Education in Microscopy: Taking a Closer Look with Jennifer Waters

Abstract

Jennifer Waters (Nikon Imaging Center, Harvard Medical School, MA, USA) spoke to Ebony Torrington (Future Science Group, London, UK) about her career in microscopy and the importance of education. Jennifer is the Director of the Nikon Imaging Center (NIC) at Harvard Medical School and a Chan Zuckerberg Initiative (CZI) Imaging Scientist. She was trained in cell biology and microscopy by Ted Salmon at University of North Carolina (UNC) at Chapel Hill (NC, USA), where her research focused on mitosis and cell cycle regulation. Jennifer's main focus today, in addition to running the NIC, is developing light microscopy educational resources.

Keywords::

• education
• imaging
• microscopy

What inspired you to start building microscopes?

We have a couple of simple home-built microscopes in the core that we use for educational purposes, but I don't have experience building novel microscopes. My experience is primarily with commercial systems. As a graduate student, I was certainly very interested in biology, but as I began my project, I found that I was much more curious about microscopes. My graduate advisor, Ted Salmon, was trained as an engineer, and has a deep understanding of how microscopes work. I was working on a project that involved using UV light to photoactivate green fluorescence. I was using red fluorescence to find a focal plane in the sample but was seeing little to no photoactivation with UV. I recall sitting down at the microscope with Ted to trouble shoot. He quickly recognized that the UV was not focusing on the image plane due to chromatic aberration. He gave me a piece of glass to insert into the light path during photoactivation, which caused the UV to come into focus at the image plane and, just like that, the photoactivation worked! I was amazed and awakened to the power of understanding how microscopes work. My advisor taught several different microscopy courses, and I took every opportunity to join him as a teaching assistant. I learned so much being a part of his courses, and it is how I discovered my own passion for teaching.

I love talking to people about their research, but the technology is what really engages me, so, when deciding what to do after graduate school, I looked in that direction. At the time, in the late 1990s, PhD-level core microscopy facility jobs were rare. I didn't know anyone who was doing that sort of thing. I was fortunate to get a position teaching a light microscopy graduate course at Wake Forest University (NC, USA) before I moved to my current position, which I've held since 2001.

This year we celebrate the 40^th Anniversary of BioTechniques. To celebrate, we are looking back at technological developments over the past 40 years. With that in mind, what do you believe the biggest technological developments in microscopy have been over the past 40 years?

There have been so many developments! If I had to choose one, it would be far more sensitive and lower noise detectors. When I was a graduate student, we were primarily using what is now outdated technology – tube cameras. At that time, sensitive and relatively low noise charge coupled device (CCD) cameras for microscopy were pretty new, and cameras have improved so much since then. The other thing that comes to mind is green fluorescent protein (GFP) and other fluorescent proteins. GFP was cloned when I was a graduate student. At that time, live quantitative fluorescence microscopy experiments were much harder to perform. We had to purify proteins, label them with fluorophores and microinject them back into single cells. Although GFP isn't strictly microscopy, it is a huge reason why microscopy has become so popular.

Can you tell us about the core facility that you run & some of the challenges that you face?

Funding is always an issue for core facilities. I'm very fortunate in that I have the support of three of the preclinical departments at Harvard Medical School (MA, USA), who make sure that all of our operating expenses are covered. Many core facilities struggle to recoup costs with user chargebacks for microscope use, and fortunately, that is not something that I have had to worry about. The CZI Imaging Scientist Award has been instrumental in allowing me to pursue interests outside of my core, as I was able to use some of the funds to hire an Associate Director of Imaging Education, Anna Jost.

I do struggle with keeping our existing equipment updated, as do many cores. There are no external funding sources for upgrading existing equipment, only for bringing in new instruments. That is important too, but I pride myself in keeping our existing workhorse instruments operating optimally for as long as possible. Harvard Medical School does offer an internal source of competitive funding for technology, and the departments who support the core have been generous over the years in that area as well, but keeping technology up to date is a continuous struggle. Identifying novel instruments that will best support the local research community takes research, planning and securing funding, all of which can be challenging.

Your Microcourses channel on YouTube [1] provides informative educational videos on light microscopy. What inspired you to launch it & how do you think it has helped the imaging community?

The idea was floating around in my head for many years before I actually started the channel. I've seen microscopy education positively impact so many research projects and scientists' careers, and I want developing microscopy education tools and resources to be my major contribution to science.

