UIC biochemists advance 3D brain mapping

Nearsighted people understand the microscopist's plight.

"Do I want a clear image of what's right in front of me, or a blurrier image of the bigger picture?" said Ruixuan Gao, a UIC professor of chemistry and biological sciences in the College of Liberal Arts and Sciences. "With most microscopy methods, you can either generate a large image or a clear one, but not both."

Determined to have it all, Gao and his colleagues developed a fluorescence imaging method that captures sharp, detailed images of large biological specimens. They used their method to examine and computationally reconstruct part of a mouse brain in 3D. Their work appeared in the Oct. 16 issue of Science.

Fluorescence microscopy is often used to examine biological samples, such as cells and tissues. Scientists tag molecules of interest with dyes or proteins that light up under colored lasers, enabling highly specific and distraction-free observation.

For cells and thin tissue sections, fluorescence microscopy works like a charm. But larger, thicker samples - for example, a whole organ or a large portion of one - are more difficult to see in high resolution. The researchers overcame this tradeoff by developing a method that achieves extensive imaging depth and high resolution.

They tested their method on a mouse's olfactory bulb - the brain structure that processes smells.

First, the researchers embedded the brain sample in a light-sensitive hydrogel, a jelly-like material that dissolves when exposed to ultraviolet light. Then, they used a UV laser beam - think a Jedi lightsaber - to shear thin layers off the top. The microscope captured a new image with each layer removed.

The result was a stack of images that, when stitched together, created a detailed, structurally accurate 3D map of the whole olfactory bulb.

"We're creating a new surface every time we take an image, so we're technically still doing high-resolution, shallow imaging while achieving great sample depth at the same time," said Wei Wang, a chemistry graduate student in the College of Liberal Arts and Sciences who made this UV lightsaber approach possible.

Wang said reconstructing the olfactory bulb took more than a week and generated a dataset equivalent in size to 65 million songs.

The researchers hope their method can also advance spatial omics, the study of a cell or tissue's molecular and spatial properties, as well as 3D histology, the microscopic examination of tumors and organs such as kidneys, lungs and lymph nodes.

Wenping Li, a visiting research assistant professor at UIC, is also a coauthor. The research was performed in collaboration with Srigokul Upadhyayula's research team from the University of California, Berkeley, as well as the Howard Hughes Medical Institute, the Chan Zuckerberg Biohub and Lawrence Berkeley National Laboratory.

The research received funding from the National Institutes of Health.