A team of scientists has developed a free, open-access VR program that allows anyone to interact with single-cell datasets using a headset costing less than $10.

While often thought of as being limited to expensive hardware for dedicated gamers, virtual reality (VR) has become a lot more affordable in recent years with entry-level hardware – such as Google Cardboard – costing less than $10. With this headset, anyone with a smartphone can place their device into the headset and view VR content through its large screen. 

With the barrier to entry now greatly reduced, scientists and engineers are trying to figure out ways of bringing VR to the masses and, potentially, using it to unlock breakthrough discoveries. One such team of researchers from some of the US’s top medical centers and institutions has now published a paper in Frontiers in Genetics documenting a VR tool they created called ‘singlecellVR’ that allows anyone to explore single-cell datasets.

Dr. Luca Pinello, an Associate Professor at Massachusetts General Hospital and Harvard Medical School, as well as the corresponding author of the paper, originally pitched the concept at a hackathon in 2019 alongside his colleagues David Stein, Dr. Huidong Chen, and Mike Vinyard. After gaining a lot of attention from their peers at the event, they decided to develop a working prototype. New features were later added with the help of Dr. Qian Qin and others in the Pinello Lab.

Learning new things in a fun and interactive way’ 

“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,” Pinello said. “I hope the general public could appreciate the new opportunities that new VR/AR technologies are bringing to us to interact with reality, to explore biological data, or just to learn new things in a fun and interactive way.”

The free, open-access web app allows anyone to easily visualize single-cell assays in VR and requires no advanced technical skills from the user. Single-cell assays have transformed our ability to model heterogeneity within cell populations and help identify the function and behavior of individual cells within a much larger population of cells.

Having access to this data and knowing which cell states and genes are present is crucial in helping scientists better understand how, for example, various cancers spread in the human body.

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 pre-computed data directly from the most commonly used single-cell analysis tools including Scanpy, Seurat, PAGA, STREAM, scVelo, and EpiScanpy.

How to access it 

“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 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.

Plans for the future

Looking to the future, the team sees singlecellVR having more applications related to new single-cell technologies (eg multi-omics or spatial profiling) and expects singlecellVR to expand support to more powerful devices such as the Oculus VR headsets from Facebook (costing approximately $300).

 “My hope is that by lowering the barrier to adopt or explore these new technologies, more people will become excited about this space, and we will create a community interested in developing VR applications focused on the exploration and analysis of biological data,” Pinello said.

A Brazilian study shows how wildfires and forest burning for agriculture influence rain cloud formation in the Amazon. According to the authors, aerosols (tiny solid particles and liquid droplets emitted into the atmosphere by fire) hinder the freezing of cloud droplets when the atmosphere is humidified, but can also promote freezing when the atmosphere is dry. This alters the natural functioning of clouds and their typical height, and may also affect precipitation and the amount of sunlight reaching the ground. 

To arrive at this conclusion, the scientists used a large dataset collected over 15 years, from 2000 to 2014, involving satellite imagery from the United States National Oceanic and Atmospheric Administration (NOAA), measurements of atmospheric aerosols from fires made by NASA’s Aerosol Robotic Network (AERONET), and reanalysis data from the European Center for Medium-Range Weather Forecasts (ECMWF). Reanalysis data provides the most complete picture currently possible of past weather and climate, blending observations and past forecasts rerun with modern forecasting models, according to ECMWF.

The satellite images and reanalysis data covered the entire Amazon region. The aerosol data referred to five locations in southern Amazonia: Alta Floresta and Cuiabá in Mato Grosso state; Rio Branco in Acre state; and Ji-Paraná and Ouro Preto do Oeste in Rondônia state.

The purpose of the investigation was to perform an observational study of the temperature at which droplets freeze in convective clouds, which form vertically and can reach heights exceeding 10 km, to identify the key drivers of the phenomenon. The presence of ice in clouds is important since it influences the formation of rain and the average time clouds remain in the atmosphere. “The longer clouds last on average, the more solar radiation is reflected back into space, contributing to the cooling of the planet,” said Alexandre Correia, a professor in the Department of Applied Physics at the University of São Paulo’s Institute of Physics (IF-USP) and first author of the article.

The study was supported by FAPESP. The co-authors were Elisa Sena (Federal University of São Paulo), Maria A. F. Silva Dias (Institute of Astronomy, Geophysics and Atmospheric Sciences, IAG-USP), and Ilan Koren (Weizmann Institute of Science, Israel).

The findings show that freezing, which in this case occurs not at 0 °C, as it does in our day-to-day lives, but at about -10 °C, depends mainly on a combination of three factors: atmospheric humidification, solar radiation, and aerosols. In southern Amazonia’s rainy season (roughly December-April), the atmosphere is extremely clear and the origin of the particles in the aerosols is natural. They come from the condensation of gases emitted by the forest, and from wind abrasion of soil and vegetation. They typically contain pollen, microorganisms, and sea salt, among other kinds of particles. In the burning season, which occurs annually in August-October, large-scale fires emit a huge amount of smoke, which spreads throughout the region and is blown by the wind to other regions. “They produce much worse pollution than urban activities in the city of São Paulo, for example,” Correia said.

The study contributes to the knowledge of the behavior of clouds in the Amazon and can be enriched by further research. “The influence of clouds on the climate is very important. This is the most complex topic in climate models that set out to forecast what will happen with regard to this theme in the future, so any improvement in knowledge of how clouds function is a major contribution to the advancement of climate science,” he stressed.