Jonathan T. Elliott, Ph.D.

I'm a Research Assistant Professor of Engineering Sciences at Dartmouth College in New Hampshire. I work in the Optics in Medicine Group at Thayer School of Engineering. My research strives to apply biotechnology--including imaging and sensing--to improve cancer surgery. Right now, I work mostly in the fluorescence-guided surgery space, where I develop smart probes that target tumors based on molecular expression. These imaging agents have the potential to dramatically improve cancer resection by highlighting cells that overexpress certain markers which are found primarily in cancer. 

I am also passionate about human-centered design: how can I provide high-level information to surgeons during complicated cancer surgery, in a way that is helpful and natural. This problem intersects medical imaging, tracer kinetics, computer vision, optical engineering, physiology, oncology, molecular biology, to name a few...which is perfect, since I love to learn new things every day!

Finally, I am advancing methodologies to more effectively and efficiently use this novel information in real time, so surgeons can make the best decisions on when to resect tissue, and when to spare it. This is particularily important in balancing the risk of recurrence with quality of life and morbidity due to surgery. I explore this concept in fluorescence guided surgery, as well as breast conserving surgery, and employ technologies and visualization methods to enhance contrast and support decision making based on multiparametric data, intraoperatively.

My teaching focus is on biomedical engineering for global health. I have developed, and instruct, an undergraduate survey-level course which challenges students to develop and apply skills in biomedical engineering to solve health challenges for low- and middle-income countries. I am passionate about improving the access and quality of healthcare for everyone, through research, teaching, and raising awareness of these under-researchered areas of BME.

When I'm not playing around with lasers, I am almost certainly hiking, skiing, or kicking around a ball with my two wonderful kids. I am fortunate to have the support of my wonderful wife Laura, the "high-fives" of our son, Yianni, and smiles of our daughter, Ruby, which encourage me each day. Thanks for visiting my website, where you'll find some information on my current projects. Feel free to contact me if you have any questions!

Curriculum Vitae


2013-2015 Postdoctoral Fellowship in Cancer Research
Thayer School of Engineering, Dartmouth College, Hanover NH USA
Research Mentor: Brian W. Pogue
Topics: Fluorescence guided surgery, photodynamic therapy, tracer kinetic modeling, and structured light imaging. Salary supported by the Canadian Institutes of Health Research.
2013 Doctor of Philosophy (Medical Biophysics)
The University of Western Ontario, London ON Canada
Thesis Committee: Keith St. Lawrence (advisor), Ting-Yim Lee, Vladislav Toronov
" On the development of a dynamic contrast-enhanced near-infrared technique to measure cerebral blood flow in the neurocritical care unit”
2008 Bachelors of Medical Science (Hon.)
The University of Western Ontario, London ON Canada
Double Major in Physiology and Medical Biophysics

Academic Appointments

2015 - Present Research Assistant Professor, Thayer School of Engineering at Dartmouth
2014 - Present Lecturer, Thayer School of Engineering at Dartmouth
2013 - 2015 Research Associate, Thayer School of Engineering at Dartmouth

Research Grants

2016-2018  K99 Pathway to Independence Award (K99CA190890)
2016-2017  ZOLL Academic Industry Grant
2016-2017  Neukom Foundation Faculty CompX Award
2015-2016  Hitchcock Foundation Pilot Project Grant
2013-2015  Canadian Institutes of Health Research Postdoctoral Fellowship

Teaching, Mentoring and Outreach

2015 - 2016 Faculty Advisor, Healthcare Policy, Innovation and Delivery Living Learning Community
2015 Faculty Advisor, Dartmouth Team in Emory Global Health Case Competition

Complete CV available upon request.


Almost 1 in 4 people will get cancer in their lifetime. When that happens, it is hoped that chemotherapy, radiation and surgery will contribute to a postivie patient outcome. I work with surgeons and other researchers to help improve the outcomes of three significant types of cancer: brain cancer, pancreatic cancer and breast cancer.


Top row: Accumulation of EGFR-targeted tracer ABY029 in F98 rat gloma ex vivo tissue sections, compared with IRDye680RD and 5-ALA enhanced PpIX. Bottom row: A fusion image (left) shows the similarity and differences in spatial distribution, while (right) the contrast enhanced T2 MRI image shows the location of the tumor.

Glioma surgery is challenging because the tumor invades into the normal brain, making it difficult to know which tissue to remove. I research and design image-guided surgical tools and analytics to improve the visualization and resection of tumor during open craniotomy. I have the privlege of working with a team of world-class Dartmouth researchers who are involved in several NIH funded projects including a grant to develop a safe antibody fragment based imaging agent and a grant that enabled the construction of a intraoperative CT and MRI suite.

