Dr. Martin Yaffe

Co-Program Director, Imaging Program

Dr. Martin Yaffe’s research is directed toward development and improvement of imaging techniques for the earlier detection, diagnosis and treatment of cancer, with a strong focus on breast cancer. His team is also interested in methods for analyzing image patterns to predict breast cancer risk and using these as tools to study the causes of breast cancer and to help develop preventive measures.

His team has established a comprehensive program in biomarker imaging research, which includes development of new techniques for 3D pathology including whole mount large format tissue slides development and analysis. These techniques are used for validation of new in vivo imaging methods, as well as for investigating approaches to improving accuracy of pathology, and adding prognostic and predictive information in management of cancer.

Currently the effort of the laboratory is largely focused on developing biomarker multiplexing techniques in cancer studies to examine molecular changes in different areas of the tumours and to define the extent of cancer heterogeneity by characterizing each clone with biomarker signatures, as well as investigating potential functional relationships between them. This information could also be used to further delineate subtypes of cancers for developing treatments that can target heterogeneous tumours. In this area we are currently involved in collaborative projects developing biomarker panels for ductal carcinoma in situ (DCIS), ovarian cancer and immune checkpoint inhibitors.

As well, we are developing an alternative method for biomarker multiplexing based on simultaneous immunohistochemical staining with different chromogens and imaging with a multispectral deconvolution system which can unmix and quantify wavelengths of the different chromogens applied.

The two main foci of Yaffe’s research are integrated in a number of radiomics and radiogenomics studies that compare biomarker and molecular signatures of tumour cells and microenvironment with imaging biomarkers derived from medical breast images.

Yaffe’s lab made fundamental contributions to the technical development and clinical evaluation of digital mammography. Yaffe is part of the leadership team of TMIST, a randomized trial of digital breast tomosynthesis for earlier detection of potentially lethal breast cancers.

Current affiliations

  • Program Director, Imaging Program, OICR;
  • Tory Family Chair in Cancer Research;
  • Chief Scientific Officer, Centre for Imaging Technology Commercialization;
  • Professor, Departments of Medical Biophysics and Medical Imaging, University of Toronto;
  • Senior Scientist, Sunnybrook Research Institute (SRI).

Research interests

  • Breast cancer;
  • Earlier detection;
  • Screening;
  • Digital breast tomosynthesis;
  • Biomarkers;
  • Precision medicine;
  • Over/under treatment;
  • Multiplexing;
  • Multispectral deconvolution;
  • Whole mount immunohistochemistry;
  • Imaging-pathology validation;
  • 3D Pathology tools;
  • Image analysis.

Select publications

Sun L, Wang D, Zubovits JT, Yaffe MJ, Clarke GM.
An improved processing method for breast whole-mount serial sections for three-dimensional histopathology imaging.
Am J Clin Pathol 2009;131:383-392.

Clarke GM, Zubovits JT, Shaikh KA, Wang D, Dinn SR, Corwin AD, Santamaria-Pang A, Li Q, Nofech-Mozes S, Liu K, Pang Z, Filkins RJ, Yaffe MJ.
A novel, automated technology for multiplex biomarker imaging and application to breast cancer.
Histopathology. 2014 Jan;64(2):242-55. 48.

Clarke GM, Holloway CMB, Zubovits JT, Nofech-Mozes S, Liu K, Murray M, Wang D, Yaffe MJ.
Whole-mount pathology of breast lumpectomy specimens improves detection of tumour margins and focality.
Histopathology. 2016 Jul;69(1):35-44. doi: 10.1111/his.12912. Epub 2016 Jan 19.

