The microscopy revolution – How the CVL is leveraging new imaging modalities

The microscopy revolution – How the CVL is leveraging new imaging modalities
July 31, 2017 Karen Mecoles
CVL polarised light image

How the Characterisation Virtual Lab (CVL) is leveraging new imaging modalities to deliver increased research investment impact and collaboration

The Characterisation Virtual Laboratory (CVL)  is a NeCTAR-funded project connecting Australia’s characterisation instruments with rich online data analysis environments. It underpins researchers and facilitates research collaboration by integrating analysis and visualisation tools with high-performance computing and data storage infrastructure.

“We are experiencing a microscopy revolution and CVL is pleased to play a leading role in developing and supporting research collaborations between facilities, fellows, instruments and eResearch providers.” According to Dr Wojtek James Goscinski, CVL Manager.

Integrating world-leading instruments and computing power

CVL integrates world-leading high-value Australian imaging instruments, including MR imaging equipment, electron microscopes, light microscopes, and cytometry equipment, with specialised computing capabilities and offers a remote desktop environment that supports analysis and collaboration. Available free of charge to researchers, the CVL is underpinned by the NeCTAR research cloud with computational power provided by the MASSIVE – the Multi-Modal Australian Sciences Imaging and Visualisation Environment.

“We are experiencing a microscopy revolution” says Wojtek. “4D imaging (3D imaging plus time sequencing information) is shaping the future of imaging.” Desktop analysis environments are no longer able to store or analysis the resulting terabyte data sets. That’s why CVL is needed.”

Easily access advanced imaging services and captured data

CVLData is captured directly from high-value specialised instrumentation, before being transported to a managed environment for processing by tools available in the CVL and the NeCTAR Cloud. Researchers can access a range of advanced imaging workbench services including Atom Probe, Cytometry, Cryo-Electron Microscopy, Light Microscopy, Neutron, Neuroimaging, Neutron Beam Imaging, Structural Biology, X-ray and General Imaging. Together, these workbenches provide access to over 100 scientific applications. “The increase in availability of next-generation imaging techniques has resulted in a rapid rise in CVL users”.

“CVL demonstrates increased return on research investment by providing a real-time research solution with in-experiment access.”

By putting imaging instrumentation into the hands of the people running MRI machines and microscopes, researchers can run and modify experiments and other research activities in real time. Impacts of changes can be immediately identified, and modifications can be quickly determined to provide the most use of the available time across the range of high-value instrumentation.

Collaboration across sectors

The collaborative impact of this initiative extends broadly across the eResearch, higher education, health and medical sectors. As a key driver behind the CVL, NeCTAR was instrumental in funding its initial establishment as well as offering continued support over the following years.

Leading examples of research collaboration facilitated by the CVL include helping unravel the secrets of cancer and other diseases using the world-class Titan Krios electron microscope at Monash University – a first of its kind microscope in Australia, that can image biological molecules at near-atomic scale. Using this microscope, researchers are able to reconstruct the molecular structure of proteins that were previously too complicated to resolve. However, this technique produces immense volumes of data that must be processed and visualised, which is what the CVL is built to do.

“This is essentially understanding how the building blocks of life work – which understandably has immense applications.”

CVL polarised light

Jade Barbuto, Hudson Institute of Medical Research Description: Polarised light microscopy image from a section of a cartilage plate in lung tissue captured at Monash Micro Imaging on microscopes integrated through CVL.

The CVL has also been instrumental in helping position research communities in esteemed regard within international spheres. Lattice Light Sheet Microscopy (LLSM) is a new technique, developed at Janelia Farm, that is now being deployed at four sites in Australia. Under the banner of the CVL, Monash University, University of Queensland, and University of New South Wales, are partnering to develop critical post-processing and visualisation techniques for LLSM that do not currently exist because the technique is so new.

Researcher engagement

CVL regards researcher engagement as a key demonstration of its on-going collaborative benefit. Current statistics indicate that the researcher base has run over 23 000 user sessions to date in 2017 with “over 50% of our current CVL user base have used the facility more than 10 times during the last 12 months.” Researchers seem to agree with the old saying “when you’re onto a good thing – stick with it!”

CVL partners include NeCTAR, Monash University, Australian Synchrotron, Australian Nuclear Science and Technology Organisation (ANSTO), Australian Microscopy and Microanalysis Research Facility (AMMRF), National Imaging Facility (NIF), University of Sydney, Australian National University, the University of Queensland, University of Western Australia, and University of New South Wales.

“Imaging is transitioning to a new modality – which offers a raft of opportunities, in addition to a number of new challenges.”

Ensuring future scalability is the greatest challenge currently facing the CVL. The CVL currently supports 30-40 concurrent users deployed across the MASSIVE M3 supercomputer. “Current instrumentation is operating at capacity – which is a good problem to have!”

The future

CVL is currently undertaking two programs – connecting instrumentation and further developing its rich online environments.

CVL has identified a cohort of 120+ instruments that are candidates for connecting to the data management infrastructure. Of these, only 60-70 are currently integrated into CVL, representing an outstanding capital value investment of $250-260 Million.

In addition to the increased size and volume of datasets, there has been a corresponding increase in instrumentation. With over 20 new instruments already added in 2017, “Supporting the data needs of the proposed instrumentation increase is a top priority for CVL to provide an on-going ROI for both the instrument facilities as well as their supporting user communities.”

CVL is also planning to further develop and enrich its online environment. Once data is created by the instrument and ingested into the NeCTAR research cloud, the CVL environment becomes a key portal for researchers. “CVL provides much richer environments than those currently available”. Ensuring the on-going expansion and sustainability of these environments is critical to the extension of CVL offerings, and for ensuring on-going research impact.

With the microscopy revolution underway, a line-up of high-value instruments awaiting inclusion, and the on-going development of a rich analysis environment, CVL is perfectly positioned to continue leading the areas of research impact and collaboration throughout Australian and international research communities.

NeCTAR has been proud to support the CVL from initial investment through to continued on-going support. We look forward to sharing their continued success as their exciting developments mature. For more information on the CVL, visit https://nectar.org.au/?portfolio=characterisation-virtual-lab

By Loretta Davis