Director of Communications, Biological Sciences Division
In the pre-dawn winter darkness of a cold January morning, workers at the University of Chicago used a forklift to unload several large wooden crates from the back of a flatbed semi-truck trailer. The largest of these crates, weighing over one-and-a-half tons, contained a photoemission electron microscope (PEEM) that had just cleared customs on its journey from a manufacturer in Germany.
The new microscope is the biggest piece of equipment needed in the quest by a team of UChicago researchers to build a complete wiring diagram of the brain. This diagram – known as the connectome – will help researchers reverse engineer the brain and unlock secrets of how it works by mapping every single connection between brain cells.
In 2024, Gregg Wildenberg, PhD, a Research Assistant Professor in the Department of Neurobiology at UChicago, Narayanan “Bobby” Kasthuri, PhD, Assistant Professor of Neurobiology at UChicago and neuroscience researcher at Argonne National Laboratory, and Sarah King,PhD, Assistant Professor of Chemistry at UChicago, received a $4.8 million, three-year grant from the Brain Research Through Advancing Innovative Neurotechnologies (BRAIN) Initiative, part of the National Institutes of Health (NIH), to purchase the microscope and customize it for connectome imaging.
The project is a collaboration with researchers at Chicago State University and the University of Illinois at Chicago to drastically increase the speed of capturing brain images and build a pipeline of students who are trained to work with such powerful microscopes and analyze the imaging data.
Adapting old technology for higher volume
PEEM is an older imaging technology first developed in the 1980s, mostly used to scan two-dimensional hard surfaces and materials. Until now, connectome researchers used two other kinds of microscopes: scanning electron microscopy (SEM) and transmission electron microscopy (TEM), each with their own advantages and disadvantages. SEM can accommodate a wide variety of samples, but capturing images can be very slow. TEM captures images much more quickly, but the samples must be extremely thin and mounted on fragile grids, which are difficult to work with in large volumes.
Wildenberg and Kasthuri believe that PEEM can overcome these bottlenecks because it combines elements of SEM and TEM, using photons to capture a large field of view quickly like TEM but with sturdier equipment for mounting the samples like SEM. They have perfected preparation techniques that essentially turn ultra-thin slices of brains into hard 2D materials by fixing them in resin, more appropriate for PEEM’s usual applications.
The team successfully scanned a few brain images with PEEM on a microscope in King’s lab, which was enough proof of concept to receive the grant. But the biggest challenge remained: how to capture the hundreds of thousands of images at the resolution needed to map an entire mouse brain, not to mention the exponentially bigger number necessary for building a human brain connectome someday.
Traveling the world to gather data
Since they received the grant, the team has traveled the world to experiment with microscopes operating at other institutions to dial in the specifications they’ll need to scan brain images at scale. It took some convincing to get these partners to lend their equipment to help, however.
“These labs live and breathe on these instruments. So, any time you want to put something foreign into their system, there's always hesitation,” Wildenberg said. “It took finding people who not only had the right tools but had the right sort of courage and spirit of adventure to try something new.”
Wildenberg worked with a team at Leiden University in the Netherlands and established a collaboration with the Okinawa Institute of Science and Technology in Japan. Lola Lambert, a fourth-year undergraduate student majoring in chemistry, traveled to Oxford University in the United Kingdom to take hundreds of images on their microscope.
Lola Lambert at Oxford University
Lambert has been working in Kasthuri’s lab since her freshman year, an experience that has defined her time at UChicago. "The mentorship I've received and the ability I've had to grow through this project has been really incredible,” she said.
Not only did her trip to Oxford gather crucial data for the PEEM project, but it also provided a unique opportunity to shape her career plans. “The Oxford trip was amazing and probably one of the highlights of my undergraduate career,” she said. “To be able to go there by myself and just run the experiments and collect the data was unforgettable. It really has transformed how I think about science and the type of science I want to pursue. It's been amazing.”
Pushing the technology forward
After the workers unboxed the microscope on the loading dock, they carefully lowered it on a freight elevator into a subbasement, where it was then transported to a core facility lab where it will be installed and configured.
The research team’s fact-finding trips showed that with the right optimizations, like modifying it to hold more samples at once or using brighter light sources, PEEM can indeed capture images at a high enough resolution to trace brain circuits and do so at a fast enough pace to handle the enormous volume of samples. They published these findings in a recent paper in the Proceedings of the National Academy of Sciences.
“We think we can get to imaging rates that put doing something like a whole mouse brain within the time frame of several months, as opposed to 20 to 30 years it would take with existing technology,” Wildenberg said. “We've been putting together the pieces of the puzzle over the past year and a half, so now that the microscope is here, we have a very clear vision of what we need to do to push the technology forward.”
