A new imaging data tool launched for Australian researchers
December 16, 2022
A new imaging tool to assist Australian researchers in processing cryogenic electron microscopy (CryoEM) data was launched earlier this month.
The EM Data Processing Portal was created and launched through the ARDC platform project Australian Characterisation Commons at Scale (ACCS) utilising ARDC-funded specialised compute infrastructure provided by QCIF and Monash University.
In recent years the number of electron microscopy (EM) instruments, especially in CryoEM, has increased nationally and internationally. The large data sets produced by these instruments have elevated demand for compute capability to process them.
The EM Data Processing Portal provides access to high-performance GPU clusters for processing EM data using CryoSPARC and LiberTEM software services.
Once a CryoSPARC or LiberTEM service has been started, it can run continuously for 14 days.
Access is open to all staff and HDR students at Australian universities as well as CSIRO and other government research agencies that are members of the Australian Access Federation (AAF).
Data are transferred in and out of the portal using Globus (v5). Currently, eligible users of the portal must then be at organisations that are also members of the Educational Global Authentication Infrastructure (eduGAIN) as this is a restriction of Globus v5. If you are unsure of whether your organisation is a member of the eduGAIN global network, please contact the IT or eResearch service at your organisation.
Information about how to access and run the EM Data Processing Portal is on the ImagingTools platform.
ImagingTools is an initiative of ACCS. This platform has training material available for the neuroimaging and microscopy community. ImagingTools also provides access to XNAT and the Characterisation Data Virtual Laboratory (CVL). Opendata.fit, a tool for bio-nano science, will be added soon.
Characterisation Virtual Laboratory (CVL)
The CVL desktop is a remote desktop environment that provides researchers with access to imaging tools and data, and a range of tools to process atom probe, neuroimaging, structural biology, X-ray, and general imaging data.
Instruments are integrated with the CVL desktop so data is captured directly from the imaging instrument and transported to a managed environment, where it can be processed using software tools stored in the CVL and the ARDC Nectar Research Cloud, which features QCIF cloud compute service QRIScloud as the Queensland node.
The CVL is available to all Australian researchers working in imaging and characterisation sciences. Using their AAF login, researchers can access the virtual laboratory using their choice of desktop client or web-based interface.
The CVL allows researchers to easily access high-performance computing (HPC) setups over the internet using their own computers for processing large volumes of imaging data on remote systems.
RCC operates a CVL node on HPC Wiener that is available to researchers from all QCIF Member institutions (including UQ) who need a GPU for their work.
Other tools also available through the ImagingTools website:
XNAT
XNAT is an open-source data platform for management and quality assurance tasks of imaging and associated data. It may be used for storing, managing, and analysing imaging data.
XNAT is one of the most popular tools for managing neuroimaging data collections. The tool is being used to manage Australian multi-site data collections.
RCC and the QUT eResearch teams have been working on institutional XNAT services in collaboration with other project members of the ARDC’s Australian Imaging Service (AIS), with the University of Sydney as the lead agent in this ARDC platform project.
AIS provides a distributed federation linking member institutions, including the UQ XNAT service, with a federated search layer, common community practice, support for expanded data types and a Trusted Data Repository ensuring ongoing ownership and accountability of data.
Globus
Globus is a high-speed file transfer system that enables researchers to securely move large volumes of data to other Globus-connected sites across the world efficiently and quickly, all via a web-based platform.
RCC staff built the local Globus service with infrastructure funded by QCIF and AARNET’s assistance for network performance and optimisation. It is an ‘opt-in’ service and is currently only available for QRISdata Q-collections (see the QRIScloud webpage titled “Using QRISdata Collections for UQ RDM Collection users” for more information about Q-collections).
Article written by The University of Queensland Research Computing Centre (RCC) and QCIF and originally posted on their websites.
Special thanks to ACCS’ partner organisations The University of Queensland Research Computing Centre (RCC) and QCIF for writing this insightful article about ImagingTools and its newly deployed tool, the EM Data Processing Portal.
