Astronomical Image Handling - Application to TMA Analysis: Exploiting AstroGrid/ CancerGrid Systems

Lead Research Organisation: University of Cambridge
Department Name: Institute of Astronomy

Abstract

Cancers result from the accumulation of genetic changes, with changes
in the genome of the cancer cells disrupting normal cellular
functions. Tracking the causes, and predicting the effects and impact
of treatments is a complex problem, involving the the integration and
analysis of multi-dimensional datasets. Large clinical studies,
involving many thousands of patients) are now underway in the UK aimed
at providing vital evidence to support the investigation of the causes
of a significant range of cancers. A key challenge is providing an
interface between for instance epidemiological trials data and high
volume data from tissue micro-arrays (used to for instance identify
markers for breast cancer classification).

The CancerGrid project is providing an e-infrastructure to to support
e-clinical trials. AstroGrid has developed a framework to support the
the discovery and analysis of large distributed astronomical images
using the latest developments in distributed computation. The
scientific data itself is generated by sophisticated image processing
pipelines acting on the raw observational data.

The aim of this programme is explore novel uses of techniques
developed in the astronomical domain to provide solutions for the
challenges inherent in the analysis and integration of the large
medical imagery. This will include use of image analysis algorithms
optimised for feature classification, integration of statistical
applications in a workflow environment, and interface of the resulting
richly annotated results to the medical CancerGrid created information
infrastructure.

Outcomes from this programme will be designs and prototypes of new
information systems to support the handling of these large distributed
data flows, and increased collaborative pathways between these key
medical and astronomical groups.

Technical Summary

CancerGrid is a key MRC eScience programme that is developing open
standards for clinical cancer informatics by developing a
model-driven, document-centric architecture to manage and use the
complex data gathered in cancer clinical trials so that this can be
used for linked translational tissue-based research. Tissue
microarrays (TMA) from approximately 10,000 breast cancer samples from
four clinical studies are being constructed and will be linked to
their associated clinical data using a set of interoperable Common
Data Elements (CDEs) to represent concepts and measurements from the
trial. Analysis of this extensive image and clinical data is being
carried out to identify markers for breast cancer classification and
outcome. AstroGrid (http://www.astrogrid.org) has developed a Virtual
Observatory (VO) infrastructure, based on open standards, which
provides a data discovery and analysis environment for
astronomers. The Cambridge AstroGrid Survey Unit (CASU)
(http://casu.ast.cam.ac.uk) has developed a sophisticated image
analysis pipeline system.

This programme will bring together key intellectual leaders of these
two major eScience projects located in Cambridge. It will enable the
investigation of novel techniques to be transferred to provide
solutions to a number of key needs, supporting the integration of
digital imaging data with clinical trials information. These
techniques include the application of astronomical image analysis
algorithms optimised for feature recognition, the application of
statistical environments such as R, through an integrated workflow
system to enable large scale statistical analysis of resulting
annotated object catalogues, use of distributed e-science
infrastructural frameworks to facilitate multi-TB image data flows.

In the longer term improved collaborative work between the larger
multi-institute groups associated with these projects will result,
thereby leveraging the value of capabilities developed in the PPARC
eScience to the benefit of the CancerGrid and related
projects. Techniques investigated during this programme will be further
developed to form the basis of significant new information handling
systems supporting research programmes such determining markers for
breast cancer.

Publications

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publication icon
Walton NA (2010) PathGrid: a service-orientated architecture for microscopy image analysis. in Philosophical transactions. Series A, Mathematical, physical, and engineering sciences

publication icon
Walton, Nicholas (2009) PathGrid: The Transfer of Astronomical Image Algorithms to the Analysis of Medical Microscopy Data in Astronomical Data Analysis Software and Systems XVIII ASP Conference Series

 
Description STFC Impact Acceleration Account Pilot Program
Amount £9,250 (GIP)
Organisation Science and Technologies Facilities Council (STFC) 
Sector Academic/University
Country United Kingdom
Start 05/2014 
End 12/2014
 
Description miniPIPSS
Amount £83,604 (GBP)
Funding ID ST/G003556/1 
Organisation Science and Technologies Facilities Council (STFC) 
Sector Academic/University
Country United Kingdom
Start 10/2008 
End 10/2009
 
Description Oracle - PathGrid partnership 
Organisation Oracle Corporation
Department Oracle EMEA
Country United States 
Sector Private 
PI Contribution Further development of the PathGrid infrastructure
Collaborator Contribution Oracle have provided technical advice and expertise in the form of contributed effort to the PathGrid team
Impact The Oracle partnership has provided additional support to the development of the PathGrid project - through the STFC miniPIPSS programme, and now (2009) through potential direct support.
Start Year 2008
 
Description PathGrid-CRUK 
Organisation Cancer Research UK Cambridge Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution The IoA provide acces to astronomical image analysis techniques, and workflow and data distribution mechanisms.
Collaborator Contribution The CR-UK team is now an active partner in the continuing PathGrid programme.
Impact Multi-disciplinary - astronomy, computation, image analysis, cancer genomics Paper: PathGrid: a service-orientated architecture for microscopy image analysis, N. A. Walton, J. D. Brenton et al, Phil. Trans. R. Soc. A 28 August 2010 vol. 368 no. 1925 3937-3952 Paper: PathGrid: The Transfer of Astronomical Image Algorithms to the Analysis of Medical Microscopy Data - Walton, N. A.; Brenton, J. D.; Caldas, C.; Irwin, M. J.; Akram, A.; Gonzalez-Solares, E.; Lewis, J. R.; MacCullum, P.; Morris, L. J.; Rixon, G. T.: Astronomical Data Analysis Software and Systems XVIII ASP Conference Series, Vol. 411, proceedings of the conference held 2-5 November 2008 at Hotel Loews Le Concorde, Québec City, QC, Canada. Edited by David A. Bohlender, Daniel Durand, and Patrick Dowler. San Francisco: Astronomical Society of the Pacific, 2009., p.77
Start Year 2006
 
Title PathGrid-Pipeline 
Description PathGrid has developed a flexible and scalable image processing, access and databasd infrastructure for IHC microscopy data. This is supporting the discovery of new Bio-Markers at CRI, CR-UK. 
Type Support Tool - For Medical Intervention
Current Stage Of Development Early clinical assessment
Year Development Stage Completed 2009
Development Status Actively seeking support
Impact The image analysis pipeline from PathGrid is being used in support of biomarker diiscovery at CRI, CR-UK. It is also under trial for use within the Institute for Food research. 
 
Description Cancer Research UK Legacy Presentation Jul 13 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact LEGACY PIONEERS EVENT - LEICESTER 2 Jul 2013.

EVENT INFO
Our pioneer event is designed to engage supporters who have helped in the work that we do and inspire them to consider leaving a gift to Cancer Research UK in their Will

I gave a talk on the PathGrid work.

Increased legacy donations to Cancer Research UK
Year(s) Of Engagement Activity 2013
 
Description Science Data Article 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Major component of a main news and analysis article in a Science special issue on Data - Is There an Astronomer in the House? - vol 331 Feb 2011

Followup interest from academics and media.
Year(s) Of Engagement Activity 2011
 
Description Times PathGrid news article 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Page article in The Times - Sat Aug 14 2010 - 'Advances in cancer
treatment could be astronomical: Stargazer technology can monitor tumours'

This is leading to further interest - for instance a long news article will shortly be published in Science highlighting the knowledge transfer aspects of this collaboration with the interactions between the astronomy and medical domains.
Year(s) Of Engagement Activity 2010