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Faculty of Science Radiation Sciences Graduate Program (RadGrad)
Faculty of Science

Radiation Sciences Graduate Program (RadGrad)

Michael Farquharson

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Supervisor, Associate Dean (Academic), School of Interdisciplinary Science

Office: Burke Science Building 129

Phone: (905) 525-9140 ext. 23021

Fax: (905) 546-9995

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  • My research interests are in the application of x-ray techniques to answer questions and solve problems related to human health. My PhD was in Advanced X-Ray Instrumentation developing technology that would enable the measurement of trabecular bone density in-vivo for the early diagnosis of the onset of osteoporosis. Instrumentation development still plays an important part of the laboratories research. An example of this is the design and build of an x-ray device that simultaneously measures the trace element content of human tissue as well as electron density and fat to fibrous ratio of the tissue. This data is obtained by using x-ray fluorescence (XRF), Compton scatter and angular dispersive x-ray diffraction. The motivation for this instrument is the development of technology that can determine margins in surgical oncology, particularly breast cancer surgery. This is an active area of research in my group. The instrument is shown below:


    Focus of the work conducted by my group:

    Mic3 The Development of Instrumentation and X-Ray Analysis Systems for the Identification and Characterization of Human Tissue and Other Materials Composition. This work involves the development of a tri-axial XRF instrument, and an energy dispersive x-ray diffraction system for tissue analysis. The tri-axial system reduces scatter and hence increases signal enabling us to improve on our minimum detectable limits by an order of magnitude and reduce data acquisition times.

    Normal and cancer tissue characterization for applications in surgery and histology. Measurements of radiation interaction properties of breast, colon, prostate, liver and kidney tissue e.g. attenuation coefficients, trace element levels, electron densities and scatter properties. This project is in collaboration with St Joseph’s Hospital in Hamilton, the Juravinski Cancer Centre and with the Centre for Surgical Invention and Innovation.

    Mic4 A further development of the surgical margin technology is the use optical spectroscopy and fluorescence system to characterize cancer and normal tissue. The aim is to develop a rapid and accurate diagnostic tool that can differentiate tumour from normal tissue in breast cancer at the time of biopsy as well as supply surgeons with a decision support tool that can provide an immediate intra-operative margin assessment at time of surgery. This work is in collaboration with Dr. Peter Lovrics, Dr. Tom Farrell and Dr. Qiyin Fang.

    Mic6Mic5Trace element analysis of biological samples as markers of disease particularly cancers and brain disorders. This work is mainly synchrotron based and involves the micro mapping of the distribution of trace elements in tissue using a synchrotron XRF microprobe. I have also examined the oxidization state of Zn, Fe and Cu in tumour and normal tissue using X-ray absorption near edge structure (XANES) techniques. Synchrotron facilities used for this work include, DESY synchrotron in Hamburg, Germany, ANKA synchrotron in Karlsruhe, Germany, Diamond Light Source UK, Canadian Light Source CLS Canada, and the Paul Schirrer Institute (PSI) in Switzerland. Many of my students have participated in synchrotron studies as part of their project work. Our latest work in this area, being carried out at the CLS in Canada and Diamond in the UK, is looking at the distribution of zinc in prostate cancer to be used as registration information for MRI techniques to image prostate cancer.

    Mic7Mic8 Monitoring iron levels in the skin as a surrogate marker for iron concentration in critical organs using x-ray fluorescence. Beta Thalassemia and Hemochromatosis are conditions that result in iron overload in the body. This can cause serious problems if the iron builds up in critical organs such as the heart and liver. We are developing a technique that can measure iron levels stored in the skin and correlate those levels to iron levels in critical organs. In order to use this in-vivo we are hoping to use a novel handheld XRF instrument available in the laboratory. This will help greatly in the treatment of thalassemia and hemochromatosis patients.

