University of Cambridge Ph.D. student Anoushka Handa recently stood inside of and explored her own immune cell. While this may sound like a really good episode of The Magic School Bus, Handa unfortunately didn’t have Ms. Frizzle around to help. Instead, she relied on virtual reality (VR) technology developed by her principal investigator, Steven Lee.
vLume was created by Lee, colleagues at the University of Cambridge, and 3D image analysis company Lume VR. The software allows super-resolution microscopy data to be visualized in virtual reality, essentially allowing researchers to “walk” inside individual cells.
Super-resolution microscopy, which was awarded the Nobel Prize for Chemistry in 2014, is a blessing for scientists looking to obtain images at the nanoscale. The optical microscopy technique can capture images that have higher resolutions than those imposed by the diffraction limit. While this bought scientists into the nanoscale, the lack of ways to visualize and analyze resulting data has been a problem—until now.
“Visualizing 3D data on a 2D screen is difficult,” Lee told Laboratory Equipment. “By implementing data into a VR environment, one can intuitively walk around in that data. This allows you to view all three dimensions in one setting.”
The software allows multiple datasets with millions of data points to be loaded in and finds patterns in the complex data using in-built clustering algorithms.
“vLUME instantaneously allows you to visualize artefacts, clusters and various characteristics in VR that would be time consuming otherwise,” said Lee. “It takes a matter of seconds for a dataset consisting of a million localizations to open up in vLUME.”
The Lee Lab has been using vLUME to understand and analyze various biological samples, ranging from T-cells to synapses within mice brain tissue. For example, researchers within the group have been using vLUME to study how antigen cells trigger an immune response in the human body. Through segmenting and viewing the data, they were able to quickly rule out certain hypotheses and even propose new ones.
In fact, the researchers say proposing new initiatives and ideas is one of the main benefits of vLUME—viewing the data in three dimensions gets them thinking in a diverse way.
“It’s incredible—it gives you an entirely different perspective on your work,” Handa said.
vLUME findings can be shared with collaborators worldwide using image and video features in the software, which feels apt since the product itself is a collaboration—one that came about through a serendipitous meeting.
The Lee Lab was hosting a talk about “how a gin and tonic can save your life” at a public engagement event at the Science Museum in London. Representatives from LumeVR loved the data—which was generated by super-resolution microscopy—but thought they could help present it in a more intuitive manner. Two years later, vLUME was a (virtual) reality.
Currently, vLUME is primarily suited for 3D single-molecule localization microscopy (SMLM). It can be used to further our understanding of fundamental problems in biology and develop possible new treatments for disease. Of course, this may only be the beginning.
“Future directions could include the incorporation of a multi-user tool for numerous users to use vLUME within the same environment, as well as the incorporation of advanced computation imaging tools, such as focused training methods for machine learning,” Lee said.
Photo: vLUME in action. Credit: University of Cambridge