About Sickkids
About SickKids

Mark Henkelman, PhD

Research Institute
Senior Scientist
Physiology & Experimental Medicine

Mouse Imaging Centre

University of Toronto
Department of Medical Biophysics and Medical Imaging

Phone: 647-837-5820
Fax: 647-837-5832
e-mail: mhenkel@mouseimaging.ca
Alternate Contact: Lynda Cockroft
Alternate Phone: 647-837-5820
Alternate Fax: 647-837-5832
Alternate e-mail: cockroft@mouseimaging.ca

For more information, visit:

Mouse Imaging Centre
Toronto Centre for Phenogenomics

Brief Biography

I am Director of the Mouse Imaging Centre (MICe) which became operational in 2002. The centre is staffed by an exciting team of about 25 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

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

I am co-author on 273 publications and an author for over 498 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 or 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 we look 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, my 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 will screen 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. Preliminary 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
  • National Cancer Institute of Canada - Terry Fox Foundation
  • National Institutes of Health (U.S.A.)
  • Ontario Innovation Trust
  • Ontario Institute for Cancer Research
  • Ontario Research Development Challenge Fund
  • Ontario Research Fund


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)


Dorr AE, Lerch JP, Spring S, Kabani N, Henkelman RM. High resolution three dimensional brain atlas using an average magnetic resonance imaging of 40 adult C57BL/6J mice. NeuroImage 42(1):60-69, 2008. DOI 10.1016/j.neuroimage.2008.03.037

Walls JR, Coultas L, Rossant J, Henkelman RM. Three-dimensional analysis of vascular development in the mouse embryo. PLoS-ONE 3(8):e2853, 2008. DOI 10.1371/journal.pone.0002853.

Clapcote SJ, Lipina TV, Millar JK, Mackie S, Christie S, Ogawa F, Lerch JP, Trimble K, Uchiyama M, Sakuraba Y, Kaneda H, Shiroishi T, Houslay MD, Henkelman RM, Sled JG, Gondo Y, Porteous DJ, Roder JC. Behavioral phenotypes of disc1 missense mutations in mice. Neuron 54:387-402, 2007. DOI 10.1016/j.neuron.2007.04.015

Nieman BJ, Lerch JP, Bock NA, Chen XJ, Sled JG, Henkelman RM. Mouse behavioral mutants have neuroimaging abnormalities. Human Brain Mapping 28(6):567-575, 2007. DOI 10.1002/hbm.20408

Bock NA, Kovacevic N, Lipina TV, Roder JC, Ackerman SL, Henkelman RM. In vivo magnetic resonance imaging and semi-automated image analysis extend the brain phenotype for cdf/cdf mice. J Neuroscience 26:4455-4459, 2006 (Cover Illustration). DOI 10.1523/JNEUROSCI.5438-05.2006

Bock NA, Nieman BJ, Bishop JB, Henkelman RM. In vivo multiple-mouse MRI at 7 tesla. Magn. Reson. Med. 54(5):1311-1316, 2005.DOI 10.1002/mrm.20683

Lickert H, Takeuchi JK, von Both I, Walls JR, McAuliffe F, Adamson SL, Henkelman RM, Wrana JL, Rossant J, Bruneau BG. Baf60c is essential for function of BAF chromatin remodeling complexes in heart development. Nature 432(7013):107-112, 2004. DOI 10.1038/nature03071

Singh SK, Hawkins C, Clarke ID, Squire JA, Bayani J, Hide T, Henkelman RM, Cusimano MD, Dirks PB. Identification of human brain tumour initiating cells. Nature 432(7015):396-401, 2004. DOI 10.1031/nature03031