A press release relating to our 3D pathology work is available here. This work is featured on the front cover of May's edition of the Americal Journal of Pathology. It's got a lot of press including from the BBC, Lancet Oncology, Wired, CNET, The Naked scientists, Science Omega, Medical News Today, Labmedica, and the Yorkshire Post. A webpage on this work is available here.

Bio


I have been employed as a Lecturer within the School of Computing at the University of Leeds since 2008, where previously I held a 5 year University Research Fellowship (2003-2008). My main research interests are in the medical domain, relating to medical image/volume (MRI, CT, PET and ultrasound) analysis and surgical simulation, and in visual surveillance, analysis of remote sensing data, and visual learning. I am a member of the Vision Group, a research group based within the school of computing. I completed my PhD within the group in 2000 (supervised by Prof. Roger Boyle) and was subsequently employed on a project relating to analysis of CT volumes for automatic generation of 3D anatomical models, for training and decision making in keyhole vascular intervention. Subsequently, I was employed on the Cognitive Vision project with Prof. David Hogg and Prof. Tony Cohn. For more details of my research follow the links:

Current Research

2D/3D Analysis of Digital Pathology Images
Fusion and Visualization of 3D Magnetic Resonance Angiography and Multi-slice 2D Dynamic Contrast-Enhanced Magnetic Resonance Imaging for Improved Diagnosis of Coronary Heart Disease (Supervising 2 PhDs)
EU Panorama project relating to high bandwidth video analysis (in particular X-ray dose control)
Learning to Recognise Dynamic Visual Content from Broadcast Footage EPSRC project relating to tracking and learning sign language with Andrew Zisserman (Oxford) and Richard Bowden (Surrey).
EU NetTUN project relating to remote sensing (GPR and seismic) data analysis and visualisation for tunnel boring
Asessing the Underworld Collaborative EPSRC project on multi-modal remote sensing based analysis of burried assets led by Chris Rogers (Birmingham). Starting soon!
The DART Project Open Science project relating to assessing the best use of various types of remote sensing in Archeology (I am an academic consultant)

Previous Research

Non-rigid multi-modal PET-MRI registration
Simulation of ultrasound guided needle insertion procedures
The CRaIVE Consortium Collaboration in Radiological Interventional Virtual Environments
The Cognitive Vision Project
Automatic Generation of 3D Anatomical Models: training and decision making in keyhole vascular intervention
Football (Soccer) tracking and analysis (Industrial Consultancy)
The Electronic Stockmans Eye (PhD Project)

Some of my cow images have been included in the PASCAL object recognition database: http://www.pascal-network.org/challenges/VOC/. A short (ground-truthed) sequence is also available as part of the Oxford Moseg Data here.

Teaching

In the 2012/13 session I am teaching Web Development (level 1) and Computer Vision (level 3). Formerly I taught the Speech, Audio and Image Processing module (level 2) for 4 years, and Artificial Intelligence (level 2) for 3 years.

Research Students and Postdocs

I am always keen to hear from potential students, in particular people interested in areas relating to medical image analysis. Current PhD students and postdocs are:

James Charles Postdoc: EPSRC Funded Learning to Recognise Dynamic Visual Content from Broadcast Footage project relating to tracking and learning sign language with Andrew Zisserman (Oxford) and Richard Bowden (Surrey).

Kyaw Kyaw Htike Postdoc: EPSRC Funded Learning to Recognise Dynamic Visual Content from Broadcast Footage project relating to tracking and learning from video with Andrew Zisserman (Oxford) and Richard Bowden (Surrey).

Matthew Benatan PhD student: Synchronisation of audio and video for film production applications [Co-supervision with Kia Ng, EPSRC CASE award from Zoo Digital]

Stephen Kengyelics PhD student: Dose and Image Quality control in real-time X-ray [Co-supervision with Andy Davies (Medical Physics), sponsored by the EU Panorama project ]

Alex Wright PhD student: Colorectal image analysis using virtual slides (Funded by Yorkshire Cancer Research) . [Co-supervision with Phil Quirke and Darren Treanor (Pathology)]

Tze Wah PhD student (Part Time): Optimisation of image based planning protocol for RFA [Co-supervision with David Buckley (Medical Physics) and Peter Selby (Oncology)]

Former Research Students and Postdocs

Constantine Zakkaroff PhD student: Analysis of Multi-modal Cardiac MRI Data [Co-supervision with Sasha Radjenovic (Medical Physics)]

Sophie Greene PhD Student: Multi-camera applications in medical imaging. Yi Song Postdoc: Working on multi-modal registration and 3D histopathology as part of the Wellmec Centre of Excellence in Medical Engineering.

