QuArray: an application for tissue array whole slide image export and signal analysis
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1Prostate Cancer Research Centre at the Centre for Stem Cells and Regenerative Medicine, King's College London, SE1 9RT London, UK.
Motivation:
Tissue array (TA) staining, combined with whole slide imaging (WSI) methods facilitate discovery of biomarkers for diagnosis, prognostication and disease stratification. A key impediment in TA WSI analysis is handling missing tissue and artefacts when identifying tissue cores before quantitative, standardized downstream analysis. There is a need for an open access, user friendly, integrated analysis of the WSI generated using TAs in clinical and scientific research laboratories.
Results:
We have developed QuArray (Quantitative Array Application) for image export and signal analysis of TAs using WSI. The application input is a WSI and a corresponding TA configuration file. QuArray identifies and exports core images and analyses chromogen staining in a simple graphical user interface. Output data is saved to file for further analysis including indexed data.
Availabilityand Implementation:
Available for download from https://github.com/c-arthurs/QuArray under an MIT licence.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
