• Share
  • Email
  • Embed
  • Like
  • Save
  • Private Content
Vre ci presentation -ric workshop - july 26th

Vre ci presentation -ric workshop - july 26th






Total Views
Views on SlideShare
Embed Views



0 Embeds 0

No embeds



Upload Details

Uploaded via as Microsoft PowerPoint

Usage Rights

© All Rights Reserved

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
Post Comment
Edit your comment
  • Extend the functionality of the Research Information Centre (RIC) and include tools for articulating and sharing imaging algorithms through the integration of Trident.
  • Multiple layers at different resolutionsEnable quick zooming and panning of large imagesRequires Silverlight browser plugin
  • Yes

Vre ci presentation -ric workshop - july 26th Vre ci presentation -ric workshop - july 26th Presentation Transcript

  • A Virtual Research Environment for Cancer Imaging (VRE-CI)
    RIC Workshop
    26 July 2010
  • Outline
    Project Overview
    Current activities
    Future Work
  • A Virtual Research Environment for Cancer Imaging (VRE-CI)
    VRE-CIproject is funded by the Joint Information Systems Committee (JISC) to provide a framework to allow researchers and clinicians involved in Cancer Imaging to share information, images and algorithms.
    • JISC VRE frameworks phase 3.
    • 22 months 01/05/2009 – 28/02/2011.
    • Project Partner: Microsoft Research
    • Lee Dirks
    • Alex Wade
    • Roger Barga
    • Oscar Naim
    • Team members:
    • PI. Prof. Anne E. Trefethen
    • Co-I. Dr. Vicente Grau
    • Project Manager Dr. M. Susana Avila-Garcia.
    • Technical developers:
    • Xin Xiong, Charles Crichton and Andrew Tsui.
    • http://www.oerc.ox.ac.uk/research/vre-ci
  • Background
    • Implementing algorithms developed in the past by other researchers.
    • Sharing is an issue since they commonly use different programming tools, data sources and formats.
    • Reusing existing pieces of code.
    They work at different locations
    Computing Lab
    • Feedback
    • Researchers show resultson a computer/laptop screen.
    • Clinician do not have the opportunity to interact with the applications.
    • No user interface defined for clinicians.
  • Virtual Research Environment
    Sharing algorithm to:
    • Reuse it as it is.
    • Reuse it as part of a bigger solution.
    • Modify it.
    End users
    Research Context
    Share associated objects:
    • Original data sets.
    • Papers
    • Logs,
    • Links, etc.
    Web Services
    Test the algorithm:
    • Original data
    • Own data
    • Different image formats
    Scientific Workflows/
    • Open discussion forums.
    • Feedback
  • Scientific Workflows/ Trident
    • http://www.microsoft.com/mscorp/tc/trident.mspx
    This graphical representation hides the complexity of the applications allowing to:
    • understand at a high level how the application works,
    • modify the flow of activities in an easy way and
    • analyse the application into the level of required detail
  • VRE-CI
    Extend the functionality of the Research Information Centre (RIC) and include tools for articulating and sharing imaging algorithms through the integration of Trident.
  • Oxford University Groupware
    Oxford University has adopted a Microsoft solution as the integrated framework to support future communications and collaboration across the University.
    This project will provide an exemplar within the realm of the Virtual Research Environment and will result, we hope in a model that can be utilised in other parts of the University.
  • Use cases
    • Oncological image analysis
    • Researchers at Oxford University, Churchill Hospital and Microsoft Research Cambridge. Novel segmentation algorithms for colorectal cancer images.
    • Define research objects for the project and make them available to the team members.
    • Fluorescent microscopy.
    • Gray Institute for Radiation, Oncology and Biology.
    • Ensure the system is interoperable with existing image management systems.
  • Oncological image analysis
    Developments focus on:
    Image analysis:
    Define web services and web parts.
    Image functionality:
    Load Images
    DICOM, regular image formats.
    Search on image metadata.
    Image viewer.
  • Image analysis
  • Image analysis - Results
  • Loading images
  • Image metadata
    SharePoint Lists:
    • DICOM_Image
    • DICOM_Metadata
  • Search on image metadata
    Search on image metadata.
    Modality, Study Description and Keyword
    Keyword. (Modality, Anatomical part, Manufacturer, Place, Person, Date, Disease).
    • Search Operation: And, Or
  • Image Viewer
    Adapt an existing Deep Zoom viewer [http://images.cancergrid.org/score/]
    Need a DICOM image filter to convert to bmp or jpeg format.
    Developed using the Insight Toolkit ITK.
  • What is Silverlight DeepZoom?
    Multiple layers at different resolutions
    Enables quick zooming and panning of large images
    Requires Silverlight browser plugin
  • Trident Integration in RIC
    Demo developed in Microsoft Research:
    Kindly demonstrated by project manager Oscar Naim.
    Final deployment will require SharePoint 2010.
    Demo includes functionality to perform and track workflow executions.
    Future developments will include the workflow composer => Highly important for our project.
    At OeRC
    Tests to install RIC on SharePoint 2010.
    By defining our image processing as web-services we will easily be able to integrate them when they arrive
  • Summary
    Project update:
    Web service and web part defined for Level set algorithm.
    To be integrated as workflow activity.
    Information model definition for regular formats and MR, CT, US and PET DICOM images.
    Advanced search functionality
    Adaptation of Image viewer.
    Current activities:
    Installing the RIC on SharePoint 2010.
    Integrating image viewer and search functionality
    Feedback is being collected from the user pilot group to improve and enhance the system before making it available to a wider imaging research community.
  • Future work
    Image-based functionality
    Anonymise DICOM files uploaded into the system.
    Include functionality for additional formats: Analyze, Mhd images ROB image formats .
    Image viewer integration.
    • Remote Image Access
    • Create link to original datasets and keep low resolution copy at the server.
    Trident integration:
    Test Trident demo application in our setup.
    Define catalogue of activities for Trident.
  • Acknowledgements
    British Library – Stephen Andrews
    Niranjan Joshi
    Interviewees at Gray Institute of Radiation Oncology and Biology.
    Sean Smart, Danny Allen
  • Thanks!