John Biglands PhD student: Analysis of Cardiac DCE MRI Sequences [Co-supervision with Roger Boyle and Sasha Radjenovic (Medical Physics)]

Phattthanaphong (Joe) Chomphuwiset PhD student: Automatic analyis of Digital Histopathology Images of the Liver [Co-supervision with Roger Boyle and Darren Treanor]

Darren Treanor PhD student (Part Time): Computer aided analysis of electronic pathology images [Co-supervision with Phil Quirke (Pathology) and Andy Bulpitt]

Andrew Hume PhD student: Behaviour Modelling and Indexing of Team Sports (supported by a CASE award from ProZone Ltd.) (Graduated 2012)

Jonathan Sykes PhD student: Optimisation of dose and image quality in cone beam CT for radiotherapy (Co-supervision with DS Brettle (Medical Physics, LGI), D Thwaites (Medical Physics, Cookridge) and A Morgan (Medical Physics, Cookridge)) (Graduated 2011)

Tracy Petrie PhD student: Improving Image quality in 4D Cone Beam CT (Graduated 2011)

Andrew Bennett PhD student: Autonomous visual learning and representation using Genetic Programming (Graduated 2010)

Yanong (Allen) Zhu Postdoc: Computer simulation of ultrasound guided procedures (EPSRC funded grant), and Breast cancer analysis

Dan Hart Postdoc: Working on an industrially funded research project for ProZone Ltd.

Chris Needham Postdoc: Working on an industrially funded research project for ProZone Ltd.

Garsah Al-qarni PhD student: Wide area surveillance using shoe appearance and other cues (Co-supervision with Roger Boyle)

Software

Various bits of software that I have written (and helped to write) are available here. Other useful bits and bobs are:

Microscopy colour normalisation toolkit developed in collaboration with Adnan Mudjahid at Warwick University.

  • A perl script to rename a MS Visual C++ project (.NET 2003, but will probably work for other versions)
  • Prizes

    I have won the following prizes:

  • The Best Poster Prize at the British Machine Vision Conference 2014

  • 1st Prize for "Publications and Training Materials" in Medipex Yorkshire and Humber NHS Innovations Competition 2007 (for ultrasound simulator)

  • 2nd Prize for ICT in Medipex national NHS Innovations Competition 2007

  • "Certificate of Merit" at Cardiovascular and Interventional Radiological Society of Europe Conference, 2006 (see publications below)

  • British Computer Society Machine Intelligence Prize 2004 (more details here)

  • The Industry Prize at the British Machine Vision Conference 2000
  • Scholarly Activities

    I was/am on the program committees for the British Machine Vision Conference (2003-12), (and on the organising committee for 2008), and Area Chair 10-12, Medical Image Understanding and Analysis (2005,2007) and IEEE International Workshop on Visual Surveillance (2006). I am a reviewer for Medical Image Computing and Computer Assisted Intervention (MICCAI). I also have reviewed for the following journals; IEEE Transactions on Pattern Analysis and Machine Intelligence (PAMI), IEEE Transactions on Medical Imaging, Medical Image Analysis, IEEE Transactions on Biomedical Engineering, Computer Vision and Image Understanding, Pattern Recognition Letters, IEE Proceedings on Vision, Image & Signal Processing, Machine Vision Applications, Radiotherapy and Oncology, Information Fusion, Computerized Medical Imaging and Graphics, Simulation Modelling Practice and Theory, and EURASIP Journal on Applied Signal Processing. I was the co-chair of the following workshop:

    CVBASE '06 - ECCV Workshop on Computer Vision Based Analysis in Sport Environments.

