SinglecellVR Facilitates Virtual Reality Visualization of Single-Cell Data

A new virtual reality (VR) tool called singlecellVR has been launched. It is a free, open-access web app that allows anyone to easily visualize single-cell assays in VR and requires no advanced technical skills from the user.

“I believe VR and augmented reality (AR) technologies are just getting started in terms of the spaces to which they are applicable, especially in the sciences,” explained Luca Pinello, first author of the paper published today in Frontiers in Genetics.

Previous tools used to view single-cell data visualizations in VR have been limited to the most expensive hardware, costing upwards of $2,500. However, singlecellVR is built on previous advancements in VR by allowing users to visualize their own precomputed data directly from the most commonly used single-cell analysis tools including Scanpy, Seurat, PAGA, STREAM, scVelo, and EpiScanpy. “We have simplified conversion of data output from these tools, enabling users to easily contribute to a growing database of datasets from key studies that are preprocessed and available for VR visualization,” the authors wrote.

“Ultimately, these tools seek to empower non-computational biologists to explore their data and make rapid hypotheses otherwise difficult to attain from traditional 2D visualizations.” The authors go on to say that despite tools having been developed in the past, there are currently no peer-reviewed tools available for the visualization of single-cell data in VR, illustrating the novelty in the area of single-cell RNA sequencing.

While smartphone-based VR headsets are limited in the amount the user can navigate and interact with their digital surroundings, Pinello said that the addition of an inexpensive Bluetooth keyboard or controller (approximately $20) should make for a better experience. 

The singlecellVR website,  which requires no installation on a device, allows users to explore several preloaded datasets or upload their own datasets for VR visualization across Google Chrome, Safari and Firefox on Android and Apple devices.

Once users have uploaded their data to singlecellVR, they have the option to view and explore the data in 3D directly in their web browser or to quickly jettison the data to their mobile device for visualization in a VR headset. One of the biggest challenges in visualizing single-cell data, the team said, was taking data compiled on a desktop computer and displaying it through a smartphone.

To overcome this challenge and enable a seamless transition to a smartphone for VR view, the team’s website dynamically generates a QR code that enables users to open the VR view on their phone to view data uploaded through a personal computer.