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Single-cell analysis enters the third dimension

A man using a VR headset and hand controllers
The virtual reality environment CellexalVR is built on gaming technology and allows single-cell data to be analysed in 3D using hand controllers, here demonstrated by the PhD student Mikael Sommarin. (Foto credit: Shamit Soneji)

The Soneji lab has developed an open-source virtual reality environment enabling scientists to analyse their single-cell sequencing data in 3D.

Current single cell sequencing technology enable researchers to measure transcriptome-wide gene expression within thousands of individual cells in a single experiment. These type of projects generates enormous amounts of data which needs to be made comprehensible to humans, often achieved by dimension reduction methods where each cell is mathematically positioned in two or three dimensions to form “maps” of cells and how they relate to each other.

Data obtained from populations with complex heterogeneity would benefit from three dimensions, however current methods to visualise 3D reductions are poor, offering very little opportunity for the scientist to interact with the data in a meaningful way. Shamit Soneji and is research group have found a solution to this problem by developing a new way to visualize and analyse single cell data.

They have created CellexalVR, which is a free and open-source virtual reality environment that allows researchers complete access to 3D data using simple hand controllers. As space is near limitless, many cellular maps can be visualised and compared simultaneously. Moreover, as CellexalVR is built on gaming technology several people can meet in VR at once and analyse data collaboratively, regardless of geographical location.

Related links for further reading:

The full article "CellexalVR: A virtual reality platform to visualize and analyze single-cell omics data" published in iScience

An interview with Shamit Soneji about CellexalVR at Lund University's homepage "VR i kampen mot sjukdom" (in Swedish) .

The Soneji lab homepage

Download the software for free at the CellexalVR website