    I was local arrangements chair for British Machine Vision Conference 2008

    I was guest editor for a special issue of CVIU on Computer Vision Based Analysis in Sport Environments (Volume 113 , Issue 5 (May, 2009)) with Janez Pers.

    I was guest editor for a special issue of Machine Vision and Applications (MVA) on Microscopy Image Analysis for Biomedical Applications with Stephen McKenna and Nasir Rajpoot. (Volume 23, Issue 4, 2012)

    Journal Publications

  • Khan, A.M., Rajpoot, N, Treanor, D., Magee, D, A Non-Linear Mapping Approach to Stain Normalisation in Digital Histopathology Images using Image-Specific Colour Deconvolution, IEEE Transactions on Biomedical Engineering, To Appear, 2014 (PDF)

  • Song, Y., Treanor D., Bulpitt, A.J., Wijayathunga N., Roberts N., Wilcox R., Magee D., Unsupervised Content Classification Based Non-rigid Registration of Differently Stained Histology Images, IEEE Transactions on Biomedical Engineering,Vol 61(1), 2014 (PDF)

  • Song, Y., Treanor D., Bulpitt, A.J., Magee D., 3D reconstruction of multiple stained histology images, Journal of Pathology Informatics, Vol 4(1), 2013 (Available Here)

  • Zhou, Y., Magee, D., Treanor D., Bulpitt, A., Stain guided mean-shift filtering in automatic detection of human tissue nuclei , Journal of Pathology Informatics, Vol 4(1), 2013 (Available Here)

  • Roberts N, Magee D, Song Y, Brabazon K, Shires M, Crellin D, Orsi N, Quirke P, Treanor D, Toward Routine Use of 3D Histopathology as a Research Tool, American Journal of Pathology, Vol. 180(5), 2012 (Available Here)

  • Biglands J, Magee D, Boyle R, Larghat A, Plein S and Radjenovic A, Evaluation of the effect of myocardial segmentation errors on myocardial blood flow estimates from DCE-MRI , Physics in Medicine and Biology, Vol 56, pp2423-2443, 2011 Available Here

  • Magee D, Tanner S, Waller M, Tan A-L, McGonagle D, and Jeavons A, Combining variational and model-based techniques to register PET and MR images in hand osteoarthritis, Physics in Medicine and Biology, Vol 55(16), pp4755-4769, 2010 Available Here

  • Sykes J, Brettle D, Magee D, and Thwaites D, Investigation of uncertainties in image registration of cone beam CT to CT on an image guided radiotherapy system, Physics in Medicine and Biology, Vol 54, pp7263-7283, 2009 Available Here

  • Treanor D, Quirke P, Magee D, and Bulpitt A, Tracking with virtual slides: A tool to study diagnostic error in histopathology, Histopathology, Vol. 55, pp37-45, 2009. Available Here

  • Santos P., Needham C., and Magee D., Inductive Learning Spatial Attention, Revista Controle & Automacao, Vol.19(3), 2008 PDF

  • Sykes J, Lindsay R, Dean C, Brettle D, Magee D, and Thwaites D, Measurement of a cone beam CT coincidence with a megavoltage isocentre and image sharpness using the QUASAR Penta-Guide phantom, Physics in Medicine and Biology, Vol. 53, pp5275-5293, 2008. Available here

  • Bennett B., Magee D., Cohn A.G., and Hogg, D.C., Enhanced tracking and recognition of moving objects by reasoning about spatio-temporal continuity Image and Vision Computing, Vol. 26(1), pp67-81, 2008. Available here.

  • Magee D., Zhu Y., Ratnalingam R., Gardner P., and Kessel D., An Augmented Reality Simulator for Ultrasound Guided Needle Placement Training, Journal of Medical & Biological Engineering & Computing, Vol. 45, pp957-967, 2007 Available from the publisher here, or White Rose repository here.

  • Needham C.J., Santos P.E., Magee D.R., Devin V., Hogg, D.C. and Cohn A.G., Protocols from perceptual observations Artificial Intelligence Journal, Vol. 167, Issues 1-2, pp103-136, 2005. Available here.