In general, to meet the needs of students, educational resources need to be available online and on demand. I thought that a graphical and fun approach to microscopy education would have an impact. The channel has been very successful, shockingly so! The numerical aperture video, which was one of the first, just passed 60,000 views. I never expected that.

Aaron Straight from Stanford University (CA, USA), who I've known since graduate school, was also an inspiration. He emailed me because someone in his lab had damaged one of their total internal reflection fluorescence (TIRF) objective lenses. He said, “How does this happen? What can we do to educate our microscope users so this doesn't happen again?” The very first video I made was on avoiding what I call ‘objective lens blunt force trauma’ [2]. I made that one with Aaron's lab in mind, and the channel progressed from there.

It is incredible that so many people are viewing your videos

It has even gone beyond our imaging community. In the YouTube comments, I hear from college students, high-school students and folks that are teaching microscopy at different levels and in different disciplines, such as engineering, physics and astronomy.

It must be inspiring younger people who may be interested in getting into that field of research. What is your favorite imaging technique at the moment & why?

I always find this to be a loaded question. I sometimes get excited, like many do, when a new technique comes out. But at this stage in my career, to really get excited I have to see a technique have an impact on biological discovery. I've seen so many new things come out over the years. People get excited about them, there's a lot of buzz, and then they just slowly dissipate. That's usually because the instruments are hard to use, more limited than is clear from the original publication, or the commercial version may not be quite as good as the developer's version. So, my standard answer to that question is that I like the technique that is best for solving the biological problem at hand. In recent years, some of the newer single-lens light-sheet instruments designed for intracellular imaging and ease of use are quite exciting.

Could you give some background to light-sheet microscopy & describe what it can be used for?

Light-sheet microscopy has been around for a very long time, but it didn't hit most biologists radar until the early 2000s, when Jan Huisken, University of Göttingen (Germany), who was working in Ernst Stelzer's lab, Goethe University Frankfurt (Germany) at that time, developed what they called selective plane illumination microscopy (SPIM) [3]. He demonstrated a remarkable increase in axial resolution in live samples, which he achieved by using a high-quality objective, in conjunction with a cylindrical lens, to generate a light sheet that was much thinner than the depth of focus of the objective lens. That was a key part of the design of his microscope.

Anybody out there who's done any sort of live-cell imaging knows that photobleaching and phototoxicity can be a big problem. A key strength of light-sheet microscopy is in reducing photobleaching and phototoxicity. In techniques such as widefield or confocal, the entire 3D sample is illuminated with each image you acquire. When performing multidimensional live imaging of fluorescent samples – for example, collecting Z sections and multiple wavelengths over time – that adds up to a lot of illumination. Conversely, light-sheet microscopes are intended to only illuminate the plane of the sample that you're imaging. Light-sheet microscopes are also designed to collect images very quickly, allowing increased temporal resolution in 3D imaging.

What do you think could be the next big development to advance the imaging field even further?

Continued developments in image-analysis tools are critical to moving the field forward. There are now more computer scientists than ever working on bioimage analysis, and the expertise they have brought to our field is having, and will continue to have, a huge impact. Big efforts are being made to provide image-analysis education and support for research scientists. Hopefully, those efforts will continue to receive funding.

Biologists are very excited about machine-learning and deep-learning techniques for bioimage analysis. These methods are very powerful, but, as with every technique, it is important that the biologists who use them understand all of the caveats and limitations, and that they validate performance for their particular application. In many cases, biologists with little experience with these methods are better off collaborating with an expert [4].

Thinking about yourself & your career, what are you looking to do next & where do you see your career progressing to?

I have a project that we're just getting started on that I'd love to share. Anna Jost is the coordinating principal investigator, and it is a collaboration with Gleb Grebnev from Global BioImaging (GBI), and a team of imaging scientists: Michelle Itano (UNC Chapel Hill), Abhishek Kumar (University of Chicago, IL, USA), Bryan Millis (Vanderbilt University, TN, USA), Uri Manor (University of California San Diego, CA, USA), Talley Lambert (Harvard Medical School), Martin Fischer (Duke University, NC, USA), and Beth Cimini (Broad Institute of MIT and Harvard, MA, USA). We were recently awarded funding from the Chan Zuckerberg Initiative for the project.

