Dr Rubbiya Akram Ali1, Dr Hoang Nguyen2, Professor David Abramson2, Professor Roger Wepf1
1Centre For Microscopy And Microanalysis, The University of Queensland, Australia, 2Research Computing Center, The University Of Queensland, Australia
Scientific imaging instruments with modern fast CMOS detectors are generating increasingly large datasets, and hence, data management becomes more critical. This is particularly true in the context of large multiuser facilities such as the Centre for Microscopy and Microanalysis (CMM) at UQ as it operates a wide range of microscopes and many of them are big data producers. A central data repository to store, index, annotate data not only allows its researchers to search, browse and retrieve their data easily but also has the potential to harvest metadata to enrich these datasets.
Particle Imaging depoT using Storage CacHing Infrastructure (PITSCHI) is a central data repository for CMM instruments that adheres to FAIR data principles. This is part of the Australian Characterisation Commons at Scale project, funded by the Australian Research Data Commons. PITSCHI is based on the opensource Clowder data management framework, and fully integrated with the instrument booking system and the storage infrastructure at UQ. PITSCHI provides end-to-end process data management, from capturing raw data to transferring them to storage collection, ingesting/indexing the data into the repository leading to an automated metadata extraction. The data ingested in PITSCHI are available in various platforms such as HPCs, personal computers, and processing platforms (e.g., CVL). Data transport is arranged transparently using the Metropolitan Data Caching Infrastructure (MeDICI).
We presented PITSCHI in eResearch Australasia 2021. This year, we would like to share our experience in the development and operation of PITSCHI.
Biography:
Dr Rubbiya Ali completed her PhD from the Institute for Molecular Bioscience, the University of Queensland, Australia. She developed three dimensional computational methods (3D BLE, RAZA and RAZAps) for edge detection, segmentation and particle picking of 3D organelles, macromolecules, and membrane proteins. She currently works at the Centre for Microscopy and Microanalysis (CMM) as Data Informatics Manager. Her major research activities are 2D/3D image processing and establishing scientific workflows for microscopic data management to facilitate entire data lifecycle at CMM.