̽��ֱ�� of Cambridge - Steven Lee

New virtual reality software allows scientists to ‘walk’ inside cells

sc604 — Mon, 12 Oct 2020 15:00:15 +0000

̽��ֱ��software, called vLUME, was created by scientists at the ̽��ֱ�� 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.”

̽��ֱ��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.

̽��ֱ��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.”

̽��ֱ��team is 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.”

Reference:
Alexander Spark et al. ‘vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy.’ Nature Methods (2020). DOI: 10.1038/s41592-020-0962-1

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.

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

Steven Lee

Alexandre Kitching

DBScan analysis being performed a mature neuron in a typical vLUME workspace.

̽��ֱ��text in this work is licensed under a Creative Commons Attribution 4.0 International License. Images, including our videos, are Copyright © ̽��ֱ�� of Cambridge and licensors/contributors as identified. All rights reserved. We make our image and video content available in a number of ways – as here, on our main website under its Terms and conditions, and on a range of channels including social media that permit your use and sharing of our content under their respective Terms.

Yes

New imaging technique measures toxicity of proteins associated with Alzheimer’s and Parkinson’s diseases

sc604 — Wed, 23 Nov 2016 09:57:57 +0000

Researchers have developed a new imaging technique that makes it possible to study why proteins associated with Alzheimer’s and Parkinson’s diseases may go from harmless to toxic. ̽��ֱ��technique uses a technology called multi-dimensional super-resolution imaging that makes it possible to observe changes in the surfaces of individual protein molecules as they clump together. ̽��ֱ��tool may allow researchers to pinpoint how proteins misfold and eventually become toxic to nerve cells in the brain, which could aid in the development of treatments for these devastating diseases.

̽��ֱ��researchers, from the ̽��ֱ�� of Cambridge, have studied how a phenomenon called hydrophobicity (lack of affinity for water) in the proteins amyloid-beta and alpha synuclein – which are associated with Alzheimer’s and Parkinson’s respectively – changes as they stick together. It had been hypothesised that there was a link between the hydrophobicity and toxicity of these proteins, but this is the first time it has been possible to image hydrophobicity at such high resolution. Details are reported in the journal Nature Communications.

“These proteins start out in a relatively harmless form, but when they clump together, something important changes,” said Dr Steven Lee from Cambridge’s Department of Chemistry, the study’s senior author. “But using conventional imaging techniques, it hasn’t been possible to see what’s going on at the molecular level.”

In neurodegenerative diseases such as Alzheimer’s and Parkinson’s, naturally-occurring proteins fold into the wrong shape and clump together into filament-like structures known as amyloid fibrils and smaller, highly toxic clusters known as oligomers which are thought to damage or kill neurons, however the exact mechanism remains unknown.

For the past two decades, researchers have been attempting to develop treatments which stop the proliferation of these clusters in the brain, but before any such treatment can be developed, there first needs to be a precise understanding of how oligomers form and why.

“There’s something special about oligomers, and we want to know what it is,” said Lee. “We’ve developed new tools that will help us answer these questions.”

When using conventional microscopy techniques, physics makes it impossible to zoom in past a certain point. Essentially, there is an innate blurriness to light, so anything below a certain size will appear as a blurry blob when viewed through an optical microscope, simply because light waves spread when they are focused on such a tiny spot. Amyloid fibrils and oligomers are smaller than this limit so it’s very difficult to directly visualise what is going on.

However, new super-resolution techniques, which are 10 to 20 times better than optical microscopes, have allowed researchers to get around these limitations and view biological and chemical processes at the nanoscale.

Lee and his colleagues have taken super-resolution techniques one step further, and are now able to not only determine the location of a molecule, but also the environmental properties of single molecules simultaneously.