  • Magee D. Tracking Multiple Vehicles using Foreground, Background and Motion Models , Image and Vision Computing , vol 22(2), pp143-155, 2004. Available here.

  • Magee D. and Boyle R. Detecting Lameness using `Re-sampling condensation' and `Multi-stream Cyclic Hidden Markov Models' . Image and Vision Computing , vol 20(8), pp 581-594, 2002. Available as a Research Report.
  • Other Refereed Publications

    Note: Only full publications (not abstracts) are listed here.

  • Charles, J., Pfister, T., Magee, D., Hogg D. and Zisserman A. Upper Body Pose Estimation with Temporal Sequential Forests. Proc. in British Machine Vision Conference (BMVC), 2014. PDF Winner of Best Poster Award

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

  • Charles, J., Pfister, T., Zisserman A., Magee D., Hogg D., Domain Adaptation for Upper Body Pose Tracking in Signed TV Broadcasts, Proc. British Machine Vision Conference, 2013 (Available Here)

  • A. Johannes Pretorius, D. Treanor, D. Magee, R. Ruddle, Visual Parameter Optimization for Biomedical Image Analysis: A Case Study, Proc. SIGRAD, 2012 (Avalilable Here)

  • Y. Song, A. Bulpitt, D. Treanor, D. Magee, 3D reconstruction of multiple stained histology images, Proc. MICCAI Workshop on Histopathology Image Analysis, 2012

  • Y. Zhou, D. Magee, D. Treanor, and A. Bulpitt, Stain Guided Mean-Shift Filtering in Automatic Detection of Human Tissue Nuclei, Proc. MICCAI Workshop on Histopathology Image Analysis, 2012

  • Zakkaroff, C., Radjenovic A., Greenwood J., Magee D. Recovery of Slice Rotations with the Stack Alignment Transform in Cardiac MR Series, Proc. British Machine Vision Conference, pp35.1-35.11, 2012 PDF

  • Zakkaroff, C., Radjenovic A., Greenwood J., Magee D. Stack Alignment Transform for Misalignment Correction in Cardiac MR Cine Series Proc. Medical Image Understanding and Analysis, 2012 PDF

  • P. Chomphuwiset, D. Treanor, D.Magee, et al. Context-Based Classification of Cell Nuclei and Tissue Area in Liver Histology, Proc. Medical Image Understanding and Analysis , 2011 PDF

  • D. Magee, P. Chomphuwiset, D. Treanor, et al. Context Aware Colour Classification in Digital Microscopy Proc. Medical Image Understanding and Analysis , 2011 PDF

  • Zakkaroff, C., Magee D., Radjenovic A., Boyle R., Mediated Spatiotemporal Fusion of Multiple Cardiac Magnetic Resonance Datasets for Patient-specific Perfusion Analysis Computing in Cardiology 37 p. 1-4 , 2010 PDF

  • Zakkaroff, C., Magee D., Radjenovic A., Boyle R., Mediated Spatiotemporal Registration of Cardiac DCE-MRI and Coronary MR Angiography Proc. Spatio-Temporal Image Analysis for Longitudinal and Time-Series Image Data (MICCAI Workshop) , 2010 PDF

  • P. Chomphuwiset, D. Magee, R. Boyle, D. Treanor, Nucleus classication and bile duct detection in liver histology, Proc. MICCAI Workshop on Machine Learning in Medical Imaging, 2010 PDF

  • Petrie T, Magee D R, and Sykes J, Binning Without a Model For Cone-Beam CT Proc. Medical Image Understanding and Analysis (MIUA), , pp1245-1248, 2010 PDF

  • Petrie T, Magee D R, and Sykes J, Modeless motion binning in Cone Beam CT International Symposium on Biomedical Imaging, , pp1245-1248, 2010 PDF

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

  • Zhu, Y., Magee D., Ratnalingam, R. and Kessel D., A Physics Based Method for Combining Multiple Anatomy Models with Application to Medical Simulation Proc. Medicine Meets Virtual Reality, pp465-467, 2009 PDF

  • Magee D., Treanor D., and Quirke P., A New Image Registration algorithm with application to 3D Histopathology Proc. Microscopic Image Analysis with Applications in Biology (MICCAI Workshop), 2008 PDF

