Literature DB >> 18348945

Large-scale biomedical image analysis in grid environments.

Vijay S Kumar1, Benjamin Rutt, Tahsin Kurc, Umit V Catalyurek, Tony C Pan, Sunny Chow, Stephan Lamont, Maryann Martone, Joel H Saltz.   

Abstract

This paper presents the application of a component-based Grid middleware system for processing extremely large images obtained from digital microscopy devices. We have developed parallel, out-of-core techniques for different classes of data processing operations employed on images from confocal microscopy scanners. These techniques are combined into a data preprocessing and analysis pipeline using the component-based middleware system. The experimental results show that: 1) our implementation achieves good performance and can handle very large datasets on high-performance Grid nodes, consisting of computation and/or storage clusters and 2) it can take advantage of Grid nodes connected over high-bandwidth wide-area networks by combining task and data parallelism.

Mesh:

Year:  2008        PMID: 18348945      PMCID: PMC3294419          DOI: 10.1109/TITB.2007.908466

Source DB:  PubMed          Journal:  IEEE Trans Inf Technol Biomed        ISSN: 1089-7771


  6 in total

1.  The virtual microscope.

Authors:  Umit Catalyürek; Michael D Beynon; Chialin Chang; Tahsin Kurc; Alan Sussman; Joel Saltz
Journal:  IEEE Trans Inf Technol Biomed       Date:  2003-12

2.  Automated microscopy system for mosaic acquisition and processing.

Authors:  S K Chow; H Hakozaki; D L Price; N A B MacLean; T J Deerinck; J C Bouwer; M E Martone; S T Peltier; M H Ellisman
Journal:  J Microsc       Date:  2006-05       Impact factor: 1.758

Review 3.  Informatics in radiology: GridCAD: grid-based computer-aided detection system.

Authors:  Tony C Pan; Metin N Gurcan; Stephen A Langella; Scott W Oster; Shannon L Hastings; Ashish Sharma; Benjamin G Rutt; David W Ervin; Tahsin M Kurc; Khan M Siddiqui; Joel H Saltz; Eliot L Siegel
Journal:  Radiographics       Date:  2007 May-Jun       Impact factor: 5.333

4.  Integrating Open Grid Services Architecture Data Access and Integration with computational Grid workflows.

Authors:  Tamas Kukla; Tamas Kiss; Peter Kacsuk; Gabor Terstyanszky
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2009-06-28       Impact factor: 4.226

5.  Digital dynamic telepathology--the Virtual Microscope.

Authors:  A Afework; M D Beynon; F Bustamante; S Cho; A Demarzo; R Ferreira; R Miller; M Silberman; J Saltz; A Sussman; H Tsang
Journal:  Proc AMIA Symp       Date:  1998

6.  caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid.

Authors:  Joel Saltz; Scott Oster; Shannon Hastings; Stephen Langella; Tahsin Kurc; William Sanchez; Manav Kher; Arumani Manisundaram; Krishnakant Shanbhag; Peter Covitz
Journal:  Bioinformatics       Date:  2006-06-09       Impact factor: 6.937

  6 in total
  3 in total

1.  An Integrated Framework for Parameter-based Optimization of Scientific Workflows.

Authors:  Vijay S Kumar; P Sadayappan; Gaurang Mehta; Karan Vahi; Ewa Deelman; Varun Ratnakar; Jihie Kim; Yolanda Gil; Mary Hall; Tahsin Kurc; Joel Saltz
Journal:  Proc Int Symp High Perform Distrib Comput       Date:  2009

2.  Database-managed grid-enabled analysis of neuroimaging data: the CNARI framework.

Authors:  Steven L Small; Michael Wilde; Sarah Kenny; Michael Andric; Uri Hasson
Journal:  Int J Psychophysiol       Date:  2009-02-20       Impact factor: 2.997

3.  Parameterized Specification, Configuration and Execution of Data-Intensive Scientific Workflows.

Authors:  Vijay S Kumar; Tahsin Kurc; Varun Ratnakar; Jihie Kim; Gaurang Mehta; Karan Vahi; Yoonju Lee Nelson; P Sadayappan; Ewa Deelman; Yolanda Gil; Mary Hall; Joel Saltz
Journal:  Cluster Comput       Date:  2010-09       Impact factor: 1.809

  3 in total

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