My research is unique in that I exploit tracer kinetic methods from PET imaging, mainly arterial input based methods[1], to quantify binding and kinetic parameters. These provide a direct assessment of the molecular composition and physiological status of cancer tissue. Currently I am developing the appropriate arterial input models and means by which these can be evaluated [2,3].

Another major part of my research involves understanding how information can be effectively and efficiently communicated to the surgeon during a procedure [4]. This draws on elements of visual perception, computer vision and cognitive science, to better understand how different sources of information can be selectively attended and acted upon during resection. For example, colocalized information (such as in an image fusion) can be selectively attended to if it occupies a unique locus on a particular pereceptual dimension. This perceptual dimension can be "color", i.e., chromaticity or luminance, for example. Therefore, I seek to maximize contrast between different elements of a fused image such that perception of one aspect (the white-light image of tissue) is distinct and augmented by another aspect (the colormap representation of a kinetic parameter). I maintain an open-source MATLAB-based program to assist in developing and understanding these types of images ( http://www.dartmouth.edu/~overlay )

I'm also part of a research team looking at using targeted photosensitizing agents to improve photodynamic therapy for unresectable pancreatic cancer and oral cancer. Our most recent work is in understanding how contrast enhanced CT can be used to guide PDT has been published. [5]

Finally, a third area of focus is in wide field scatter-based imaging as a way of evaluating the ultrastructure of tissue in a macroscopic scale. Currently, about 35% of patients undergoing breast conserving therapy must return to the hospital for a second surgery because some tumor was left int he patient. This is because many tumors are being discovered early and are difficult to palpate (so the surgeon is cutting blind) and the histopathology cannot be performed intraoperatively due to problems with frozen section analysis of breast tissue. We have developed a rapid wide-field technique that provides contrast on the basis of scattering properties of tissue -- properties that are modified by cancer cells as they reorganize the extracellular matrix in order to expand. [6]


Colorimetry is an important aspect of data visualization when multimple images are fused and information must be selectively attended to based on a unique perceptual dimension. Optimizing the color contrast between two sources of information may reduce interpretive error.

[1] Elliott JT et al. (2014) Quantifying cerebral blood flow in an adult pig ischemia model by a depth-resolved dynamic contrast-enhanced optical method. Neuroimage .
[2] Elliott JT et al. (2014) Direct characterization of arterial input functions by fluorescence imaging of exposed carotid artery to facilitate kinetic analysis. Molecular Imaging in Biology.
[3] Elliott JT et al. (2015) Image-derived arterial input function for quantitative fluorescence imaging of receptor-drug binding in vivo. J Biophotonics 
[4] Elliott JT et al. (2015) Review of fluorescence guided surgery visualization and overlay techniques. Biomed Opt Expr
[5] Elliott JT et al. (2014) Perfusion CT estimates PS uptake and biodistribution in a rabbit orthotopic pancreatic cancer model: a pilot study Acad Radiol DOI: 10.1016/j.acra.2014.12.014
[6] Krishnaswamy V, Elliott JT, et al. (2014) Structured Light Scatteroscopy. J Biomed Opt 7(19): 070504.


The Winter 2016 term will mark the second time I have the privilege of coordinating and instructing undergraduate students in biomedical engineering for global health (ENGS16). This offering is a comprehensive, survey-level course designed to equip students with the skills necessary to develop global health technology for low- and middle-income countries. My teaching approach to this course strives to make the experience: experiential, extreme, and empowering.

Engineering forms the bridge between scientific discovery and human experience—it is by its very nature, concerned with applying the scientific process to fill a human need. Global health encapsulates the breadth of human joy (the birth of a child) and human suffering from illness and death. My goal in ENGS 16 is for each student to experience these things through discussions, lab work, group projects, case studies and tear-downs. 

Paradoxically, extreme conditions can impose constraints on an engineer that will result in more creative solutions. It’s my goal to push through the everyday and mundane and challenge you to come up with solutions that are outlandish and bold. I’m guided by the principle that every human deserves health, even if they live in war-torn Afghanistan or 16,500 feet above sea level in the Peruvian Andes. These are extreme scenarios--and my goal is to curate as many of these as I can, so we can ideate, prototype and test solutions.

My goal is to run ENGS 16 very agile—perhaps an extreme idea in it’s own right. I firmly believe that the student should be in the drivers seat as much as possible. ENGS 16 will give every student the chance to develop a solution to a real global health challenge in less than 6 weeks!

