizations. Compliance with Open Specifications for data collection, storage and distribution is the first step toward the creation of systems that are capable of interacting and exchanging data in a seamlessly (interoperable) way. The features of Free and Open Source Software (FOSS) offer low access cost that facilitate scalability and long-term viability of information systems. The World Wide Web (the Web) will be the platform of choice to deploy and access these systems. Geospatial capabilities for mapping, visualization, and spatial analysis will be important components of these new generation of Web-based interoperable information systems in the water domain. The purpose of this presentation is to increase the awareness of scientists, IT personnel and agency managers about the advantages offered by the combined use of Open Data, Open Specifications for geospatial and water-related data collection, storage and sharing, as well as mature FOSS projects for the creation of interoperable Web-based information systems in the water domain. A case study is used to illustrate how these principles and technologies can be integrated to create a system with the previously mentioned characteristics for managing and responding to flood events.

smokeSALUD: exploring the effect of demographic change on the smoking prevalence at municipality level in Austria.

PubMed

Tomintz, Melanie; Kosar, Bernhard; Clarke, Graham

2016-10-07

Reducing the smoking population is still high on the policy agenda, as smoking leads to many preventable diseases, such as lung cancer, heart disease, diabetes, and more. In Austria, data on smoking prevalence only exists at the federal state level. This provides an interesting overview about the current health situation, but for regional planning authorities these data are often insufficient as they can hide pockets of high and low smoking prevalence in certain municipalities. This paper presents a spatial-temporal change of estimated smokers for municipalities from 2001 and 2011. A synthetic dataset of smokers is built by combining individual large-scale survey data and small area census data using a deterministic spatial microsimulation approach. Statistical analysis, including chi-square test and binary logistic regression, are applied to find the best variables for the simulation model and to validate its results. As no easy-to-use spatial microsimulation software for non-programmers is available yet, a flexible web-based spatial microsimulation application for health decision support (called simSALUD) has been developed and used for these analyses. The results of the simulation show in general a decrease of smoking prevalence within municipalities between 2001 and 2011 and differences within areas are identified. These results are especially valuable to policy decision makers for future planning strategies. This case study shows the application of smokeSALUD to model the spatial-temporal changes in the smoking population in Austria between 2001 and 2011. This is important as no data on smoking exists at this geographical scale (municipality). However, spatial microsimulation models are useful tools to estimate small area health data and to overcome these problems. The simulations and analysis should support health decision makers to identify hot spots of smokers and this should help to show where to spend health resources best in order to reduce health inequalities.

SU-C-201-04: Quantification of Perfusion Heterogeneity Based On Texture Analysis for Fully Automatic Detection of Ischemic Deficits From Myocardial Perfusion Imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fang, Y; Huang, H; Su, T

Purpose: Texture-based quantification of image heterogeneity has been a popular topic for imaging studies in recent years. As previous studies mainly focus on oncological applications, we report our recent efforts of applying such techniques on cardiac perfusion imaging. A fully automated procedure has been developed to perform texture analysis for measuring the image heterogeneity. Clinical data were used to evaluate the preliminary performance of such methods. Methods: Myocardial perfusion images of Thallium-201 scans were collected from 293 patients with suspected coronary artery disease. Each subject underwent a Tl-201 scan and a percutaneous coronary intervention (PCI) within three months. The PCImore » Result was used as the gold standard of coronary ischemia of more than 70% stenosis. Each Tl-201 scan was spatially normalized to an image template for fully automatic segmentation of the LV. The segmented voxel intensities were then carried into the texture analysis with our open-source software Chang Gung Image Texture Analysis toolbox (CGITA). To evaluate the clinical performance of the image heterogeneity for detecting the coronary stenosis, receiver operating characteristic (ROC) analysis was used to compute the overall accuracy, sensitivity and specificity as well as the area under curve (AUC). Those indices were compared to those obtained from the commercially available semi-automatic software QPS. Results: With the fully automatic procedure to quantify heterogeneity from Tl-201 scans, we were able to achieve a good discrimination with good accuracy (74%), sensitivity (73%), specificity (77%) and AUC of 0.82. Such performance is similar to those obtained from the semi-automatic QPS software that gives a sensitivity of 71% and specificity of 77%. Conclusion: Based on fully automatic procedures of data processing, our preliminary data indicate that the image heterogeneity of myocardial perfusion imaging can provide useful information for automatic determination of the myocardial ischemia.« less

Approach to data exchange: the spatial data transfer standard

USGS Publications Warehouse

Rossmeissl, Hedy J.; Rugg, Robert D.

1992-01-01

Significant developments have taken place in the disciplines of cartography and geography in recent years with the advent of computer hardware and software that manipulate and process digital cartographic and geographic data more efficiently. The availability of inexpensive and powerful hardware and software systems offers the capability of displaying and analyzing spatial data to a growing number of users. As a result, developing and using existing digital cartographic databases are becoming very popular. However, the absence of uniform standards for the transfer of digital spatial data is hindering the exchange of data and increasing costs. Several agencies of the U.S. government and the academic community have been working hard over the last few years to develop a spatial data transfer standard that includes definitions of standard terminology, a spatial data transfer specification, recommendations on reporting digital cartographic data quality, and standard topographic and hydrographic entity terms and definitions. This proposed standard was published in the January 1988 issue of The American Cartographer. Efforts to test and promote this standard were coordinated by the U.S. Geological Survey. A Technical Review Board was appointed with representatives from the U.S. government, the private sector, and the academic community to complete the standard for submittal to the National Institute of Standards and Technology for approval as a Federal Information Processing Standard. The proposed standard was submitted in February 1992 for final approval.

A spatial database for landslides in northern Bavaria: A methodological approach

NASA Astrophysics Data System (ADS)

Jäger, Daniel; Kreuzer, Thomas; Wilde, Martina; Bemm, Stefan; Terhorst, Birgit

2018-04-01

Landslide databases provide essential information for hazard modeling, damages on buildings and infrastructure, mitigation, and research needs. This study presents the development of a landslide database system named WISL (Würzburg Information System on Landslides), currently storing detailed landslide data for northern Bavaria, Germany, in order to enable scientific queries as well as comparisons with other regional landslide inventories. WISL is based on free open source software solutions (PostgreSQL, PostGIS) assuring good correspondence of the various softwares and to enable further extensions with specific adaptions of self-developed software. Apart from that, WISL was designed to be particularly compatible for easy communication with other databases. As a central pre-requisite for standardized, homogeneous data acquisition in the field, a customized data sheet for landslide description was compiled. This sheet also serves as an input mask for all data registration procedures in WISL. A variety of "in-database" solutions for landslide analysis provides the necessary scalability for the database, enabling operations at the local server. In its current state, WISL already enables extensive analysis and queries. This paper presents an example analysis of landslides in Oxfordian Limestones in the northeastern Franconian Alb, northern Bavaria. The results reveal widely differing landslides in terms of geometry and size. Further queries related to landslide activity classifies the majority of the landslides as currently inactive, however, they clearly possess a certain potential for remobilization. Along with some active mass movements, a significant percentage of landslides potentially endangers residential areas or infrastructure. The main aspect of future enhancements of the WISL database is related to data extensions in order to increase research possibilities, as well as to transfer the system to other regions and countries.

Efficacy of a Newly Designed Cephalometric Analysis Software for McNamara Analysis in Comparison with Dolphin Software.

PubMed

Nouri, Mahtab; Hamidiaval, Shadi; Akbarzadeh Baghban, Alireza; Basafa, Mohammad; Fahim, Mohammad

2015-01-01

Cephalometric norms of McNamara analysis have been studied in various populations due to their optimal efficiency. Dolphin cephalometric software greatly enhances the conduction of this analysis for orthodontic measurements. However, Dolphin is very expensive and cannot be afforded by many clinicians in developing countries. A suitable alternative software program in Farsi/English will greatly help Farsi speaking clinicians. The present study aimed to develop an affordable Iranian cephalometric analysis software program and compare it with Dolphin, the standard software available on the market for cephalometric analysis. In this diagnostic, descriptive study, 150 lateral cephalograms of normal occlusion individuals were selected in Mashhad and Qazvin, two major cities of Iran mainly populated with Fars ethnicity, the main Iranian ethnic group. After tracing the cephalograms, the McNamara analysis standards were measured both with Dolphin and the new software. The cephalometric software was designed using Microsoft Visual C++ program in Windows XP. Measurements made with the new software were compared with those of Dolphin software on both series of cephalograms. The validity and reliability were tested using intra-class correlation coefficient. Calculations showed a very high correlation between the results of the Iranian cephalometric analysis software and Dolphin. This confirms the validity and optimal efficacy of the newly designed software (ICC 0.570-1.0). According to our results, the newly designed software has acceptable validity and reliability and can be used for orthodontic diagnosis, treatment planning and assessment of treatment outcome.

Evaluations of UltraiQ software for objective ultrasound image quality assessment using images from a commercial scanner.

PubMed

Long, Zaiyang; Tradup, Donald J; Stekel, Scott F; Gorny, Krzysztof R; Hangiandreou, Nicholas J

2018-03-01

We evaluated a commercially available software package that uses B-mode images to semi-automatically measure quantitative metrics of ultrasound image quality, such as contrast response, depth of penetration (DOP), and spatial resolution (lateral, axial, and elevational). Since measurement of elevational resolution is not a part of the software package, we achieved it by acquiring phantom images with transducers tilted at 45 degrees relative to the phantom. Each measurement was assessed in terms of measurement stability, sensitivity, repeatability, and semi-automated measurement success rate. All assessments were performed on a GE Logiq E9 ultrasound system with linear (9L or 11L), curved (C1-5), and sector (S1-5) transducers, using a CIRS model 040GSE phantom. In stability tests, the measurements of contrast, DOP, and spatial resolution remained within a ±10% variation threshold in 90%, 100%, and 69% of cases, respectively. In sensitivity tests, contrast, DOP, and spatial resolution measurements followed the expected behavior in 100%, 100%, and 72% of cases, respectively. In repeatability testing, intra- and inter-individual coefficients of variations were equal to or less than 3.2%, 1.3%, and 4.4% for contrast, DOP, and spatial resolution (lateral and axial), respectively. The coefficients of variation corresponding to the elevational resolution test were all within 9.5%. Overall, in our assessment, the evaluated package performed well for objective and quantitative assessment of the above-mentioned image qualities under well-controlled acquisition conditions. We are finding it to be useful for various clinical ultrasound applications including performance comparison between scanners from different vendors. © 2018 The Authors. Journal of Applied Clinical Medical Physics published by Wiley Periodicals, Inc. on behalf of American Association of Physicists in Medicine.

Astrometric and Photometric Analysis of the September 2008 ATV-1 Re-Entry Event

NASA Technical Reports Server (NTRS)

Mulrooney, Mark K.; Barker, Edwin S.; Maley, Paul D.; Beaulieu, Kevin R.; Stokely, Christopher L.

2008-01-01

NASA utilized Image Intensified Video Cameras for ATV data acquisition from a jet flying at 12.8 km. Afterwards the video was digitized and then analyzed with a modified commercial software package, Image Systems Trackeye. Astrometric results were limited by saturation, plate scale, and imposed linear plate solution based on field reference stars. Time-dependent fragment angular trajectories, velocities, accelerations, and luminosities were derived in each video segment. It was evident that individual fragments behave differently. Photometric accuracy was insufficient to confidently assess correlations between luminosity and fragment spatial behavior (velocity, deceleration). Use of high resolution digital video cameras in future should remedy this shortcoming.

Computational analysis of high resolution unsteady airloads for rotor aeroacoustics

NASA Technical Reports Server (NTRS)

Quackenbush, Todd R.; Lam, C.-M. Gordon; Wachspress, Daniel A.; Bliss, Donald B.

1994-01-01

The study of helicopter aerodynamic loading for acoustics applications requires the application of efficient yet accurate simulations of the velocity field induced by the rotor's vortex wake. This report summarizes work to date on the development of such an analysis, which builds on the Constant Vorticity Contour (CVC) free wake model, previously implemented for the study of vibratory loading in the RotorCRAFT computer code. The present effort has focused on implementation of an airload reconstruction approach that computes high resolution airload solutions of rotor/rotor-wake interactions required for acoustics computations. Supplementary efforts on the development of improved vortex core modeling, unsteady aerodynamic effects, higher spatial resolution of rotor loading, and fast vortex wake implementations have substantially enhanced the capabilities of the resulting software, denoted RotorCRAFT/AA (AeroAcoustics). Results of validation calculations using recently acquired model rotor data show that by employing airload reconstruction it is possible to apply the CVC wake analysis with temporal and spatial resolution suitable for acoustics applications while reducing the computation time required by one to two orders of magnitude relative to that required by direct calculations. Promising correlation with this body of airload and noise data has been obtained for a variety of rotor configurations and operating conditions.

US GeoData

USGS Publications Warehouse

,

1992-01-01

US GeoData tapes are computer tapes which contain cartographic data in digital form. The 1:2,000,000-scale data are available in two forms. The graphic form can be used to generate computer-plotted maps. The content and scale of the maps can be varied to meet your needs. The topologically-structured form of US GeoData is suitable for input to geographic information systems for use in spatial analysis and geographic studies. Both forms must be used in conjunction with appropriate software. US GeoData tapes offer convenience, accuracy, flexibility, and cost effectiveness to many map users. Business, industry, and government users who are involved in network planning and analysis, transportation, demography, land use, or any activity where data can be related to, or plotted on a map will find US GeoData a valuable resource.

Design and Construction of a Field Capable Snapshot Hyperspectral Imaging Spectrometer

NASA Technical Reports Server (NTRS)

Arik, Glenda H.

2005-01-01

The computed-tomography imaging spectrometer (CTIS) is a device which captures the spatial and spectral content of a rapidly evolving same in a single image frame. The most recent CTIS design is optically all reflective and uses as its dispersive device a stated the-art reflective computer generated hologram (CGH). This project focuses on the instrument's transition from laboratory to field. This design will enable the CTIS to withstand a harsh desert environment. The system is modeled in optical design software using a tolerance analysis. The tolerances guide the design of the athermal mount and component parts. The parts are assembled into a working mount shell where the performance of the mounts is tested for thermal integrity. An interferometric analysis of the reflective CGH is also performed.

