A virtual reality platform to visualize and analyze single-cell RNA sequencing data

Avatars in virtual reality looking at cell maps

Science has the technology to measure the activity of every gene within a single individual cell, and just one experiment can generate thousands of cells worth of data. Researchers at Lund University in Sweden have now revolutionised the way this data is analysed – by using 3D video gaming technology. The study is published in the journal iScience.

Advanced techniques in DNA and RNA sequencing have opened up the possibility of studying individual cells in tissue in a more comprehensive way than was previously possible. 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 need to examine thousands of cells to get a proper understanding, which translates into enormous amounts of numerical data”, says Shamit Soneji, researcher in computational biology at Lund University.

To make this data comprehensible, each cell is mathematically positioned in three-dimensional space to form a “roadmap” of the cells, and how they relate to each other. However, these maps can be difficult to navigate using a regular desktop computer.

“To be able to walk around your own data and manipulate it intuitively and efficiently gives it a whole new understanding. I would actually go so far as to say that one thinks 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 have developed the software CellexalVR; a virtual reality environment that enables researchers to use intuitive tools to explore all 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 in front of them, and can more accurately determine how cells relate to one another. Using two hand controllers, they can select cells of interest for further analysis with simple hand gestures as if they were physical objects.

An overview of CellexalVR

(A) Single-cell data is processed using a tool of the users choice (for example Seurat/Scanpy) and these are then converted to CellexalVR input files using our cellexalvrR R package. (B) A mixed-reality shot of CellexalVR showing the user in relation to the data in VR from which objects such as heatmaps and custom cell annotations can be exported. After a session has finished, an HTML report of actions performed in CellexalVR is automatically generated. (C) An example scene from the users’ point of view in CellexalVR. The hand controllers are seen in foreground, the left one showing the menu system. A UMAP and PHATE reduction of the Liver Cell Atlas is shown where our animated RNA velocity visualization has been activated on the PHATE mapping.

Since space is not an issue, it is possible to have several cellular maps in the same “room” and compare them side by side, something that is difficult on a traditional computer screen. Researchers can also meet in this VR world to analyze data together, despite being in different places geographically.

“Even if you are not familiar with computer programming, this type of analysis is open to everyone. A virtual world is a fast developing area of research that has enormous potential for scientists that need to access and process big-data in a more interactive and collaborative way”, concludes Shamit Soneji.

Availability – The software can be downloaded for free at https://www.cellexalvr.med.lu.se/

SourceLund University

Legetth O, Rodhe J, Lang S, Dhapola P, Wallergård M, Soneji S. (2021) CellexalVR: A virtual reality platform to visualize and analyze single-cell omics data. iScience 24(11), 103251. [article]

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