Science has the technology to measure the activity of each gene in a single individual cell, and a single experiment can generate thousands of cells of data. Researchers at Lund University in Sweden have now revolutionized the way this data is analyzed, using 3D video game technology. The study is published in the journal iScience.
Advanced DNA and RNA sequencing techniques have opened up the possibility of studying individual cells in tissues in a more comprehensive way than ever before. The big challenge with these sequencing techniques is that they lead to large amounts of data.
When you want to distinguish cancer cells from normal cells, for example, you have to look at thousands of cells to fully understand, which translates into huge amounts of digital data. “
Shamit Soneji, computational biology researcher, Lund University
To make this data understandable, each cell is mathematically positioned in three-dimensional space to form a “road map” of cells and how they relate to each other. However, these maps can be difficult to navigate using a regular desktop computer.
“Being able to browse and manipulate your own data intuitively and efficiently gives them a whole new understanding. I would even go so far as to say that you think differently in VR, thanks to the technique’s ability to involve your body in the analysis process, ”explains Mattias Wallergård. researcher in interaction design and virtual reality at Lund University.
The Lund University team developed the CellexalVR software; a virtual reality environment that allows researchers to use intuitive tools to explore all of their data in one place. 3D maps of cells that have been calculated from gene activity and other information captured from individual cells can be displayed, and the researcher can clearly see which genes are active when certain cell types are formed.
Using a VR headset, the user has a complete universe of cell populations and can more precisely determine how cells relate to each other. Using two manual controllers, they can select cells of interest for further analysis with simple hand gestures as if they were physical objects.
Since space is not an issue, it is possible to have multiple cellular maps in the same “room” and compare them side by side, which is difficult on a traditional computer monitor. Researchers can also meet in this virtual reality world to analyze data together, despite being in geographically different places.
“Even if you are not familiar with computer programming, this type of analysis is open to anyone. A virtual world is a rapidly developing area of research that has enormous potential for scientists who need to access and process big data collaboratively, ”concludes Shamit Soneji.
Legetth, O., et al. (2021) CellexalVR: a virtual reality platform for visualizing and analyzing single-cell omics data. iScience. doi.org/10.1016/j.isci.2021.103251.