Demeter-W

DOE Office of Scientific and Technical Information (OSTI.GOV)

2017-09-27

Demeter-W, an open-access software written in Python, consists of extensible module packages. It is developed with statistical downscaling algorithms, to spatially and temporally downscale water demand data into finer scale. The spatial resolution will be downscaled from region/basin scale to grid (0.5 geographic degree) scale and the temporal resolution will be downscaled from year to month. For better understanding of the driving forces and patterns for global water withdrawal, the researchers is able to utilize Demeter-W to reconstruct the data sets to examine the issues related to water withdrawals at fine spatial and temporal scales.

Mapping Vegetation Community Types in a Highly-Disturbed Landscape: Integrating Hiearchical Object-Based Image Analysis with Digital Surface Models

NASA Astrophysics Data System (ADS)

Snavely, Rachel A.

Focusing on the semi-arid and highly disturbed landscape of San Clemente Island, California, this research tests the effectiveness of incorporating a hierarchal object-based image analysis (OBIA) approach with high-spatial resolution imagery and light detection and range (LiDAR) derived canopy height surfaces for mapping vegetation communities. The study is part of a large-scale research effort conducted by researchers at San Diego State University's (SDSU) Center for Earth Systems Analysis Research (CESAR) and Soil Ecology and Restoration Group (SERG), to develop an updated vegetation community map which will support both conservation and management decisions on Naval Auxiliary Landing Field (NALF) San Clemente Island. Trimble's eCognition Developer software was used to develop and generate vegetation community maps for two study sites, with and without vegetation height data as input. Overall and class-specific accuracies were calculated and compared across the two classifications. The highest overall accuracy (approximately 80%) was observed with the classification integrating airborne visible and near infrared imagery having very high spatial resolution with a LiDAR derived canopy height model. Accuracies for individual vegetation classes differed between both classification methods, but were highest when incorporating the LiDAR digital surface data. The addition of a canopy height model, however, yielded little difference in classification accuracies for areas of very dense shrub cover. Overall, the results show the utility of the OBIA approach for mapping vegetation with high spatial resolution imagery, and emphasizes the advantage of both multi-scale analysis and digital surface data for accuracy characterizing highly disturbed landscapes. The integrated imagery and digital canopy height model approach presented both advantages and limitations, which have to be considered prior to its operational use in mapping vegetation communities.

RiskChanges Spatial Decision Support system for the analysis of changing multi-hazard risk

NASA Astrophysics Data System (ADS)

van Westen, Cees; Zhang, Kaixi; Bakker, Wim; Andrejchenko, Vera; Berlin, Julian; Olyazadeh, Roya; Cristal, Irina

2015-04-01

Within the framework of the EU FP7 Marie Curie Project CHANGES and the EU FP7 Copernicus project INCREO a spatial decision support system was developed with the aim to analyse the effect of risk reduction planning alternatives on reducing the risk now and in the future, and support decision makers in selecting the best alternatives. Central to the SDSS are the stakeholders. The envisaged users of the system are organizations involved in planning of risk reduction measures, and that have staff capable of visualizing and analyzing spatial data at a municipal scale. The SDSS should be able to function in different countries with different legal frameworks and with organizations with different mandates. These could be subdivided into Civil protection organization with the mandate to design disaster response plans, Expert organizations with the mandate to design structural risk reduction measures (e.g. dams, dikes, check-dams etc), and planning organizations with the mandate to make land development plans. The SDSS can be used in different ways: analyzing the current level of risk, analyzing the best alternatives for risk reduction, the evaluation of the consequences of possible future scenarios to the risk levels, and the evaluation how different risk reduction alternatives will lead to risk reduction under different future scenarios. The SDSS is developed based on open source software and following open standards, for code as well as for data formats and service interfaces. Code development was based upon open source software as well. The architecture of the system is modular. The various parts of the system are loosely coupled, extensible, using standards for interoperability, flexible and web-based. The Spatial Decision Support System is composed of a number of integrated components. The Risk Assessment component allows to carry out spatial risk analysis, with different degrees of complexity, ranging from simple exposure (overlay of hazard and assets maps) to quantitative analysis (using different hazard types, temporal scenarios and vulnerability curves) resulting into risk curves. The platform does not include a component to calculate hazard maps, and existing hazard maps are used as input data for the risk component. The second component of the SDSS is a risk reduction planning component, which forms the core of the platform. This component includes the definition of risk reduction alternatives (related to disaster response planning, risk reduction measures and spatial planning) and links back to the risk assessment module to calculate the new level of risk if the measure is implemented, and a cost-benefit (or cost-effectiveness/ Spatial Multi Criteria Evaluation) component to compare the alternatives and make decision on the optimal one. The third component of the SDSS is a temporal scenario component, which allows to define future scenarios in terms of climate change, land use change and population change, and the time periods for which these scenarios will be made. The component doesn't generate these scenarios but uses input maps for the effect of the scenarios on the hazard and assets maps. The last component is a communication and visualization component, which can compare scenarios and alternatives, not only in the form of maps, but also in other forms (risk curves, tables, graphs)

HydroClimATe: hydrologic and climatic analysis toolkit

USGS Publications Warehouse

Dickinson, Jesse; Hanson, Randall T.; Predmore, Steven K.

2014-01-01

The potential consequences of climate variability and climate change have been identified as major issues for the sustainability and availability of the worldwide water resources. Unlike global climate change, climate variability represents deviations from the long-term state of the climate over periods of a few years to several decades. Currently, rich hydrologic time-series data are available, but the combination of data preparation and statistical methods developed by the U.S. Geological Survey as part of the Groundwater Resources Program is relatively unavailable to hydrologists and engineers who could benefit from estimates of climate variability and its effects on periodic recharge and water-resource availability. This report documents HydroClimATe, a computer program for assessing the relations between variable climatic and hydrologic time-series data. HydroClimATe was developed for a Windows operating system. The software includes statistical tools for (1) time-series preprocessing, (2) spectral analysis, (3) spatial and temporal analysis, (4) correlation analysis, and (5) projections. The time-series preprocessing tools include spline fitting, standardization using a normal or gamma distribution, and transformation by a cumulative departure. The spectral analysis tools include discrete Fourier transform, maximum entropy method, and singular spectrum analysis. The spatial and temporal analysis tool is empirical orthogonal function analysis. The correlation analysis tools are linear regression and lag correlation. The projection tools include autoregressive time-series modeling and generation of many realizations. These tools are demonstrated in four examples that use stream-flow discharge data, groundwater-level records, gridded time series of precipitation data, and the Multivariate ENSO Index.

Environmental statistics with S-Plus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Millard, S.P.; Neerchal, N.K.

1999-12-01

The combination of easy-to-use software with easy access to a description of the statistical methods (definitions, concepts, etc.) makes this book an excellent resource. One of the major features of this book is the inclusion of general information on environmental statistical methods and examples of how to implement these methods using the statistical software package S-Plus and the add-in modules Environmental-Stats for S-Plus, S+SpatialStats, and S-Plus for ArcView.

A computer software system for the generation of global ocean tides including self-gravitation and crustal loading effects

NASA Technical Reports Server (NTRS)

Estes, R. H.

1977-01-01

A computer software system is described which computes global numerical solutions of the integro-differential Laplace tidal equations, including dissipation terms and ocean loading and self-gravitation effects, for arbitrary diurnal and semidiurnal tidal constituents. The integration algorithm features a successive approximation scheme for the integro-differential system, with time stepping forward differences in the time variable and central differences in spatial variables.

Atmospheric and wind modeling for ATC

NASA Technical Reports Server (NTRS)

Slater, Gary L.

1990-01-01

The section on atmospheric modeling covers the following topics: the standard atmosphere, atmospheric variations, atmosphere requirements for ATC, and implementation of a software model for Center/Tracon Advisory System (CTAS). The section on wind modeling covers the following topics: wind data -- NOAA profiler system; wind profile estimation; incorporation of various data types into filtering scheme; spatial and temporal variation; and software implementation into CTAS. The appendices contain Matlab codes for atmospheric routines and for wind estimation.

Debugging and Performance Analysis Software Tools for Peregrine System |

Science.gov Websites

High-Performance Computing | NREL Debugging and Performance Analysis Software Tools for Peregrine System Debugging and Performance Analysis Software Tools for Peregrine System Learn about debugging and performance analysis software tools available to use with the Peregrine system. Allinea

Preliminary design of the spatial filters used in the multipass amplification system of TIL

NASA Astrophysics Data System (ADS)

Zhu, Qihua; Zhang, Xiao Min; Jing, Feng

1998-12-01

The spatial filters are used in Technique Integration Line, which has a multi-pass amplifier, not only to suppress parasitic high spatial frequency modes but also to provide places for inserting a light isolator and injecting the seed beam, and to relay image while the beam passes through the amplifiers several times. To fulfill these functions, the parameters of the spatial filters are optimized by calculations and analyzes with the consideration of avoiding the plasma blow-off effect and components demanding by ghost beam focus. The 'ghost beams' are calculated by ray tracing. A software was developed to evaluate the tolerance of the spatial filters and their components, and to align the whole system on computer simultaneously.

Achieving sustainable ground-water management by using GIS-integrated simulation tools: the EU H2020 FREEWAT platform

NASA Astrophysics Data System (ADS)

Rossetto, Rudy; De Filippis, Giovanna; Borsi, Iacopo; Foglia, Laura; Toegl, Anja; Cannata, Massimiliano; Neumann, Jakob; Vazquez-Sune, Enric; Criollo, Rotman

2017-04-01

In order to achieve sustainable and participated ground-water management, innovative software built on the integration of numerical models within GIS software is a perfect candidate to provide a full characterization of quantitative and qualitative aspects of ground- and surface-water resources maintaining the time and spatial dimension. The EU H2020 FREEWAT project (FREE and open source software tools for WATer resource management; Rossetto et al., 2015) aims at simplifying the application of EU water-related Directives through an open-source and public-domain, GIS-integrated simulation platform for planning and management of ground- and surface-water resources. The FREEWAT platform allows to simulate the whole hydrological cycle, coupling the power of GIS geo-processing and post-processing tools in spatial data analysis with that of process-based simulation models. This results in a modeling environment where large spatial datasets can be stored, managed and visualized and where several simulation codes (mainly belonging to the USGS MODFLOW family) are integrated to simulate multiple hydrological, hydrochemical or economic processes. So far, the FREEWAT platform is a large plugin for the QGIS GIS desktop software and it integrates the following capabilities: • the AkvaGIS module allows to produce plots and statistics for the analysis and interpretation of hydrochemical and hydrogeological data; • the Observation Analysis Tool, to facilitate the import, analysis and visualization of time-series data and the use of these data to support model construction and calibration; • groundwater flow simulation in the saturated and unsaturated zones may be simulated using MODFLOW-2005 (Harbaugh, 2005); • multi-species advective-dispersive transport in the saturated zone can be simulated using MT3DMS (Zheng & Wang, 1999); the possibility to simulate viscosity- and density-dependent flows is further accomplished through SEAWAT (Langevin et al., 2007); • sustainable management of combined use of ground- and surface-water resources in rural environments is accomplished by the Farm Process module embedded in MODFLOW-OWHM (Hanson et al., 2014), which allows to dynamically integrate crop water demand and supply from ground- and surface-water; • UCODE_2014 (Poeter et al., 2014) is implemented to perform sensitivity analysis and parameter estimation to improve the model fit through an inverse, regression method based on the evaluation of an objective function. Through creating a common environment among water research/professionals, policy makers and implementers, FREEWAT aims at enhancing science and participatory approach and evidence-based decision making in water resource management, hence producing relevant outcomes for policy implementation. Acknowledgements This paper is presented within the framework of the project FREEWAT, which has received funding from the European Union's HORIZON 2020 research and innovation programme under Grant Agreement n. 642224. References Hanson, R.T., Boyce, S.E., Schmid, W., Hughes, J.D., Mehl, S.M., Leake, S.A., Maddock, T., Niswonger, R.G. One-Water Hydrologic Flow Model (MODFLOW-OWHM), U.S. Geological Survey, Techniques and Methods 6-A51, 2014 134 p. Harbaugh A.W. (2005) - MODFLOW-2005, The U.S. Geological Survey Modular Ground-Water Model - the Ground-Water Flow Process. U.S. Geological Survey, Techniques and Methods 6-A16, 253 p. Langevin C.D., Thorne D.T. Jr., Dausman A.M., Sukop M.C. & Guo Weixing (2007) - SEAWAT Version 4: A Computer Program for Simulation of Multi-Species Solute and Heat Transport. U.S. Geological Survey Techniques and Methods 6-A22, 39 pp. Poeter E.P., Hill M.C., Lu D., Tiedeman C.R. & Mehl S. (2014) - UCODE_2014, with new capabilities to define parameters unique to predictions, calculate weights using simulated values, estimate parameters with SVD, evaluate uncertainty with MCMC, and more. Integrated Groundwater Modeling Center Report Number GWMI 2014-02. Rossetto, R., Borsi, I. & Foglia, L. FREEWAT: FREE and open source software tools for WATer resource management, Rendiconti Online Società Geologica Italiana, 2015, 35, 252-255. Zheng C. & Wang P.P. (1999) - MT3DMS, A modular three-dimensional multi-species transport model for simulation of advection, dispersion and chemical reactions of contaminants in groundwater systems. U.S. Army Engineer Research and Development Center Contract Report SERDP-99-1, Vicksburg, MS, 202 pp.

Investigating the spatial accuracy of CBCT-guided cranial radiosurgery: A phantom end-to-end test study.

