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

Hybrid rendering of exploded views for medical image atlas visualization

Medical image atlases contain much information about human anatomy, but learning the shapes of anatomical regions and making sense of the overall structure defined in the atlas can be problematic. Atlases may contain hundreds of regions with complex shapes which can be tightly packed together. This makes visualisation difficult since the shapes can fit together in complex ways and visually obscure each other. In this work, we describe a technique which enables interactive exploration of medical image atlases that permits the hierarchical structure of the atlas and the content of an underlying medical image to be investigated simultaneously. Our method enables a user to create visualizations of the atlas similar to the exploded views used in technical illustrations to show the structure of mechanical assemblies. These views are constrained by the geometry of the atlas and the hierarchical structure to reduce the complexity of user interaction. We also enable the user to explode the atlas meshes themselves. The atlas meshes are registered with a medical image which is displayed on the cut surfaces of the meshes using raycasting. Results from the AAL human brain atlas are presented and discussed

Hierarchical Control of the ATLAS Experiment

Control systems at High Energy Physics (HEP) experiments are becoming increasingly complex mainly due to the size, complexity and data volume associated to the front-end instrumentation. In particular, this becomes visible for the ATLAS experiment at the LHC accelerator at CERN. ATLAS will be the largest particle detector ever built, result of an international collaboration of more than 150 institutes. The experiment is composed of 9 different specialized sub-detectors that perform different tasks and have different requirements for operation. The system in charge of the safe and coherent operation of the whole experiment is called Detector Control System (DCS). This thesis presents the integration of the ATLAS DCS into a global control tree following the natural segmentation of the experiment into sub-detectors and smaller sub-systems. The integration of the many different systems composing the DCS includes issues such as: back-end organization, process model identification, fault detection, synchronization with external systems, automation of processes and supervisory control. Distributed control modeling is applied to the widely distributed devices that coexist in ATLAS. Thus, control is achieved by means of many distributed, autonomous and co-operative entities that are hierarchically organized and follow a finite-state machine logic. The key to integration of these systems lies in the so called Finite State Machine tool (FSM), which is based on two main enabling technologies: a SCADA product, and the State Manager Interface (SMI++) toolkit. The SMI++ toolkit has been already used with success in two previous HEP experiments providing functionality such as: an object-oriented language, a finite-state machine logic, an interface to develop expert systems, and a platform-independent communication protocol. This functionality is then used at all levels of the experiment operation process, ranging from the overall supervision down to device integration, enabling the overall sequencing and automation of the experiment. Although the experience gained in the past is an important input for the design of the detector's control hierarchy, further requirements arose due to the complexity and size of ATLAS. In total, around 200.000 channels will be supervised by the DCS and the final control tree will be hundreds of times bigger than any of the antecedents. Thus, in order to apply a hierarchical control model to the ATLAS DCS, a common approach has been proposed to ensure homogeneity between the large-scale distributed software ensembles of sub-detectors. A standard architecture and a human interface have been defined with emphasis on the early detection, monitoring and diagnosis of faults based on a dynamic fault-data mechanism. This mechanism relies on two parallel communication paths that manage the faults while providing a clear description of the detector conditions. The DCS information is split and handled by different types of SMI++ objects; whilst one path of objects manages the operational mode of the system, the other is to handle eventual faults. The proposed strategy has been validated through many different tests with positive results in both functionality and performance. This strategy has been successfully implemented and constitutes the ATLAS standard to build the global control tree. During the operation of the experiment, the DCS, responsible for the detector operation, must be synchronized with the data acquisition system which is in charge of the physics data taking process. The interaction between both systems has so far been limited, but becomes increasingly important as the detector nears completion. A prototype implementation, ready to be used during the sub-detector integration, has achieved data reconciliation by mapping the different segments of the data acquisition system into the DCS control tree. The adopted solution allows the data acquisition control applications to command different DCS sections independently and prevents incorrect physics data taking caused by a failure in a detector part. Finally, the human-machine interface presents and controls the DCS data in the ATLAS control room. The main challenges faced during the design and development phases were: how to support the operator in controlling this large system, how to maintain integration across many displays, and how to provide an effective navigation. These issues have been solved by combining the functionalities provided by both, the SCADA product and the FSM tool. The control hierarchy provides an intuitive structure for the organization of many different displays that are needed for the visualization of the experiment conditions. Each node in the tree represents a workspace that contains the functional information associated with its abstraction level within the hierarchy. By means of an effective navigation, any workspace of the control tree is accessible by the operator or detector expert within a common human interface layout. The interface is modular and flexible enough to be accommodated to new operational scenarios, fulfil the necessities of the different kind of users and facilitate the maintenance during the long lifetime of the detector of up to 20 years. The interface is in use since several months, and the sub-detector's control hierarchies, together with their associated displays, are currently being integrated into the common human-machine interface

Near-IR Atlas of S0-Sa galaxies (NIRS0S)

An atlas of Ks-band images of 206 early-type galaxies is presented, including 160 S0-S0/a galaxies, 12 ellipticals, and 33 Sa galaxies. A majority of the Atlas galaxies belong to a magnitude-limited (mB<12.5 mag) sample of 185 NIRS0S (Near-IR S0 galaxy Survey) galaxies. To assure that mis-classified S0s are not omitted, 25 ellipticals from RC3 classified as S0s in the Carnegie Atlas were included in the sample. The images are 2-3 mag deeper than 2MASS images. Both visual and photometric classifications are made. Special attention is paid to the classification of lenses, coded in a systematic manner. A new lens-type, called a 'barlens', is introduced. Also, boxy/peanut/x-shaped structures are identified in many barred galaxies, even-though the galaxies are not seen in edge-on view, indicating that vertical thickening is not enough to explain them. Multiple lenses appear in 25% of the Atlas galaxies, which is a challenge to the hierarchical evolutionary picture of galaxies. Such models need to explain how the lenses were formed and survived in multiple merger events that galaxies may have suffered during their lifetimes. Following the early suggestion by van den Bergh, candidates of S0c galaxies are shown, which galaxies are expected to be former Sc-type spirals stripped out of gas.Comment: 67 pages (include 16 figures and 6 tables). Accepted to MNRAS 2011 June 1

Naturally split supersymmetry

Nonobservation of superparticles till date, new Higgs mass limits from the CMS and ATLAS experiments, WMAP constraints on relic density, various other low energy data, and the naturalness consideration, all considered simultaneously imply a paradigm shift of supersymmetric model building. In this paper we perform, for the first time, a detailed numerical study of brane-world induced supersymmetry breaking for both minimal and next-to-minimal scenarios. We observe that a naturally hierarchical spectrum emerges through an interplay of bulk, brane-localized and quasi-localized fields, which can gain more relevance in the subsequent phases of the LHC run.Comment: 6 pages, 6 eps figures; v2: minor updates, to appear in JHE

RNA-seq based transcriptomic map reveals new insights into mouse salivary gland development and maturation

Heatmap depicting the hierarchical clustering of the 45 genes that are conserved between the mouse adult salivary gland gene signature and the RNA-seq data obtained from the Human Protein Atlas. The values reported represent Z-scores of the conserved genes in their respective datasets. (PDF 737 kb