In 2018, UK Research and Innovation (UKRI) awarded £10m funding for the PathLAKE project as part of the Industrial Strategy Challenge Fund. Project PathLAKE partners will embed and demonstrate the diagnostic efficiency of digital pathology, computer-aided testing of pathology samples, and develop novel AI tools to personalised medicine by selecting the right patients for the best therapy.
The OXFORD TEAM
Professor CLARE VERRILL is the Pathlake Oxford consortium co-lead with Professor Jens Rittscher. The Oxford team is a unique multi-disciplinary team which will provide knowledge, skills and expertise in prostate pathology, image analysis and AI.
In Oxford we have a strong NHS digital pathology platform through work already undertaken to instigate an initial Digital Pathology reporting infrastructure and Oxford hosts a unique set of clinically annotated mature prostate cancer cohorts of over 5000 cases.
Oxford will contribute to all four tenets of the programme, that is: Data Lake; Discovery and Adoption (D & A); AI Capability and Education.
The project will create a secure data-lake of tens of thousands of professionally annotated images for building deep learning algorithms that can automatically detect cancer. These images and tools will be made available across the consortium including a growing number of SME partners in this sector to develop AI to overcome burgeoning workloads in the UK and establish a world-leading UK digital health industry.
Kieron White and digital scanner
Professor Verrill is also the lead for Work Package 5; Engagement and is developing a portfolio of diverse engagement and training opportunities. Clare will also lead engagement activities with ISCF centres, SMEs, CM Path, RCPath,RCR and the National Physical Laboratory using existing links with these bodies ( many of which have been established via the Technology and Informatics lead role held by Professor Verrill with the NCRI CM-Path) she will seek to promote the understanding of the work of the centre in AI with patients and the public via open days and social media and will work with the NCRI to ensure that the project is linked to national cancer research engagement efforts.
Dr Lisa Browning and Professor Clare Verrill
The Oxford Projects:
1.Creating a fully digital NHS lab. The cellular pathology NHS lab at Oxford University Hospitals NHS Foundation Trust is undergoing a transformation to digital reporting. The aim is fully digital reporting by 2021. We anticipate efficiency gains and patient benefits from transition to this technology such as quicker results. Together with other partner hospitals in our region who also have the technology we will create increased opportunity for networked working across the region with better access to second opinions.
2. Datalake. Oxford is contributing cases to the central PathLAKE across multiple tissue types. Many of these will undergo detailed annotation by our expert pathologist team.
The Oxford exemplar project is focussed on prostate cancer and has 2 subprojects:
1.Improving workflow efficiency for reporting of prostate biopsies using AI which will lead to NHS efficiency gains and improved turn-around times.
2. Developing novel subtypes of prostate cancer using AI to mine for these new groups, which will lead to new insights into cancer biology and prognosis
Other members of the OXFORD TEAM include:
Professor Jens Rittscher
Prof. Jens Rittscher's research aim is to enable biomedical imaging through the development of new algorithms and novel computational platforms. The current focus of his research is to improve mechanistic understanding of cancer and patient care through quantitative analysis of image data. In 2013 he was appointed to the first joint academic appointment between the Department of Engineering Science and the Nuffield Department of Medicine at the University of Oxford. He has been awarded the title of Professor of Engineering Science. He is a group leader at the Big Data Institute and is a adjunct member of the Ludwig Institute of Cancer Research.
Prior to coming to Oxford Professor Rittscher was a senior research scientist and manager at GE Global Research in Niskayuna (NY, USA), one of the world’s largest and most diversified industrial research laboratories. Building on his extensive expertise in computer vision, probabilistic modelling and statistical learning, he developed new theoretical approaches that address specific real-world challenge problems in automated video annotation, visual surveillance, and biomedical imaging. In the context of biomedical imaging he worked on applications ranging from monitoring cellular processes and computational pathology to the development of an anatomical atlas for zebrafish imaging. In addition he held a position as an adjunct professor at the Rensselear Polytechnic Institute in Troy (NY, USA).