PubMed

Calvo-Ortega, Juan-Francisco; Hermida-López, Marcelino; Moragues-Femenía, Sandra; Pozo-Massó, Miquel; Casals-Farran, Joan

2017-03-01

To evaluate the spatial accuracy of a frameless cone-beam computed tomography (CBCT)-guided cranial radiosurgery (SRS) using an end-to-end (E2E) phantom test methodology. Five clinical SRS plans were mapped to an acrylic phantom containing a radiochromic film. The resulting phantom-based plans (E2E plans) were delivered four times. The phantom was setup on the treatment table with intentional misalignments, and CBCT-imaging was used to align it prior to E2E plan delivery. Comparisons (global gamma analysis) of the planned and delivered dose to the film were performed using a commercial triple-channel film dosimetry software. The necessary distance-to-agreement to achieve a 95% (DTA95) gamma passing rate for a fixed 3% dose difference provided an estimate of the spatial accuracy of CBCT-guided SRS. Systematic (∑) and random (σ) error components, as well as 95% confidence levels were derived for the DTA95 metric. The overall systematic spatial accuracy averaged over all tests was 1.4mm (SD: 0.2mm), with a corresponding 95% confidence level of 1.8mm. The systematic (Σ) and random (σ) spatial components of the accuracy derived from the E2E tests were 0.2mm and 0.8mm, respectively. The E2E methodology used in this study allowed an estimation of the spatial accuracy of our CBCT-guided SRS procedure. Subsequently, a PTV margin of 2.0mm is currently used in our department. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Spatial Distribution of Bed Particles in Natural Boulder-Bed Streams

NASA Astrophysics Data System (ADS)

Clancy, K. F.; Prestegaard, K. L.

2001-12-01

The Wolman pebble count is used to obtain the size distribution of bed particles in natural streams. Statistics such as median particle size (D50) are used in resistance calculations. Additional information such as bed particle heterogeneity may also be obtained from the particle distribution, which is used to predict sediment transport rates (Hey, 1979), (Ferguson, Prestegaard, Ashworth, 1989). Boulder-bed streams have an extreme range of particles in the particle size distribution ranging from sand size particles to particles larger than 0.5-m. A study of a natural boulder-bed reach demonstrated that the spatial distribution of the particles is a significant factor in predicting sediment transport and stream bed and bank stability. Further experiments were performed to test the limits of the spatial distribution's effect on sediment transport. Three stream reaches 40-m in length were selected with similar hydrologic characteristics and spatial distributions but varying average size particles. We used a grid 0.5 by 0.5-m and measured four particles within each grid cell. Digital photographs of the streambed were taken in each grid cell. The photographs were examined using image analysis software to obtain particle size and position of the largest particles (D84) within the reach's particle distribution. Cross section, topography and stream depth were surveyed. Velocity and velocity profiles were measured and recorded. With these data and additional surveys of bankfull floods, we tested the significance of the spatial distributions as average particle size decreases. The spatial distribution of streambed particles may provide information about stream valley formation, bank stability, sediment transport, and the growth rate of riparian vegetation.

gPhoton: The GALEX Photon Data Archive

NASA Astrophysics Data System (ADS)

Million, Chase; Fleming, Scott W.; Shiao, Bernie; Seibert, Mark; Loyd, Parke; Tucker, Michael; Smith, Myron; Thompson, Randy; White, Richard L.

2016-12-01

gPhoton is a new database product and software package that enables analysis of GALEX ultraviolet data at the photon level. The project’s stand-alone, pure-Python calibration pipeline reproduces the functionality of the original mission pipeline to reduce raw spacecraft data to lists of time-tagged, sky-projected photons, which are then hosted in a publicly available database by the Mikulski Archive at Space Telescope. This database contains approximately 130 terabytes of data describing approximately 1.1 trillion sky-projected events with a timestamp resolution of five milliseconds. A handful of Python and command-line modules serve as a front end to interact with the database and to generate calibrated light curves and images from the photon-level data at user-defined temporal and spatial scales. The gPhoton software and source code are in active development and publicly available under a permissive license. We describe the motivation, design, and implementation of the calibration pipeline, database, and tools, with emphasis on divergence from prior work, as well as challenges created by the large data volume. We summarize the astrometric and photometric performance of gPhoton relative to the original mission pipeline. For a brief example of short time-domain science capabilities enabled by gPhoton, we show new flares from the known M-dwarf flare star CR Draconis. The gPhoton software has permanent object identifiers with the ASCL (ascl:1603.004) and DOI (doi:10.17909/T9CC7G). This paper describes the software as of version v1.27.2.

A WebGIS-based system for analyzing and visualizing air quality data for Shanghai Municipality

NASA Astrophysics Data System (ADS)

Wang, Manyi; Liu, Chaoshun; Gao, Wei

2014-10-01

An online visual analytical system based on Java Web and WebGIS for air quality data for Shanghai Municipality was designed and implemented to quantitatively analyze and qualitatively visualize air quality data. By analyzing the architecture of WebGIS and Java Web, we firstly designed the overall scheme for system architecture, then put forward the software and hardware environment and also determined the main function modules for the system. The visual system was ultimately established with the DIV + CSS layout method combined with JSP, JavaScript, and some other computer programming languages based on the Java programming environment. Moreover, Struts, Spring, and Hibernate frameworks (SSH) were integrated in the system for the purpose of easy maintenance and expansion. To provide mapping service and spatial analysis functions, we selected ArcGIS for Server as the GIS server. We also used Oracle database and ESRI file geodatabase to store spatial data and non-spatial data in order to ensure the data security. In addition, the response data from the Web server are resampled to implement rapid visualization through the browser. The experimental successes indicate that this system can quickly respond to user's requests, and efficiently return the accurate processing results.

Spatiotemporal hurdle models for zero-inflated count data: Exploring trends in emergency department visits.

PubMed

Neelon, Brian; Chang, Howard H; Ling, Qiang; Hastings, Nicole S

2016-12-01

Motivated by a study exploring spatiotemporal trends in emergency department use, we develop a class of two-part hurdle models for the analysis of zero-inflated areal count data. The models consist of two components-one for the probability of any emergency department use and one for the number of emergency department visits given use. Through a hierarchical structure, the models incorporate both patient- and region-level predictors, as well as spatially and temporally correlated random effects for each model component. The random effects are assigned multivariate conditionally autoregressive priors, which induce dependence between the components and provide spatial and temporal smoothing across adjacent spatial units and time periods, resulting in improved inferences. To accommodate potential overdispersion, we consider a range of parametric specifications for the positive counts, including truncated negative binomial and generalized Poisson distributions. We adopt a Bayesian inferential approach, and posterior computation is handled conveniently within standard Bayesian software. Our results indicate that the negative binomial and generalized Poisson hurdle models vastly outperform the Poisson hurdle model, demonstrating that overdispersed hurdle models provide a useful approach to analyzing zero-inflated spatiotemporal data. © The Author(s) 2014.

ASAP (Automatic Software for ASL Processing): A toolbox for processing Arterial Spin Labeling images.

PubMed

Mato Abad, Virginia; García-Polo, Pablo; O'Daly, Owen; Hernández-Tamames, Juan Antonio; Zelaya, Fernando

2016-04-01

The method of Arterial Spin Labeling (ASL) has experienced a significant rise in its application to functional imaging, since it is the only technique capable of measuring blood perfusion in a truly non-invasive manner. Currently, there are no commercial packages for processing ASL data and there is no recognized standard for normalizing ASL data to a common frame of reference. This work describes a new Automated Software for ASL Processing (ASAP) that can automatically process several ASL datasets. ASAP includes functions for all stages of image pre-processing: quantification, skull-stripping, co-registration, partial volume correction and normalization. To assess the applicability and validity of the toolbox, this work shows its application in the study of hypoperfusion in a sample of healthy subjects at risk of progressing to Alzheimer's disease. ASAP requires limited user intervention, minimizing the possibility of random and systematic errors, and produces cerebral blood flow maps that are ready for statistical group analysis. The software is easy to operate and results in excellent quality of spatial normalization. The results found in this evaluation study are consistent with previous studies that find decreased perfusion in Alzheimer's patients in similar regions and demonstrate the applicability of ASAP. Copyright © 2015 Elsevier Inc. All rights reserved.

Spatial variability and long-term analysis of groundwater quality of Faisalabad industrial zone

NASA Astrophysics Data System (ADS)

Nasir, Muhammad Salman; Nasir, Abdul; Rashid, Haroon; Shah, Syed Hamid Hussain

2017-10-01

Water is the basic necessity of life and is essential for healthy society. In this study, groundwater quality analysis was carried out for the industrial zone of Faisalabad city. Sixty samples of groundwater were collected from the study area. The quality maps of deliberately analyzed results were prepared in GIS. The collected samples were analyzed for chemical parameters and heavy metals, such as total hardness, alkalinity, cadmium, arsenic, nickel, lead, and fluoride, and then, the results were compared with the WHO guidelines. The values of these results were represented by a mapping of quality parameters using the ArcView GIS v9.3, and IDW was used for raster interpolation. The long-term analysis of these parameters has been carried out using the `R Statistical' software. It was concluded that water is partially not fit for drinking, and direct use of this groundwater may cause health issues.

Detecting spatial patterns of rivermouth processes using a geostatistical framework for near-real-time analysis

USGS Publications Warehouse

Xu, Wenzhao; Collingsworth, Paris D.; Bailey, Barbara; Carlson Mazur, Martha L.; Schaeffer, Jeff; Minsker, Barbara

2017-01-01

This paper proposes a geospatial analysis framework and software to interpret water-quality sampling data from towed undulating vehicles in near-real time. The framework includes data quality assurance and quality control processes, automated kriging interpolation along undulating paths, and local hotspot and cluster analyses. These methods are implemented in an interactive Web application developed using the Shiny package in the R programming environment to support near-real time analysis along with 2- and 3-D visualizations. The approach is demonstrated using historical sampling data from an undulating vehicle deployed at three rivermouth sites in Lake Michigan during 2011. The normalized root-mean-square error (NRMSE) of the interpolation averages approximately 10% in 3-fold cross validation. The results show that the framework can be used to track river plume dynamics and provide insights on mixing, which could be related to wind and seiche events.

Open source tools for the information theoretic analysis of neural data.

PubMed

Ince, Robin A A; Mazzoni, Alberto; Petersen, Rasmus S; Panzeri, Stefano

2010-01-01

The recent and rapid development of open source software tools for the analysis of neurophysiological datasets consisting of simultaneous multiple recordings of spikes, field potentials and other neural signals holds the promise for a significant advance in the standardization, transparency, quality, reproducibility and variety of techniques used to analyze neurophysiological data and for the integration of information obtained at different spatial and temporal scales. In this review we focus on recent advances in open source toolboxes for the information theoretic analysis of neural responses. We also present examples of their use to investigate the role of spike timing precision, correlations across neurons, and field potential fluctuations in the encoding of sensory information. These information toolboxes, available both in MATLAB and Python programming environments, hold the potential to enlarge the domain of application of information theory to neuroscience and to lead to new discoveries about how neurons encode and transmit information.

Development and implementation of a low cost micro computer system for LANDSAT analysis and geographic data base applications

NASA Technical Reports Server (NTRS)

Faust, N.; Jordon, L.

1981-01-01

Since the implementation of the GRID and IMGRID computer programs for multivariate spatial analysis in the early 1970's, geographic data analysis subsequently moved from large computers to minicomputers and now to microcomputers with radical reduction in the costs associated with planning analyses. Programs designed to process LANDSAT data to be used as one element in a geographic data base were used once NIMGRID (new IMGRID), a raster oriented geographic information system, was implemented on the microcomputer. Programs for training field selection, supervised and unsupervised classification, and image enhancement were added. Enhancements to the color graphics capabilities of the microsystem allow display of three channels of LANDSAT data in color infrared format. The basic microcomputer hardware needed to perform NIMGRID and most LANDSAT analyses is listed as well as the software available for LANDSAT processing.

Opto-thermal analysis of a lightweighted mirror for solar telescope.

PubMed

Banyal, Ravinder K; Ravindra, B; Chatterjee, S

2013-03-25

In this paper, an opto-thermal analysis of a moderately heated lightweighted solar telescope mirror is carried out using 3D finite element analysis (FEA). A physically realistic heat transfer model is developed to account for the radiative heating and energy exchange of the mirror with surroundings. The numerical simulations show the non-uniform temperature distribution and associated thermo-elastic distortions of the mirror blank clearly mimicking the underlying discrete geometry of the lightweighted substrate. The computed mechanical deformation data is analyzed with surface polynomials and the optical quality of the mirror is evaluated with the help of a ray-tracing software. The thermal print-through distortions are further shown to contribute to optical figure changes and mid-spatial frequency errors of the mirror surface. A comparative study presented for three commonly used substrate materials, namely, Zerodur, Pyrex and Silicon Carbide (SiC) is relevant to vast area of large optics requirements in ground and space applications.

A manual for microcomputer image analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rich, P.M.; Ranken, D.M.; George, J.S.

1989-12-01

This manual is intended to serve three basic purposes: as a primer in microcomputer image analysis theory and techniques, as a guide to the use of IMAGE{copyright}, a public domain microcomputer program for image analysis, and as a stimulus to encourage programmers to develop microcomputer software suited for scientific use. Topics discussed include the principals of image processing and analysis, use of standard video for input and display, spatial measurement techniques, and the future of microcomputer image analysis. A complete reference guide that lists the commands for IMAGE is provided. IMAGE includes capabilities for digitization, input and output of images,more » hardware display lookup table control, editing, edge detection, histogram calculation, measurement along lines and curves, measurement of areas, examination of intensity values, output of analytical results, conversion between raster and vector formats, and region movement and rescaling. The control structure of IMAGE emphasizes efficiency, precision of measurement, and scientific utility. 18 refs., 18 figs., 2 tabs.« less

Maximum unbiased validation (MUV) data sets for virtual screening based on PubChem bioactivity data.

PubMed

Rohrer, Sebastian G; Baumann, Knut

2009-02-01

Refined nearest neighbor analysis was recently introduced for the analysis of virtual screening benchmark data sets. It constitutes a technique from the field of spatial statistics and provides a mathematical framework for the nonparametric analysis of mapped point patterns. Here, refined nearest neighbor analysis is used to design benchmark data sets for virtual screening based on PubChem bioactivity data. A workflow is devised that purges data sets of compounds active against pharmaceutically relevant targets from unselective hits. Topological optimization using experimental design strategies monitored by refined nearest neighbor analysis functions is applied to generate corresponding data sets of actives and decoys that are unbiased with regard to analogue bias and artificial enrichment. These data sets provide a tool for Maximum Unbiased Validation (MUV) of virtual screening methods. The data sets and a software package implementing the MUV design workflow are freely available at http://www.pharmchem.tu-bs.de/lehre/baumann/MUV.html.

