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UPDATE: We are delighted to announce that EPSRC have funded our CDT for five more years under the new name EPSRC Centre for Doctoral Training in Intelligent Integrated Imaging in Healthcare (i4health).

Visit our new website at:

Dr Matt Clarkson

UCL Department of Medical Physics and biomedical engineering

8th Floor
Malet Place Engineering Building
UCL, London


My Ph.D., which was funded by the EPSRC, addressed the registration of 2D video images to 3D pre-operative scans such as magnetic resonance imaging, or computed tomography. This topic is an example of the classical pose-estimation problem in computer vision. With an interest in image-guided interventions, my research led to the invention of “photo-consistency” as a similarity measure, enabling registration between a 3D model and multiple 2D video images. This method proved to be reliable, accurate, and could be suitable for radiotherapy patient positioning, and some image-guided intervention applications. I then spent 8 years in industry in a wide range of software related roles. In 2008, I joined the Centre For Medical Image Computing (CMIC) to focus on computational neuro-imaging and bio-marker development under Prof. Sebastien Ourselin. I validated the use of 9 degree-of-freedom registration for correction of MR scanner drift in large clinical trials, which impacts clinical trial design such as in ADNI2. This validation was part of a larger initiative to improve the accuracy and reliability of imaging bio-markers for Alzheimer’s Disease including whole brain and hippocampal atrophy measurement. We additionally developed methods for voxel-based cortical thickness measurement, where the newly developed voxel-based methods were orders of magnitude quicker. Between May 2010 to October 2012 I lead a team to develop the NifTK platform. We have developed semi-automated brain, hippocampal and ventricle segmentation tools for the imaging trials work at the UCL Dementia Research Centre, and an image-guided surgery platform for various research projects at CMIC and the image-guided surgery program at the National Hospital for Neurology and Neurosurgery at Queen Square. Since November 2012 I am Senior Research Associate on a Wellcome Trust and Department of Health funded project to deliver a system for Laparoscopic Liver Resection. I additionally continue to lead the development of the NifTK platform.

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