The idea is to build a curated online educational resource for imaging scientists. There are a lot of online resources out there already, but the quality of teaching and the target audience varies greatly. There are in fact so many resources available, it's hard for students to find high quality content that is presented in a way that's complete, easy to absorb and with minimal assumptions about what they already know.

At the same time, most students don't know what they need to learn! A learner might think, “I want to do some super-resolution microscopy work, so I need to learn about super-res.” However, there are critical fundamental principles that must be mastered to fully understand super-resolution microscopy. Students benefit from a structured curriculum they can work through to reach their learning objectives.

My fellow grantees and I are microscopy experts with teaching experience and a passion for microscopy education. The aim of our project is to design a microscopy education website that offers a complete curriculum that can be tailored to meet a student's particular learning objectives and provides curated high-quality online content that makes learning accessible to a wide audience. The website will build upon the existing GBI Virtual Training Portal.

We began the project by scavenging the internet for every microscopy education lecture and resource we could find; we currently have a database of over 600 lectures. We are in the process of screening each video, assessing them for quality of teaching, audio and video quality, content and accuracy. As we narrow down candidate lectures, the goal is to identify content that the whole team agrees is the best out there to cover the curriculum. We've also already identified gaps: some topics aren't covered in existing materials, or we haven't found a lecture of the quality we're looking for. So, we also plan to fill in the gaps by generating content ourselves and soliciting content from other experienced educators in our community.

We are thinking carefully about the format of the learning modules, taking into account our current understanding of how students best learn and what they need to retain information. Alongside lectures, we will provide supporting materials, such as virtual lab exercises, self-grading quizzes and simulators. Each module will be interactive – as students work through the material, they will be presented with self-graded quizzes or offered the choice to dig into additional content on topics that they find particularly interesting. We hope that the format will be appealing and facilitate learning.

We will not only provide content that students can work through themselves, but also resources for them to interact with educators. For example, we will host remote ‘flipped-classroom courses’ with specific learning objectives. Students will be assigned dates by which they need to complete assigned content. After each due date, we will host a remote session where several members of our team will answer questions and facilitate discussion on the assigned content. For each course, we will also set up a private discussion room on Microforum [5], which is an online discussion forum that my group and I developed. As the students work through the material, they can post questions that our team will answer.

Another aim of the project is to provide resources for educators. There are many microscopy educators who could benefit from shared teaching content and tools, as well as community support. When you are just starting your career running a core facility, for example, putting together lectures and lab exercises is a big time sink. We plan to provide slide decks for each lecture on the resource, and corresponding lab exercises. This will both help educators to fill in any holes in their understanding of the subject by watching the lectures, and they can modify or add to the slide decks depending on their needs.

We are very excited about this initiative. I think it has a lot of potential. There's a lot of work in front of us, but we have put together a dedicated team of teachers who, with Anna at the helm, are ready to take it on.

My final question is, do you have any advice for your younger self or for any people who are looking to start a career in microscopy?

The first thing that comes to mind is, don't let anyone discourage you from pursuing your passions. As a junior core director, I was fortunate to work with and learn from many excellent and encouraging scientists. However, I also came across a few who were not as supportive. I started designing and teaching microscopy workshops at Harvard in my first year. Soon after, I also began teaching short intensive microscopy courses at places like the Marine Biological Laboratory (MA, USA) and Cold Spring Harbor Laboratory (NY, USA). I was both a student and teaching assistant in these types of courses as a grad student, and it was my dream to run my own. At the time, to my knowledge, there had never been a woman or a core director running one of these microscopy courses. I was told I was not “eligible” to be listed as an instructor in some of the courses I was teaching in, even though I was lecturing and developing lab exercises, because I was not a principal investigator. My good ideas were at times dismissed, and I was told my teaching style was too “basic”. There were plenty of times it would have been easier to give up, and I am so glad I didn't. My patience and hard work paid off, and I am now very proud to have been running an annual two-week course on ‘Quantitative Imaging: From Acquisition to Analysis’ at Cold Spring Harbor Laboratory since 2011.

Disclaimer

The opinions expressed in this interview are those of Jennifer Waters and do not necessarily reflect the views of Future Science Ltd.

Financial & competing interests disclosure

Jennifer Waters is funded by CZI grant DAF2019-198157, and grant DOI https://doi.org/10.37921/132216bkquwf from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Additional information

Funding

Jennifer Waters is funded by CZI grant DAF2019-198157, and grant DOI https://doi.org/10.37921/132216bkquwf from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.