Anne Carpenter shows that, in biomedicine, a picture can be worth a million data points

In a #WhyIScience Q&A, the director of the Broad’s Imaging Platform discusses her trailblazing work developing tools that analyze biological images

When Anne Carpenter started her career in biomedicine, she couldn’t have envisioned the path she would take to her current role as director of the Broad’s Imaging Platform. After all, the tools that now define her work hadn’t even been invented yet: she had to make them.

As a postdoctoral researcher at the Whitehead Institute, Carpenter, a cell biologist by training, hit a snag in her research when she couldn’t find useful tools to measure cells in her Drosophila fruit fly experiments. Though she knew relatively little at the time about computer science, she still decided to tackle the problem herself; she taught herself how to use MATLAB, a programming language for numerical computation, to help write the software she needed.

That early work ultimately led to the development of CellProfiler and CellProfiler Analyst, complementary, foundational tools she and colleagues created to extract meaningful, measurable data from microscopic cellular images. Today, Carpenter’s lab continues those efforts as her team works to accelerate drug discovery by writing software to automatically analyze the deluge of cellular images generated by today’s powerful, robotic microscopes.

Carpenter describes her unusual career path and what she’s learned along the way in a #WhyIScience Q&A:

Q: Even as a relatively young scientist, you’re considered a leader in your field. Of what, so far in your career, are you most proud?
I’m proud that I’ve pushed biologists to see images as a data source, and not just a pretty picture. Our software (especially CellProfiler) and methods (especially Cell Painting) allow people to create images and analyze them at a large scale so they can test more potential drugs, faster.

I find it enormously satisfying that my lab’s work has already made major discoveries possible across biological disciplines, including drugs that are moving toward patient treatment. I’ve no idea what the future holds scientifically, but having an impact on human health is what motivates me.

Q: What got you interested in science to begin with, and what led you to your particular field of study?
I liked all my subjects in school, especially reading and writing. I was not specifically interested in science or math from an early age. But it became clear during college that everyone liked their literature classes and very few people liked the sciences, while I loved them all equally. It is not a very romantic story, but I picked the sciences because it seemed like no one else did! And I chose cell biology specifically because the other sciences seemed relatively dry and straightforward whereas biology clearly had tons of mysteries to be solved.

Then, my transition to computer science after my PhD came out of necessity: for my postdoctoral project no software existed to analyze the images I was collecting on the microscope so I set out to solve my own problem. And it became clear many other biologists needed software for these tasks so it was super satisfying to make a toolbox to help everyone else too.

Although my path to leading a computational group at a top-notch biomedical research institute seems a bit random, it is clear that it’s a great fit for the things I love doing and that it’s making an impact on the world. When I think of my journey, I’m reminded of a quote from Frederick Buechner: “The place God calls you to is the place where your deep gladness and the world’s deep hunger meet.”

Q: Did you have a mentor who was particularly helpful along the way?
I’m grateful for the training I received during my PhD and postdoc stages, but I have to say one of my most important mentors has been the internet. I’ve been very lucky to grow up in the age of blogs and Twitter where you can get advice about very specific issues in science from kind strangers who take the time to share their guidance publicly. I think this is especially valuable for scientists from under-represented groups, who receive less informal mentoring from senior scientists.

Q: What is your approach to mentoring others?

Photograph of members of the Carpenter lab.The Carpenter Lab at the Broad Institute.

A: Because I’ve personally had times in my career where I didn’t feel like I had anyone advocating for me, I go out of my way to be an available mentor for members of my lab and others. I would encourage people not to be shy about asking for mentoring, and try to find several people who fill different roles. Some mentors might be there for feedback on minor issues or for emotional support (they might be peers, even), but also try to find a mentor who is powerful and willing to be tangibly influential for you. Again, that is easier said than done. I wish I had been more bold and outgoing in seeking this for myself.

Q: What is one of the biggest challenges you’ve faced in your career and what did you learn from it?
Impostor Syndrome is prevalent in the sciences and definitely I felt insecurity during my training years. A grad school buddy advised me, “Don’t compare other peoples’ outsides to your insides,” which led me to adopt a strategy whenever I felt anxious: I would look through my folder of past awards and grade reports to remind myself that I was pretty awesome from the outside, too. As I’ve moved along in my career and gotten to know other senior researchers, that insecurity is almost gone. (It’s been years since I looked through my awards folder!) It’s been replaced by a strong sense of gratitude for where I am. My faith is an important part of that shift: I know that my true value and identity have nothing to do with success or failure in science, so that frees me to just do the best I can.