Using their technique, known as sPAINT (spectrally-resolved points accumulation for imaging in nanoscale topography), the researchers used a dye molecule to map the hydrophobicity of amyloid fibrils and oligomers implicated in neurodegenerative diseases. ̽��ֱ��sPAINT technique is easy to implement, only requiring the addition of a single transmission diffraction gradient onto a super-resolution microscope. According to the researchers, the ability to map hydrophobicity at the nanoscale could be used to understand other biological processes in future.

̽��ֱ��research was supported by the Medical Research Council, the Engineering and Physical Sciences Research Council, the Royal Society and the Augustus Newman Foundation.

Reference
Marie N. Bongiovanni et al. ‘Multi-dimensional super-resolution imaging enables surface hydrophobicity mapping.’ Nature Communications (2016). DOI: 10.1038/NCOMMS13544

A new super-resolution imaging technique allows researchers to track how surface changes in proteins are related to neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases.

These proteins start out in a relatively harmless form, but when they clump together, something important changes.

Steven Lee

ZEISS Microscopy

Brain showing hallmarks of Alzheimer's disease (plaques in blue)

̽��ֱ��text in this work is licensed under a Creative Commons Attribution 4.0 International License. For image use please see separate credits above.

Yes

Licence type:

Attribution-Noncommerical

̽��ֱ��super-resolution revolution

lw355 — Fri, 27 Feb 2015 09:30:07 +0000

There has been a revolution in optical microscopy and it’s been 350 years in the making. Ever since Robert Hooke published his Physiological Descriptions of Minute Bodies in 1665, the microscope has opened up the world in miniature. But it has also been limited by the wavelength of light.

Anything smaller than the size of a bacterial cell (around 250 nanometres) appears as a blurred blob through an optical microscope, simply because light waves spread when they are focused on a tiny spot. As a result, resolving two tiny spots that lie close together has been tantalisingly out of reach using an optical microscope. Unfortunately, many biological interactions occur at a spatial scale much smaller than this.

But, thanks to recent breakthroughs, a new era of super-resolution microscopy has begun. ̽��ֱ��developments earned inventors Eric Betzig and William E Moerner (USA) and Stefan Hell (Germany) the 2014 Nobel Prize for Chemistry, and are based on clever physical tricks that work around the problem of light diffraction.

Professor Clemens Kaminski, whose team in the Department of Chemical Engineering and Biotechnology designs and builds super-resolution microscopes to study Alzheimer’s disease, explained: “ ̽��ֱ��technology is based on a conceptual change, a different way of thinking about how we resolve tiny structures. By imaging blobs of light at separate points in time, we are able to discriminate them spatially, and thus prevent image blur.”

Imagine taking a photo of a tree lit by the glow of ten thousand tiny lights scattered over its branches. ̽��ֱ��emission from each light would overlap. At best you would see a fuzzy, glowing shape lacking in detail. But if you were to switch on only a few lights at a time, locate the centre of each glow and take a picture, and then repeat this process thousands of times for different lights, the composite image would resolve into a myriad of distinguishable dots, denoting the exact position of each individual light on the tree.

This is analogous to the techniques developed by the Nobel Prize winners: in one technique, a sample is tagged with light-activated markers called fluorophores that can be switched on and off with pulses of light, like a switchable light bulb; in another, the light at the outer edges of each blob of light is selectively blocked.

Either way, by imaging a sparse subset of lights, they can be localised with nanometre precision. When combined, a picture starts to emerge that features a resolution that is 10 to 100 times better than previously possible.

“It’s been hailed as revolutionary because it means that biologists can validate some of their hypotheses for the first time,” said Dr Kevin O’Holleran who co-leads the Cambridge Advanced Imaging Centre (CAIC), which is currently building two super-resolution microscopes. “Although electron microscopy has very high resolution, it can’t be performed on live cells. With super-resolution optical microscopy, scientists can track molecular processes as they happen and in three dimensions.”

Meanwhile, Dr Steven Lee and Professor David Klenerman in the Department of Chemistry have built what they believe is the first 3D super-resolution microscope of its kind in Europe. They are using the machine to watch the organisation of cell-surface proteins at the point when an immune cell is triggered into action. Before super-resolution, they needed to artificially reduce the number of proteins on the cell surface to make visualisation easier; now, they can work with normal levels of up to 10,000 proteins at a time on the cell surface.