Individuals living in resource-limited settings deal with diseases that are stigmatizing and poverty promoting. Global health technology can connect, educate, diagnose and monitor individuals. Rapidly deployable microcomputers can allow the end-user to hack their own solution to a health need.

ENGS 16 will also empower students. Fears waste human time, effort, and creativity we need to solve global health challenges. These include fear of the unknown, fear of making mistakes, and fear of losing control. A major goal of ENGS 16 is to employ participatory teaching methods to overcome these fears and enable the student to develop and retain knowledge and skills that can be used to make an impact into the future.

Peer-Reviewed Publications

Selected Publications (click to view)
opmi boe JBP neuroimage
Microdose imaging of ABY-029 with customized OPMI
Review of FGR visualization techniques
Image-derived AIF for receptor-drug imaging
Quantitative NIRS in adult TBI model

Most Recent Publications

  1. JT Elliott, AV Dsouza, K Marra, BW Pogue, DW Roberts, KD Paulsen. Microdose fluorescence imaging of ABY-029 on an operating microscope adapted by custom illumination and imaging modules. Biomed Opt Expr 2016; 7(9):3280-3288.
  2. BW Pogue, KD Paulsen, KS Samkoe, JT Elliott T Hasan, TV Strong, DR Draney, J Feldwisch. Vision 20/20: Molecular-guided surgical oncology based upon tumor metabolism or immunologic phenotype Med Phys 2016; 43(6):3143-3156.
  3. BW Pogue, JT Elliott , SC Kanick, SC Davis, KS Samkoe, EV Maytin, SP Pereira, and T Hasan. Revisiting photodynamic therapy dosimetry: reductionist & surrogate approaches to facilitate clinical success. Phys Med Biol 2016; 61(7):R57.
  4. JT Elliott, AV Dsouza, SC Davis, JD Olson, KD Paulsen, DW Roberts, and BW Pogue. Review of fluorescence guided surgery visualization and overlay techniques. Biomed Opt Expr 2015; 6(10):3765-3782.
  5. JT Elliott, KS Samkoe, SC Davis, JR Gunn, KD Paulsen, DW Roberts, BW Pogue. Image-derived arterial input function for quantitative fluorescence imaging of receptor-drug binding in vivo. J Biophotonics 2015; (DOI: 10.1002/jbio.201500162).
  6. DM McClatchy, V Krishnaswamy, SC Kanick, JT Elliott, WA Wells, RJ Barth, KD Paulsen, and BW Pogue. Molecular dyes used for surgical specimen margin orientation allow for intraoperative optical assessment during breast conserving surgery. J Biomed Opt 2015: 20(4):40504.
  7. AV DSouza, JT Elliott, JR Gunn, RJ Barth, KS Samkoe, KM Tichauer, and Pogue BW. Nodal lymph flow quantified with afferent vessel input function allows differentiation between normal and cancer-bearing nodes. Biomed Opt Expr 2015: 6(4):1304-1317.
  8. SC Kanick, DM McClatchy III, V Krishnaswamy, JT Elliott, KD Paulsen, BW Pogue. Sub-diffusive scattering parameter maps recovered using wide-field high-frequency structured light imaging. Biomed Opt Expr 2014; 5(10):3376-90.
  9. JT Elliott, KS Samkoe, JR Gunn, Errol E. Stewart, Timothy B. Gardner, KM Tichauer, T-Y Lee, P. Jack Hoopes, Stephen P. Pereira, T Hasan, BW Pogue. Perfusion CT estimates photosensitizer quantification and biodistribution in a rabbit orthotopic pancreas cancer model. Academic Radiology 2014; 22(5):572-579.
  10. JT Elliott, M Diop, LB Morrison, Christopher D. d’Esterre, T-Y Lee, K St. Lawrence. Quantifying cerebral blood flow in an adult pig ischemia model by a depth-resolved dynamic contrast-enhanced optical method. Neuroimage 2014; 94:303-11 DOI10.1016/j.neuroimage.2014.03.023.
  11. V Krishnaswamy, JT Elliott, DM McClatchy III, BW Pogue, KD Paulsen. Structured light scatteroscopy. Journal of Biomedical Optics 2014; 19(7):070504.
  12. N Hamzei, KS Samkoe, JT Elliott, JR Gunn, T Hasan, BW Pogue, KM Tichauer. Comparison of kinetic models for dual-tracer receptor concentration imaging in tumors. Austin Journal of Biomedical Engineering 2014 ; 1(1):9.