  • A. Bennett and D. Magee, Using Genetic Programming to Learn Models Containing Temporal Relations from Spatio-Temporal Data, Proc. 1st International Workshop on Combinations of Intelligent Methods and Applications , pp7-12, 2008. PDF
     
  • A. Bennett and D. Magee , Learning Sets of Sub-Models for Spatio-Temporal Prediction , Proc. SGAI International Conference on Artificial Intelligence (AI-2007), pp123-136, 2007
     
  • Y. Zhu, D. Magee, R. Ratnalingam, and D. Kessel, A Training System for Ultrasound-Guided Needle Insertion Procedures , Proc. International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), pp566-574, 2007
     
  • R.A. Ratnalingam, D. Coates, J. Leong, D.O. Kessel, D. Magee, Y. Zhu, Computer assisted simulation of ultrasound guided procedures , Proc. Cardiovascular and Interventional Radiological Society of Europe Conference,, Poster 64, pp233, 2006 e-poster, CIRSE Abstracts Winner of Certificate of Merit
     
  • Zhu, Y., Magee D., Ratnalingam, R., Kessel, D., A Virtual Ultrasound Imaging System for the Simulation of Ultrasound-Guided Needle Insertion Procedures Proc. Medical Image Understanding and Analysis (MIUA), pp61-65, vol 1., 2006 PDF
     
  • Santos P., Magee D., Colton S., Predictive and Descriptive Approaches to Learning Game Rules from Vision Data Proc. Ibero-American Artificial Intelligence Conference, pp349-359, 2006 (Springer LNCS 2709) PDF
     
  • Jones, A. Wilcox, R., Magee, D., and Bulpitt, A., Level-set based medical image segmentation tools for the creation of spinal finite element models Proc. 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering (CMBBE), 2006 (To Appear)
     
  • Magee, D., Tanner, S., Waller, M., McGonagle, D., and Jeavons, A. Registration of PET and MR hand volumes using Bayesian Networks Proc. ICCV Workshop on Computer Vision for Biomedical Image Applications, pp437-448, 2005 PDF.
     
  • Magee D.R., Needham C.J., Santos P.E. and Rao S., Inducing the focus of attention by observing patterns in space Proceedings Workshop on Modelling Others from Observations (MOO 2005), pp47-52, 2005
     
  • Magee D. and Kessel D., A Computer Based Simulator for Ultrasound Guided Needle Insertion Procedure, Proc. IEE International Conference on Visual Information Engineering, pp301-308, 2005. Available to PDF.
     
  • Bennett B., Magee D., Cohn A.G., and Hogg D.C., Using Spatio-temporal Continuity Constraints to Enhance Visual Tracking of Moving Objects, Proc. European Conference on Artificial Intelligence, pp 922-926, 2004. Available to PDF.
     
  • Santos P., Magee D., Cohn A.G., and Hogg D.C., Combining Multiple Answers for Learning Mathematical Structures from Visual Observation, Proc. European Conference on Artificial Intelligence, pp 544-548, 2004. PDF
     
  • Magee D., Needham C.J., Santos P., Cohn A.G. and Hogg D.C., Autonomous learning for a cognitive agent using continuous models and inductive logic programming from audio-visual input, Proc. AAAI Workshop on Anchoring Symbols to Sensor Data, (AAAI Press TR WS-04-03), pp17-24, 2004. PDF
     
  • Santos P., Magee D. and Cohn A., Looking for Logic in Vision, Proc. Eleventh Workshop on Automated Reasoning, pp61-62, 2004.
     
  • Magee D. and Leibe B., Online Face Tracking Using a Feature Driven Level-set, Proc. British Machine Vision Conference, pp419-428, 2003.
     
  • Magee D., A Sequential Scheduling Approach to Combining Multiple Object Classifiers Using Cross-entropy . Proc. IAPR International Workshop on Multiple Classifier Systems , pp135-145, 2003 (Springer LNCS 2709).
     
  • Magee D., Tracking Multiple Vehicles Using Foreground, Background and Motion Models . Proc. ECCV Workshop on Statistical Methods in Video Processing , pp7-12, June 2002. Available as a Research Report.
     