    Mic9Investigation of the relative contributions of transition metals to magnetic resonance imaging (MRI) for structural imaging in animals and humans to develop a cutting-edge protocol for brain metal imaging.

  • Selected Recent Publications:

    My research team produce many of outstanding research contributions to the field of biomedical research with a total of over 71 articles. I strongly encourage my students to publish and be lead author on papers. Members of my research group are in bold.

    1. Oakden W, Bock NA, Al-Ebraheem A, Farquharson MJ, Stanisz GJ.(2016). Early Regional Cuprizone Induced Demyelination in a Rat Model Revealed with MRI. NeuroImage. Submitted November 2016

    2. Shalaby N., Al-Ebraheem A., Le D., Fang Q., Farrell T., Lovrics P., and Farquharson M.J. (2016). A Comparison Study of Time-Resolved Fluorescence (TRF) and Diffuse Reflectance Spectroscopy (DRS) between Fresh and Pre-Frozen Breast Tissue. Medical Physics. Submitted October 2016

    3. Johnston E. M., Byun S. H., and Farquharson M. J. (2016). Determination of Optimal Metallic Secondary Target Thickness, Collimation, and Exposure Parameters for X-Ray Tube Based Polarized EDXRF. X-Ray Spectrometry. Accepted with minor corrections November 2016

    4. Desmond K, Al-Ebraheem A, Dabrowski W, Rola R, Stanisz GJ, Janik R, Oakden W, Kwiecien JM, Geraki K, Stanisz G, Farquharson MJ, and Bock NA .(2016). Differences in iron and manganese concentration may confound the measurement of myelin from R1 and R2 relaxation rates in studies of dysmyelination. NMR in Biomedicine. 29: 985-998.

    5. Al Ebraheem A., Miller L., Geraki K., Desmond K., Stanisz J., Bock N., and Farquharson M.J. (2016). Transition Metal Distribution in the Brain and Spinal Cord of a Dysmyelinated Rodent Model. American Institute of Physics (AIP) Conference Proceedings. 1764: 030005-1- 030005-11.

    6. Al-Ebraheem, Alia; Dao, Erica; Desouza, Elstan; Li, Christine; Wainman, Bruce; McNeill, Fiona; and Farquharson, Michael. (2015). Effect of sample preparation techniques on the concentrations and distributions of elements in biological tissues using µSRXRF: a comparative study. Physiological Measurement. 36(3): N51-60.

    7. Moldovan, N, Al-Ebraheem A, Lobo L, Park R, Farquharson MJ, and Bock NA. (2015). Altered Transition Metal Homeostasis in the Cuprizone Model of Demyelination. Neurotoxicology. 48: 1-8.

    8. Mersov A, Mersov G, Al-Ebraheem A, Cornacchi S, Gohla G, Lovrics P, and Farquharson MJ. (2014). The differentiation of malignant and benign human breast tissue at surgical margins and biopsy using x-ray interaction data and Bayesian classification. Radiation Physics and Chemistry. 95: 210-213.

    9. Al-Ebraheem A, Dao E, Geraki K, and Farquharson MJ. (2014). Emerging Patterns in the Distribution of Trace Elements in Ovarian, Invasive and In-Situ Breast Cancer. Journal of Physics: Conference Series. 499: 1-8.

    10. Moldovan N, Al-Ebraheem A, Miksys NA , Farquharson MJ, Bock NA. (2013). Altered transition metal homeostasis in mice following manganese injections for manganese-enhanced magnetic resonance imaging. Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine 26(1): 179-187.

    11. Darvish-Molla S. Al-Ebraheem A. Farquharson M.J. (2013). The identification and differentiation of secondary colorectal cancer in human liver tissue using x-ray fluorescence, coherent scatter spectroscopy and multivariate analysis.Applied Spectroscopy. 68: 79-87.

    12. Al-Ebraheem. A., Geraki. K., Leek. R., Harris. A.L. and Farquharson. M.J. (2013). The use of bio- metal concentrations correlated with clinical prognostic factors to assess human breast tissue. X-Ray Spectrometry. 42: 330-336.

