Design of a "Digital Atlas Vme Electronics" (DAVE) Module

ATLAS-SCT has developed a new ATLAS trigger card, 'Digital Atlas Vme Electronics' ("DAVE"). The unit is designed to provide a versatile array of interface and logic resources, including a large FPGA. It interfaces to both VME bus and USB hosts. DAVE aims to provide exact ATLAS CTP (ATLAS Central Trigger Processor) functionality, with random trigger, simple and complex deadtime, ECR (Event Counter Reset), BCR (Bunch Counter Reset) etc. being generated to give exactly the same conditions in standalone running as experienced in combined runs. DAVE provides additional hardware and a large amount of free firmware resource to allow users to add or change functionality. The combination of the large number of individually programmable inputs and outputs in various formats, with very large external RAM and other components all connected to the FPGA, also makes DAVE a powerful and versatile FPGA utility cardComment: 8 pages, 4 figures, TWEPP-2011; E-mail: [email protected]

Digital Atlas of American Religion

poster abstractOur poster presentation will introduce DAAR, the Digital Atlas of American Religion (http://www.religionatlas.org). DAAR is a web-based research platform with innovative data exploration and visualization tools to support research in the humanities. Time and location are essential components of humanities exploratory research; however, GIS technology, especially in its web form, does not support the easy exploration and visualization of the complex spatio-temporal data manipulated by humanists. DAAR presents researchers with an integrated solution stemming from several fields including GIS, visualization, and classification theory. Researchers using DAAR are provided with the following exploration/visualization techniques: maps, cartograms, tree maps, pie charts, and motion charts. Using these tools and methods, researchers can explore patterns, trends, and relationships in the data that otherwise are not apparent with traditional GIS or statistical software. DAAR allows researchers to understand the multiple dimensions and diversity of religion across geographies, or within geographies. Paired with historic census data, it allows them to explore relationships to give better context and meaning to the patterns and trends. Maps provide the spatial patterns and relationships, tree maps show relative strength and relationships, charts show trends, cartograms reveal relative numbers of adherence, and motion charts animate trends over time

A Digital Atlas of the Dog Brain

There is a long history and a growing interest in the canine as a subject of study in neuroscience research and in translational neurology. In the last few years, anatomical and functional magnetic resonance imaging (MRI) studies of awake and anesthetized dogs have been reported. Such efforts can be enhanced by a population atlas of canine brain anatomy to implement group analyses. Here we present a canine brain atlas derived as the diffeomorphic average of a population of fifteen mesaticephalic dogs. The atlas includes: 1) A brain template derived from in-vivo, T1-weighted imaging at 1 mm isotropic resolution at 3 Tesla (with and without the soft tissues of the head); 2) A co-registered, high-resolution (0.33 mm isotropic) template created from imaging of ex-vivo brains at 7 Tesla; 3) A surface representation of the gray matter/white matter boundary of the high-resolution atlas (including labeling of gyral and sulcal features). The properties of the atlas are considered in relation to historical nomenclature and the evolutionary taxonomy of the Canini tribe. The atlas is available for download (https://cfn.upenn.edu/aguirre/wiki/public:data_plosone_2012_datta)

Automated Annotation in the GEBCO Digital Atlas

The GEBCO series of bathymetric charts of the world's oceans has developed over a long time, with many changes in format, content and detail. A digital version, the GEBCO Digital Atlas, is currently under preparation using the present (fifth) edition as a starting point. One of the methods for distribution will be the CD-ROM optical disk. With the potential of this medium for handling considerably more information than can be portrayed on paper and the use of the electronic medium for mapping applications, a number of cartographic issues are raised, one of which is feature annotation. Research into techniques for carrying out this process automatically has focused almost exclusively on land-based applications. The application of these techniques to bathymetric mapping is discussed, with particular attention paid to the problems involved with viewing data at arbitrary scale factors, and a number of possible solutions are presented

An Improved Portrayal of the Floor of the Arctic Ocean, Based on a Grid Derived from GEBCO Bathymetric Contours

Digital descriptions of sea floor relief and land topography in the Arctic are useful for scientific and illustrative purposes, however existing public-domain data sets, such as the ET0P05 grid and extracts from the GEBCO Digital Atlas, don’t lend themselves particularly well to visualization and other processes that work best with uniformly-spaced data. A technique has been developed for converting isobaths from the GEBCO Digital Atlas into a uniform 5 km X 5 km grid of depth values. At the same time, the land component of ET0P05 has been re-sampled at a similar grid spacing. When combined, these two grid sets yield convincing shaded relief portrayals of the Arctic region. The methodologies described here are not restricted to the Arctic, but may be applied with minor modification to other regions as well

Digital Three-Dimensional Atlas of Quail Development Using High-Resolution MRI

We present an archetypal set of three-dimensional digital atlases of the quail embryo based on microscopic magnetic resonance imaging (µMRI). The atlases are composed of three modules: (1) images of fixed ex ovo quail, ranging in age from embryonic day 5 to 10 (e05 to e10); (2) a coarsely delineated anatomical atlas of the µMRI data; and (3) an organ system–based hierarchical graph linked to the anatomical delineations. The atlas is designed to be accessed using SHIVA, a free Java application. The atlas is extensible and can contain other types of information including anatomical, physiological, and functional descriptors. It can also be linked to online resources and references. This digital atlas provides a framework to place various data types, such as gene expression and cell migration data, within the normal three-dimensional anatomy of the developing quail embryo. This provides a method for the analysis and examination of the spatial relationships among the different types of information within the context of the entire embryo

A Digital Atlas to Characterize the Mouse Brain Transcriptome

Massive amounts of data are being generated in an effort to represent for the brain the expression of all genes at cellular resolution. Critical to exploiting this effort is the ability to place these data into a common frame of reference. Here we have developed a computational method for annotating gene expression patterns in the context of a digital atlas to facilitate custom user queries and comparisons of this type of data. This procedure has been applied to 200 genes in the postnatal mouse brain. As an illustration of utility, we identify candidate genes that may be related to Parkinson disease by using the expression of a dopamine transporter in the substantia nigra as a search query pattern. In addition, we discover that transcription factor Rorb is down-regulated in the barrelless mutant relative to control mice by quantitative comparison of expression patterns in layer IV somatosensory cortex. The semi-automated annotation method developed here is applicable to a broad spectrum of complex tissues and data modalities