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SJ Roostee, J Staaf, M Aine (Department of Clinical Sciences Division of Oncology Lund University Medicon Village SE-223 81 Lund Sweden)
The work we present here revolves around standardising the quantification of tissue microarray cores and increasing throughput of them in a research setting. We have developed an unsupervised image analysis pipeline for this and tested it on a breast cancer cohort. Breast cancer is the most common cancer among women world wide. Immunohistochemical examination is used here for molecular subtyping. This manual work is carried out by pathologists. However, standardisation and high throughput are ongoing challenges here. The development of automated tools could improve reproducibility and increase the throughput of TMA analysis. The results we show here are from the B-cell marker CD20 and are compared to pathologist estimates. We show that estimated positive cell counts output by this pipeline show a trend that matches pathologist estimates.