MIAL

Jingyun Chen

PhD Student, Medical Image Analysis Lab

Ph.D. candidate, School of Engineering Science, Simon Fraser University, Present
Certificate of University Teaching and Learning, Simon Fraser University, 2010
Summer school, Institute for Pure and Applied Mathematics, University of California-Los Angeles, 2008
M.Sc, Institute of Nuclear and New Energy Technology, Tsinghua University, 2006
B.Sc, School of Information Science and Technology, Tsinghua University, 2003

 
Office
SFU TASC 9400

Phone
Office
1-778-782-5509

 

Research Interests

My research interest involves processing and analyzing digital tomography images such as x-ray computed tomography (CT) images, magnetic resonance images (MRI), and electron microscope cross-section images. My main contributions to this area include: 2D histogram for CT image segmentation, brain MRI scan segmentation and registration for Parkinson’s disease study, Matlab toolbox for functional MRI signal processing (fPipe), and electron microscope image segmentation for animal peripheral nervous system study.

Teaching is also my interest. I use to work as a teaching assistant of two courses: “digital image processing”, and “human factor & usability engineering”. I completed the certificate program of university teaching & learning, and was elected the trustee of teaching support staff union for two terms.

Most of time I work as an image/data analyst in a team consists of neurologists, radiologists, system analysts, and patients. I really enjoy working in such teams, where I can contribute my expertise and be covered by other members’ expertise. Both my research and teaching skills will help. It’s also kind cool as it reminds me of those fantasy role-playing teams - melee fighters, archers, spellcasters and healers - every class is uniquely needed in its own way.

Some posters of my previous work can be found on our Auto Brain Mapping website:

Multi-channel Registration of Susceptibility Weighted Imaging Scans

Investigation of Anatomical Variability in Basal Ganglia Structures

Automated Brain Segmentation for Parksinson's Study

Selected Publications

Journal Papers:

  • J. Chen, M. J. McKeown, and M. F. Beg, “Brain Morphometry analysis by assessing initial momentum: independent components application to Parkinson's disease”. IEEE Transactions on Medical Imaging, 2010. (under review)
  • H. L. More, J. Chen (Co-first Author), E. Gibson, J. M. Donelan, and M. F. Beg, “A semi-automated method for quantifying axon and myelin size distribution in scanning electron microscope images”, Journal of Neuroscience Method, 2010. (under review)
  • J. Chen, P. Cong and Q. Song, “Thresholding Using two-dimensional histogram and watershed algorithm in the luggage inspection system”, Nuclear Electronics & Detection Technology, 2006 vol26, pp901-904,954
  • Q. Song, P. Cong and J. Chen, “Image segmentation based on level set method in the luggage Inspection system”, Atomic Energy Science and Technology, 2006 vol40, pp745-748
  • J. Chen and X. Zhou, “ZigBee wireless communication technology in Industrial controls”, Radio Engineering of China, 2006 vol36, pp61-64

Conference Presentations:

  • J. Chen, A. R. Khan, M. J. McKeown, and M. F. Beg, “Momentum-based morphometric analysis with application to Parkinson's Disease”, SPIE Symposium on Medical Imaging. Orlando USA, 2011
  • J. Chen, A. R. Khan, C. Denk, S. Galley, A. Rauscher, M.J. McKeown and M.F. Beg, “Multi-structure registration allows group interpretation of midbrain iron content in Parkinson's”, 16th Annual Meeting of the Organization for Human Brain Mapping,  Barcelona Spain, 2010
  • J. Chen, M.J. McKeown and M.F. Beg, "Variability of basal ganglia morphology after spatial normalization: Implications for group studies", 33rd Conference of the Canadian Medical and Biological Engineering Society, Vancouver Canada, 2010
  • J. Chen, H.L. More, J.M. Donelan and M.F. Beg, “Automated methods for neuron segmentation and analysis of electron microscope images”, 33rd Conference of the Canadian Medical and Biological Engineering Society, Vancouver Canada, 2010
  • H.L. More, J.R. Hutchinson, D.F. Collins, D.J. Weber, S.K.H. Aung, J. Chen, M.F. Beg, and J.M. Donelan, "Tradeoffs in responsiveness and resolution in the peripheral nervous system", The Society for Integrative and Comparative Biology Annual Meeting, Seattle USA, 2010.
  • J. Chen, S.J. Palmer, A.R. Khan, M.J. McKeown, M.F. Beg, “Freesurfer-Initialized Large Deformation Diffeomorphic Metric Mapping with application to Parkinson's Disease”, SPIE Symposium on Medical Imaging, Orlando USA, 2009

Theses:

  • J. Chen, P.Cong, X. Xiang, "Two-dimensional histogram thresholding method for digital radiograph segmentation", M.Sc thesis, Institute of Nuclear and New Energy Technology, Tsinghua University, 2006
  • J. Chen, W. Xue, Y. Dou, "Industrial web-database development, a national key technologies research and development project", B.Sc thesis, School of Information Science and Technology, Tsinghua University, 2003

Brief bio

I came to Canada in 2006, and have since then been living in Vancouver - the great city that brought us 2010 Winter Olympics. The way people live here really inspired me, and no matter how long I’ve stayed, the magnificent nature environment never failed to amaze me. An interesting article revealing my early days in Vancouver can be found on a local newspaper The Geogia Straight:

Chinese students adjust via noodles and new year

Current Funding

NSERC Collaborative Health Research Projects Program

Research Projects

FreeSurfer-Initiated Putamen, Cadate and Thalamus Segmentation in MRI Using Large Deformation Diffeomorphic Metric Mapping

Site by Faculty of Applied Science web team, Simon Fraser University