Hope , Dan Wang, S. Nofech-Mozes, Kela Liu, S. Kaanumalle, Y. Al-Kohafi, K. Shaikh, R.Filkins, M. Yaffe.
Single Section Biomarker Measurement and Colocalization via a Novel Multiplexing Staining Technology, Single Section Biomarker Measurement and Colocalization via a Novel Multiplexing Staining Technology,
Chapter, Breast Imaging, Volume 9699 of the series Lecture Notes in Computer Science pp 265-273,17 June 2016


Various display and analysis tools for:

  • 3D image reconstruction of slide images – this includes corrections for distortion;
  • Interactive 3D image display and analysis;
  • Colour calibration: Pipeline for the correlation of 3D in vivo imaging to histopathology.


  • Cumulus 6 and Cumulus V Software for quantitative assessment of breast density. Used worldwide;
  • DMISTIFIER – software for measurement of image quality of digital radiographs;
  • Software for Quality Control for large mammography screening programs;
  • Software for Quality Control in a large randomized study of breast tomosynthesis.

Other achievements

  • Founder of two start-up companies: Volpara Solutions and Mammographic Physics Inc.;
  • Patent # 4,638,502, January 20, 1987
    “Anthropomorphic Phantoms”;
  • Patent #8,120,683 B1
    “High resolution digital imaging apparatus”;
  • Patent # 7,286,632, October 23, 2007
    “Method and apparatus for measuring the thickness of compressed objects”;
  • Patent # A61B6/00; A61B6/03; A61B6/12 Dec 30, 2015
    “Systems and methods for generating an imaging biomarker that indicates detectability or conspicuity of lesions in a mammographic image”;
  • Disclosure ”Rapid-Setting Adhesive Hydrogel to Support Rapid Grossing and Hypersampling of Large Surgical Specimens” (2012);
  • Disclosure ”Tissue Slicing Mould for Rapid Grossing and Hypersampling of Large Surgical Specimens”(2012).


  • Physics in Medicine and Biology – top 25 most important publications in 60 years;
  • Member, Order of Canada, July 1, 2015;
  • Honorary Fellow, The Society of Breast Imaging, 2014;
  • Cause Leadership Award, Canadian Breast Cancer Foundation April, 2011;
  • Tory Chair in Cancer Research, 2007;
  • Sylvia Sorkin Greenfield Award, August, 2003;
  • Cum Laude Award, RSNA for INFORAD exhibit, A Functional Demonstration of the National Digital Mammography Archive Testbed@, with MD Schnall et al, Nov., 2001;
  • Fellow, American Association of Physicists in Medicine July, 1997;
  • Sylvia Fedoruk Prize in Medical Physics, with R.M. Nishikawa, G.E. Mawdsley, A. Fenster. Presented at the World Congress on Medical Physics, San Antonio, TX, August 1988;
  • Runner-up of Sylvia Fedoruk Prize, with P.C. Johns, August, 1988;
  • Sylvia Greenfield Award. Presented to P.C. Johns and M. Yaffe by American Association of Physicists in Medicine, July, 1984;
  • Charles E. Ives Engineering Award, 1984. Presented by the Society of Photographic Scientists and Engineers.

Previous experience and education

  • Program Director, Smarter Imaging Program, OICR;
  • Co-Program Director, Imaging Translation Program, OICR;
  • Associate Professor, Departments of Radiology and Medical Biophysics, University of Toronto;
  • Senior Scientist Physics Division, the Ontario Cancer Institute, University Health Network;
  • Consultant Physicist, St. Michael’s Hospital, Toronto;
  • Consultant Physicist: National Cancer Institute of Canada, National Breast Screening Study, Ontario Breast Screening Program;
  • PhD, Medical Biophysics, University of Toronto.

Opportunities to collaborate

Yaffe welcomes collaborators in many areas of research that involve the development of more accurate quantitative techniques, validation of novel medical imaging methods and design of new therapies including:

  • Whole mount technique development;
  • Biomarker panel multiplexing;
  • Intelligent image analysis tools;
  • Imaging/pathology correlation for imaging clinical trials and pilot projects.

Visit OICR’s Collaborative Research Resources directory for more opportunities to collaborate with Dr. Yaffe.

Related links


Yulia Yerofeyeva
Program Manager
Sunnybrook Research Institute