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Open Access Research article

The development and validation of the Virtual Tissue Matrix, a software application that facilitates the review of tissue microarrays on line

Catherine M Conway1, Deirdre O'Shea2, Sallyann O'Brien3, Darragh K Lawler1, Graham D Dodrill1, Anthony O'Grady2, Helen Barrett2, Christian Gulmann2, Lorraine O'Driscoll1, William M Gallagher3, Elaine W Kay2 and Daniel G O'Shea1*

Author affiliations

1 Medical Informatics Group, School of Biotechnology, Dublin City University, Dublin, Ireland and National Institute for Cellular Biotechnology, Dublin City University, Dublin, Ireland

2 Department of Histopathology, Beaumont Hospital and Royal College of Surgeons, Dublin, Ireland

3 Centre for Molecular Medicine, Conway Institute of Biomolecular and Biomedical Research University College Dublin, Ireland

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Citation and License

BMC Bioinformatics 2006, 7:256  doi:10.1186/1471-2105-7-256

Published: 17 May 2006



The Tissue Microarray (TMA) facilitates high-throughput analysis of hundreds of tissue specimens simultaneously. However, bottlenecks in the storage and manipulation of the data generated from TMA reviews have become apparent. A number of software applications have been developed to assist in image and data management; however no solution currently facilitates the easy online review, scoring and subsequent storage of images and data associated with TMA experimentation.


This paper describes the design, development and validation of the Virtual Tissue Matrix (VTM). Through an intuitive HTML driven user interface, the VTM provides digital/virtual slide based images of each TMA core and a means to record observations on each TMA spot. Data generated from a TMA review is stored in an associated relational database, which facilitates the use of flexible scoring forms. The system allows multiple users to record their interpretation of each TMA spot for any parameters assessed. Images generated for the VTM were captured using a standard background lighting intensity and corrective algorithms were applied to each image to eliminate any background lighting hue inconsistencies or vignetting.

Validation of the VTM involved examination of inter-and intra-observer variability between microscope and digital TMA reviews. Six bladder TMAs were immunohistochemically stained for E-Cadherin, β-Catenin and PhosphoMet and were assessed by two reviewers for the amount of core and tumour present, the amount and intensity of membrane, cytoplasmic and nuclear staining.


Results show that digital VTM images are representative of the original tissue viewed with a microscope. There were equivalent levels of inter-and intra-observer agreement for five out of the eight parameters assessed. Results also suggest that digital reviews may correct potential problems experienced when reviewing TMAs using a microscope, for example, removal of background lighting variance and tint, and potential disorientation of the reviewer, which may have resulted in the discrepancies evident in the remaining three parameters.