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Research Publications

Publication List


Here you will find a comprehensive list of publications from members of our team.

2020


Emily L. Clarke, Craig Munnings, Bethany Williams, David Brettle, Darren Treanor (2020) Display evaluation for primary diagnosis using digital pathology external site symbol (White Rose Research Online) J. Med. Imag. 7(2), 027501 (2020), doi: 10.1117/1.JMI.7.2.027501.

Bethany Jill Williams, David Brettle, Muhammad Aslam, Paul Barrett, Gareth Bryson, Simon Cross, David Snead, Clare Verrill, Emily Clarke, Alexander Wright, Darren Treanor (2020) Guidance for remote reporting of digital pathology slides during periods of exceptional service pressure: An emergency response from the UK royal college of pathologists. external site symbol J Pathol Inform 2020, 11:12

Bethany Jill Williams, Azzam Ismail, Arundhati Chakrabarty, Darren Treanor (2020) Clinical digital neuropathology: experience and observations from a departmental digital pathology training programme, validation and deployment. external site symbol Journal of Clinical Pathology 2019;


2019


Williams BJ, Knowles C, Treanor D (2019)
Maintaining quality diagnosis with digital pathology: a practical guide to ISO 15189 accreditation external site symbol

Journal of Clinical Pathology 2019;72:663-668.

Williams BJ, Jayewardene D, Treanor D (2019)
Digital immunohistochemistry implementation, training and validation: experience and technical notes from a large clinical laboratory external site symbol

Journal of Clinical Pathology 2019;72:373-378.

Clarke EL, Brettle D, Sykes A, Wright A, Boden A, Treanor D (2019)
Development and Evaluation of a Novel Point-of-Use Quality Assurance Tool for Digital Pathology external site symbol

Arch Pathol Lab Med. 2019. doi: 10.5858/arpa.2018-0210-OA


2018


Lockwood C, Hussain B (2018)
Total Digital Pathology  pdf document symbol

This article appeared in the November issue of the IBMS magazine, The Biomedical Scientist. For more information, visit ibms.org external site symbol and thebiomedicalscientist.net external site symbol

Falk M, Ynnerman A, Treanor D, Lundström C (2018)
Interactive Visualization of 3D Histopathology in Native Resolution  pdf document symbol

Capitanio A, Dina RE, Treanor D (2018)
Digital cytology: A short review of technical and methodological approaches and applications external site symbol Cytopathology. 2018;29:317-325.

Treanor D, Williams BJ (2018)
The Leeds Guide to Digital Pathology  pdf document symbol The Leeds Teaching Hospitals NHS / University of Leeds

Williams BJ, Hanby H, Millican-Slater R, Nijhawan A, Verghese E, Treanor D. (2018)
Digital pathology for the primary diagnosis of breast histopathological specimens: an innovative validation and concordance study on digital pathology validation and training  pdf document symbol Histopathology 72, 662-671. https://doi.org/10.1111/his.13403.

Williams BJ, Lee J, Oien KA, Treanor D. (2018)
Digital pathology access and usage in the UK: results from a national survey on behalf of the National Cancer Research Institute's CM-Path initiative  pdf document symbol J Clin Pathol: first published as 10.1136/jclinpath-2017-204808 on 9 January 2018.

Williams BJ, Bottoms D, Clark D, Treanor D. (2018)
Future-proofing pathology part 2: building a business case for digital pathology  pdf document symbol J Clin Pathol: first published as 10.1136/jclinpath-2017-204926 on 16 March 2018.

Dessauvagie BF, Lee AHS, Meehan K, Nijhawan A, Tan PH, Thomas J, Tie B, Treanor D, Umar S, Hanby AM, Millican-Slater R. (2018)
Interobserver variation in the diagnosis of fibroepithelial lesions of the breast: a multicentre audit by digital pathology  pdf document symbol JCP Online First, published on February 13, 2018 as 10.1136/jclinpath-2017-204977

Clarke EL, Revie C, Brettle D, Shires M, Jackson P, Cochrane R, Wilson R, Mello-Thoms C, Treanor D. (2017)
Development of a novel tissue-mimicking color calibration slide for digital microscopy. Color Res Appl. 2018;43:184-197. external site symbol


