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Gates Funding VR with Expansion Microscopes

Virtual reality, expansion microscopy

Graduate student Brendan Gallagher uses virtual reality to examine 3-D biological data gathered using expansion microscopy. (Carnegie Mellon University)

14 June 2019. The Bill and Melinda Gates Foundation is backing research to combine a microscopy technique that grows the size of samples being examined with virtual reality, or VR. The project underway at Carnegie Mellon University in Pittsburgh and Benaroya Research Institute in Seattle is funded by a $200,000 Gates Foundation Grand Challenges grant.

The Carnegie Mellon-Benaroya researchers are seeking better tools to diagnose infectious and and autoimmune diseases that with today’s standard light microscopes can get clinicians closer to and provide 2-D images of samples, but no more. The project team aims to combine techniques that expand the size of the specimens, as well as apply virtual reality to go inside the cells and explore the samples in 3 dimensions.

The bioengineering lab of Yongxin (Leon) Zhao at Carnegie Mellon develops tools for better analyzing biological processes, such as tracking indicators of cell signaling and molecular events. One of the techniques devised in Zhao’s lab is expansion microscopy, where biopsy samples are expanded in volume as much as 100 times with hydrogels, water-based polymers. The hydrogels loosen the tissues allowing for expanding the biopsy samples without sacrificing the original tissue structure. This expansion microscopy allows for more detailed images and data, including interactions of cells within the biopsies.

While the expansion of biopsy samples adds more detailed images and data, a fuller understanding of their tissue and cells can be gained by processing those larger volumes of data to allow for exploring inside the expanded structure. That task is undertaken by the labs of Lynda Stuart and Adam Lacey-Hulbert at Benaroya Research Institute, or BRI. The institute studies autoimmune disorders, such as type 1 diabetes and multiple sclerosis, where the immune system is tricked into attacking healthy cells and tissue. The Stuart and Lacey-Hulbert labs study mechanisms for the immune system to tell friend from foe, and technologies to aid in that task.

One of those technologies is virtual reality. In this case, VR represents the much larger volumes of data produced by expansion microscopy, translating the data into detailed 3-D images that allow researchers to view inside cells, zoom in and out, and rotate the images to better understand the processes in real time. The scientific VR technology is being enhanced and refined at Immersive Science, a spin-off company from BRI, and part of the Gates Foundation-funded project.

Tom Skillman, founder of Immersive Science and former research technology director at BRI, says in a joint statement, “Bringing all that data into VR not only allows the scientist to see their 2-D microscope images in full 3-D, 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.”

Caroline Stefani, a postdoctoral researcher at BRI, explains the working protocol between the two research groups, “At BRI,” says Stefani, “we’ll prepare the live infectious and autoimmune disease samples. We’ll send those to Carnegie Mellon, where they will enlarge the samples and send images back to BRI to be viewed in VR.”

The researchers plan to make the VR system called ExMicroVR available on a shared platform with expansion microscopy. The system is expected to allow for up to 6 people working remotely to simultaneously view and collaborate on the same image.

In this video hosted at Eurekalert, Zhao and Stefani tell more about and demonstrate the system.

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