Dr Lisa Browning
Dr Lisa Browning is a consultant histopathologist (uropathologist) within the Department of Cellular Pathology at the John Radcliffe Hospital, Oxford, and an Honorary Senior Clinical Lecturer at the University of Oxford.
As a diagnostic pathologist her work covers the entire range of urological pathology seen within the regional tertiary referral centre. Dr Browning has a specialist interest and an increasing national referral practice in renal tumours, and has developed a specialist local service to facilitate this, including specialist immunohistochemical and molecular diagnostic tests.
Complementing clinical practice, Dr Browning is a member of the Oxford Renal Tumour Interest Group, and through this group she works alongside leading research groups within the University. She is partly funded by the Experimental Pathology subtheme of the Oxford BRC, and played a role in the pilot studies for Genomics England, undertaking some of the experimental work leading to the development of tissue handling protocols for the 100,000 Genomes Project.
More recently Dr Browning has joined the PathLAKE initiative in Oxford.
Dr Browning has an established background in education both at undergraduate and postgraduate level. She is currently the honorary meetings secretary for the British Division of the International Academy of Pathology, and Education Secretary for the British Association of Urological Pathologists. Dr Browning is an examiner for the Royal College of Pathologists, and at undergraduate level she has acted as internal examiner for University of Oxford, and is currently external examiner for histopathology at the University of Cambridge School of Clinical Medicine and at Imperial College School of Medicine. She regularly lectures within the UK (and beyond) on urological pathology, particularly renal tumours.
Dr Richard Colling
Richard Colling is a Senior Clinical Research Fellow at the University of Oxford and a Consultant Histopathologist at the John Radcliffe Hospital. Richard joined the PathLAKE project Oxford site in 2019 and will be contributing histopathology input, annotations and validation work across the portfolio of Oxford exemplar projects. Clinically, Richard specialises in urological pathology and his wider research interests include digital pathology, evidence-based healthcare and urological cancer.
Korsuk Sirinukunwattana is a postdoctoral research assistant in Rittscher's group at the Institute of Biomedical Engineering (IBME), Department of Engineering Science and the Big Data Institute, Oxford University. His main interest is the applications of image analysis and machine learning in medical research. He has been actively involved in several research projects in computational pathology focusing on colon, breast, and prostate cancers. He completed his doctoral research in the group of Nasir Rajpoot at the University of Warwick and held a postdoc position in Andrew Beck's lab at Harvard Medical School, and worked as a consultant for Robert West's lab at Stanford School of Medicine.
Maryam Haghighat joined the BDI in August 2019 to persue her research in biomedical image analysis under the supervision of Prof. Jens Rittscher.
She did her PhD under the supervision of Prof. David Taubman and Dr. Reji Mathew in the School of Electrical Engineering and Telecommunications, UNSW, Sydney, Australia. Her Ph.D. thesis is on over-complete decomposition of imagery for the purpose of compression. She proposed rate-distortion driven frameworks to separate illumination and specularities from image data. Her proposed approach not only improves the compression performance, but also provides a meaningful and tractable procedure for data separation.
In 2015, she was with Intelligent Transport Systems (ITS) lab at Swinburne University of Technology, Melbourne, Australia, where she began to work on large-scale data processing.
Her research interests are in signal, image and video processing, inverse problems and artificial intelligence.
OCHRe - The Oxford Centre for Histopathology Research
OCHRe facilitates research taking place in Oxford and elsewhere by giving access to researchers to human tissue samples and associated data such as clinical information and digital images. At the same time, OCHRe's role is to ensure that the distribution, use and storage of human samples and associated date for research complies with all relevant regulations such as HTA (Human Tissue Act) and GDPR (General Date Protection Regulations).
OCHRe is able to source tissue samples for research through a close relationship with the Oxford University Hospitals (OUH) Pathology department and the Oxford Radcliffe Biobank (ORB).The OCHRe team are actively involved in supporting the Oxford PathLAKE project.