Improved spatial resolution in PET scanners using sampling techniques

PubMed Central

Surti, Suleman; Scheuermann, Ryan; Werner, Matthew E.; Karp, Joel S.

2009-01-01

Increased focus towards improved detector spatial resolution in PET has led to the use of smaller crystals in some form of light sharing detector design. In this work we evaluate two sampling techniques that can be applied during calibrations for pixelated detector designs in order to improve the reconstructed spatial resolution. The inter-crystal positioning technique utilizes sub-sampling in the crystal flood map to better sample the Compton scatter events in the detector. The Compton scatter rejection technique, on the other hand, rejects those events that are located further from individual crystal centers in the flood map. We performed Monte Carlo simulations followed by measurements on two whole-body scanners for point source data. The simulations and measurements were performed for scanners using scintillators with Zeff ranging from 46.9 to 63 for LaBr3 and LYSO, respectively. Our results show that near the center of the scanner, inter-crystal positioning technique leads to a gain of about 0.5-mm in reconstructed spatial resolution (FWHM) for both scanner designs. In a small animal LYSO scanner the resolution improves from 1.9-mm to 1.6-mm with the inter-crystal technique. The Compton scatter rejection technique shows higher gains in spatial resolution but at the cost of reduction in scanner sensitivity. The inter-crystal positioning technique represents a modest acquisition software modification for an improvement in spatial resolution, but at a cost of potentially longer data correction and reconstruction times. The Compton scatter rejection technique, while also requiring a modest acquisition software change with no increased data correction and reconstruction times, will be useful in applications where the scanner sensitivity is very high and larger improvements in spatial resolution are desirable. PMID:19779586

Integration of LCoS-SLM and LabVIEW based software to simulate fundamental optics, wave optics, and Fourier optics

NASA Astrophysics Data System (ADS)

Lyu, Bo-Han; Wang, Chen; Tsai, Chun-Wei

2017-08-01

Jasper Display Corp. (JDC) offer high reflectivity, high resolution Liquid Crystal on Silicon - Spatial Light Modulator (LCoS-SLM) which include an associated controller ASIC and LabVIEW based modulation software. Based on this LCoS-SLM, also called Education Kit (EDK), we provide a training platform which includes a series of optical theory and experiments to university students. This EDK not only provides a LabVIEW based operation software to produce Computer Generated Holograms (CGH) to generate some basic diffraction image or holographic image, but also provides simulation software to verity the experiment results simultaneously. However, we believe that a robust LCoSSLM, operation software, simulation software, training system, and training course can help students to study the fundamental optics, wave optics, and Fourier optics more easily. Based on these fundamental knowledges, they could develop their unique skills and create their new innovations on the optoelectronic application in the future.

Technological evaluation of gesture and speech interfaces for enabling dismounted soldier-robot dialogue

NASA Astrophysics Data System (ADS)

Kattoju, Ravi Kiran; Barber, Daniel J.; Abich, Julian; Harris, Jonathan

2016-05-01

With increasing necessity for intuitive Soldier-robot communication in military operations and advancements in interactive technologies, autonomous robots have transitioned from assistance tools to functional and operational teammates able to service an array of military operations. Despite improvements in gesture and speech recognition technologies, their effectiveness in supporting Soldier-robot communication is still uncertain. The purpose of the present study was to evaluate the performance of gesture and speech interface technologies to facilitate Soldier-robot communication during a spatial-navigation task with an autonomous robot. Gesture and speech semantically based spatial-navigation commands leveraged existing lexicons for visual and verbal communication from the U.S Army field manual for visual signaling and a previously established Squad Level Vocabulary (SLV). Speech commands were recorded by a Lapel microphone and Microsoft Kinect, and classified by commercial off-the-shelf automatic speech recognition (ASR) software. Visual signals were captured and classified using a custom wireless gesture glove and software. Participants in the experiment commanded a robot to complete a simulated ISR mission in a scaled down urban scenario by delivering a sequence of gesture and speech commands, both individually and simultaneously, to the robot. Performance and reliability of gesture and speech hardware interfaces and recognition tools were analyzed and reported. Analysis of experimental results demonstrated the employed gesture technology has significant potential for enabling bidirectional Soldier-robot team dialogue based on the high classification accuracy and minimal training required to perform gesture commands.

Facilitating text reading in posterior cortical atrophy.

PubMed

Yong, Keir X X; Rajdev, Kishan; Shakespeare, Timothy J; Leff, Alexander P; Crutch, Sebastian J

2015-07-28

We report (1) the quantitative investigation of text reading in posterior cortical atrophy (PCA), and (2) the effects of 2 novel software-based reading aids that result in dramatic improvements in the reading ability of patients with PCA. Reading performance, eye movements, and fixations were assessed in patients with PCA and typical Alzheimer disease and in healthy controls (experiment 1). Two reading aids (single- and double-word) were evaluated based on the notion that reducing the spatial and oculomotor demands of text reading might support reading in PCA (experiment 2). Mean reading accuracy in patients with PCA was significantly worse (57%) compared with both patients with typical Alzheimer disease (98%) and healthy controls (99%); spatial aspects of passages were the primary determinants of text reading ability in PCA. Both aids led to considerable gains in reading accuracy (PCA mean reading accuracy: single-word reading aid = 96%; individual patient improvement range: 6%-270%) and self-rated measures of reading. Data suggest a greater efficiency of fixations and eye movements under the single-word reading aid in patients with PCA. These findings demonstrate how neurologic characterization of a neurodegenerative syndrome (PCA) and detailed cognitive analysis of an important everyday skill (reading) can combine to yield aids capable of supporting important everyday functional abilities. This study provides Class III evidence that for patients with PCA, 2 software-based reading aids (single-word and double-word) improve reading accuracy. © 2015 American Academy of Neurology.

Facilitating text reading in posterior cortical atrophy

PubMed Central

Rajdev, Kishan; Shakespeare, Timothy J.; Leff, Alexander P.; Crutch, Sebastian J.

2015-01-01

Objective: We report (1) the quantitative investigation of text reading in posterior cortical atrophy (PCA), and (2) the effects of 2 novel software-based reading aids that result in dramatic improvements in the reading ability of patients with PCA. Methods: Reading performance, eye movements, and fixations were assessed in patients with PCA and typical Alzheimer disease and in healthy controls (experiment 1). Two reading aids (single- and double-word) were evaluated based on the notion that reducing the spatial and oculomotor demands of text reading might support reading in PCA (experiment 2). Results: Mean reading accuracy in patients with PCA was significantly worse (57%) compared with both patients with typical Alzheimer disease (98%) and healthy controls (99%); spatial aspects of passages were the primary determinants of text reading ability in PCA. Both aids led to considerable gains in reading accuracy (PCA mean reading accuracy: single-word reading aid = 96%; individual patient improvement range: 6%–270%) and self-rated measures of reading. Data suggest a greater efficiency of fixations and eye movements under the single-word reading aid in patients with PCA. Conclusions: These findings demonstrate how neurologic characterization of a neurodegenerative syndrome (PCA) and detailed cognitive analysis of an important everyday skill (reading) can combine to yield aids capable of supporting important everyday functional abilities. Classification of evidence: This study provides Class III evidence that for patients with PCA, 2 software-based reading aids (single-word and double-word) improve reading accuracy. PMID:26138948

Optimization design and dynamic analysis on the drive mechanisms of flapping-wing air vehicles based on flapping trajectories

NASA Astrophysics Data System (ADS)

Xie, Lingwang; Zhang, Xingwei; Luo, Pan; Huang, Panpan

2017-10-01

The optimization designs and dynamic analysis on the driving mechanism of flapping-wing air vehicles on base of flapping trajectory patterns is carried out in this study. Three different driving mechanisms which are spatial double crank-rocker, plane five-bar and gear-double slider, are systematically optimized and analysed by using the Mat lab and Adams software. After a series debugging on the parameter, the comparatively ideal flapping trajectories are obtained by the simulation of Adams. Present results indicate that different drive mechanisms output different flapping trajectories and have their unique characteristic. The spatial double crank-rocker mechanism can only output the arc flapping trajectory and it has the advantages of small volume, high flexibility and efficient space utilization. Both planar five-bar mechanism and gear-double slider mechanism can output the oval, figure of eight and double eight flapping trajectories. Nevertheless, the gear-double slider mechanism has the advantage of convenient parameter setting and better performance in output double eight flapping trajectory. This study can provide theoretical basis and helpful reference for the design of the drive mechanisms of flapping-wing air vehicles with different output flapping trajectories.

An algorithm for automated detection, localization and measurement of local calcium signals from camera-based imaging.

PubMed

Ellefsen, Kyle L; Settle, Brett; Parker, Ian; Smith, Ian F

2014-09-01

Local Ca(2+) transients such as puffs and sparks form the building blocks of cellular Ca(2+) signaling in numerous cell types. They have traditionally been studied by linescan confocal microscopy, but advances in TIRF microscopy together with improved electron-multiplied CCD (EMCCD) cameras now enable rapid (>500 frames s(-1)) imaging of subcellular Ca(2+) signals with high spatial resolution in two dimensions. This approach yields vastly more information (ca. 1 Gb min(-1)) than linescan imaging, rendering visual identification and analysis of local events imaged both laborious and subject to user bias. Here we describe a routine to rapidly automate identification and analysis of local Ca(2+) events. This features an intuitive graphical user-interfaces and runs under Matlab and the open-source Python software. The underlying algorithm features spatial and temporal noise filtering to reliably detect even small events in the presence of noisy and fluctuating baselines; localizes sites of Ca(2+) release with sub-pixel resolution; facilitates user review and editing of data; and outputs time-sequences of fluorescence ratio signals for identified event sites along with Excel-compatible tables listing amplitudes and kinetics of events. Copyright © 2014 Elsevier Ltd. All rights reserved.

Adaptation of video game UVW mapping to 3D visualization of gene expression patterns

NASA Astrophysics Data System (ADS)

Vize, Peter D.; Gerth, Victor E.

2007-01-01

Analysis of gene expression patterns within an organism plays a critical role in associating genes with biological processes in both health and disease. During embryonic development the analysis and comparison of different gene expression patterns allows biologists to identify candidate genes that may regulate the formation of normal tissues and organs and to search for genes associated with congenital diseases. No two individual embryos, or organs, are exactly the same shape or size so comparing spatial gene expression in one embryo to that in another is difficult. We will present our efforts in comparing gene expression data collected using both volumetric and projection approaches. Volumetric data is highly accurate but difficult to process and compare. Projection methods use UV mapping to align texture maps to standardized spatial frameworks. This approach is less accurate but is very rapid and requires very little processing. We have built a database of over 180 3D models depicting gene expression patterns mapped onto the surface of spline based embryo models. Gene expression data in different models can easily be compared to determine common regions of activity. Visualization software, both Java and OpenGL optimized for viewing 3D gene expression data will also be demonstrated.

Development of management information system for land in mine area based on MapInfo

NASA Astrophysics Data System (ADS)

Wang, Shi-Dong; Liu, Chuang-Hua; Wang, Xin-Chuang; Pan, Yan-Yu

2008-10-01

MapInfo is current a popular GIS software. This paper introduces characters of MapInfo and GIS second development methods offered by MapInfo, which include three ones based on MapBasic, OLE automation, and MapX control usage respectively. Taking development of land management information system in mine area for example, in the paper, the method of developing GIS applications based on MapX has been discussed, as well as development of land management information system in mine area has been introduced in detail, including development environment, overall design, design and realization of every function module, and simple application of system, etc. The system uses MapX 5.0 and Visual Basic 6.0 as development platform, takes SQL Server 2005 as back-end database, and adopts Matlab 6.5 to calculate number in back-end. On the basis of integrated design, the system develops eight modules including start-up, layer control, spatial query, spatial analysis, data editing, application model, document management, results output. The system can be used in mine area for cadastral management, land use structure optimization, land reclamation, land evaluation, analysis and forecasting for land in mine area and environmental disruption, thematic mapping, and so on.

Using GIS to analyze animal movements in the marine environment

USGS Publications Warehouse

Hooge, Philip N.; Eichenlaub, William M.; Solomon, Elizabeth K.; Kruse, Gordon H.; Bez, Nicolas; Booth, Anthony; Dorn, Martin W.; Hills, Susan; Lipcius, Romuald N.; Pelletier, Dominique; Roy, Claude; Smith, Stephen J.; Witherell, David B.

2001-01-01

Advanced methods for analyzing animal movements have been little used in the aquatic research environment compared to the terrestrial. In addition, despite obvious advantages of integrating geographic information systems (GIS) with spatial studies of animal movement behavior, movement analysis tools have not been integrated into GIS for either aquatic or terrestrial environments. We therefore developed software that integrates one of the most commonly used GIS programs (ArcView®) with a large collection of animal movement analysis tools. This application, the Animal Movement Analyst Extension (AMAE), can be loaded as an extension to ArcView® under multiple operating system platforms (PC, Unix, and Mac OS). It contains more than 50 functions, including parametric and nonparametric home range analyses, random walk models, habitat analyses, point and circular statistics, tests of complete spatial randomness, tests for autocorrelation and sample size, point and line manipulation tools, and animation tools. This paper describes the use of these functions in analyzing animal location data; some limited examples are drawn from a sonic-tracking study of Pacific halibut (Hippoglossus stenolepis) in Glacier Bay, Alaska. The extension is available on the Internet at www.absc.usgs.gov/glba/gistools/index.htm.

Performance analysis of a film dosimetric quality assurance procedure for IMRT with regard to the employment of quantitative evaluation methods.

PubMed

Winkler, Peter; Zurl, Brigitte; Guss, Helmuth; Kindl, Peter; Stuecklschweiger, Georg

2005-02-21

A system for dosimetric verification of intensity-modulated radiotherapy (IMRT) treatment plans using absolute calibrated radiographic films is presented. At our institution this verification procedure is performed for all IMRT treatment plans prior to patient irradiation. Therefore clinical treatment plans are transferred to a phantom and recalculated. Composite treatment plans are irradiated to a single film. Film density to absolute dose conversion is performed automatically based on a single calibration film. A software application encompassing film calibration, 2D registration of measurement and calculated distributions, image fusion, and a number of visual and quantitative evaluation utilities was developed. The main topic of this paper is a performance analysis for this quality assurance procedure, with regard to the specification of tolerance levels for quantitative evaluations. Spatial and dosimetric precision and accuracy were determined for the entire procedure, comprising all possible sources of error. The overall dosimetric and spatial measurement uncertainties obtained thereby were 1.9% and 0.8 mm respectively. Based on these results, we specified 5% dose difference and 3 mm distance-to-agreement as our tolerance levels for patient-specific quality assurance for IMRT treatments.

