RIC Workshop 26 July 2010 A Virtual Research Environment for Cancer Imaging (VRE-CI)
Outline <ul><li>Background </li></ul><ul><li>Project Overview </li></ul><ul><li>DICOM Image functionality </li></ul><ul><l...
Background <ul><li>Implementing algorithms developed in the past by other researchers. </li></ul><ul><li>Reusing existing ...
Virtual Research Environment Research Context Web Services  Code  Scientific Workflows/ Activities  End users <ul><li>Shar...
VRE-CI   project is funded by the Joint Information Systems Committee (JISC) to provide a framework to allow researchers a...
VRE-CI
Use cases <ul><li>Oncological image analysis </li></ul><ul><ul><ul><li>Leveraging the work of an existing Microsoft funded...
Project Outputs <ul><li>Module for Cancer Imaging: </li></ul><ul><ul><li>Sharing DICOM images </li></ul></ul><ul><ul><ul><...
Loading images into the system <ul><li>More secure way to make images available to researchers.  </li></ul><ul><ul><li>Ens...
Subjects Confidential information Anonymised data sets No confidential information No need to remove any metadata Define p...
Configuration Files Use of configuration files to personalise metadata filters according to each user preferences.
Loading images
Image Metadata
Dicom Image Properties / Zoom in
Image Viewer <ul><li>Adapt an existing Deep Zoom viewer  [ http://images.cancergrid.org/score/ ] </li></ul><ul><li>Need a ...
What is Silverlight DeepZoom? <ul><li>Multiple layers at different resolutions </li></ul><ul><li>Enables quick zooming and...
Image Viewer / Deep zoom functionality
 
Image analysis
Scientific Workflows/ Trident <ul><li>This graphical representation hides the complexity of the applications allowing to: ...
Oxford University Groupware <ul><li>Oxford University has adopted a Microsoft solution as the integrated framework to supp...
SharePoint 2010 Pros & Cons <ul><li>Pros: </li></ul><ul><li>When University has the license </li></ul><ul><li>Can be suppo...
Acknowledgements <ul><li>Dr Niranjan Joshi </li></ul><ul><li>Interviewees at Gray Institute of Radiation Oncology and Biol...
Thanks!
Questions? <ul><li>Project website:    http://www.oerc.ox.ac.uk/research/vre-ci </li></ul>
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Virtual Research Environment for Cancer Imaging

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Presented by Maria Susanna Avila Garcia at the JISC Future of Research Conference, 19th October 2010

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  • Multiple layers at different resolutions Enable quick zooming and panning of large images Requires Silverlight browser plugin
  • Virtual Research Environment for Cancer Imaging