  • Galata A., Cohn A., Magee D. and Hogg D., Modeling Interaction Using Learnt Qualitative Spatial Relations and Variable Length Markov Models, Proc. 15th European Conference on Artificial Intelligence, Lyon, 2002. Available Here.
     
  • Magee D., A Qualitative, Multi-scale Grammar For Image Description and Analysis, Proc. British Machine Vision Conference, pp293-302, 2002.
     
  • Cohn A., Magee D., Galata A., Hogg D., Hazarika S., Towards an Architecture for Cognitive Vision using Qualative Spatio-Temporal Representations and Abduction . Proc. Spatial Cognition , June 2002, (Published in Spatial Cognition III, Freksa, C., Habel, C., & Wender, K.F. (Eds.)).
     
  • Galata A., Cohn A., Magee D. and Hogg D., Learning temporal and qualitative spatial components of an interaction model , Proc. ECCV Workshop on Vision and Modelling of Dynamic Scenes, 2002
     
  • Magee D., Bulpitt A. and Berry E. Combining 3D Deformable Models and Level Set Methods for the Segmentation of Abnormal Aortic Aneurysms . Proc. British Machine Vision Conference , September 2001, p333-342.
     
  • Magee D., Bulpitt A. and Berry E. 3D Automated Segmentation and Structural Analysis of Vascular Trees Using Deformable Models . Proc. IEEE Workshop on Variational and Level Set Methods (ICCV2001) , July 2001, pp119-126.
     
  • Magee D., Bulpitt A. and Berry E. Level Set Methods for the 3D Segmentation of CT Images of Abnormal Aortic Aneurysms . Proc. Medical Image Understanding and Analysis (MIUA) , July 2001, pp141-144.
     
  • Magee D. and Boyle R. Detecting lameness in livestock using resampling Condensation and multi-stream cyclic hidden markov models. Proc. British Machine Vision Conference , BMVA, September 2000, pp332-341. Available as a Research Report.  Winner of Best Industrial Paper Award
     
  • Magee D. and Boyle R. Spatio-temporal Modeling in the Farmyard Domain. Proc. IAPR International Workshop on Articulated Motion and Deformable Objects (AMDO'2000), Palma de Mallorca, Spain, September 2000, pp83-95. (Springer LNCS 1899) Available as a Research Report.
     
  • Magee D. and Boyle R. Building Class Sensitive Models for Tracking Applications. Proc. British Machine Vision Conference, BMVA, September 1999. Available as a Research Report.
     
  • Magee D. and Boyle R. Feature tracking in real world scenes (or how to track a cow). Proc. IEE Colloquium on Motion Analysis and Tracking, IEE, May 1999. Available as a Research Report.
     
  • Magee D. and Boyle R. Building Shape Models from Image Sequences Using Piecewise Linear Approximation. Proc. British Machine Vision Conference, pages 398-408. BMVA, September 1998. Available as a Research Report.
  • Other Publications (Invited)

    Hogg, D; Cohn, A G; Devin, V; Magee, D; Needham, C; Santos, P. Learning about objects and activites in 24th L.A.S.R (Leeds Annual Statistical Research) Workshop pp. 79-82, 2005. PDF

    Book Chapters

    Cohn, A G; Hogg, D C; Bennett B, Devin, V; Galata A, Magee, D; Needham, C; Santos, P. Cognitive Vision: Integrating Symbolic Qualitative Representations with Computer Vision in Cognitive Vision Systems: Sampling the spectrum of approaches, H. Christensen and H-H. Nagel (eds.), Springer Verlag, 2006.

    PhD Thesis (2000)

  • Magee D. Machine Vision Techniques for the Evaluation of Animal Behaviour PhD Thesis. Available for download here.
  • Personal

    Some Photos

    Have a look at the page about my old band SLIDE.

    Contact Details

    photo of me email:          D.R.Magee AT leeds DOT ac DOT uk
    tel:               +44 113 343 6819
    fax:              +44 113 343 5468
    room:          7.11 E C Stoner
    address:      School of Computing, The University of Leeds, Leeds, LS2 9JT