New virtual reality software allows scientists to 'walk' inside cells


Date:
October 12, 2020
Source:
University of Cambridge
Summary:
Virtual reality software which allows researchers to 'walk' inside
and analyze individual cells could be used to understand fundamental
problems in biology and develop new treatments for disease.



FULL STORY ========================================================================== Virtual reality software which allows researchers to 'walk' inside and
analyse individual cells could be used to understand fundamental problems
in biology and develop new treatments for disease.


==========================================================================
The software, called vLUME, was created by scientists at the University
of Cambridge and 3D image analysis software company Lume VR Ltd. It
allows super- resolution microscopy data to be visualised and analysed
in virtual reality, and can be used to study everything from individual proteins to entire cells.

Details are published in the journal Nature Methods.

Super-resolution microscopy, which was awarded the Nobel Prize for
Chemistry in 2014, makes it possible to obtain images at the nanoscale
by using clever tricks of physics to get around the limits imposed by
light diffraction. This has allowed researchers to observe molecular
processes as they happen. However, a problem has been the lack of ways
to visualise and analyse this data in three dimensions.

"Biology occurs in 3D, but up until now it has been difficult to interact
with the data on a 2D computer screen in an intuitive and immersive
way," said Dr Steven F. Lee from Cambridge's Department of Chemistry,
who led the research.

"It wasn't until we started seeing our data in virtual reality that
everything clicked into place." The vLUME project started when Lee and
his group met with the Lume VR founders at a public engagement event
at the Science Museum in London. While Lee's group had expertise in super-resolution microscopy, the team from Lume specialised in spatial computing and data analysis, and together they were able to develop
vLUME into a powerful new tool for exploring complex datasets in virtual reality.

"vLUME is revolutionary imaging software that brings humans into the nanoscale," said Alexandre Kitching, CEO of Lume. "It allows scientists
to visualise, question and interact with 3D biological data, in real time
all within a virtual reality environment, to find answers to biological questions faster. It's a new tool for new discoveries." Viewing data in
this way can stimulate new initiatives and ideas. For example, Anoushka
Handa -- a PhD student from Lee's group -- used the software to image
an immune cell taken from her own blood, and then stood inside her own
cell in virtual reality. "It's incredible -- it gives you an entirely
different perspective on your work," she said.

The software allows multiple datasets with millions of data points
to be loaded in and finds patterns in the complex data using in-built clustering algorithms.

These findings can then be shared with collaborators worldwide using
image and video features in the software.

"Data generated from super-resolution microscopy is extremely complex,"
said Kitching. "For scientists, running analysis on this data can be very
time consuming. With vLUME, we have managed to vastly reduce that wait
time allowing for more rapid testing and analysis." The team are mostly
using vLUME with biological datasets, such as neurons, immune cells or
cancer cells. For example, Lee's group has been studying how antigen cells trigger an immune response in the body. "Through segmenting and viewing
the data in vLUME, we've quickly been able to rule out certain hypotheses
and propose new ones," said Lee. This software allows researchers to
explore, analyse, segment and share their data in new ways. All you need
is a VR headset."

========================================================================== Story Source: Materials provided by University_of_Cambridge. The original
story is licensed under a Creative_Commons_License. Note: Content may
be edited for style and length.


========================================================================== Journal Reference:
1. Alexander Spark, Alexandre Kitching, Daniel Esteban-Ferrer, Anoushka
Handa, Alexander R. Carr, Lisa-Maria Needham, Aleks Ponjavic, Ana
Mafalda Santos, James Mccoll, Christophe Leterrier, Simon J. Davis,
Ricardo Henriques & Steven F. Lee. vLUME: 3D virtual reality for
single-molecule localization microscopy. Nature Methods, 2020 DOI:
10.1038/s41592-020- 0962-1 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/10/201012120005.htm

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