    1. 1. RIC Workshop 26 July 2010 A Virtual Research Environment for Cancer Imaging (VRE-CI)
    2. 2. Outline <ul><li>Background </li></ul><ul><li>Project Overview </li></ul><ul><li>DICOM Image functionality </li></ul><ul><li>Image analysis </li></ul><ul><li>Sharing project outputs </li></ul><ul><li>Questions </li></ul>
    3. 3. Background <ul><li>Implementing algorithms developed in the past by other researchers. </li></ul><ul><li>Reusing existing pieces of code. </li></ul><ul><li>Sharing is an issue since they commonly use different programming tools, data sources and formats. </li></ul><ul><li>Feedback </li></ul><ul><ul><li>Show result on a computer/laptop screen. </li></ul></ul><ul><ul><li>Do not have the opportunity to interact with the applications. </li></ul></ul><ul><ul><li>No user interface defined for them </li></ul></ul>They work at different locations Computing Lab Hospital Sharing image datasets.
    4. 4. Virtual Research Environment Research Context Web Services Code Scientific Workflows/ Activities End users <ul><li>Sharing algorithm to: </li></ul><ul><li>Reuse it as it is. </li></ul><ul><li>Reuse it as part of a bigger solution. </li></ul><ul><li>Modify it. </li></ul><ul><li>Test the algorithm: </li></ul><ul><li>Original data </li></ul><ul><li>Own data </li></ul><ul><ul><li>Different image formats </li></ul></ul>
    5. 5. VRE-CI project 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. A Virtual Research Environment for Cancer Imaging (VRE-CI) <ul><li>JISC VRE frameworks phase 3. </li></ul><ul><li>22 months 01/05/2009 – 28/02/2011. </li></ul><ul><li>Project Partner: Microsoft Research </li></ul><ul><ul><li>Lee Dirks </li></ul></ul><ul><ul><li>Alex Wade </li></ul></ul><ul><ul><li>Roger Barga </li></ul></ul><ul><li>Team members: </li></ul><ul><ul><li>PI. Prof. Anne E. Trefethen </li></ul></ul><ul><ul><li>Co-I. Dr. Vicente Grau </li></ul></ul><ul><ul><li>Project Manager Dr. M. Susana Avila-Garcia. </li></ul></ul><ul><ul><li>Technical developers: Xin Xiong, Charles Crichton and Andrew Tsui. </li></ul></ul>
    6. 6. VRE-CI
    7. 7. Use cases <ul><li>Oncological image analysis </li></ul><ul><ul><ul><li>Leveraging the work of an existing Microsoft funded project on the development of novel segmentation algorithms for colorectal cancer images. </li></ul></ul></ul><ul><ul><ul><li>Use case to ensure that the main elements of cancer imaging research are considered. </li></ul></ul></ul><ul><li>Fluorescent microscopy. </li></ul><ul><ul><ul><li>Gray Institute of Radiation, Oncology and Biology. </li></ul></ul></ul><ul><ul><ul><li>Ensure the system is interoperable with existing image management systems . </li></ul></ul></ul>
    8. 8. Project Outputs <ul><li>Module for Cancer Imaging: </li></ul><ul><ul><li>Sharing DICOM images </li></ul></ul><ul><ul><ul><li>Load in the system </li></ul></ul></ul><ul><ul><ul><li>Creating links to other servers </li></ul></ul></ul><ul><ul><li>Sharing Image processing algorithms: </li></ul></ul><ul><ul><ul><li>Workflows/activities </li></ul></ul></ul><ul><ul><ul><li>Web services </li></ul></ul></ul><ul><ul><li>Advanced search. </li></ul></ul><ul><ul><ul><li>Image DICOM & Keyword metadata </li></ul></ul></ul><ul><ul><ul><li>Algorithms </li></ul></ul></ul><ul><li>Architecture being defined to add more image formats, algorithms. </li></ul>
    9. 9. Loading images into the system <ul><li>More secure way to make images available to researchers. </li></ul><ul><ul><li>Ensuring datasets are ‘validated’. </li></ul></ul><ul><ul><li>Avoid storing data in media that might not be stored/managed securely. </li></ul></ul><ul><li>Clinicians may have a way to track which datasets they have made available and the associated results back from researchers. </li></ul>
    10. 10. Subjects Confidential information Anonymised data sets No confidential information No need to remove any metadata Define personalised filters to fit needs from each user/research scenario
    11. 11. Configuration Files Use of configuration files to personalise metadata filters according to each user preferences.
    12. 12. Loading images
    13. 13. Image Metadata
    14. 14. Dicom Image Properties / Zoom in
    15. 15. Image Viewer <ul><li>Adapt an existing Deep Zoom viewer [ http://images.cancergrid.org/score/ ] </li></ul><ul><li>Need a DICOM image filter to convert to bmp or jpeg format. </li></ul><ul><ul><li>Developed using the Insight Toolkit ITK. </li></ul></ul>
    16. 16. What is Silverlight DeepZoom? <ul><li>Multiple layers at different resolutions </li></ul><ul><li>Enables quick zooming and panning of large images </li></ul><ul><li>Requires Silverlight browser plugin </li></ul>
    17. 17. Image Viewer / Deep zoom functionality
    18. 19. Image analysis
    19. 20. Scientific Workflows/ Trident <ul><li>This graphical representation hides the complexity of the applications allowing to: </li></ul><ul><li>understand at a high level how the application works, </li></ul><ul><li>modify the flow of activities in an easy way and </li></ul><ul><li>analyse the application into the level of required detail </li></ul><ul><ul><li>http://www.microsoft.com/mscorp/tc/trident.mspx </li></ul></ul>
    20. 21. Oxford University Groupware <ul><li>Oxford University has adopted a Microsoft solution as the integrated framework to support future communications and collaboration across the University. </li></ul><ul><li>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. </li></ul>
    21. 22. SharePoint 2010 Pros & Cons <ul><li>Pros: </li></ul><ul><li>When University has the license </li></ul><ul><li>Can be supported on the cloud </li></ul><ul><ul><li>SP admin not required </li></ul></ul><ul><ul><li>Could lead to more effective (cheaper) use of computer systems. </li></ul></ul><ul><ul><li>Could lead to less computer support required. </li></ul></ul><ul><li>Cons: </li></ul><ul><li>If not this is expensive </li></ul><ul><li>Uncertain business model at this time </li></ul>
    22. 23. Acknowledgements <ul><li>Dr Niranjan Joshi </li></ul><ul><li>Interviewees at Gray Institute of Radiation Oncology and Biology. </li></ul><ul><ul><li>Sean Smart, Danny Allen </li></ul></ul><ul><ul><li>Veerle Kersemans & Bart Cornelissen. </li></ul></ul><ul><li>Advisory committee. </li></ul><ul><ul><li>Peter Jezzard, Paul Watson. </li></ul></ul>British Library – Stephen Andrews
    23. 24. Thanks!
    24. 25. Questions? <ul><li>Project website: http://www.oerc.ox.ac.uk/research/vre-ci </li></ul>

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