Inside the Light Microscopy Core: Q&A with Frederic Bonnet, Ph.D.

Microscopy

Inside the Light Microscopy Core: Q&A with Frederic Bonnet, Ph.D.

• May 9, 2025

The microscope is perhaps the most instantly recognizable scientific instrument, but the technology utilized today is light years from the simple compound scope invented in the late 16th century. The people of MDI Biological Laboratory's Light Microscopy Facility Core (LMF) are experts in image capture, working alongside our faculty to dive deeper with what can be seen and understood through the lens of a scope.

We sat down with core Director and Staff Scientist, Frederic Bonnet, Ph.D., to find out more about this specialized and centralized resource group.

1. Can you explain, in plain language, what the Light Microscopy Facility Core (LMF) does?

While we facilitate access to the sophisticated microscopes we have on campus, the LMF also provides comprehensive support throughout the entire imaging process: consulting on experimental design, offering technical expertise in sample preparation, providing access to appropriate imaging technologies, delivering thorough training, and assisting with data analysis and interpretation.

Microscopy excellence isn't about having the newest equipment-it's about aligning technology with meaningful scientific questions. The LMF embodies this philosophy by serving as a true research partner that helps scientists design experiments where the imaging approach perfectly matches their scientific inquiry.

After images are captured, we support faculty preparing for publication by reviewing their microscopy images and the materials and methods sections. Our goal is to ensure high quality and adherence to good research practices. Just like experimental data, the ability to reproduce an image is essential to scientific rigor.

We're proud that the LMF has been recognized as one of the top microscopy facilities in the country-placing in the top 5 according to Bioimaging North America's Michael W. Davidson Memorial Award 2024.

2. How does the LMF Core benefit MDI Bio Lab, support faculty, and help enhance research?

The LMF works with a five-dimensional approach to excellence: innovation, technical precision, accessibility, collaboration, and efficiency. Rather than functioning as a mere equipment repository, we actively monitor emerging developments in microscopy and implement new techniques that expand our overall visualization capabilities. We ensure technical precision by maintaining reliable imaging systems calibrated to capture exactly what researchers need to answer their specific questions. These resources are accessible to researchers of all experience levels, accompanied with appropriate training and support.

Most importantly, the LMF functions as an active collaborative partner in research. We contribute methodological expertise that enhances experimental design in the earliest stages of planning. This collaborative approach, combined with streamlined workflows that minimize time from concept to publishable image, significantly accelerates research productivity and enables scientific discoveries that wouldn't be possible without this kind of specialized partnership.

3. Can you describe the collaboration process when you work with a faculty member?

We believe that the technology isn't the most important thing to be successful. The most important thing is having a good scientific question that matches the technology. We do our utmost to embody this philosophy when we work alongside our faculty, as well as our INBRE partners.

We start with in-depth consultations that focus on understanding their scientific questions. We help clarify what our researchers need to visualize and why, ensuring that imaging becomes an integral part of experimental design rather than an afterthought. Once we've established clear imaging goals, we work together to align the right microscopy technologies with the questions they are trying to answer. For researchers requiring hands-on assistance, we offer comprehensive training. Going beyond teaching just which button to push, we work to build competency in understanding the underlying principles and critical thinking skills needed for high quality microscopy work.

Throughout the process, we remain active partners, providing guidance on sample preparation, image acquisition, data analysis, and interpretation-ensuring that researchers not only collect beautiful images but meaningful data that advances their scientific goals. For remote collaborations, we've developed innovative solutions where samples can be sent to our facility, and researchers can work virtually with our team through video interfaces.

4. What does the future of the LMF look like?

In terms of innovation, we already have the bespoke-built mesoSPIM light sheet microscope to image larger tissue-cleared sample (several mm in size) and will continue to expand its capabilities to address different types of samples and research questions. We hope to also add the capability for light sheet live imaging in 3D, which would allow us to capture things like zebrafish brain activity, and blood vessel development in a zebrafish kidney or retina.

Technological advances require the development of expertise-so we've recruited a specialist in image analysis to build sophisticated data processing workflows that transform raw imaging into actionable scientific insights. We're also closely monitoring developments in artificial intelligence and will leverage these technologies to help researchers answer new questions that were previously inaccessible. We're working with another MDI Bio Lab Core Facility, the Comparative Genomics and Data Science Core, to explore cloud computing and processing solutions that will enable more sophisticated analysis of complex microscopy data.

This year, for the first time, MDI Bio Lab will host a Light Microscopy Course, the largest of its kind in the U.S. We already host a Quantitative Fluorescence Microscopy course. As education remains a central tenet of our operation, we want to continue to expand our training programs to build competency and cultivate the next generation of imaging scientists.

By focusing on these initiatives, we will continue to redefine what excellence in microscopy means-moving beyond equipment inventories to become a true catalyst for scientific discovery where technology and scientific questions perfectly align.