2017


Williams, B., Bottoms, D., Treanor, D (2017) Future-proofing pathology: the case for clinical adoption of digital pathology external site symbol Journal of Clinical Pathology Published: December 2017 - Volume 70 - 12

Williams, B., DaCosta, P., Goacher, E. and Treanor, D (2017) A Systematic Analysis of Discordant Diagnoses in Digital Pathology Compared With Light Microscopy external site symbol ARCHIVES of Pathology & Laboratory Medicine


2016


Clarke, EL and Treanor, D (2016) Colour in Digital Pathology: A Review. external site symbol (White Rose Research Online) Histopathology. ISSN 0309-0167

Clarke, EL, Mello-Thoms, C, Magee, D and Treanor, D (2016) A response to Campbell WS, Talmon GA, Foster KW, Lele SM, Kozel JA, West WW. Sixty-five thousand shades of gray: importance of color in surgical pathology diagnoses. external site symbol (White Rose Research Online) Human Pathology, 56. pp. 204-205. ISSN 0046-8177

Goacher, E., Randell, R., Williams, B., Treanor, D. (2016) The diagnostic concordance of whole slide imaging and light microscopy: a systematic review external site symbol Archives of Pathology & Laboratory Medicine. ISSN 0003-9985 (White Rose Research Online)

Finlay, S., Seedhom, BB., Carey, D., Bulpitt, A., Treanor, D. and Kirkham, J. (2016) In-vitro engineering of high modulus cartilage-like constructs. external site symbol Tissue engineering. Part C, Methods, 22 (4). ISSN 1937-3384 (White Rose Research Online)

McCarthy, R., Orsi, NM., Treanor, D., Moran, O., Vernooij, M., Magee, DR., Roberts, N., Stahlschmidt, J. and Simpson, NAB. (2016) Three-dimensional digital reconstruction of human placental villus architecture in normal and complicated pregnancies. external site symbol European Journal of Obstetrics and Gynecology and Reproductive Biology, 197. pp. 130-135. ISSN 0301-2115 (White Rose Research Online)

Ruddle, RA., Thomas, RG., Randell, R., Quirke, P. and Treanor, D. (2016) The design and evaluation of interfaces for navigating gigapixel images in digital pathology. external site symbol ACM Transactions on Computer-Human Interaction, 23 (1). 5. ISSN 1073-0516 (White Rose Research Online)

Wright, A. I., Magee D. R., Quirke, P., Treanor, D. (2016) Incorporating Local and Global Context for Better Automated Analysis of Colorectal Cancer on Digital Pathology Slides external site symbol 20th Conference on Medical Image Understanding and Analysis (MIUA 2016) Proc Comp Science. Vol 90, pp 125-131; doi:10.1016/j.procs.2016.07.034

Ruddle, R. A., Thomas, R. G., Randell, R., Quirke, P., & Treanor, D. (2016). The design and evaluation of interfaces for navigating gigapixel images in digital pathology  pdf document symbol ACM Transactions on Computer-Human Interaction, 23(1), Article No. 5. DOI external site symbol Also featured as the Editor's Spotlight external site symbol


2015


Treanor, D.,Gallas, B. D., Gavrielides, M. A., Hewitt, S. M. (2015) Evaluating whole slide imaging: A working group opportunity. external site symbol Journal of Pathology Informatics. 2015;6:4

Wright, A. I., Grabsch, H. I., Treanor, D. E. (2015) RandomSpot: A web-based tool for systematic random sampling of virtual slides. external site symbol Journal of Pathology Informatics. 2015;6:8

Wright, A. I., Magee, D. R., Quirke, P., Treanor, D. E. (2015) Prospector: A web-based tool for rapid acquisition of gold standard data for pathology research and image analysis. external site symbol Journal of Pathology Informatics. 2015;6:21

Magee, D. R., Song, Y., Gilbert, S., Roberts, N., Wijayathunga, N., Wilcox, R., Bulpitt, A.,Treanor, D. (2015) Histopathology in 3D: From three-dimensional reconstruction to multi-stain and multi-modal analysis external site symbol Journal of Pathology Informatics. 2015;6:6

Booth, M. E., Treanor, D.,Roberts, N., Magee, D. R., Spiers, V., Hanby, A. M. (2015) Three-dimensional reconstruction of ductal carcinoma in situ with virtual slides external site symbol Histopathology. Volume 66, Issue 7, June 2015, Pages 966-973

