QCIF supports big imaging data

QCIF and UQ’s Research Computing Centre (RCC) are leading the development of dedicated computing and storage infrastructure to handle the big data volumes expected to be generated by a revolutionary new microscope being installed at UQ’s Institute for Molecular Bioscience (IMB).

The Lattice Light Sheet Microscope (LLSM), a new modality for 4D imaging of live biological specimens ranging from individual molecules to small organisms, is expected to generate up to 7 TBs of imaging data per day.

This new type of microscope enables unprecedented imaging of live specimens without phototoxicity or photobleaching, enabling prolonged imaging of significant physiological or biophysical events. It was developed by 2014 Nobel laureate, Dr Eric Betzig of the Howard Hughes Medical Institute, Janelia Farm Research Campus, Virginia, USA.

Installation of a LLSM at UQ is the result of successful funding bids to the Australian Research Council’s LIEF scheme and the Australian Cancer Research Fund by an international consortium of researchers led by IMB’s Professor Jenny Stow. 

“The LLSM being installed at IMB is one of only a handful in the world and the third in Australia,” said Prof. Stow, “It will be used to generate exciting new insights into cancer and cell biology, immunology, virology, pathogens and bacterial infection, brain and organ development.”

QCIF is supporting the development of dedicated computing and storage infrastructure to support the LLSM and avoid critical bottlenecks in imaging as terabytes of data can be generated by a single microscope in a matter of hours.

Once captured on the LLSM, the data will be stored and made available via MeDiCI (Metropolitan Data Caching Infrastructure), a high-performance data storage fabric that has been deployed in QRIScloud and several UQ institutes.

MeDiCI delivers seamless ultra-fast multi-site data access, saving researchers valuable time since manual movement of data is not required. Whether the researcher wishes to access their data from their desktop, via the OMERO image database hosted in QRIScloud (see below), or on high performance computers, such as Tinaroo (UQ only) or FlashLite (offered via QRIScloud) that access QRIScloud data collections, the data will appear without the need to move multiple terabytes of data.

Using funding from the Research Data Services (RDS) project, QCIF, in collaboration with UQ’s RCC, IMB, Queensland Brain Institute, and Centre of Microscopy and Microanalysis, has created an instance of the OMERO image database for use by all UQ researchers. OMERO allows secure image data storage and access via desktop clients or through web browsers. As well as sharing data within groups at UQ, OMERO allows easy and secure sharing with research collaborators, and public access where appropriate. QCIF is investigating broadening this OMERO deployment to support its other member universities.

With supporting funding from the Australian National Data Service (ANDS), QCIF and RCC are working as part of a national consortium to develop digital tools to work with the LLSM. At UQ these include tools for visualisation and to interact with the massive image sets, as well as ensuring that the OMERO database can deal with and make easily available the microscope’s data. At Monash University tools are being developed to create workflows and to pre-process LLSM data, as well as to capture important imaging metadata and create trusted data that researchers can analyse, share and re-use. Researchers at UNSW are enabling integration of these data and methods into the Characterisation Virtual Laboratory environment.

Together, these new initiatives in big data storage, advanced data processing and data access will ensure that UQ researchers can fully leverage the power of exciting new data sources from cutting-edge technologies such as the LLSM, and facilitate the breakthroughs in biological and medical sciences they enable. QCIF looks forward to the results of this work benefiting the other Queensland universities in time. 

The new Lattice Light Sheet Microscope currently being installed at IMB. (Image: Dr Nick Hamilton, QCIF/RCC/IMB.)