Co-simulation coupling spectral/finite elements for 3D soil/structure interaction problems

NASA Astrophysics Data System (ADS)

Zuchowski, Loïc; Brun, Michael; De Martin, Florent

2018-05-01

The coupling between an implicit finite elements (FE) code and an explicit spectral elements (SE) code has been explored for solving the elastic wave propagation in the case of soil/structure interaction problem. The coupling approach is based on domain decomposition methods in transient dynamics. The spatial coupling at the interface is managed by a standard coupling mortar approach, whereas the time integration is dealt with an hybrid asynchronous time integrator. An external coupling software, handling the interface problem, has been set up in order to couple the FE software Code_Aster with the SE software EFISPEC3D.

Teaching the Blind to Find Their Way by Playing Video Games

PubMed Central

Merabet, Lotfi B.; Connors, Erin C.; Halko, Mark A.; Sánchez, Jaime

2012-01-01

Computer based video games are receiving great interest as a means to learn and acquire new skills. As a novel approach to teaching navigation skills in the blind, we have developed Audio-based Environment Simulator (AbES); a virtual reality environment set within the context of a video game metaphor. Despite the fact that participants were naïve to the overall purpose of the software, we found that early blind users were able to acquire relevant information regarding the spatial layout of a previously unfamiliar building using audio based cues alone. This was confirmed by a series of behavioral performance tests designed to assess the transfer of acquired spatial information to a large-scale, real-world indoor navigation task. Furthermore, learning the spatial layout through a goal directed gaming strategy allowed for the mental manipulation of spatial information as evidenced by enhanced navigation performance when compared to an explicit route learning strategy. We conclude that the immersive and highly interactive nature of the software greatly engages the blind user to actively explore the virtual environment. This in turn generates an accurate sense of a large-scale three-dimensional space and facilitates the learning and transfer of navigation skills to the physical world. PMID:23028703

Protecting the privacy of individual general practice patient electronic records for geospatial epidemiology research.

PubMed

Mazumdar, Soumya; Konings, Paul; Hewett, Michael; Bagheri, Nasser; McRae, Ian; Del Fante, Peter

2014-12-01

General practitioner (GP) practices in Australia are increasingly storing patient information in electronic databases. These practice databases can be accessed by clinical audit software to generate reports that inform clinical or population health decision making and public health surveillance. Many audit software applications also have the capacity to generate de-identified patient unit record data. However, the de-identified nature of the extracted data means that these records often lack geographic information. Without spatial references, it is impossible to build maps reflecting the spatial distribution of patients with particular conditions and needs. Links to socioeconomic, demographic, environmental or other geographically based information are also not possible. In some cases, relatively coarse geographies such as postcode are available, but these are of limited use and researchers cannot undertake precision spatial analyses such as calculating travel times. We describe a method that allows researchers to implement meaningful mapping and spatial epidemiological analyses of practice level patient data while preserving privacy. This solution has been piloted in a diabetes risk research project in the patient population of a practice in Adelaide. The method offers researchers a powerful means of analysing geographic clinic data in a privacy-protected manner. © 2014 Public Health Association of Australia.

Design and demonstration of automated data analysis algorithms for ultrasonic inspection of complex composite panels with bonds

NASA Astrophysics Data System (ADS)

Aldrin, John C.; Forsyth, David S.; Welter, John T.

2016-02-01

To address the data review burden and improve the reliability of the ultrasonic inspection of large composite structures, automated data analysis (ADA) algorithms have been developed to make calls on indications that satisfy the detection criteria and minimize false calls. The original design followed standard procedures for analyzing signals for time-of-flight indications and backwall amplitude dropout. However, certain complex panels with varying shape, ply drops and the presence of bonds can complicate this interpretation process. In this paper, enhancements to the automated data analysis algorithms are introduced to address these challenges. To estimate the thickness of the part and presence of bonds without prior information, an algorithm tracks potential backwall or bond-line signals, and evaluates a combination of spatial, amplitude, and time-of-flight metrics to identify bonded sections. Once part boundaries, thickness transitions and bonded regions are identified, feature extraction algorithms are applied to multiple sets of through-thickness and backwall C-scan images, for evaluation of both first layer through thickness and layers under bonds. ADA processing results are presented for a variety of complex test specimens with inserted materials and other test discontinuities. Lastly, enhancements to the ADA software interface are presented, which improve the software usability for final data review by the inspectors and support the certification process.

Instant Grainification: Real-Time Grain-Size Analysis from Digital Images in the Field

NASA Astrophysics Data System (ADS)

Rubin, D. M.; Chezar, H.

2007-12-01

Over the past few years, digital cameras and underwater microscopes have been developed to collect in-situ images of sand-sized bed sediment, and software has been developed to measure grain size from those digital images (Chezar and Rubin, 2004; Rubin, 2004; Rubin et al., 2006). Until now, all image processing and grain- size analysis was done back in the office where images were uploaded from cameras and processed on desktop computers. Computer hardware has become small and rugged enough to process images in the field, which for the first time allows real-time grain-size analysis of sand-sized bed sediment. We present such a system consisting of weatherproof tablet computer, open source image-processing software (autocorrelation code of Rubin, 2004, running under Octave and Cygwin), and digital camera with macro lens. Chezar, H., and Rubin, D., 2004, Underwater microscope system: U.S. Patent and Trademark Office, patent number 6,680,795, January 20, 2004. Rubin, D.M., 2004, A simple autocorrelation algorithm for determining grain size from digital images of sediment: Journal of Sedimentary Research, v. 74, p. 160-165. Rubin, D.M., Chezar, H., Harney, J.N., Topping, D.J., Melis, T.S., and Sherwood, C.R., 2006, Underwater microscope for measuring spatial and temporal changes in bed-sediment grain size: USGS Open-File Report 2006-1360.

Accuracy of Bolton analysis measured in laser scanned digital models compared with plaster models (gold standard) and cone-beam computer tomography images.

PubMed

Kim, Jooseong; Lagravére, Manuel O

2016-01-01

The aim of this study was to compare the accuracy of Bolton analysis obtained from digital models scanned with the Ortho Insight three-dimensional (3D) laser scanner system to those obtained from cone-beam computed tomography (CBCT) images and traditional plaster models. CBCT scans and plaster models were obtained from 50 patients. Plaster models were scanned using the Ortho Insight 3D laser scanner; Bolton ratios were calculated with its software. CBCT scans were imported and analyzed using AVIZO software. Plaster models were measured with a digital caliper. Data were analyzed with descriptive statistics and the intraclass correlation coefficient (ICC). Anterior and overall Bolton ratios obtained by the three different modalities exhibited excellent agreement (> 0.970). The mean differences between the scanned digital models and physical models and between the CBCT images and scanned digital models for overall Bolton ratios were 0.41 ± 0.305% and 0.45 ± 0.456%, respectively; for anterior Bolton ratios, 0.59 ± 0.520% and 1.01 ± 0.780%, respectively. ICC results showed that intraexaminer error reliability was generally excellent (> 0.858 for all three diagnostic modalities), with < 1.45% discrepancy in the Bolton analysis. Laser scanned digital models are highly accurate compared to physical models and CBCT scans for assessing the spatial relationships of dental arches for orthodontic diagnosis.

Multi-Spacecraft Analysis with Generic Visualization Tools

NASA Astrophysics Data System (ADS)

Mukherjee, J.; Vela, L.; Gonzalez, C.; Jeffers, S.

2010-12-01

To handle the needs of scientists today and in the future, software tools are going to have to take better advantage of the currently available hardware. Specifically, computing power, memory, and disk space have become cheaper, while bandwidth has become more expensive due to the explosion of online applications. To overcome these limitations, we have enhanced our Southwest Data Display and Analysis System (SDDAS) to take better advantage of the hardware by utilizing threads and data caching. Furthermore, the system was enhanced to support a framework for adding data formats and data visualization methods without costly rewrites. Visualization tools can speed analysis of many common scientific tasks and we will present a suite of tools that encompass the entire process of retrieving data from multiple data stores to common visualizations of the data. The goals for the end user are ease of use and interactivity with the data and the resulting plots. The data can be simultaneously plotted in a variety of formats and/or time and spatial resolutions. The software will allow one to slice and separate data to achieve other visualizations. Furthermore, one can interact with the data using the GUI or through an embedded language based on the Lua scripting language. The data presented will be primarily from the Cluster and Mars Express missions; however, the tools are data type agnostic and can be used for virtually any type of data.

U.S. Geological Survey spatial data access

USGS Publications Warehouse

Faundeen, John L.; Kanengieter, Ronald L.; Buswell, Michael D.

2002-01-01

The U.S. Geological Survey (USGS) has done a progress review on improving access to its spatial data holdings over the Web. The USGS EROS Data Center has created three major Web-based interfaces to deliver spatial data to the general public; they are Earth Explorer, the Seamless Data Distribution System (SDDS), and the USGS Web Mapping Portal. Lessons were learned in developing these systems, and various resources were needed for their implementation. The USGS serves as a fact-finding agency in the U.S. Government that collects, monitors, analyzes, and provides scientific information about natural resource conditions and issues. To carry out its mission, the USGS has created and managed spatial data since its inception. Originally relying on paper maps, the USGS now uses advanced technology to produce digital representations of the Earth’s features. The spatial products of the USGS include both source and derivative data. Derivative datasets include Digital Orthophoto Quadrangles (DOQ), Digital Elevation Models, Digital Line Graphs, land-cover Digital Raster Graphics, and the seamless National Elevation Dataset. These products, created with automated processes, use aerial photographs, satellite images, or other cartographic information such as scanned paper maps as source data. With Earth Explorer, users can search multiple inventories through metadata queries and can browse satellite and DOQ imagery. They can place orders and make payment through secure credit card transactions. Some USGS spatial data can be accessed with SDDS. The SDDS uses an ArcIMS map service interface to identify the user’s areas of interest and determine the output format; it allows the user to either download the actual spatial data directly for small areas or place orders for larger areas to be delivered on media. The USGS Web Mapping Portal provides views of national and international datasets through an ArcIMS map service interface. In addition, the map portal posts news about new map services available from the USGS, many simultaneously published on the Environmental Systems Research Institute Geography Network. These three information systems use new software tools and expanded hardware to meet the requirements of the users. The systems are designed to handle the required workload and are relatively easy to enhance and maintain. The software tools give users a high level of functionality and help the system conform to industry standards. The hardware and software architecture is designed to handle the large amounts of spatial data and Internet traffic required by the information systems. Last, customer support was needed to answer questions, monitor e-mail, and report customer problems.

Data analysis software for the autoradiographic enhancement process. Volumes 1, 2, and 3, and appendix

NASA Technical Reports Server (NTRS)

Singh, S. P.

1979-01-01

The computer software developed to set up a method for Wiener spectrum analysis of photographic films is presented. This method is used for the quantitative analysis of the autoradiographic enhancement process. The software requirements and design for the autoradiographic enhancement process are given along with the program listings and the users manual. A software description and program listings modification of the data analysis software are included.

Bushland Evapotranspiration and Agricultural Remote Sensing System (BEARS) software

NASA Astrophysics Data System (ADS)

Gowda, P. H.; Moorhead, J.; Brauer, D. K.

2017-12-01

Evapotranspiration (ET) is a major component of the hydrologic cycle. ET data are used for a variety of water management and research purposes such as irrigation scheduling, water and crop modeling, streamflow, water availability, and many more. Remote sensing products have been widely used to create spatially representative ET data sets which provide important information from field to regional scales. As UAV capabilities increase, remote sensing use is likely to also increase. For that purpose, scientists at the USDA-ARS research laboratory in Bushland, TX developed the Bushland Evapotranspiration and Agricultural Remote Sensing System (BEARS) software. The BEARS software is a Java based software that allows users to process remote sensing data to generate ET outputs using predefined models, or enter custom equations and models. The capability to define new equations and build new models expands the applicability of the BEARS software beyond ET mapping to any remote sensing application. The software also includes an image viewing tool that allows users to visualize outputs, as well as draw an area of interest using various shapes. This software is freely available from the USDA-ARS Conservation and Production Research Laboratory website.

High-Resolution C-Arm CT and Metal Artifact Reduction Software: A Novel Imaging Modality for Analyzing Aneurysms Treated with Stent-Assisted Coil Embolization.

PubMed

Yuki, I; Kambayashi, Y; Ikemura, A; Abe, Y; Kan, I; Mohamed, A; Dahmani, C; Suzuki, T; Ishibashi, T; Takao, H; Urashima, M; Murayama, Y

2016-02-01

Combination of high-resolution C-arm CT and novel metal artifact reduction software may contribute to the assessment of aneurysms treated with stent-assisted coil embolization. This study aimed to evaluate the efficacy of a novel Metal Artifact Reduction prototype software combined with the currently available high spatial-resolution C-arm CT prototype implementation by using an experimental aneurysm model treated with stent-assisted coil embolization. Eight experimental aneurysms were created in 6 swine. Coil embolization of each aneurysm was performed by using a stent-assisted technique. High-resolution C-arm CT with intra-arterial contrast injection was performed immediately after the treatment. The obtained images were processed with Metal Artifact Reduction. Five neurointerventional specialists reviewed the image quality before and after Metal Artifact Reduction. Observational and quantitative analyses (via image analysis software) were performed. Every aneurysm was successfully created and treated with stent-assisted coil embolization. Before Metal Artifact Reduction, coil loops protruding through the stent lumen were not visualized due to the prominent metal artifacts produced by the coils. These became visible after Metal Artifact Reduction processing. Contrast filling in the residual aneurysm was also visualized after Metal Artifact Reduction in every aneurysm. Both the observational (P < .0001) and quantitative (P < .001) analyses showed significant reduction of the metal artifacts after application of the Metal Artifact Reduction prototype software. The combination of high-resolution C-arm CT and Metal Artifact Reduction enables differentiation of the coil mass, stent, and contrast material on the same image by significantly reducing the metal artifacts produced by the platinum coils. This novel image technique may improve the assessment of aneurysms treated with stent-assisted coil embolization. © 2016 by American Journal of Neuroradiology.

imzML: Imaging Mass Spectrometry Markup Language: A common data format for mass spectrometry imaging.

