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Open Access Software

A metadata-aware application for remote scoring and exchange of tissue microarray images

Lorna Morris1, Andrew Tsui4, Charles Crichton4, Steve Harris4, Peter H Maccallum1, William J Howat1, Jim Davies4, James D Brenton123 and Carlos Caldas123*

Author Affiliations

1 Department of Oncology, University of Cambridge and Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK

2 Cambridge Experimental Cancer Medicine Centre, Li Ka Shing Centre, Cambridge, CB2 0RE, UK

3 Addenbrooke’s Hospital, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 2QQ, UK

4 Department of Computer Science, University of Oxford, Wolfson Building, Parks Road, Oxford, OX1 3QD, UK

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BMC Bioinformatics 2013, 14:147  doi:10.1186/1471-2105-14-147

Published: 1 May 2013

Abstract

Background

The use of tissue microarrays (TMA) and advances in digital scanning microscopy has enabled the collection of thousands of tissue images. There is a need for software tools to annotate, query and share this data amongst researchers in different physical locations.

Results

We have developed an open source web-based application for remote scoring of TMA images, which exploits the value of Microsoft Silverlight Deep Zoom to provide a intuitive interface for zooming and panning around digital images. We use and extend existing XML-based standards to ensure that the data collected can be archived and that our system is interoperable with other standards-compliant systems.

Conclusion

The application has been used for multi-centre scoring of TMA slides composed of tissues from several Phase III breast cancer trials and ten different studies participating in the International Breast Cancer Association Consortium (BCAC). The system has enabled researchers to simultaneously score large collections of TMA and export the standardised data to integrate with pathological and clinical outcome data, thereby facilitating biomarker discovery.

Keywords:
Tissue microarray; TMA; Metadata; XML; Software