(Cover page article, Histopathology June 2015)

The Design and Evaluation of Interfaces for Navigating Gigapixel Images

Figure 2 - example 1   Figure 2 - example 2

Randell, R.,Ambepitiya, T., Mello-Thoms, C., Ruddle, R. A., Brettle, D., Thomas, R. G., Treanor, D. (2015) Effect of Display Resolution on Time to Diagnosis with Virtual Pathology Slides in a Systematic Search Task external site symbol Journal of Digital Imaging February 2015, Volume 28, Issue 1, pp 68-76 (First online: 16 August 2014)


2014


Gray, A., Wright, A., Jackson, P., Hale, M., Treanor, D. (2014) Quantification of histochemical stains using whole slide imaging: development of a method and demonstration of its usefulness in laboratory quality control.  pdf document symbol and at http://jcp.bmj.com external site symbol J Clin Pathol. 2014 Dec 5. pii: jclinpath-2014-202526. doi: 10.1136/jclinpath-2014-202526.

Randell, R., Ruddle, R. A., Thomas, R. G., Mello-Thoms, C., Treanor, D. (2014) Diagnosis of major cancer resection specimens with virtual slides: Impact of a novel digital pathology workstation.  pdf document symbol Human Pathology In press. DOI: 10.1016/j.humpath.2014.06.017 external site symbol

Song, Y., Treanor, D., Bulpitt, A. J., Wijayathunga, N., Roberts, N., Wilcox, R., Magee D. R. (2014) Unsupervised content classification based nonrigid registration of differently stained histology images. external site symbol IEEE Trans Biomed Eng. 2014 Jan;61(1):96-108. doi: 10.1109/TBME.2013.2277777. Epub 2013 Aug 8.

Badano, A., Revie, C., Casertano, A., Cheng, W., Green, P., Kimpe, T., Krupinski, E., Sisson, C., Skrøvseth, S., Treanor, D., Boynton, P., Clunie, D., Flynn, M. J., Heki, T., Hewitt, S., Homma, H., Masia, A., Matsui, T., Nagy, B., Nishibori, M., Penczek, J., Schopf, T., Yagi, Y., Yokoi, H. (2014) Consistency and Standardization of Color in Medical Imaging: a Consensus Report. external site symbol Journal of Digital Imaging, The Journal of the Society for Computer Applications in Radiology 2014

Khan, A. M., Rajpoot, N., Treanor, D., Magee D. R. (2014) A Non-Linear Mapping Approach to Stain Normalisation in Digital Histopathology Images using Image-Specific Colour Deconvolution. external site symbol IEEE Transactions on Biomedical Engineering, Vol. 61, No. 6, June 2014

Gilbert, S., Bernus, O., White E., Roberts, N., Treanor, D., Magee D. R. (2014) A Framework for Quantification of Regional Cardiac Fibrosis from Serial Sections using 3D Whole Slide Imaging. external site symbol Proc. International Conference of the IEEE Engineering in Medicine and Biology Society, 2014

Wright, A. I., Magee D. R., Quirke, P., Treanor, D. (2014) Towards automatic patient selection for chemotherapy in colorectal cancer trials external site symbol Proc. SPIE 9041, Medical Imaging 2014: Digital Pathology, 90410A (March 20, 2014); doi:10.1117/12.2043220


2013


Randell, R., Ruddle, R. A., Mello-Thoms, C., Thomas, R. G., Quirke, P. and Treanor, D. (2013) Virtual reality microscope versus conventional microscope regarding time to diagnosis: an experimental study.  pdf document symbol Histopathology, 62: 351-358. doi: 10.1111/j.1365-2559.2012.04323.x

Song, Y., Treanor, D. Bulpitt, A. J., Magee D. R., (2013) 3D reconstruction of multiple stained histology images. external site symbol Journal of Pathology Informatics, Vol 4(1), 2013

Zhou, Y., Magee D. R., Treanor, D., Bulpitt, A. J.(2013) Stain guided mean-shift filtering in automatic detection of human tissue nuclei. external site symbol Journal of Pathology Informatics, Vol 4(1), 2013


2012


Randell, R., Hutchins, G., Sandars, J., Ambepitiya, T., Treanor, D., Thomas R. G., Ruddle, R.A. (2012) Using a high-resolution wall-sized virtual microscope to teach undergraduate medical students.  pdf document symbol CHI 2012, May 5-10, 2012, Austin, TX, USA

Roberts, N., Magee, D., Song, Y., Brabazon, K., Shires, M., Crellin, D., Orsi, N. M., Quirke, R., Quirke, P., Treanor, D. (2012) Toward Routine Use of 3D Histopathology as a Research Tool.  pdf document symbol Am J Pathol. 2012 May;180(5):1835-42. Epub 2012 Apr 9.