    13. Desouza ED, Abu Atiya I, Al-Ebraheem A, Wainman BC, Fleming DEB, Fiona E. McNeill and Farquharson MJ. (2013). Characterization of the depth distribution of Ca, Fe and Zn in skin samples, using synchrotron micro-X- Ray Fluorescence (S-microXRF) to help quantify in-vivo measurements of elements in the skin. Applied Radiation and Isotopes. 77: 68-75.

    14. Farquharson M.J. Al-Ebraheem A. Cornacchi S. Gohla G. Lovrics P. (2013). The use of X- Ray interaction data to differentiate malignant from normal breast tissue at surgical margins and biopsy analysis. X-ray Spectrometry. 42: 349-358.

    15. Al- Ebraheem A, Gurusamy K, Mersov A and Farquharson MJ. (2010). Distribution of Ca,Fe, Cu and Zn in Primary Colorectal Cancer and Secondary Colorectal Liver Metastases. Nuclear Instruments and Methods in Physics Research A. 619: 338-343.

    16. Ryan EA and Farquharson MJ. (2010). The differentiation between malignant and nonmalignant breast tissue using Compton scattering. Nuclear Instruments and Methods in Physics Research A.619: 379-384.

    17. Al- Ebraheem A Goettlicher A. Geraki K. Steininger R. Farquharson M.J. (2010). The determination of zinc, copper and iron oxidation state in invasive ductal carcinoma of breast tissue and normal surrounding tissue using XANES. X-Ray Spectrometry. 39(5): 332-337.
  • Current research group members:

    Research Associate. Alia Al-Ebraheem. 2014 - current

    PhD student. “Design and development of a combined Tri-Axial XRF system and energy dispersive diffraction instrumentation for material analysis” Eric Johhston. Started at McMaster in September 2012, transferred to PhD 2014.

    Masters Student. “Development of an intra-surgical decision support system for use by breast cancer surgeons to identify tumour and margin locations” Nourhan Shalaby. Started at McMaster in May 2015. Awarded second place prize for the graduate students at the Radiation research day April 2016.

    Masters Student. “Correlation between iron levels in the skin and critical organs in rats” Erica Dao. Started at McMaster in September 2015.

    Masters Student. “Breast tissue classification using x-ray diffraction techniques” Duaa Faisal. Started at McMaster in September 2016.

    Former Graduate Students:

    MSc “SPECT Quality Control; an investigation into parameters for centre-of-rotation offset measurement” (nuclear medicine). Successfully completed 1997.

    MSc “2D vs 3D tumour volume determination. Is there a constant?” (computed tomography). Successfully completed June 1998.

    MSc “Filtered beams and x-ray fluorescence for photon attenuation measurements in biological samples”. (MSc student collaborating from Surrey University). Successfully completed September 1998.

    MSc “Comparison of filtered back projection technique for SPECT imaging” (Nuclear Medicine). Successfully completed June 1999.

    MSc “Comparison of two software programs using the filtered back projection algorithm for first generation tomographic set up”. (MSc student collaborating from University College London). Successfully completed August 1999

    MSc project “Attenuation correction techniques in SPECT cardiac imaging”. (Nuclear Medicine). Successfully completed January 2000.

    MSc “Measuring trabecular bone in archaeological femurs using EDXRD”. (MSc student collaborating from Southampton University). Successfully completed November 2000.

    MSc “A European wide trial on the dose given to patients during high resolution computed tomography of the chest. (computed tomography). Successfully completed 2000.

    MSc “Optimisation of magnetic resonance cholangiopanceatography (MRCP) at 1.5 T” (MRI). Successfully completed July 2000.

    MSc “Evaluation of sequences for quantitative contrast enhanced MRI” (MRI). Successfully completed 2003.

