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QuPath: Open source software for digital pathology image analysis

View ORCID ProfilePeter Bankhead, Maurice B Loughrey, José A Fernández, Yvonne Dombrowski, Darragh G McArt, Philip D Dunne, Stephen McQuaid, Ronan T Gray, Liam J Murray, Helen G Coleman, Jacqueline A James, Manuel Salto-Tellez, Peter W Hamilton
doi: https://doi.org/10.1101/099796
Peter Bankhead
1Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland, UK
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  • ORCID record for Peter Bankhead
Maurice B Loughrey
1Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland, UK
2Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland, Northern Ireland, UK
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José A Fernández
1Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland, UK
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Yvonne Dombrowski
3Centre for Experimental Medicine, Queen’s University Belfast, Belfast, Northern Ireland, UK
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Darragh G McArt
1Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland, UK
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Philip D Dunne
1Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland, UK
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Stephen McQuaid
1Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland, UK
2Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland, Northern Ireland, UK
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Ronan T Gray
4Cancer Epidemiology and Health Services Research Group, Centre for Public Health, Queen’s University Belfast, Belfast, Northern Ireland, UK
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Liam J Murray
4Cancer Epidemiology and Health Services Research Group, Centre for Public Health, Queen’s University Belfast, Belfast, Northern Ireland, UK
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Helen G Coleman
4Cancer Epidemiology and Health Services Research Group, Centre for Public Health, Queen’s University Belfast, Belfast, Northern Ireland, UK
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Jacqueline A James
1Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland, UK
2Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland, Northern Ireland, UK
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Manuel Salto-Tellez
1Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland, UK
2Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland, Northern Ireland, UK
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  • For correspondence: m.Salto-tellez@qub.ac.uk p.hamilton@qub.ac.uk
Peter W Hamilton
1Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland, UK
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  • For correspondence: m.Salto-tellez@qub.ac.uk p.hamilton@qub.ac.uk
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Abstract

QuPath is new bioimage analysis software designed to meet the growing need for a user-friendly, extensible, open-source solution for digital pathology and whole slide image analysis. In addition to offering a comprehensive panel of tumor identification and high-throughput biomarker evaluation tools, QuPath provides researchers with powerful batch-processing and scripting functionality, and an extensible platform with which to develop and share new algorithms to analyze complex tissue images. Furthermore, QuPath’s flexible design makes it suitable for a wide range of additional image analysis applications across biomedical research.

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Posted March 06, 2017.
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QuPath: Open source software for digital pathology image analysis
Peter Bankhead, Maurice B Loughrey, José A Fernández, Yvonne Dombrowski, Darragh G McArt, Philip D Dunne, Stephen McQuaid, Ronan T Gray, Liam J Murray, Helen G Coleman, Jacqueline A James, Manuel Salto-Tellez, Peter W Hamilton
bioRxiv 099796; doi: https://doi.org/10.1101/099796
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QuPath: Open source software for digital pathology image analysis
Peter Bankhead, Maurice B Loughrey, José A Fernández, Yvonne Dombrowski, Darragh G McArt, Philip D Dunne, Stephen McQuaid, Ronan T Gray, Liam J Murray, Helen G Coleman, Jacqueline A James, Manuel Salto-Tellez, Peter W Hamilton
bioRxiv 099796; doi: https://doi.org/10.1101/099796

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