PubMed

Römpp, Andreas; Schramm, Thorsten; Hester, Alfons; Klinkert, Ivo; Both, Jean-Pierre; Heeren, Ron M A; Stöckli, Markus; Spengler, Bernhard

2011-01-01

Imaging mass spectrometry is the method of scanning a sample of interest and generating an "image" of the intensity distribution of a specific analyte. The data sets consist of a large number of mass spectra which are usually acquired with identical settings. Existing data formats are not sufficient to describe an MS imaging experiment completely. The data format imzML was developed to allow the flexible and efficient exchange of MS imaging data between different instruments and data analysis software.For this purpose, the MS imaging data is divided in two separate files. The mass spectral data is stored in a binary file to ensure efficient storage. All metadata (e.g., instrumental parameters, sample details) are stored in an XML file which is based on the standard data format mzML developed by HUPO-PSI. The original mzML controlled vocabulary was extended to include specific parameters of imaging mass spectrometry (such as x/y position and spatial resolution). The two files (XML and binary) are connected by offset values in the XML file and are unambiguously linked by a universally unique identifier. The resulting datasets are comparable in size to the raw data and the separate metadata file allows flexible handling of large datasets.Several imaging MS software tools already support imzML. This allows choosing from a (growing) number of processing tools. One is no longer limited to proprietary software, but is able to use the processing software which is best suited for a specific question or application. On the other hand, measurements from different instruments can be compared within one software application using identical settings for data processing. All necessary information for evaluating and implementing imzML can be found at http://www.imzML.org .

Distributed Visualization Project

NASA Technical Reports Server (NTRS)

Craig, Douglas; Conroy, Michael; Kickbusch, Tracey; Mazone, Rebecca

2016-01-01

Distributed Visualization allows anyone, anywhere to see any simulation at any time. Development focuses on algorithms, software, data formats, data systems and processes to enable sharing simulation-based information across temporal and spatial boundaries without requiring stakeholders to possess highly-specialized and very expensive display systems. It also introduces abstraction between the native and shared data, which allows teams to share results without giving away proprietary or sensitive data. The initial implementation of this capability is the Distributed Observer Network (DON) version 3.1. DON 3.1 is available for public release in the NASA Software Store (https://software.nasa.gov/software/KSC-13775) and works with version 3.0 of the Model Process Control specification (an XML Simulation Data Representation and Communication Language) to display complex graphical information and associated Meta-Data.

Three-dimensional perspective software for representation of digital imagery data. [Olympic National Park, Washington

NASA Technical Reports Server (NTRS)

Junkin, B. G.

1980-01-01

A generalized three dimensional perspective software capability was developed within the framework of a low cost computer oriented geographically based information system using the Earth Resources Laboratory Applications Software (ELAS) operating subsystem. This perspective software capability, developed primarily to support data display requirements at the NASA/NSTL Earth Resources Laboratory, provides a means of displaying three dimensional feature space object data in two dimensional picture plane coordinates and makes it possible to overlay different types of information on perspective drawings to better understand the relationship of physical features. An example topographic data base is constructed and is used as the basic input to the plotting module. Examples are shown which illustrate oblique viewing angles that convey spatial concepts and relationships represented by the topographic data planes.

[Spatial analysis of autumn-winter type scrub typhus in Shandong province, 2006-2014].

PubMed

Yang, H; Bi, Z W; Kou, Z Q; Zheng, L; Zhao, Z T

2016-05-01

To discuss the spatial-temporal distribution and epidemic trends of autumn-winter type scrub typhus in Shandong province, and provide scientific evidence for further study for the prevention and control of the disease. The scrub typhus surveillance data during 2006-2014 were collected from Shandong Disease Reporting Information System. The data was analyzed by using software ArcGIS 9.3(ESRI Inc., Redlands, CA, USA), GeoDa 0.9.5-i and SatScan 9.1.1. The Moran' s I, log-likelihood ratio(LLR), relative risk(RR)were calculated and the incidence choropleth maps, local indicators of spatial autocorrelation cluster maps and space scaning cluster maps were drawn. A total of 4 453 scrub typhus cases were reported during 2006-2014, and the annual incidence increased with year. Among the 17 prefectures(municipality)in Shandong, 13 were affected by scrub typhus. The global Moran's I index was 0.501 5(P<0.01). The differences in local Moran' s I index among 16 prefectures were significant(P<0.01). The " high-high" clustering areas were mainly Wulian county, Lanshan district and Juxian county of Rizhao, Xintai county of Tai' an, Gangcheng and Laicheng districts of Laiwu, Yiyuan county of Zibo and Mengyin county of Linyi. Spatial scan analysis showed that an eastward moving trend of high-risk clusters and two new high-risk clusters were found in Zaozhuang in 2014. The centers of the most likely clusters were in the south central mountainous areas during 2006-2010 and in 2012, eastern hilly areas in 2011, 2013 and 2014, and the size of the clusters expanded in 2008, 2011, 2013 and 2014. One spatial-temporal cluster was detected from October 1, 2014 to November 30, 2014, the center of the cluster was in Rizhao and the radius was 222.34 kilometers. A positive spatial correlation and spatial agglomerations were found in the distribution of autumn-winter type scrub typhus in Shandong. Since 2006, the epidemic area of the disease has expanded and the number of high-risk areas has increased. Moreover, the eastward moving and periodically expanding trends of high-risk clusters were detected.

Harnessing cell-to-cell variations to probe bacterial structure and biophysics

NASA Astrophysics Data System (ADS)

Cass, Julie A.

Advances in microscopy and biotechnology have given us novel insights into cellular biology and physics. While bacteria were long considered to be relatively unstructured, the development of fluorescence microscopy techniques, and spatially and temporally resolved high-throughput quantitative studies, have uncovered that the bacterial cell is highly organized, and its structure rigorously maintained. In this thesis I will describe our gateTool software, designed to harness cell-to-cell variations to probe bacterial structure, and discuss two exciting aspects of structure that we have employed gateTool to investigate: (i) chromosome organization and the cellular mechanisms for controlling DNA dynamics, and (ii) the study of cell wall synthesis, and how the genes in the synthesis pathway impact cellular shape. In the first project, we develop a spatial and temporal mapping of cell-cycle-dependent chromosomal organization, and use this quantitative map to discover that chromosomal loci segregate from midcell with universal dynamics. In the second project, I describe preliminary time- lapse and snapshot imaging analysis suggesting phentoypical coherence across peptidoglycan synthesis pathways.

Land-use evaluation for sustainable construction in a protected area: A case of Sara mountain national park.

PubMed

Ristić, Vladica; Maksin, Marija; Nenković-Riznić, Marina; Basarić, Jelena

2018-01-15

The process of making decisions on sustainable development and construction begins in spatial and urban planning when defining the suitability of using land for sustainable construction in a protected area (PA) and its immediate and regional surroundings. The aim of this research is to propose and assess a model for evaluating land-use suitability for sustainable construction in a PA and its surroundings. The methodological approach of Multi-Criteria Decision Analysis was used in the formation of this model and adapted for the research; it was combined with the adapted Analytical hierarchy process and the Delphi process, and supported by a geographical information system (GIS) within the framework of ESRI ArcGIS software - Spatial analyst. The model is applied to the case study of Sara mountain National Park in Kosovo. The result of the model is a "map of integrated assessment of land-use suitability for sustainable construction in a PA for the natural factor". Copyright © 2017 Elsevier Ltd. All rights reserved.

X-Ray Microanalysis and Electron Energy Loss Spectrometry in the Analytical Electron Microscope: Review and Future Directions

NASA Technical Reports Server (NTRS)

Goldstein, J. I.; Williams, D. B.

1992-01-01

This paper reviews and discusses future directions in analytical electron microscopy for microchemical analysis using X-ray and Electron Energy Loss Spectroscopy (EELS). The technique of X-ray microanalysis, using the ratio method and k(sub AB) factors, is outlined. The X-ray absorption correction is the major barrier to the objective of obtaining I% accuracy and precision in analysis. Spatial resolution and Minimum Detectability Limits (MDL) are considered with present limitations of spatial resolution in the 2 to 3 microns range and of MDL in the 0.1 to 0.2 wt. % range when a Field Emission Gun (FEG) system is used. Future directions of X-ray analysis include improvement in X-ray spatial resolution to the I to 2 microns range and MDL as low as 0.01 wt. %. With these improvements the detection of single atoms in the analysis volume will be possible. Other future improvements include the use of clean room techniques for thin specimen preparation, quantification available at the I% accuracy and precision level with light element analysis quantification available at better than the 10% accuracy and precision level, the incorporation of a compact wavelength dispersive spectrometer to improve X-ray spectral resolution, light element analysis and MDL, and instrument improvements including source stability, on-line probe current measurements, stage stability, and computerized stage control. The paper reviews the EELS technique, recognizing that it has been slow to develop and still remains firmly in research laboratories rather than in applications laboratories. Consideration of microanalysis with core-loss edges is given along with a discussion of the limitations such as specimen thickness. Spatial resolution and MDL are considered, recognizing that single atom detection is already possible. Plasmon loss analysis is discussed as well as fine structure analysis. New techniques for energy-loss imaging are also summarized. Future directions in the EELS technique will be the development of new spectrometers and improvements in thin specimen preparation. The microanalysis technique needs to be simplified and software developed so that the EELS technique approaches the relative simplicity of the X-ray technique. Finally, one can expect major improvements in EELS imaging as data storage and processing improvements occur.

Real-time SHVC software decoding with multi-threaded parallel processing

NASA Astrophysics Data System (ADS)

Gudumasu, Srinivas; He, Yuwen; Ye, Yan; He, Yong; Ryu, Eun-Seok; Dong, Jie; Xiu, Xiaoyu

2014-09-01

This paper proposes a parallel decoding framework for scalable HEVC (SHVC). Various optimization technologies are implemented on the basis of SHVC reference software SHM-2.0 to achieve real-time decoding speed for the two layer spatial scalability configuration. SHVC decoder complexity is analyzed with profiling information. The decoding process at each layer and the up-sampling process are designed in parallel and scheduled by a high level application task manager. Within each layer, multi-threaded decoding is applied to accelerate the layer decoding speed. Entropy decoding, reconstruction, and in-loop processing are pipeline designed with multiple threads based on groups of coding tree units (CTU). A group of CTUs is treated as a processing unit in each pipeline stage to achieve a better trade-off between parallelism and synchronization. Motion compensation, inverse quantization, and inverse transform modules are further optimized with SSE4 SIMD instructions. Simulations on a desktop with an Intel i7 processor 2600 running at 3.4 GHz show that the parallel SHVC software decoder is able to decode 1080p spatial 2x at up to 60 fps (frames per second) and 1080p spatial 1.5x at up to 50 fps for those bitstreams generated with SHVC common test conditions in the JCT-VC standardization group. The decoding performance at various bitrates with different optimization technologies and different numbers of threads are compared in terms of decoding speed and resource usage, including processor and memory.

Detecting Spatial Patterns in Biological Array Experiments

PubMed Central

ROOT, DAVID E.; KELLEY, BRIAN P.; STOCKWELL, BRENT R.

2005-01-01

Chemical genetic screening and DNA and protein microarrays are among a number of increasingly important and widely used biological research tools that involve large numbers of parallel experiments arranged in a spatial array. It is often difficult to ensure that uniform experimental conditions are present throughout the entire array, and as a result, one often observes systematic spatially correlated errors, especially when array experiments are performed using robots. Here, the authors apply techniques based on the discrete Fourier transform to identify and quantify spatially correlated errors superimposed on a spatially random background. They demonstrate that these techniques are effective in identifying common spatially systematic errors in high-throughput 384-well microplate assay data. In addition, the authors employ a statistical test to allow for automatic detection of such errors. Software tools for using this approach are provided. PMID:14567791

Infusing Reliability Techniques into Software Safety Analysis

NASA Technical Reports Server (NTRS)

Shi, Ying

2015-01-01

Software safety analysis for a large software intensive system is always a challenge. Software safety practitioners need to ensure that software related hazards are completely identified, controlled, and tracked. This paper discusses in detail how to incorporate the traditional reliability techniques into the entire software safety analysis process. In addition, this paper addresses how information can be effectively shared between the various practitioners involved in the software safety analyses. The author has successfully applied the approach to several aerospace applications. Examples are provided to illustrate the key steps of the proposed approach.

Open-Source web-based geographical information system for health exposure assessment

PubMed Central

2012-01-01

This paper presents the design and development of an open source web-based Geographical Information System allowing users to visualise, customise and interact with spatial data within their web browser. The developed application shows that by using solely Open Source software it was possible to develop a customisable web based GIS application that provides functions necessary to convey health and environmental data to experts and non-experts alike without the requirement of proprietary software. PMID:22233606

Application of a newly developed software program for image quality assessment in cone-beam computed tomography.

PubMed

de Oliveira, Marcus Vinicius Linhares; Santos, António Carvalho; Paulo, Graciano; Campos, Paulo Sergio Flores; Santos, Joana

2017-06-01

The purpose of this study was to apply a newly developed free software program, at low cost and with minimal time, to evaluate the quality of dental and maxillofacial cone-beam computed tomography (CBCT) images. A polymethyl methacrylate (PMMA) phantom, CQP-IFBA, was scanned in 3 CBCT units with 7 protocols. A macro program was developed, using the free software ImageJ, to automatically evaluate the image quality parameters. The image quality evaluation was based on 8 parameters: uniformity, the signal-to-noise ratio (SNR), noise, the contrast-to-noise ratio (CNR), spatial resolution, the artifact index, geometric accuracy, and low-contrast resolution. The image uniformity and noise depended on the protocol that was applied. Regarding the CNR, high-density structures were more sensitive to the effect of scanning parameters. There were no significant differences between SNR and CNR in centered and peripheral objects. The geometric accuracy assessment showed that all the distance measurements were lower than the real values. Low-contrast resolution was influenced by the scanning parameters, and the 1-mm rod present in the phantom was not depicted in any of the 3 CBCT units. Smaller voxel sizes presented higher spatial resolution. There were no significant differences among the protocols regarding artifact presence. This software package provided a fast, low-cost, and feasible method for the evaluation of image quality parameters in CBCT.