    MSc “Developing a phantom for the quantitative measurment of diffusion coefficients in MRI” (MRI). Successfully completed September 2003.

    MSc “Measuring linear attenuation coefficients of normal and diseased breast tissue using CT. Successfully completed October 2003.

    MSc “ A comparative study on the image quality of teleradiology images” (Digital imaging). Successfully completed July 2003.

    MSc “To develop a brain phantom for sequence development and system performance in MRI 1.5 T.” Successfully completed July 2005.

    MPhil student "Characterisation of skin disorders using XRF particularly iron concentrations in thalassaemia patients", Tarjani Patel, registered November 2000. Successfully completed February 2003.

    PhD student “Minimum detectable limits of trabecular bone density using EDXRD”. Allan Allday, registered October 1998. MPhil transfer completed March 1999. Successfully completed with minor corrections May 2004.

    PhD student “Breast tissue characterisation and mammography” Kalotina Geraki, registered October 1999. Mphil transfer completed February 2002. Successfully completed with no corrections June 2003.

    PhD student "Magnetic Resonance Imaging (MRI) and its value in the investigation of trabecular bone" Marios Yiannakas, registered October 2000. Mphil transfer complete June 2002. Successfully completed with minor corrections July 2004.

    PhD student “Hydrophilic materials as a suitable breast tissue equivalent phantom material”. Sabar Bauk (Collaborating student from University of Surrey). Successfully completed October 2000.

    PhD student “Determination of electron density, coherent scatter properties and trace elements as a histopathology tool in mammography”. Elaine Ryan, registered August 2002. Mphil transfer completed February 2004. Successfully completed with minor corrections June 2006.

    PhD student. “Knowledge, attitude, belief, behavior and breast cancer screening practices in developing countries – A case study for Ghana. Samuel Opoku, registered 2002. Mphil transfer February 2005. Successfully completed October 2007.

    PhD student. “Minimum temporal resolution of scatter signals from normal and diseased tissue and the development of an excision margin detection device”. Ekaterina Aristovich. This was the anual studentship awarded by the University from over 100 entries. Start date May 2008.

    PhD student (part time external). “Bone mineral density, Diet and Exercise in Students at the University of Shajah UAE”. Penelope Bell, registered January 2001. MPhil transfer competed January 2005. Successfully completed April 2006.

    Research Assistant. Dr. Andrew Bagshaw. Line manager for full time RA working in the radiation laboratory on Fe XRF measurements on the skin from 2000 –2001 funded by the UK Thalassaemia Society.

    Research Assistant. Dr. Kalotina Geraki. Line manager for full time RA funded by the City University Research Fellowship for two years 2003 – 2005.

    Research Assistant. Dr. Elaine Ryan. Line manager for full time RA funded by Tissuomics project from 2005 - 2008.

    Research Assistant. Dr. Chrysoula Theodorakou. Line manager to full time RA funded by the NEAT program and EPSRC. Started February 2006 on a one year contract.

    PhD student. “Trace element micromapping and their role in cancer” Alia Al-Ebraheem. Completed with no corrections September 2010. Alia was awarded top City University student research prize in the university annual poster competition. The prize was funding to attend and present at an international conference (EXRS2008, Croatia).

    PhD Student. “The role of trace elements in colorectal liver cancer” Kuinchi Gurusamy. University College London, UK. Completed November 2010.

    Master Student. “Development of an intra surgical decision support system”. Sahar Darvish Molla. Completed September 2012.

    Master Student. “Fe in the skin as a surrogate marker for total body iron burden” Ibrahim Abuatiya. Completed September 2010.

    Master Student (co supervisor) “Investigation of transition metals in the brain” Natilia Moldova. Started at McMaster in September 2010.

    Completed July 2012.

    Post Doctoral Fellow. “The role of trace metals in cancer: quantification and distribution using synchrotron micro probe techniques” Alia Al-Ebraheem.2010-2014

    Masters Student. “Measurement of Fe and Zn in rodent brains using NAA and XRF to examine myelin degradation” Fozeyah Hamzi. Completed 2015.