“These exciting discoveries have emerged through years of painstaking research by physical scientists trying to better understand how light interacts with matter at a fundamental level,” explained Lee. “This work has enabled us to gain insight into biological processes by simply ‘looking’ at dynamic events at spatial scales that much better approximate the physical dimension that biomolecules interact on.”

Kaminski’s team has been visualising the ultrastructure of the clumps of misfolded proteins that cause Alzheimer’s disease. “We’d like to study what causes proteins to become toxic when they aggregate, and visualise them as they move from cell to cell to see whether there are opportunities early in the process to halt their progression.”

Like any fast-moving and transformative technology, super-resolution microscopy has required researchers to drive forward the capabilities of the lenses and light sources, as well as the chemistry of the fluorophores and the mathematical algorithms for image analysis. As a result, designing and building their own microscopes, rather than waiting for commercial devices to become available, has been the best option.

“ ̽��ֱ��field is dynamic and no instrument is exactly right for the questions you want to answer. We have to build the instrument around the science,” explained Dr George Sirinakis, who works with Professor Daniel St Johnston in the Gurdon Institute. His machines will be used to understand cell polarity and visualise the movement of thousands of tiny sacs called vesicles as they transport their cargo within cells. This process has never been seen before because the vesicles are so small and move fast.

No longer are these benchtop machines. Super-resolution microscopes resemble an army of lenses and mirrors marching across a table top, each minutely turning, concentrating and shaping the light beam that falls onto the sample stained with fluorescence markers. Tens of thousands of images are collected from any one sample – creating a deluge of ‘big data’ that requires complex mathematical algorithms to make sense of the information.

Quite simply, super-resolution microscopy is a feat of engineering, physics, chemistry, mathematics, computer science and biology, and it’s therefore out of reach to researchers who lack the necessary expertise or funds to take a step into this field.

CAIC has recently been created to meet super-resolution and other microscopy needs in the biological sciences. “We are a research and development facility. We have state-of-the- art commercial microscopes and we build our own, tailoring them to the needs of the biologists who come to us as a service facility or as a collaborative venture,” explained O’Holleran, who estimates that around 100 researchers will become part of the CAIC community.

“We’re also a hub. We connect researchers who’ve built their own devices and we train PhD students in the cross-disciplinary skills needed for cutting-edge imaging.”

CAIC, Klenerman, Kaminski and others have now been awarded funding as part of the Next Generation Microscopy Initiative Programme led by the Medical Research Council to help establish Cambridge as a national centre of excellence in microscopy. Part of this funding is being used for the two new super-resolution microscopes currently being built in CAIC.

̽��ֱ��researchers hope that super-resolution microscopes will one day become the workhorse of biology, allowing ever-deeper probing of living structures. Breaking the diffraction barrier of light had seemed an insurmountable barrier until recent years. With continuing advances, biologists are beginning to look beyond imaging single cells to the possibility of moving through tissues, tracking the movement of molecules in three dimensions and visualising the process of life unfolding.

Inset image: What was once a fuzzy glow (left of image) can now be super-resolved (right) even if, as here, the structures are smaller than the wavelength of light; credit: Laurie Young, Florian Stroehl and Clemens Kaminski

Cambridge scientists are part of a resolution revolution. Building powerful instruments that shatter the physical limits of optical microscopy, they are beginning to watch molecular processes as they happen, and in three dimensions.

These exciting discoveries have emerged through years of painstaking research by physical scientists trying to better understand how light interacts with matter at a fundamental level

Steven Lee

̽��ֱ��Super-Resolution Revolution

̽��ֱ��text in this work is licensed under a Creative Commons Licence. If you use this content on your site please link back to this page. For image rights, please see the credits associated with each individual image.

Yes