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About Sickkids
About SickKids

Mark Henkelman, PhD

Research Institute
Senior Scientist Emeritus
Translational Medicine

University of Toronto
Professor, University of Toronto
Department of Medical Biophysics and Medical Imaging

Chair Positions
Canda Research Chair
Imaging Technologies in Human Disease & Preclinical Models

Phone: 416-813-7654 ext. 309556
Fax: 647-837-5832
Email: mhenkel@mouseimaging.ca
Alternate Contact: Katie Polanic
Alternate Phone: 416-813-7654 ext. 309536
Alternate Fax: 647-837-5832
Alternate Email: katie.polanic@sickkids.ca

For more information, visit:

Mouse Imaging Centre
The Centre for Phenogenomics

Brief Biography

Mark Henkelman is the Director of the Mouse Imaging Centre (MICe) which became operational in 2002. The centre is staffed by an exciting team of about 40 investigators with expertise in imaging techniques, computer science, imaging processing, developmental biology and mouse pathology.

Research Interests

  • Imaging for mouse phenotyping
  • Vascular development
  • Multiple mouse MR imaging
  • Micro CT and ultrasound biomicroscopy of mice
  • Optical and bioluminescent imaging of mice

Research Activities

Henkelman is a professor in the Departments of Medical Biophysics and Medical Imaging at the University of Toronto, a Senior Scientist in the Translational Medicine program at SickKids and the Director of the Mouse Imaging Centre (MICe). At MICe, his research is focused on providing a comprehensive assessment of mice using various imaging modalities as a critical resource for genome research.

He is co-author on 350 publications, > 26,000 citations (Google) and an author for over 620 abstracts and numerous presentations worldwide.

Future Research Interests

With the completion of the human genome, a major outstanding question in biomedical research is the relationship between genes and normal development of disease. Over this century, much of this will be worked out using mouse models of human diseases, because the genes and their function in the mouse are very similar to the human.

When looking for human diseases in the human population, we make extensive use of medical imaging. Therefore, it makes sense to have available the same imaging capabilities as we investigate mice for models of human disease.

As director, Henkelman's research is focused on building the Mouse Imaging Centre (MICe) with high field magnetic resonance imaging microscopy, ultrasound biomicroscopy, micro computed tomography, and optical techniques. With these imaging tools, the centre screens randomly and targeted mutagenized mice to look for phenotypes that represent human diseases and will take established human disease models in mice and use imaging to follow the progression of disease and response to treatment over time. Present results have shown that imaging has a major contribution to make to phenotyping genetic variants and to characterizing mouse disease models. Imaging is also critical for assessing mammalian development and environmental effects such as learning.

External Funding

  • Canada Foundation for Innovation
  • Canadian Institutes of Health Research
  • Genome Canada
  • Ontario Research Fund


  • Officer of the Order of Canada (2019)
  • Killam Prize in Health Sciences from the Canada Council (2010)
  • University Professor from the University of Toronto (2005)
  • Fellow of the Royal Society of Canada (2005)
  • Gold Medal from the International Society of Magnetic Resonance in Medicine (1998)


M.D. Wong, Y. Maezawa, J.P. Lerch, R.M. Henkelman.  Automated Pipeline for Anatomical Phenotyping of Mouse Embryos using Micro-CT.  Development 141(12):2533-2541, 2014.  DOI 10.1242/dev.107722  PMID 24850858

M.D. Wong, J. Dazai, J.R. Walls, R.M. Henkelman.  Design and Implementation of a Custom Built Optical Projection Tomographic System.  PLoS One 8(9):e73491, 2013.  DOI 10.1371/journal.pone.0073491  PMID 24023880

M. Hayes, X. Gao, L.X. Yu, N. Paria, R.M. Henkelman, C.A. Wise, B. Ciruna.  ptk7 Mutant Zebrafish Models of Congenital and Idiopathic Scoliosis implicates Dysregulated Wnt Signalling in Disease.  Nature Communications 5:4777, 2014.  DOI 10.38/ncomms5777  PMID 25182715

M.C. van Eede, J. Scholz, M.M. Chakravarty, R.M. Henkelman, J.P. Lerch.  Mapping Registration Sensitivity in MR Mouse Brain Images.  NeuroImage 82C:226-236, 2013.  DOI 10.1016/j.neuroimage.2013.06.004.  PMID 23756204

D.A. Vousden, J. Epp, H. Okuno, B.J. Nieman, M. van Eede, J. Dazai, T. Ragan, H, Bito, P.W. Frankland, J.P. Lerch, R.M. Henkelman.  Whole-brain Mapping of Behaviorally-induced Neural Activation in Mice.  Brain Structure and Function 220(4):2043-2057, 2014.  DOI 10.1007/s00429-014-0774-0 PMID 24760545

J. Ellegood, E. Anagnostou, B.A. Babineau, J.N. Crawley, L. Lin, M. Genestine, E. DiCicco-Bloom, J.K. Lai, J.A. Foster, O. Peñagarikano, D.H. Geschwind, L.K. Pacey, D.R. Hampson, C.L. Laliberté, A.A. Mills, E. Tam, L.R. Osborne, M. Kouser, F. Espinosa-Becerra, Z. Xuan, C.M. Powell, A. Raznahan, D.M. Robins, N. Nakai, J. Nakatani, T. Takumi, M.C. van Eede, T.M. Kerr, C. Muller, R.D. Blakely, J. Veenstra-VanderWeele, R.M. Henkelman, J.P. Lerch.  Clustering Autism: Using Neuroanatomical Differences in 26 Mouse Models Related to Autism to Gain Insight into the Heterogeneity.  Molecular Psychiatry 20(1):188-25, 2015. DOI 10.1038/mp.2014.98  PMID 25199916

D. Adams, R. Baldock, S. Bhattacharya, A.J. Copp, M. Dickinson, N.D. Greene, R.M. Henkelman, M. Justice, T. Mohun, S.A. Murray, E. Pauws, M. Raess, J. Rossant, T. Weaver, D. West.  Bloomsbury Report on Mouse Embryo Phenotyping: Recommendations from the IMPC Workshop on Embryonic Lethal Screening.  Disease Models and Mechanisms 6(3):571-579, 2013.  DOI 10.1242/dmm.011833  PMID 23519032

J. Ellegood, N. Nakai, J. Nakatani, M. Henkelman, T. Takumi and J. Lerch.  Neuroanatomical Phenotypes Are Consistent With Autism-Like Behavioral Phenotypes in the 15q11-13 Duplication Mouse Model.  Autism Research, 7 March 2015. DOI 10.1002/aur.1469 PMID 25755142

K. Lau, H. Tao, H. Liu, J. Wen, K. Sturgeon, N. Sorfazlian, S. Lazic,  J.T.A. Burrows,  M.D. Wong, D. Li, S. Deimling, B. Ciruna , I. Scott, C. Simmons, R.M. Henkelman, T. Williams, A.K. Hadjantonakis, R. Fernandez-Gonzalez, Y. Sun. S. Hopyan.  Anisotropic Stress Orients Remodeling of Mammalian Limb Bud Ectoderm.  Nature Cell Biology 17(5): 569-579, 2015. DOI 10.1038/ncb3156  PMID25893915