NASA Tech Briefs, November 2003

NASA Technical Reports Server (NTRS)

2003-01-01

Topics covered include: Computer Program Recognizes Patterns in Time-Series Data; Program for User-Friendly Management of Input and Output Data Sets; Noncoherent Tracking of a Source of a Data-Modulated Signal; Software for Acquiring Image Data for PIV; Detecting Edges in Images by Use of Fuzzy Reasoning; A Timer for Synchronous Digital Systems; Prototype Parts of a Digital Beam-Forming Wide-Band Receiver; High-Voltage Droplet Dispenser; Network Extender for MIL-STD-1553 Bus; MMIC HEMT Power Amplifier for 140 to 170 GHz; Piezoelectric Diffraction-Based Optical Switches; Numerical Modeling of Nanoelectronic Devices; Organizing Diverse, Distributed Project Information; Eigensolver for a Sparse, Large Hermitian Matrix; Modified Polar-Format Software for Processing SAR Data; e-Stars Template Builder; Software for Acoustic Rendering; Functionally Graded Nanophase Beryllium/Carbon Composites; Thin Thermal-Insulation Blankets for Very High Temperatures; Prolonging Microgravity on Parabolic Airplane Flights; Device for Locking a Control Knob; Cable-Dispensing Cart; Foam Sensor Structures Would be Self-Deployable and Survive Hard Landings; Real-Gas Effects on Binary Mixing Layers; Earth-Space Link Attenuation Estimation via Ground Radar Kdp; Wedge Heat-Flux Indicators for Flash Thermography; Measuring Diffusion of Liquids by Common-Path Interferometry; Zero-Shear, Low-Disturbance Optical Delay Line; Whispering-Gallery Mode-Locked Lasers; Spatial Light Modulators as Optical Crossbar Switches; Update on EMD and Hilbert-Spectra Analysis of Time Series; Quad-Tree Visual-Calculus Analysis of Satellite Coverage; Dyakonov-Perel Effect on Spin Dephasing in n-Type GaAs; Update on Area Production in Mixing of Supercritical Fluids; and Quasi-Sun-Pointing of Spacecraft Using Radiation Pressure.

Decision Making on Regional Landfill Site Selection in Hormozgan Province Using Smce

NASA Astrophysics Data System (ADS)

Majedi, A. S.; Kamali, B. M.; Maghsoudi, R.

2015-12-01

Landfill site selection and suitable conditions to bury hazardous wastes are among the most critical issues in modern societies. Taking several factors and limitations into account along with true decision making requires application of different decision techniques. To this end, current paper aims to make decisions about regional landfill site selection in Hormozgan province and utilizes SMCE technique combined with qualitative and quantitative criteria to select the final alternatives. To this respect, we first will describe the existing environmental situation in our study area and set the goals of our study in the framework of SMCE and will analyze the effective factors in regional landfill site selection. Then, methodological procedure of research was conducted using Delphi approach and questionnaires (in order to determine research validity, Chronbach Alpha (0.94) method was used). Spatial multi-criteria analysis model was designed in the form of criteria tree in SMCE using IL WIS software. Prioritization of respective spatial alternatives included: Bandar Abbas city with total 4 spatial alternatives (one zone with 1st priority, one zone with 3rd priority and two zones with 4thpriority) was considered the first priority, Bastak city with total 3 spatial alternatives (one zone with 2nd priority, one zone with 3rdpriorit and one zone with 4th priority) was the second priority and Bandar Abbas, Minab, Jask and Haji Abad cities were considered as the third priority.

FracPaQ: a MATLAB™ toolbox for the quantification of fracture patterns

NASA Astrophysics Data System (ADS)

Healy, David; Rizzo, Roberto; Farrell, Natalie; Watkins, Hannah; Cornwell, David; Gomez-Rivas, Enrique; Timms, Nick

2017-04-01

The patterns of fractures in deformed rocks are rarely uniform or random. Fracture orientations, sizes, shapes and spatial distributions often exhibit some kind of order. In detail, there may be relationships among the different fracture attributes e.g. small fractures dominated by one orientation, larger fractures by another. These relationships are important because the mechanical (e.g. strength, anisotropy) and transport (e.g. fluids, heat) properties of rock depend on these fracture patterns and fracture attributes. This presentation describes an open source toolbox to quantify fracture patterns, including distributions in fracture attributes and their spatial variation. Software has been developed to quantify fracture patterns from 2-D digital images, such as thin section micrographs, geological maps, outcrop or aerial photographs or satellite images. The toolbox comprises a suite of MATLAB™ scripts based on published quantitative methods for the analysis of fracture attributes: orientations, lengths, intensity, density and connectivity. An estimate of permeability in 2-D is made using a parallel plate model. The software provides an objective and consistent methodology for quantifying fracture patterns and their variations in 2-D across a wide range of length scales. Our current focus for the application of the software is on quantifying crack and fracture patterns in and around fault zones. There is a large body of published work on the quantification of relatively simple joint patterns, but fault zones present a bigger, and arguably more important, challenge. The methods presented are inherently scale independent, and a key task will be to analyse and integrate quantitative fracture pattern data from micro- to macro-scales. New features in this release include multi-scale analyses based on a wavelet method to look for scale transitions, support for multi-colour traces in the input file processed as separate fracture sets, and combining fracture traces from multiple 2-D images to derive the statistically equivalent 3-D fracture pattern expressed as a 2nd rank crack tensor.

ArcNLET: A GIS-based software to simulate groundwater nitrate load from septic systems to surface water bodies

NASA Astrophysics Data System (ADS)

Rios, J. Fernando; Ye, Ming; Wang, Liying; Lee, Paul Z.; Davis, Hal; Hicks, Rick

2013-03-01

Onsite wastewater treatment systems (OWTS), or septic systems, can be a significant source of nitrates in groundwater and surface water. The adverse effects that nitrates have on human and environmental health have given rise to the need to estimate the actual or potential level of nitrate contamination. With the goal of reducing data collection and preparation costs, and decreasing the time required to produce an estimate compared to complex nitrate modeling tools, we developed the ArcGIS-based Nitrate Load Estimation Toolkit (ArcNLET) software. Leveraging the power of geographic information systems (GIS), ArcNLET is an easy-to-use software capable of simulating nitrate transport in groundwater and estimating long-term nitrate loads from groundwater to surface water bodies. Data requirements are reduced by using simplified models of groundwater flow and nitrate transport which consider nitrate attenuation mechanisms (subsurface dispersion and denitrification) as well as spatial variability in the hydraulic parameters and septic tank distribution. ArcNLET provides a spatial distribution of nitrate plumes from multiple septic systems and a load estimate to water bodies. ArcNLET's conceptual model is divided into three sub-models: a groundwater flow model, a nitrate transport and fate model, and a load estimation model which are implemented as an extension to ArcGIS. The groundwater flow model uses a map of topography in order to generate a steady-state approximation of the water table. In a validation study, this approximation was found to correlate well with a water table produced by a calibrated numerical model although it was found that the degree to which the water table resembles the topography can vary greatly across the modeling domain. The transport model uses a semi-analytical solution to estimate the distribution of nitrate within groundwater, which is then used to estimate a nitrate load using a mass balance argument. The estimates given by ArcNLET are suitable for a screening-level analysis.

Statistical performance of image cytometry for DNA, lipids, cytokeratin, & CD45 in a model system for circulation tumor cell detection.

PubMed

Futia, Gregory L; Schlaepfer, Isabel R; Qamar, Lubna; Behbakht, Kian; Gibson, Emily A

2017-07-01

Detection of circulating tumor cells (CTCs) in a blood sample is limited by the sensitivity and specificity of the biomarker panel used to identify CTCs over other blood cells. In this work, we present Bayesian theory that shows how test sensitivity and specificity set the rarity of cell that a test can detect. We perform our calculation of sensitivity and specificity on our image cytometry biomarker panel by testing on pure disease positive (D + ) populations (MCF7 cells) and pure disease negative populations (D - ) (leukocytes). In this system, we performed multi-channel confocal fluorescence microscopy to image biomarkers of DNA, lipids, CD45, and Cytokeratin. Using custom software, we segmented our confocal images into regions of interest consisting of individual cells and computed the image metrics of total signal, second spatial moment, spatial frequency second moment, and the product of the spatial-spatial frequency moments. We present our analysis of these 16 features. The best performing of the 16 features produced an average separation of three standard deviations between D + and D - and an average detectable rarity of ∼1 in 200. We performed multivariable regression and feature selection to combine multiple features for increased performance and showed an average separation of seven standard deviations between the D + and D - populations making our average detectable rarity of ∼1 in 480. Histograms and receiver operating characteristics (ROC) curves for these features and regressions are presented. We conclude that simple regression analysis holds promise to further improve the separation of rare cells in cytometry applications. © 2017 International Society for Advancement of Cytometry. © 2017 International Society for Advancement of Cytometry.

Cyberinfrastructure for the digital brain: spatial standards for integrating rodent brain atlases

PubMed Central

Zaslavsky, Ilya; Baldock, Richard A.; Boline, Jyl

2014-01-01

Biomedical research entails capture and analysis of massive data volumes and new discoveries arise from data-integration and mining. This is only possible if data can be mapped onto a common framework such as the genome for genomic data. In neuroscience, the framework is intrinsically spatial and based on a number of paper atlases. This cannot meet today's data-intensive analysis and integration challenges. A scalable and extensible software infrastructure that is standards based but open for novel data and resources, is required for integrating information such as signal distributions, gene-expression, neuronal connectivity, electrophysiology, anatomy, and developmental processes. Therefore, the International Neuroinformatics Coordinating Facility (INCF) initiated the development of a spatial framework for neuroscience data integration with an associated Digital Atlasing Infrastructure (DAI). A prototype implementation of this infrastructure for the rodent brain is reported here. The infrastructure is based on a collection of reference spaces to which data is mapped at the required resolution, such as the Waxholm Space (WHS), a 3D reconstruction of the brain generated using high-resolution, multi-channel microMRI. The core standards of the digital atlasing service-oriented infrastructure include Waxholm Markup Language (WaxML): XML schema expressing a uniform information model for key elements such as coordinate systems, transformations, points of interest (POI)s, labels, and annotations; and Atlas Web Services: interfaces for querying and updating atlas data. The services return WaxML-encoded documents with information about capabilities, spatial reference systems (SRSs) and structures, and execute coordinate transformations and POI-based requests. Key elements of INCF-DAI cyberinfrastructure have been prototyped for both mouse and rat brain atlas sources, including the Allen Mouse Brain Atlas, UCSD Cell-Centered Database, and Edinburgh Mouse Atlas Project. PMID:25309417

Cyberinfrastructure for the digital brain: spatial standards for integrating rodent brain atlases.

PubMed

Zaslavsky, Ilya; Baldock, Richard A; Boline, Jyl

2014-01-01

Biomedical research entails capture and analysis of massive data volumes and new discoveries arise from data-integration and mining. This is only possible if data can be mapped onto a common framework such as the genome for genomic data. In neuroscience, the framework is intrinsically spatial and based on a number of paper atlases. This cannot meet today's data-intensive analysis and integration challenges. A scalable and extensible software infrastructure that is standards based but open for novel data and resources, is required for integrating information such as signal distributions, gene-expression, neuronal connectivity, electrophysiology, anatomy, and developmental processes. Therefore, the International Neuroinformatics Coordinating Facility (INCF) initiated the development of a spatial framework for neuroscience data integration with an associated Digital Atlasing Infrastructure (DAI). A prototype implementation of this infrastructure for the rodent brain is reported here. The infrastructure is based on a collection of reference spaces to which data is mapped at the required resolution, such as the Waxholm Space (WHS), a 3D reconstruction of the brain generated using high-resolution, multi-channel microMRI. The core standards of the digital atlasing service-oriented infrastructure include Waxholm Markup Language (WaxML): XML schema expressing a uniform information model for key elements such as coordinate systems, transformations, points of interest (POI)s, labels, and annotations; and Atlas Web Services: interfaces for querying and updating atlas data. The services return WaxML-encoded documents with information about capabilities, spatial reference systems (SRSs) and structures, and execute coordinate transformations and POI-based requests. Key elements of INCF-DAI cyberinfrastructure have been prototyped for both mouse and rat brain atlas sources, including the Allen Mouse Brain Atlas, UCSD Cell-Centered Database, and Edinburgh Mouse Atlas Project.

Image understanding systems based on the unifying representation of perceptual and conceptual information and the solution of mid-level and high-level vision problems

NASA Astrophysics Data System (ADS)

Kuvychko, Igor

2001-10-01

Vision is a part of a larger information system that converts visual information into knowledge structures. These structures drive vision process, resolving ambiguity and uncertainty via feedback, and provide image understanding, that is an interpretation of visual information in terms of such knowledge models. A computer vision system based on such principles requires unifying representation of perceptual and conceptual information. Computer simulation models are built on the basis of graphs/networks. The ability of human brain to emulate similar graph/networks models is found. That means a very important shift of paradigm in our knowledge about brain from neural networks to the cortical software. Starting from the primary visual areas, brain analyzes an image as a graph-type spatial structure. Primary areas provide active fusion of image features on a spatial grid-like structure, where nodes are cortical columns. The spatial combination of different neighbor features cannot be described as a statistical/integral characteristic of the analyzed region, but uniquely characterizes such region itself. Spatial logic and topology naturally present in such structures. Mid-level vision processes like clustering, perceptual grouping, multilevel hierarchical compression, separation of figure from ground, etc. are special kinds of graph/network transformations. They convert low-level image structure into the set of more abstract ones, which represent objects and visual scene, making them easy for analysis by higher-level knowledge structures. Higher-level vision phenomena like shape from shading, occlusion, etc. are results of such analysis. Such approach gives opportunity not only to explain frequently unexplainable results of the cognitive science, but also to create intelligent computer vision systems that simulate perceptional processes in both what and where visual pathways. Such systems can open new horizons for robotic and computer vision industries.

