Efficiency and Effectiveness: Shared services to support STEM subjects


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  • Efficiency and Effectiveness: Shared services to support STEM subjects

    1. 1. A Virtual Research Environment for Cancer Imaging (VRE-CI)<br />RIC Workshop<br />26 July 2010<br />
    2. 2. Outline<br />Background<br />Project Overview<br />DICOM Image functionality<br />Image analysis<br />Sharing project outputs<br />Questions<br />
    3. 3. Background<br /><ul><li>Implementing algorithms developed in the past by other researchers.
    4. 4. Reusing existing pieces of code.
    5. 5. Sharing is an issue since they commonly use different programming tools, data sources and formats. </li></ul>?<br />They work at different locations <br />Computing Lab<br />Sharing image datasets.<br /><ul><li>Feedback
    6. 6. Show result on a computer/laptop screen.
    7. 7. Do not have the opportunity to interact with the applications.
    8. 8. No user interface defined for them </li></ul>Hospital<br />
    9. 9. Virtual Research Environment<br />End users<br />Sharing algorithm to:<br /><ul><li>Reuse it as it is.
    10. 10. Reuse it as part of a bigger solution.
    11. 11. Modify it. </li></ul>Research Context<br />Code <br />Web Services <br />Test the algorithm:<br /><ul><li> Original data
    12. 12. Own data
    13. 13. Different image formats</li></ul>Scientific Workflows/<br />Activities <br />
    14. 14. A Virtual Research Environment for Cancer Imaging (VRE-CI)<br />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.<br /><ul><li> JISC VRE frameworks phase 3.
    15. 15. 22 months 01/05/2009 – 28/02/2011.
    16. 16. Project Partner: Microsoft Research
    17. 17. Lee Dirks
    18. 18. Alex Wade
    19. 19. Roger Barga
    20. 20. Team members:
    21. 21. PI. Prof. Anne E. Trefethen
    22. 22. Co-I. Dr. Vicente Grau
    23. 23. Project Manager Dr. M. Susana Avila-Garcia.
    24. 24. Technical developers: Xin Xiong, Charles Crichton and Andrew Tsui.</li></li></ul><li>VRE-CI<br />
    25. 25. Use cases<br /><ul><li>Oncological image analysis
    26. 26. Leveraging the work of an existing Microsoft funded project on the development of novel segmentation algorithms for colorectal cancer images.
    27. 27. Use case to ensure that the main elements of cancer imaging research are considered.
    28. 28. Fluorescent microscopy.
    29. 29. Gray Institute of Radiation, Oncology and Biology.
    30. 30. Ensure the system is interoperable with existing image management systems. </li></li></ul><li>Project Outputs<br />Module for Cancer Imaging:<br />Sharing DICOM images<br />Load in the system<br />Creating links to other servers<br />Sharing Image processing algorithms:<br />Workflows/activities<br />Web services<br />Advanced search. <br />Image DICOM & Keyword metadata<br />Algorithms<br />Architecture being defined to add more image formats, algorithms.<br />
    31. 31. Loading images into the system<br />More secure way to make images available to researchers. <br />Ensuring datasets are ‘validated’. <br />Avoid storing data in media that might not be stored/managed securely. <br />Clinicians may have a way to track which datasets they have made available and the associated results back from researchers. <br />
    32. 32. Subjects<br />No confidential information<br />Confidential information<br />No need to remove any metadata<br />Anonymised data sets<br />Define personalised filters to fit needs from each user/research scenario <br />
    33. 33. Configuration Files<br />Use of configuration files to personalise metadata filters according to each user preferences. <br />
    34. 34. Loading images<br />
    35. 35. Image Metadata<br />
    36. 36. Dicom Image Properties / Zoom in <br />
    37. 37. Image Viewer<br />Adapt an existing Deep Zoom viewer [http://images.cancergrid.org/score/]<br />Need a DICOM image filter to convert to bmp or jpeg format. <br />Developed using the Insight Toolkit ITK. <br />
    38. 38. What is Silverlight DeepZoom?<br />Multiple layers at different resolutions<br />Enables quick zooming and panning of large images<br />Requires Silverlight browser plugin<br />
    39. 39. Image Viewer / Deep zoom functionality<br />
    40. 40.
    41. 41. Image analysis<br />
    42. 42. Scientific Workflows/ Trident<br /><ul><li>http://www.microsoft.com/mscorp/tc/trident.mspx</li></ul>This graphical representation hides the complexity of the applications allowing to: <br /><ul><li>understand at a high level how the application works,
    43. 43. modify the flow of activities in an easy way and
    44. 44. analyse the application into the level of required detail</li></li></ul><li>Oxford University Groupware<br />Oxford University has adopted a Microsoft solution as the integrated framework to support future communications and collaboration across the University.<br />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. <br />
    45. 45. SharePoint 2010 Pros & Cons<br />Pros:<br /><ul><li>When University has the license
    46. 46. Can be supported on the cloud
    47. 47. SP admin not required
    48. 48. Could lead to more effective (cheaper) use of computer systems.
    49. 49. Could lead to less computer support required. </li></ul>Cons:<br /><ul><li>If not this is expensive
    50. 50. Uncertain business model at this time</li></li></ul><li>Acknowledgements<br />British Library – Stephen Andrews<br />Dr Niranjan Joshi<br />Interviewees at Gray Institute of Radiation Oncology and Biology. <br />Sean Smart, Danny Allen<br />VeerleKersemans & Bart Cornelissen.<br />Advisory committee.<br />Peter Jezzard, Paul Watson.<br />
    51. 51. Thanks!<br />
    52. 52. Questions?<br />Project website: http://www.oerc.ox.ac.uk/research/vre-ci<br />