Cryo-electron microscopy (cryo-EM) is a vital structural biology tool that enables the determination of three-dimensional structures of large biological macromolecules, macromolecular complexes, and cell components of biomedical interest, which bridges the gap of complementary structural biology tools such as X-ray crystallography and nuclear magnetic resonance spectroscopy (NMR). The resolution of single-particle cryo-EM has dramatically improved in the last couple of years and cryo-EM is now an essential technique for structural biology research. When operating in "molecular movie mode" the Titan Krios cryo-EM with Falcon II direct electron detector will produce major data volumes, generating terabytes of images per day. The data produced will be a significant asset to Australian and international researchers and will permit the determination of structures of large complex proteins that resist characterization through approaches such as X-ray crystallography.
The data storage made available through this proposal will allow researchers to more easily capture, share and publish images produced using the high-end microscopes of the Clive and Vera
Ramaciotti Centre for Structural Cryo-Electron Microscopy. More broadly, this undertaking is important to support Australian investment in characterization, providing the missing fabric to collect, collate, and collaborate over data. It will form the basis for a sophisticated workflow, developed under NeCTAR’s Characterisation Virtual Laboratory, that includes significant Australian research infrastructure like the NeCTAR Cloud, MASSIVE, RDSI and VicNode.
This Collection will make imaging data from research grants totalling over $100M and instrument grants totalling more than $7M accessible to researchers and provide a mechanism to make the primary research data underlying published research broadly available. This includes data produced by the TitanTM Krios cryo TEM at the Clive and Vera Ramaciotti Centre for Structural Cryo-Electron Microscopy (Monash, in collaboration with WEHI, La Trobe University, the University of Melbourne, Burnet Institute and the Peter MacCallum Cancer Centre). This collection will underpin the $27.9M ARC Centre of Excellence in Advanced Molecular Imaging, which includes collaborators from Monash University, UNSW, UQ, The University of Melbourne, La Trobe University, Australian Synchrotron, University of Warwick, ANSTO, Deutsches Elektronen-Synchrotron, Leica Microsystems Pty Ltd and Carl Zeiss Pty Ltd.
Datasets added to the collection will be assigned a DOI. The DOI landing page for individual datasets will contain metadata about the collection. This
metadata could be limited to instrument parameters and file headers at the time of data capture at
the instrument and will evolve as the data gets curated to include detailed metadata like, discipline
specific metadata and automatic processing results. This page will also contain access to the data
once the data has been published. These aspects will assist in the use and reproduction of results.
Data formates stored:
• FEI microscopes (jpg, mrc, xml, tif) .
• Hitachi/Gatan Digital Micrograph (dm3, tif)
• Leica Microscopy Formats (incl. lif, lei)
• Nikon Microscopy Formats (nd2)
• Olympus Microscopy Formats (oib, oif, vsi, apl, mtb, tnb, obsep)
• Zeiss Microscopy Formats (czi, lsm, mdb, zvi)
• Various TIFF formats (incl. tiff, ome.tif)
• JPEG (jpg, jp2)
• Bitplane Imaris (ims, hd5)
• Huygens (hd5)
• DeltaVision (dv)
• Image Cytometry Standard (ics)
• Portable Network Graphics (png)
• Video Formats (incl. avi, mpg, mov)
• Encapsulated Post Script (eps)
The instrumentation of the Clive and Vera Ramaciotti Centre of Structural Cryo-EM is unique in Australia. The centre houses the first Titan Krios TEM in Australia and is equipped with a highly efficient direct electron detector Falcon II, also the first of its kind in Australia. The facility is underpinned by sophisticated software packages for data collection generating 2TBytes of data from this instrument alone. The facility allows for shared use by several Victorian universities and MRIs including Monash, LaTrobe, WEHI, Baker, Burnet, Peter MacCallum, MIMR and St. Vincents Institute.
The proposed data library will comprise an array of cross-disciplinary multi-dimensional molecular and cellular imaging data acquired by leading researchers from these and other leading Australian institutions. In addition, the data collection will facilitate research collaboration within the $28M ARC Centre of Excellence for Advanced molecular imaging led by Professor James Whisstock.
The extraction and interpretation of biologically meaningful information from images requires sophisticated image processing, visualisation and quantitative analysis. Recent increases in image dimensionality and dataset size have put significant strain on current infrastructure for managing, handling and sharing data. This limits the use and development of tools and systems for advanced image analysis. The proposed collection will provide a foundation for fostering collaboration and development of tools for analysing image data in the future.
High-Performance Computing (HPC) platforms, including the Characterisation Virtual Laboratory (CVL), Multimodal Australian ScienceS Imaging and Visualisation Environment (MASSIVE) and National eResearch Collaboration Tools and Resources (NeCTAR), provide powerful tools to aid in the analysis of images; however, data accessibility from these systems can be restrictive. The availability of a centrally managed and integrated data storage and handling solution, such as the one proposed herein, will reduce the barriers to the use of HPC systems and provide a platform for the development and integration of other high-end image analysis tools. It will form the basis for a sophisticated workflow, developed under NeCTAR’s Characterisation Virtual Laboratory, that includes significant Australian research infrastructure like the NeCTAR Cloud, MASSIVE, RDSI and VicNode.