Rapid Prototyping of Hyperspectral Image Analysis Algorithms for Improved Invasive Species Decision Support Tools

NASA Astrophysics Data System (ADS)

Bruce, L. M.; Ball, J. E.; Evangilista, P.; Stohlgren, T. J.

2006-12-01

Nonnative invasive species adversely impact ecosystems, causing loss of native plant diversity, species extinction, and impairment of wildlife habitats. As a result, over the past decade federal and state agencies and nongovernmental organizations have begun to work more closely together to address the management of invasive species. In 2005, approximately 500M dollars was budgeted by U.S. Federal Agencies for the management of invasive species. Despite extensive expenditures, most of the methods used to detect and quantify the distribution of these invaders are ad hoc, at best. Likewise, decisions on the type of management techniques to be used or evaluation of the success of these methods are typically non-systematic. More efficient methods to detect or predict the occurrence of these species, as well as the incorporation of this knowledge into decision support systems, are greatly needed. In this project, rapid prototyping capabilities (RPC) are utilized for an invasive species application. More precisely, our recently developed analysis techniques for hyperspectral imagery are being prototyped for inclusion in the national Invasive Species Forecasting System (ISFS). The current ecological forecasting tools in ISFS will be compared to our hyperspectral-based invasives prediction algorithms to determine if/how the newer algorithms enhance the performance of ISFS. The PIs have researched the use of remotely sensed multispectral and hyperspectral reflectance data for the detection of invasive vegetative species. As a result, the PI has designed, implemented, and benchmarked various target detection systems that utilize remotely sensed data. These systems have been designed to make decisions based on a variety of remotely sensed data, including high spectral/spatial resolution hyperspectral signatures (1000's of spectral bands, such as those measured using ASD handheld devices), moderate spectral/spatial resolution hyperspectral images (100's of spectral bands, such as Hyperion imagery), and low spectral/spatial resolution images (such as MODIS imagery). These algorithms include hyperspectral exploitation methods such as stepwise-LDA band selection, optimized spectral band grouping, and stepwise PCA component selection. The PIs have extensive experience with combining these recently- developed methods with conventional classifiers to form an end-to-end automated target recognition (ATR) system for detecting invasive species. The outputs of these systems can be invasive prediction maps, as well as quantitative accuracy assessments like confusion matrices, user accuracies, and producer accuracies. For all of these research endeavors, the PIs have developed numerous advanced signal and image processing methodologies, as well a suite of associated software modules. However, the use of the prototype software modules has been primarily contained to Mississippi State University. The project described in this presentation and paper will enable future systematic inclusion of these software modules into a DSS with national scope.

[Spatial analysis of neonatal mortality in the state of São Paulo, 2006-2010].

PubMed

Almeida, Milena Cristina Silva; Gomes, Camila Moraes Santos; Nascimento, Luiz Fernando Costa

2014-12-01

The aim of this study was to identify spatial patterns of distribution of overall, early, and late neonatal mortality rates in São Paulo state. An ecological and exploratory study was carried in micro-regions of São Paulo sate. Mortality rates per 1,000 live births (LB) were calculated using data on overall, early, and late neonatal mortality in São Paulo between 2006 and 2010; these data were obtained from Information System and Information Technology Department of the Brazilian National Healthcare System (DATASUS). The global Moran's indices (I) were calculated for rates and thematic maps were built with these rates. Micro-regions with a high priority for intervention were identified by the box map. The software TerraView 4.2.1 was used for spatial analysis. The rates of early and late neonatal mortality were 6.2 per thousand LB and 2.5 per thousand LB, respectively. The global Moran's indexes (I) were I=0.13, I=0.15, and I=0.26 for overall, early, and late neonatal mortality rates, respectively; all global Moran's indices showed p-values <0.05. Thematic maps showed clusters of micro-regions with high rates located in the southwest and east of the state. The results presented in this study allow the implementation of policies by health managers, aiming to reduce neonatal mortality. Copyright © 2014 Associação de Pediatria de São Paulo. Publicado por Elsevier Editora Ltda. All rights reserved.

Inertial Upper Stage (IUS) software analysis

NASA Technical Reports Server (NTRS)

Grayson, W. L.; Nickel, C. E.; Rose, P. L.; Singh, R. P.

1979-01-01

The Inertial Upper Stage (IUS) System, an extension of the Space Transportation System (STS) operating regime to include higher orbits, orbital plane changes, geosynchronous orbits, and interplanetary trajectories is presented. The IUS software design, the IUS software interfaces with other systems, and the cost effectiveness in software verification are described. Tasks of the IUS discussed include: (1) design analysis; (2) validation requirements analysis; (3) interface analysis; and (4) requirements analysis.

Suitable Site Selection of Small Dams Using Geo-Spatial Technique: a Case Study of Dadu Tehsil, Sindh

NASA Astrophysics Data System (ADS)

Khalil, Zahid

2016-07-01

Decision making about identifying suitable sites for any project by considering different parameters, is difficult. Using GIS and Multi-Criteria Analysis (MCA) can make it easy for those projects. This technology has proved to be an efficient and adequate in acquiring the desired information. In this study, GIS and MCA were employed to identify the suitable sites for small dams in Dadu Tehsil, Sindh. The GIS software is used to create all the spatial parameters for the analysis. The parameters that derived are slope, drainage density, rainfall, land use / land cover, soil groups, Curve Number (CN) and runoff index with a spatial resolution of 30m. The data used for deriving above layers include 30 meter resolution SRTM DEM, Landsat 8 imagery, and rainfall from National Centre of Environment Prediction (NCEP) and soil data from World Harmonized Soil Data (WHSD). Land use/Land cover map is derived from Landsat 8 using supervised classification. Slope, drainage network and watershed are delineated by terrain processing of DEM. The Soil Conservation Services (SCS) method is implemented to estimate the surface runoff from the rainfall. Prior to this, SCS-CN grid is developed by integrating the soil and land use/land cover raster. These layers with some technical and ecological constraints are assigned weights on the basis of suitability criteria. The pair wise comparison method, also known as Analytical Hierarchy Process (AHP) is took into account as MCA for assigning weights on each decision element. All the parameters and group of parameters are integrated using weighted overlay in GIS environment to produce suitable sites for the Dams. The resultant layer is then classified into four classes namely, best suitable, suitable, moderate and less suitable. This study reveals a contribution to decision making about suitable sites analysis for small dams using geo-spatial data with minimal amount of ground data. This suitability maps can be helpful for water resource management organizations in determination of feasible rainwater harvesting structures (RWH).

Characterisation factors for life cycle impact assessment of sound emissions.

PubMed

Cucurachi, S; Heijungs, R

2014-01-15

Noise is a serious stressor affecting the health of millions of citizens. It has been suggested that disturbance by noise is responsible for a substantial part of the damage to human health. However, no recommended approach to address noise impacts was proposed by the handbook for life cycle assessment (LCA) of the European Commission, nor are characterisation factors (CFs) and appropriate inventory data available in commonly used databases. This contribution provides CFs to allow for the quantification of noise impacts on human health in the LCA framework. Noise propagation standards and international reports on acoustics and noise impacts were used to define the model parameters. Spatial data was used to calculate spatially-defined CFs in the form of 10-by-10-km maps. The results of this analysis were combined with data from the literature to select input data for representative archetypal situations of emission (e.g. urban day with a frequency of 63 Hz, rural night at 8000 Hz, etc.). A total of 32 spatial and 216 archetypal CFs were produced to evaluate noise impacts at a European level (i.e. EU27). The possibility of a user-defined characterisation factor was added to support the possibility of portraying the situation of full availability of information, as well as a highly-localised impact analysis. A Monte Carlo-based quantitative global sensitivity analysis method was applied to evaluate the importance of the input factors in determining the variance of the output. The factors produced are ready to be implemented in the available LCA databases and software. The spatial approach and archetypal approach may be combined and selected according to the amount of information available and the life cycle under study. The framework proposed and used for calculations is flexible enough to be expanded to account for impacts on target subjects other than humans and to continents other than Europe. © 2013 Elsevier B.V. All rights reserved.

New technology for using meteorological information in forest insect pest forecast and warning systems.

PubMed

Qin, Jiang-Lin; Yang, Xiu-Hao; Yang, Zhong-Wu; Luo, Ji-Tong; Lei, Xiu-Feng

2017-12-01

Near surface air temperature and rainfall are major weather factors affecting forest insect dynamics. The recent developments in remote sensing retrieval and geographic information system spatial analysis techniques enable the utilization of weather factors to significantly enhance forest pest forecasting and warning systems. The current study focused on building forest pest digital data structures as a platform of correlation analysis between weather conditions and forest pest dynamics for better pest forecasting and warning systems using the new technologies. The study dataset contained 3 353 425 small polygons with 174 defined attributes covering 95 counties of Guangxi province of China currently registering 292 forest pest species. Field data acquisition and information transfer systems were established with four software licences that provided 15-fold improvement compared to the systems currently used in China. Nine technical specifications were established including codes of forest districts, pest species and host tree species, and standard practices of forest pest monitoring and information management. Attributes can easily be searched using ArcGIS9.3 and/or the free QGIS2.16 software. Small polygons with pest relevant attributes are a new tool of precision farming and detailed forest insect pest management that are technologically advanced. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Semiautomated Workflow for Clinically Streamlined Glioma Parametric Response Mapping

PubMed Central

Keith, Lauren; Ross, Brian D.; Galbán, Craig J.; Luker, Gary D.; Galbán, Stefanie; Zhao, Binsheng; Guo, Xiaotao; Chenevert, Thomas L.; Hoff, Benjamin A.

2017-01-01

Management of glioblastoma multiforme remains a challenging problem despite recent advances in targeted therapies. Timely assessment of therapeutic agents is hindered by the lack of standard quantitative imaging protocols for determining targeted response. Clinical response assessment for brain tumors is determined by volumetric changes assessed at 10 weeks post-treatment initiation. Further, current clinical criteria fail to use advanced quantitative imaging approaches, such as diffusion and perfusion magnetic resonance imaging. Development of the parametric response mapping (PRM) applied to diffusion-weighted magnetic resonance imaging has provided a sensitive and early biomarker of successful cytotoxic therapy in brain tumors while maintaining a spatial context within the tumor. Although PRM provides an earlier readout than volumetry and sometimes greater sensitivity compared with traditional whole-tumor diffusion statistics, it is not routinely used for patient management; an automated and standardized software for performing the analysis and for the generation of a clinical report document is required for this. We present a semiautomated and seamless workflow for image coregistration, segmentation, and PRM classification of glioblastoma multiforme diffusion-weighted magnetic resonance imaging scans. The software solution can be integrated using local hardware or performed remotely in the cloud while providing connectivity to existing picture archive and communication systems. This is an important step toward implementing PRM analysis of solid tumors in routine clinical practice. PMID:28286871

radR: an open-source platform for acquiring and analysing data on biological targets observed by surveillance radar.

PubMed

Taylor, Philip D; Brzustowski, John M; Matkovich, Carolyn; Peckford, Michael L; Wilson, Dave

2010-10-26

Radar has been used for decades to study movement of insects, birds and bats. In spite of this, there are few readily available software tools for the acquisition, storage and processing of such data. Program radR was developed to solve this problem. Program radR is an open source software tool for the acquisition, storage and analysis of data from marine radars operating in surveillance mode. radR takes time series data with a two-dimensional spatial component as input from some source (typically a radar digitizing card) and extracts and retains information of biological relevance (i.e. moving targets). Low-level data processing is implemented in "C" code, but user-defined functions written in the "R" statistical programming language can be called at pre-defined steps in the calculations. Output data formats are designed to allow for future inclusion of additional data items without requiring change to C code. Two brands of radar digitizing card are currently supported as data sources. We also provide an overview of the basic considerations of setting up and running a biological radar study. Program radR provides a convenient, open source platform for the acquisition and analysis of radar data of biological targets.

the-wizz: clustering redshift estimation for everyone

NASA Astrophysics Data System (ADS)

Morrison, C. B.; Hildebrandt, H.; Schmidt, S. J.; Baldry, I. K.; Bilicki, M.; Choi, A.; Erben, T.; Schneider, P.

2017-05-01

We present the-wizz, an open source and user-friendly software for estimating the redshift distributions of photometric galaxies with unknown redshifts by spatially cross-correlating them against a reference sample with known redshifts. The main benefit of the-wizz is in separating the angular pair finding and correlation estimation from the computation of the output clustering redshifts allowing anyone to create a clustering redshift for their sample without the intervention of an 'expert'. It allows the end user of a given survey to select any subsample of photometric galaxies with unknown redshifts, match this sample's catalogue indices into a value-added data file and produce a clustering redshift estimation for this sample in a fraction of the time it would take to run all the angular correlations needed to produce a clustering redshift. We show results with this software using photometric data from the Kilo-Degree Survey (KiDS) and spectroscopic redshifts from the Galaxy and Mass Assembly survey and the Sloan Digital Sky Survey. The results we present for KiDS are consistent with the redshift distributions used in a recent cosmic shear analysis from the survey. We also present results using a hybrid machine learning-clustering redshift analysis that enables the estimation of clustering redshifts for individual galaxies. the-wizz can be downloaded at http://github.com/morriscb/The-wiZZ/.

radR: an open-source platform for acquiring and analysing data on biological targets observed by surveillance radar

PubMed Central

2010-01-01

Background Radar has been used for decades to study movement of insects, birds and bats. In spite of this, there are few readily available software tools for the acquisition, storage and processing of such data. Program radR was developed to solve this problem. Results Program radR is an open source software tool for the acquisition, storage and analysis of data from marine radars operating in surveillance mode. radR takes time series data with a two-dimensional spatial component as input from some source (typically a radar digitizing card) and extracts and retains information of biological relevance (i.e. moving targets). Low-level data processing is implemented in "C" code, but user-defined functions written in the "R" statistical programming language can be called at pre-defined steps in the calculations. Output data formats are designed to allow for future inclusion of additional data items without requiring change to C code. Two brands of radar digitizing card are currently supported as data sources. We also provide an overview of the basic considerations of setting up and running a biological radar study. Conclusions Program radR provides a convenient, open source platform for the acquisition and analysis of radar data of biological targets. PMID:20977735