    Current and Previous Undergraduate students:

    Jenasee Mynerich, BSc student, School of Interdisciplinary Science, Undergraduate Student, McMaster University.2016. Project Title: Characterization of breast tissue using energy-dispersive X-ray diffraction

    Kerry Chong, 3Z06 thesis project. Optimization of in-vivo skin thickness using ultrasound. Supervisor 2016

    Adrianna Mijatovic, 3Z06 thesis supervisor. Location of potential skin locations for the measurement of Fe using ultrasound. Supervisor 2016

    Erica Dao, BSc student, Department of Medical Physics and Radiation Sciences. Science 3RP3 (research practicum) supervisor 2014

    Erica Dao, BSc student, Department of Medical Physics and Radiation Sciences. Thesis supervisor 2014-2015 Project Title: Characterization of the depth distribution of trace elements in skin samples

    Lauren Miller, BSc student, Department of Medical Physics and Applied Radiation Sciences. Science 3RP3 (research practicum) supervisor 2015 Project Title: Transition Metal Distribution in the Brain and Spinal Cord of a Dysmyelinated Rodent Model

    Christine Li, BSc student, Department of Pathology and Molecular Medicine, McMaster. Thesis Student completed July 2014. Project Title: Characterization of the depth distribution of Ca, Fe and Zn in skin samples, using synchrotron micro-X-Ray Fluorescence (micro SRXRF)

    Sherry Tai, BSc student, Department of Radiography. 3Z06 Research Article 2015 Project Title: Trace Metal Quantification Using X-Ray Fluorescence

    Garrett Sawyers, BSc student, Department of Medical Physics and Applied Radiation Sciences, 3Z06 Research Article 2012. Project Title: Altered Trace elements in the Cuprizone Model of Demyelination

    Natasha Batchelor, BSc student, Department of Medical Physics and Applied Radiation Sciences, 3Z06 Research Article 2011. Project Title: Measurement of trace elements in the liver, kidney and blood of control mice using X-ray Fluorescence

    Alayna Weigel, BSc student, Department of Medical Physics and Applied Radiation Sciences, 3Z06 Research Article 2010. Project Title: Trace metal Calibration

    Nick Papalia, BSc student, Department of Medical Physics and Applied Radiation Sciences, 3Z06 Research Article 2010. Project Title: Trace Elements in Rat Brains

    Anna Mersov, BSc Honours student, Department of Medical Physics and Applied Radiation Sciences, USRA summer student 2009. Project Title: Development of Baysian classification techniques to detect tumour tissue in breast

  • Teaching Commitments at McMaster

    Med Phys 1E03: Physics in Medicine and Biology 1

    Science 1A03: level 1 undergraduate course Investigating Science: Opportunities and Experiences

    Med Rad Sci 1C03: Introductory to Physics for Medical Radiation Sciences

    Science 3RP3: Research Practicum

    Med Rad Sci 3Z06: Medical Radiation Sciences research thesis

    Med Phys 4Y06: Medical Physics research thesis

McMaster University - Faculty of Science

Mailing Address

AN Bourns Building (ABB), Room 241
McMaster University

1280 Main Street West
Hamilton, Ontario, Canada
L8S 4K1

Contact Information

Office Hours:
9:00 a.m. - 4:00 p.m.
Telephone Inquiries:
+1 (905) 525-9140 ext.27650
Email Inquiries:

McMaster University - Faculty of Science

Mailing Address

McMaster University
AN Bourns Building (ABB), Room 241
1280 Main Street West
Hamilton, Ontario, Canada
L8S 4K1

Contact Information

Office Hours:
9:00 a.m. - 4:00 p.m.
Telephone Inquiries:
(905) 525-9140 ext. 24558
Email Inquiries: