Research Staff


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3rd Floor Front Engineering Building
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Miscellaneous Information


Prior to commencing my PhD at CMIC in 2006 I spent 10 years in industry in Australia and the UK, primarily in engineering product development and project management. My subsequent research has been focused on opportunities for translational work in healthcare, finding clinical applications for novel algorithms. My PhD was focused on the development of an image guidance system for robot assisted radical prostatectomy. Following on from my PhD I have been working on the development of an image guidance system for liver surgery, initially as part of the EU funded PASSPORT project, and then with funding from the Department of Health and the Wellcome trust to develop the “SmartLiver” system.

Clinical Context of Research

Replacing traditional open surgery with minimally invasive surgery has proven benefit to the patient. Due to the requirement for smaller incisions recovery time and post operative pain can both be reduced. However not all patients are eligible for minimally invasive surgery due to the limitations imposed by the smaller ports. My research aims to enable and improve minimally invasive surgery by offering the surgeon image guidance during the procedure. Such systems enable the surgeon to refer to pre-operative scans in an intuitive way during surgery.


I am interested in the translational aspects of research, currently turning novel algorithms into working image guidance systems. Key points of my work are the use or robust software engineering principals, understanding the clinical requirements of potential systems, and developing methodologies to demonstrate the effectiveness of developing system.

The majority of my work is software development in C++ and forms part of the NifTK NiftyIGI platform [5]. The software is cross platform with unit testing to ensure it continues to meet its design requirements.

I am also very interested in better understanding the requirements for successful translation of software algorithms to the clinic. Because of the strong emotional involvement of the surgeons, the engineers, and the patients in the development of image guidance systems there is a need for robust and objective evaluation and development protocols for image guidance systems. My recent research has been focused on developing this framework, see [2,3] and the evaluation of image guidance systems [1,2].

Where these approaches identify shortfalls in the existing state of the art I have performed more basic research to improve specific areas. For example, I have invested significant effort in improving our understanding or laparoscopic tool tracking using optical marker based tracking[4]. My current work includes integration of laparoscopic ultrasound, deformable modelling of soft tissue, tissue classification from video, along with laparoscope tracking and calibration.


[1] S.Thompson, J.Totz, Y. Song, D. Stoyanov, S. Ourselin D. Hawkes M. Clarkson “Accuracy Validation of an Image Guided Laparoscopy System for Liver Resection” Proceedings of the SPIE Medical Imaging 2015 in press.

[2] Thompson, S., Penney, G., Billia, M., Challacombe, B., Hawkes, D., & Dasgupta, P. (2013). Design and evaluation of an image-guidance system for robot-assisted radical prostatectomy.. BJU Int, 111(7), 1081-1090. doi:10.1111/j.1464-410X.2012.11692.x

[3] Thompson, S. A., Hu, M., Johnsen, S., Gurusamy, K., Davidson, B., & Hawkes (2011,December 1). Towards Image Guided Laparoscopic Liver Surgery, Defining the System Requirement. In LIVIM (Living Imaging) 2011. IRCAD, Strasbourg..

[4] Thompson, S., Penney, G., Dasgupta, P., & Hawkes, D. (2013). Improved Modelling of Tool Tracking Errors by Modelling Dependent Marker Errors. IEEE TRANSACTIONS ON MEDICAL IMAGING, 32(2), 165-177. doi:10.1109/TMI.2012.2216890

[5] Clarkson, M. J., Zombori, G., Thompson, S., Totz, J., Song, Y., Espak, M., . . . Ourselin, S. (2014). The NifTK Software Platform for Image Guided Interventions. International Journal of Computer Assisted Radiology and Surgery.