Clear wins in neuroscientific imaging

Chemical engineering converges with neuroscience

First published: 22/04/2014

Updated at: 23/04/2014 at 11:01 am

New chemical engineering solutions are enabling researchers to view deep inside the brain.

And neuroscientific imaging is changing in parallel as new clearing methods allow researchers to see directly into optically transparent whole brains or thick blocks of brain tissue.

One of the clearing methods available, the CLARITY method, was devised by bioengineer and psychiatrist Karl Deisseroth and his colleagues at Stanford University. It involves infusing the brain with acrylamide which polymerises and forms a tissue-wide mesh to secure the proteins. Lipids that normally block the passage of light can then be stripped away, rendering the brain transparent.

The Florey Advanced Microscopy Facility at the Florey Institute of Neuroscience and Mental Health now offers a long working distance lens to make full use of this novel approach. Combined with a new Zeiss LSM780 confocal microscope the setup enables multi-colour deep 3D imaging in cleared brains.

“We have purchased two new state of the art confocal microscopes, a Leica SP8 and a Zeiss LSM 780, to allow maximum flexibility in imaging, including lambda scanning, mosaic imaging and high sensitivity detectors based on Gallium arsenide phosphide (GaAsP) technology,” said Imaging Facility Manager Verena Wimmer.

“We use some really high end imaging techniques and we provide analysis softwares to cope with large, high resolution data sets. Our server-based Huygens deconvolution software helps improve the quality of data for advanced analysis.

The facility also offers Amira and MetaMorph programs for 3D visualisation and quantification.

With a strong background in neuroscience and imaging herself, Verena says “If researchers can describe their research question, chances are I can help to design efficient experiments to get the best out of the imaging and analysis instrumentation available at The Florey.

“I am passionate about quantitative imaging and helping people to obtain rigorous scientifically valuable data from their experiments.

“We’re friendly and accessible and I really enjoy training people to discover science through imaging. The Facility team aim is to induce a level of confidence in people who have never done imaging and support them through all stages of their imaging experiments, from preparing the specimen, staining, imaging and analysis to development of new methods.

“When somebody books the instrumentation at the Advanced Microscopy facility, they get more than just the latest technology. They get ongoing support and help in design of their experiments and hands on support in imaging techniques for their neuroscientific research,” said Verena.

“For live cell experiments we have an Olympus FV100 confocal microscope as well as a spinning disc microscope available. We can image live cells over long periods of time in an incubator chamber or use high speed scanning to capture fast events.

Booking Florey microscopes and imaging instruments is available through the ARIN booking software at or call the Florey Advanced Microscopy Facility Manager Verena Wimmer on (03) 90356455.

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