Edinburgh Pathology

Dr Peter Bankhead

Senior Lecturer

+44 (0)131 651 8734
 

MRC Institute of Genetics and Molecular Medicine

University of Edinburgh

Western General Hospital

Crewe Road South

Edinburgh

EH4 2XR

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 I continue to develop and maintain QuPath as part of my work.

Web Links

QuPath

Full publication list

Collaborators

Dr Yvonne Dombrowski, Queen’s University Belfast

Dr Maurice Loughrey, Queen’s University Belfast

Dr Carlos Moro, Karolinska University Hospital

Selected Publications

Bankhead P, Loughrey MB, Fernández JA, Dombrowski Y, McArt DG, Dunne PD, McQuaid S, Gray RT, Murray LJ, Coleman HG, James JA, Salto-Tellez M, Hamilton PW (2017) QuPath: Open source software for digital pathology image analysis. Sci Rep 7:16878

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 (2017) Integrated tumor identification and automated scoring minimizes pathologist involvement and provides new insights to key biomarkers in breast cancer. Lab Invest 98:15–26

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 I V., Kissenpfennig A, Moynagh PN, Evergren E, Perbal B, Williams AC, Ingram RJ, Chan JR, Franklin RJM, Fitzgerald DC (2017) Regulatory T cells promote myelin regeneration in the central nervous system. Nat Neurosci 20:674–680

Hamilton PW, Bankhead P, Wang Y, Hutchinson R, Kieran D, McArt D, James J, Salto-Tellez M (2014) Digital pathology and image analysis in tissue biomarker research. Methods 70:59–73

McArt DG, Bankhead P, Dunne PD, Hamilton P, Zhang S (2013) cudaMap : a GPU accelerated program aiding in high throughput therapeutic candidate selection. Bioinformatics 14:305

Bankhead P, Scholfield CN, McGeown JG, Curtis TM (2012) Fast retinal vessel detection and measurement using wavelets and edge location refinement. PLoS One 7