Dr Peter Bankhead

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Current Research

My main research focus is bioimage analysis and digital pathology. I am especially interested in developing new and practical approaches to analyse whole slide scans of tissue, collaborating with pathologists and other researchers to apply these methods to answer important biomedical questions.

A major challenge in working with whole slide images is their size and complexity: a typical scan may be up to 50 GB in size and contain several million cells. The analysis of these datasets involves combining conventional image processing and machine learning techniques with deep learning to interrogate the data at multiple resolutions.

My work is motivated by the belief that it is not only important to develop new algorithms, but also to make these algorithms efficient, intuitive, and accessible to other researchers. With this in mind, I created the QuPath open source digital pathology platform. This software is used by labs across the world for a wide range of image analysis applications, and my research group and I continue to maintain and advance QuPath as part of our work.

Web Links

QuPath

Full publication list

Introduction to Biomage Analysis

Centre for Genomic & Experimental Medicine profile

Selected Publications

Bankhead P, Loughrey MB, Fernández JA, Dombrowski Y, McArt DG, Dunne PD, McQuaid S, Gray RT, Murray LJ, Coleman HG, James J A, Salto-Tellez M, & Hamilton PW "QuPath: Open source software for digital pathology image analysis", Scientific Reports, 7, [16878], doi:10.1038/s41598-017-17204-5, 2017

Bankhead P, "Developing image analysis methods for digital pathology", J. Pathol., 257: 391-402, doi:10.1002/path.5921, 2022

Levet F, Carpenter AE, Eliceiri KW, Kreshuk A, Bankhead P, & Haase R, "Developing open-source software for bioimage analysis: opportunities and challenges", F1000Research, 10, 302, doi:10.12688/f1000research.52531.1, 2021

Fisher NC, Loughrey MB, Coleman HG, Gelbard MD, Bankhead P, & Dunne PD, "Development of a semi‐automated method for tumour budding assessment in colorectal cancer and comparison with manual methods", Histopathology 80, 485– 500, doi:10.1111/his.14574, 2022

Bankhead P, Fernández JA, McArt DG, Boyle DP, Li G, Loughrey MB, Irwin GW, Harkin DP, James JA, McQuaid S, Salto-Tellez M, & Hamilton PW, "Integrated tumor identification and automated scoring minimizes pathologist involvement and provides new insights to key biomarkers in breast cancer", Laboratory investigation 98(1), 15-26, doi:10.1038/labinvest.2017.131, 2018

Dombrowski Y, O'Hagan T, Dittmer M, Penalva R, Mayoral SR, Bankhead P, Fleville S, Eleftheriadis G, Zhao C, Naughton M, Hassan R, Moffat J, Falconer J, Boyd A, Hamilton P, Allen IV, Kissenpfennig A, Moynagh PN, Evergren E,Perbal B, Williams AC, Ingram RJ, Chan JR, Franklin RJM, & Fitzgerald DC, "Regulatory T cells promote myelin regeneration in the central nervous system", Nature Neuroscience, 20(5), 674-680, doi:10.1038/nn.4528, 2017