  13. JT Elliott, KM Tichauer, KS Samkoe, JR Gunn, KJ Sexton, and BW Pogue. Direct characterization of tracer plasma curves by fluorescence imaging of exposed carotid artery to facilitate kinetic analysis. Molecular Imaging in Biology 2014; DOI 10.1007/s11307-013-0715-y.
  14. KM Tichauer, M Diop, JT Elliott, Kimberly S. Samkoe, Tayabba Hasan, K St. Lawrence, and BW Pogue. Accounting for pharmacokinetic differences in dual-tracer receptor density imaging. Physics in Medicine and Biology 2014; 59(10):2341-51.
  15. K St. Lawrence, Kyle Verdecchia, JT Elliott, KM Tichauer, M Diop, L Hoffman, and T-Y Lee. Kinetic model optimization for characterizing tumour physiology by dynamic contrast-enhanced near-infrared spectroscopy. Physics in Medicine and Biology 2013; 58(5): 1591.
  16. R Arora, M Ridha, JT Elliott, M Diop, DS Lee, T-Y Lee, K St. Lawrence. Preservation of the metabolic rate of oxygen in preterm infants during indomethacin therapy for closure of the ductus arteriosus. Pediatric Research 2013
  17. JT Elliott, D Milej, A Gerega, W Weigl, M Diop, LB Morrison, T-Y Lee, A Liebert and K St. Lawrence. Variance of time-of-flight distribution is sensitive to cerebral flow dynamics of indocyanine green as confirmed by comparing scalp and brain measurements in adult pigs. Biomedical Optics Express 2013; 4(2):206-218.
  18. JT Elliott, E Wright, KM Tichauer, M Diop, L Morrison, BW Pogue, T-Y Lee, K St. Lawrence. Arterial input function of an optical tracer can be determined from pulse oximetry oxygen saturation measurements. Physics in Medicine and Biology 2012; 57:8285-95.
  19. HZ Yeganeh, V Toronov, JT Elliott, M Diop, T-Y Lee, and K St. Lawrence. Broadband continuous wave technique to measure baseline values and changes in the tissue chromophore concentrations. Biomedical Optics Express 2012; 3(11):2761-70.
  20. JT Elliott, M Diop, T-Y Lee, and K St. Lawrence. Model-independent dynamic constraint to improve the optical reconstruction of regional kinetic parameters. Optics Letters 2012; 37(13): 2571-2573.
  21. JA Cooper, KM Tichauer, M Boulton, JT Elliott, M Diop, M Arango, T-Y Lee, and K St. Lawrence Continuous Monitoring of Absolute Cerebral Blood Flow by Near-Infrared Spectroscopy During Global and Focal Temporary Vessel Occlusion. Journal of Applied Physiology 2011; 110: 1691-1698.
  22. KM Tichauer, M Migueis, F Leblond, JT Elliott M Diop, K St. Lawrence, and T-Y Lee. Depth resolution and multiexponential lifetime analyses of reflectance-based time-domain fluorescence data. Applied Optics 2011; 50(21): 3962-72.
  23. M Diop, KM Tichauer, JT Elliott, M Migueis, T-Y Lee and K St. Lawrence. A comparison of time-resolved and continuous-wave near-infrared techniques measuring cerebral blood flow in piglets. Journal of Biomedical Optics 2010; 15(5), 057004.
  24. JT Elliott, M Diop, KM Tichauer, T-Y Lee and K St. Lawrence. Quantitative measurement of cerebral blood flow in a juvenile porcine model by depth-resolved near-infrared spectroscopy. Journal of Biomedical Optics 2010; 15(3), 037014.
  25. KM Tichauer, JT Elliott, JA Hadway, DS Lee, T-Y Lee and K St. Lawrence. Using near-infrared spectroscopy to measure the cerebral metabolic rate of oxygen under multiple levels of hypoxia in piglets. Journal of Applied Physiology 2010; 109(3):878-85.
  26. M Diop, JT Elliott, KM Tichauer, T-Y Lee, and K St. Lawrence. A Broadband Continuous-Wave Multi-Channel NIRS System for Measuring Regional Cerebral Blood Flow in Neonates. Review of Scientific Instruments 2009; 80(5), 054302.
  27. KM Tichauer, JT Elliott, JA Hadway, T-Y Lee, and K St. Lawrence. Cerebral metabolic rate of oxygen and amplitude-integrated electroencephalography during early reperfusion after hypoxia-ischemia in piglets. Journal of Applied Physiology 2009; 106(5):1506-12.

For an up-to-date list of my publications, please visit my Google Scholar page.