Microscopy method pairs with virtual reality to enhance cell structure analysis

Combining expansion microscopy with virtual reality enables enlarging, exploring, and analyzing cell structures beyond the capabilities of traditional light microscopy.

Biological Sciences graduate student Brendan Gallagher views expansion microscopy data using virtual reality.
Biological Sciences graduate student Brendan Gallagher views expansion microscopy data using virtual reality.
Carnegie Mellon University

A team of researchers from Carnegie Mellon University (Pittsburgh, PA) and the Benaroya Research Institute at Virginia Mason (BRI; Seattle, WA) has combined a nanoscale microscopy method called expansion microscopy with virtual reality (VR) to enable enlarging, exploring, and analyzing cell structures beyond the capabilities of traditional light microscopy. The development aims to accelerate researchers' understanding of infectious and autoimmune diseases, and enhance their ability to develop disease diagnostics and prevention and treatment methods.

Yongxin (Leon) Zhao, an assistant professor of biological sciences at Carnegie Mellon's Mellon College of Science, has been developing the expansion microscopy technique to physically magnify a biopsy, allowing researchers to see fine details in biological samples using standard microscopes. 

Zhao makes biopsy samples grow in size by chemically transforming them into water-soluble hydrogels. He then applies a treatment that loosens the tissues and allows them to expand more than 100X in volume. The tissues and molecules within the sample can then be labeled, imaged, and compiled into a complex set of data, to be used to study interactions among cells and their structures.Biological Sciences Assistant Professor Yongxin (Leon) Zhao.Biological Sciences Assistant Professor Yongxin (Leon) Zhao.Carnegie Mellon University

However, a limitation of the technology is that it extracts 2–3 orders of magnitudes more data than current techniques are able to interpret. To help solve that problem, the Gates Foundation grant pairs expansion microscopy with a VR technique developed at BRI. Through this VR technology, researchers will be able to see and manipulate the originally 2D expansion microscopy images in 3D, giving them a 360° view of tissue and protein organizations and interactions. 

"At BRI, we'll prepare the live infectious and autoimmune disease samples," says Caroline Stefani, senior postdoctoral research associate. "We'll send those to Carnegie Mellon, where they will enlarge the samples and send images back to BRI to be viewed in VR." 

"This is the future of how scientists can handle complex data," Zhao says. "It's an immersive experience, just like you are sitting inside your data. You have the freedom to explore your data from every angle and every spot." 

The VR technology was developed by Tom Skillman, BRI's former director of research technology, who has since founded a VR company, Immersive Science. 

"My role in this grant is to develop a software tool that will allow scientists studying disease a way to understand large amounts of data through a computational technique called 'immersive science,'" Skillman says. "Bringing all that data into VR not only allows the scientist to see their 2D microscope images in full 3D, but to interact with the data, selecting channels, adjusting the views, colors and contrast, and grabbing and rotating the images to quickly identify key aspects of the image that are coupled back to the disease under study." 

The eventual goal is for the VR tool, called ExMicroVR, to be shared on open platforms with other researchers along with expansion microscopy so that they, too, can view new details of disease processes and understand larger, more complex sets of data. 

The system to convert expansion microscopy data into VR 3D images will be affordable and easily accessible to researchers and physicians in developing countries. It will also allow for up to six people to collaborate and view the same sample remotely at the same time. 

The work is being funded at $200,000 through Grand Challenges, an initiative of the Bill & Melinda Gates Foundation. 

For more information, please visit cmu.edu/bio and immsci.com.

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