RIC Workshop

26 July 2010

A Virtual Research Environment for Cancer Imaging (VRE-CI)

Outline

Project Overview Background VRE-CI Progress Current activities Future Work Questions

A Virtual Research Environment for Cancer Imaging (VRE-CI)

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. JISC VRE frameworks phase 3. 22 months 01/05/2009 – 28/02/2011. Project Partner: Microsoft Research

Lee DirksAlex WadeRoger 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.

?

Feedback Researchers show results on a computer/laptop

screen. Clinician do not have the opportunity to interact with

the applications. No user interface defined for clinicians.

They work at different locations Computing Lab

Hospital

Virtual Research Environment

Research Context

• Open discussion forums.• Feedback

Web Services

Code

Scientific Workflows/Activities

End usersSharing algorithm to:• Reuse it as it is.• Reuse it as part of a bigger

solution.• Modify it.

Share associated objects:• Original data sets.• Papers• Logs,• Links, etc. Test the algorithm:

• Original data• Own data

• Different image formats

Scientific Workflows/ Trident

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

– http://www.microsoft.com/mscorp/tc/trident.mspx

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:

1. Load Images– DICOM, regular image formats.

2. Search on image metadata.

3. 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

Niranjan Joshi Interviewees at Gray Institute of Radiation

Oncology and Biology. Sean Smart, Danny Allen

British Library – Stephen Andrews

Thanks!