Student Spotlight: Amanda Bares

Amanda Bares

What is your area of research?

I am currently a fifth year Ph.D. student in the Meinig School of Biomedical Engineering, with minors in neurobiology and applied and engineering physics (AEP). I currently develop nonlinear optical instrumentation for visualizing cells and cell dynamics in living animal models of normal and disease physiology.

What inspired you to choose this field of study?

My dad is an electrical engineer working in the laser industry. I learned about the physics of light and how light could be used to manipulate matter at a young age, and never lost that fascination. Although I received my undergraduate degree in electrical engineering with a focus on optics, my true interest was in biology and medicine, so it was a natural progression into biomedical engineering. I truly enjoy engineering and its approach to problem solving through design, so my thesis project has revolved around the design of new laser microscope tools enabling researchers to visualize multiple cells and cell types simultaneously.

Why is this research important?

To understand the mechanisms of both normal and disease physiology, researchers often study animal models of disease. However, many of the previous techniques involved the slicing and visualization of many cross-sections of tissue to understand what the implicated cells may, or may not, be doing. Multiphoton microscopy, developed here at Cornell University enables researchers to track and image these cells in tissue in living animals. This allows them to watch the same cells over time and find trends and interactions in cell behavior, all in the highly relevant in vivo environment rather than a cell culture dish. Developing multiphoton microscopy tools to increase the density of information in images, such as the microscope I’ve developed, allows researchers to understand more complex cellular mechanisms involving many cells and cell types.

How has your background influenced your scholarship?

I was homeschooled up until high school, when I transitioned into a public school. The independence and freedom to learn on my own and at my own speed taught me how to learn well and synthesize information at an early age. In addition, I grew up in Bozeman, Montana, nestled in the Rocky Mountains and a short drive from Yellowstone National Park. The general culture in the area, of enjoying nature and its beauty, and taking the time to get away from the busyness of life, has stuck with me and I intentionally balance my academic life with time to relax and process.

What else has influenced your thinking as a researcher or scholar?

During my childhood and through my undergraduate years, I took piano and trombone lessons and excelled at piano, performing as a soloist, with the jazz band, as a piano accompanist, and in pit orchestras for the local opera. The techniques I learned to play and perform well have not only been crucial in my developing presentation skills, but also taught me the value of sticking with a difficult challenge until results finally begin to appear. This “doggedness” and constant fine-tuning of my approach to a problem has been key in my research.

You’re one of six doctoral students to receive a Commercialization Fellowship under the College of Engineering. Congratulations! Can you tell me a little bit about the technology you’ll be developing during this fellowship? 

Multiphoton microscopy is already an established tool in the life sciences. Researchers tag cells or subcellular structures in tissue with fluorescent labels, and then use multiphoton microscopes to visualize these cells in 3D with high resolution over time. This allows them to watch cells move and interact in living tissue and test hypotheses about normal and disease physiological mechanisms in animal models.

However, these microscopes are limited in spectral resolution, which limits the number of fluorescent label colors (and thus the number of cell types) that can be identified simultaneously. The hyperspectral multiphoton microscope I’ve developed provides 48 spectral channels, enabling the identification of a large number of labels simultaneously. Instead of observing interactions between only two cell types, this enables researchers to tag as many cell types as they like and visualize complex interactions that are potential disease mechanisms. Previously, researchers have been limited in their use of multiphoton microscopes as hypothesis testing tools, looking at the interactions between specific cell types already implicated. With the large color palette of fluorescent labels and techniques now available and the utilization of this hyperspectral multiphoton microscope, researchers could potentially observe nearly all cells in a tissue volume simultaneously and generate hypotheses based on their observations. I’ve developed a working prototype of this instrument in my thesis work, but in this fellowship I’ll take the next step and really explore the potential market for this instrument and what it would take to go from prototype to sale-ready, high-tech instrumentation.

What are you most looking forward to in this fellowship?

Many people have great ideas for “great” products, but only the products that actually meet customer needs are successful or worth developing. I hope to learn a number of tools and techniques, and develop experience in assessing user needs. I believe this will truly guide the choices I’ll make in the future on which technologies/products to develop and the features they need to have.

In what ways will the work you do during this fellowship improve or expand your scholarship?

Transitioning from a scholarly or academic approach to thinking, to an entrepreneurial or business mode can be difficult for Ph.D. students entering industry. However, learning the basics of marketing, business practices, user need assessment, hiring, and how to build a sound business plan, all revolving around a technology I know intimately through my thesis work using this fellowship, will allow me to gain experience and get a head-start on the new-to-industry learning curve. Most importantly, the entrepreneurial mindset that this fellowship will help cultivate will likely inform my final experiments as I wrap up my thesis and color my decisions about my post-Ph.D. plans.

Why did you choose Cornell to pursue your degree? 

Cornell University is well known for its Engineering School, and I expected that this excellence in scholarship likely included the biomedical engineering (BME) department as well. Although some other universities had research I initially though I was more interested in, Cornell’s BME department offered flexibility in choosing a research lab and a program catered toward the individuality of each student’s background. I was worried that a background in electrical engineering and little biology would put me at a disadvantage, and a program that could bolster my biology skills in parallel with engineering was appealing. In addition, there were several excellent labs at Cornell that I was interested in, compared to the one or two at other schools. There also appeared to be a true spirit of collaboration at Cornell as a whole, something that wasn’t as apparent at other universities. A conversation with Dr. Chris Schaffer, now my PI, confirmed this flexibility and reality of these collaborations, helping me make my decision to go to Cornell. However, I was definitely wrong about my non-biology background being a disadvantage and have learned to appreciate the technical skillset I had developed beforehand.

What’s next for you?

I would like to go into industry research and development, developing tools for researchers. However, a number of people have expressed interest in seeing the hyperspectral multiphoton microscope as an actual commercial product, and have encouraged me to consider starting a company based on this core technology. This is a direction I had never considered before now, and I hope to fully understand what this would entail through this fellowship and make an informed decision on starting a company based on what I learn.

Any advice for incoming graduate students? 

I always advise that new students take the time to do things outside of the lab and their classes. Work-life balance is incredibly important, especially during a challenging Ph.D.! Go hiking on the Finger Lakes trails, go wine tasting, learn how to play guitar, or get a dog. Form relationships with people who are different than you, and who challenge the things you always assumed and never explored. Take full advantage of the amazing breadth of opportunities Cornell offers—the people who come here, the academic challenges it provides, and the support that’s available to every member of this community.

Interview by Sally Kral, communications and outreach assistant in the Graduate School