Randell, R., Ruddle, R.A., Quirke, P., Thomas R. G., Treanor, D.(2012) Working at the microscope: analysis of the activities involved in diagnostic pathology.  pdf document symbol external site symbol (White Rose Research Online) Histopathology. 2012 Feb;60(3):504-10. doi: 10.1111/j.1365-2559.2011.04090.x. Epub 2011 Dec 16.


2011


Randell, R., Ruddle, R. A., Thomas, R. G., Treanor, D. (2011) Diagnosis at the microscope: A workplace study of histopathology.  pdf document symbol external site symbol (White Rose Research Online) Cognition Technology & Work, 1-17. DOI: 10.1007/s10111-011-0182-7

Lyttleton, O., Wright, A., Quirke, P., Treanor, D., Lewis, P. (2011) Extending the tissue microarray data exchange specification for inclusion of data analysis results. external site symbol J Pathol Inform. 2011 Mar 31;2:17.

Wright, A., Lyttleton, O., Lewis, P., Quirke, P., Treanor, D. (2011) The tissue microarray data exchange specification: Extending TMA DES to provide flexible scoring and incorporate virtual slides. external site symbol J Pathol Inform. 2011 Mar 15;2:15.

Magee, D. R., Chomphuwiset, P., Treanor, D., Quirke, P.(2011) Context Aware Colour Classification in Digital Microscopy  pdf document symbol external site symbol Proc. Medical Image Understanding and Analysis

Lyttleton, O., Wright, A., Treanor, D., Lewis, P. (2011) Using XML to encode TMA DES metadata. external site symbol J Pathol Inform. 2011;2:40. Epub 2011 Aug 24.


2010


Chomphuwiset, P., Magee, D. R., Boyle, R. D., Treanor, D. (2014) Nucleus classication and bile duct detection in liver histology.  pdf document symbol
Previously Human Pathology In press. DOI: 10.1016/j.humpath.2014.06.017


2009


Treanor, D., Jordan-Owers N, Hodrien J, Wood J, Quirke P, Ruddle R. (2009) Virtual reality Powerwall versus conventional microscope for viewing pathology slides: an experimental comparison.  pdf document symbol Histopathology 2009 Sep;55(3):294-300.

Treanor, D., Lim, C. H., Magee, D., Bulpitt, A., Quirke P. (2009) Tracking with virtual slides: a tool to study diagnostic error in histopathology.  pdf document symbol Histopathology 2009 Jul;55(1):37-45.

Magee D., Treanor, D., Crellin D., Shires M., Smith K., Mohee K., and Quirke P. (2009) Colour Normalisation in Digital Histopathology Images.  pdf document symbol external site symbol Proc. Optical Tissue Image analysis in Microscopy, Histopathology and Endoscopy (MICCAI Workshop) , pp100-111

Treanor, D. (2009) Virtual slides in diagnosis and teaching. Diagnostic Pathology 2009


2008


Magee, D. R., Treanor, D., Quirke, P. (2008) A New Image Registration algorithm with application to 3D Histopathology.  pdf document symbol external site symbol Proc. Microscopic Image Analysis with Applications in Biology, 2008


2007


Hodrien, J., Wood, J., & Ruddle, R. (2007) The design and implementation of a 50 million pixel Powerwall display.  pdf document symbol UK Visualization Support Network technical report vizNET-LEEDS-TECH-0001-070201.

Treanor D, Quirke P. (2007) The virtual slide and conventional microscope - a direct comparison of their diagnostic efficiency  pdf document symbol The Journal of Pathology [Internet]. Glasgow: Wiley; 2007 p. 1A - 65A.
Available from Wiley Online Library external site symbol