Research Computing Centre

Instruments and Managed Data Collections

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Data management at UQ 

UQ has a data management policy. The policy mandates the management and curation of research data for specified periods, depending on ARC and NHMRC funding rules and local statutes on data retention. 

RCC can help with data archiving and estimating file storage sizes to assist with data management planning and costing.   

Cloud computer QRIScloud, which RCC manages in conjunction with QCIF, can offer extensive data storage for data of national significance.  

RCC deploys tools and technologies to help UQ researchers manage their data well.  RCC currently supports OMERO,  XNAT and Pitschi (Clowder) services for the capture and management of imaging data from instruments such as Magnetic Resonance Imaging (MRI) machines and microscopes. 
 

OMERO 

Open Microscopy Remote Objects (OMERO) is a modern client-server software platform for visualising, managing, and annotating scientific image data. 

OMERO supports the importing and archiving of images, annotation and tagging, recording experimental protocols, and exporting of images in several formats. It also makes it possible to collaborate with colleagues anywhere in the world by creating user groups with different permission levels.  

The OMERO platform operated by RCC is integrated with UQ RDM collections, allowing users to manage their image files while also benefiting from RDM's features. This extends to the use of workflows involving ingesting files via OMERO onto RDM, then processing those files on the Characterisation Virtual Laboratory (CVL) or other HPC infrastructure. 

The service is available at https://omero.rcc.uq.edu.au. 
 

XNAT 

XNAT is an extensible open-source imaging informatics software platform dedicated to imaging-based research.  

The UQ XNAT service is operated by RCC as an Australian Imaging Service (AIS) node. AIS builds on XNAT investments at universities and clinical sites across Australia with enhanced data management and analysis capabilities.  

AIS operates as a federation, co-maintaining a central set of software repositories with each partner institution operating their own node matching their local governance, infrastructure, and cost structures. AIS integrates with imaging devices in a hub and spoke model, with each node integrating their local academic and clinical equipment. Data can be transferred between nodes to facilitate multi-site imaging studies. 

AIS partners include the Australian Research Data Commons (ARDC), the National Imaging Facility (NIF), the University of Sydney, and UQ and other universities and research organisations. 

Please visit the XNAT site.
 

Pitschi (Clowder) 

Pitschi (Particle Imaging depoT using Storage CacHing Infrastructure) provides end-to-end imaging data process management at the UQ Center for Microscopy and Microanalysis (CMM), from capturing raw data to transferring them to storage collection and finally ingesting/indexing the data to the repository. Metadata of supported file types are extracted automatically to facilitate search and discovery. 

Pitschi integrates the Clowder data management framework with the RIMS instrument booking system and with storage infrastructure at UQ. Data transport occurs transparently using the Metropolitan Data Caching Infrastructure (MeDICI). Data ingested in Pitschi are available in various platforms such as HPCs, personal computers, and processing platforms such as CVL. 

Pitschi was implemented as part of the Australian Characterisation Commons at Scale project, funded by the Australian Research Data Commons. Pitschi adheres to the FAIR (findable, accessible, interoperable and reusable) data principles. 

Please visit the Pitschi site.