The RCC-operated Wiener supercomputer wowed attendees of this month’s microscopy Instrument Extravaganza Workshop at UQ with its image processing speeds.
The ACRF: Cancer Biology Imaging Facility, at the Institute of Molecular Bioscience (IMB), ran a full-day, hands-on microscopy workshop on Tuesday, 5 March, prior to the Light Microscopy Australia conference held at the Translational Research Institute, 6–8 March.
At the IMB workshop, Wiener and a new cache, known as Ferdinando, ran at more than 60 GBs per second. Ferdinando is part of UQ’s Metropolitan Data Caching Infrastructure (MeDiCI) data storage fabric, and the IMB workshop showcased MeDiCI’s recent extensions.
“This allowed workshop attendees to deconvolve image stacks of multi-hundred megabyte TIF files per directory in as little as one minute and forty seconds per session,” said Jake Carroll, Associate Director, Institutes Research Computing at UQ.
Workshop co-organiser Nick Condon of IMB said, “During the day more than 10 terabytes of data was produced and processed at unprecedented speeds, which allowed for almost immediate visualisation. Attendees were left in awe of the new computing and imaging capabilities at UQ."
Wiener is a GPU-accelerated high-performance computer designed for image processing. Microscopy image data is cleaned up using mathematical modelling via a process called deconvolution. Using cutting edge software that makes use of multi-GPU support, researchers can now process their imaging data faster using this cluster.
The IMB Instrument Extravaganza Workshop invited delegates of LMA 2019 to gain hands on experience with six cutting-edge microscopes running simultaneously, using their own or provided samples to image. Participants gained access to equipment, processing time on Wiener and use of IMB’s virtualised remote analysis workstations.
As well as RCC’s contribution of computational support, two RCC staff members gave talks as part of LMA 2019, and one presented a poster.
RCC visualisation expert Oliver Cairncross gave a talk on Wednesday, 6 March, about Phoebe, an advanced data visualisation tool he developed that allows researchers to investigate large, volumetric, time-series microscopy data sets using a 3D interactive user interface.
RCC scientific workflows expert Dr Hoang Nguyen was also at LMA 2019 on 6 March to present a RCC/IMB poster about a Web portal for imaging analysis on a GPU compute cluster. The IMB Image Processing Portal, in conjunction with MeDiCI, automates the process of transferring images from instruments to HPCs for analysis, and archives the results for visualisation or further processing.
Post-conference, RCC eResearch Analyst and imaging specialist Dr Nick Hamilton presented a talk at the BioImage Analysis Satellite Symposium on Saturday, 9 March, about his work on modelling, predicting and understanding kidney development using microscopy imaging.
Dr Nick also taught in an image analysis workshop held at IMB in conjunction with the conference.
Dr Hoang Nguyen presenting a poster at LMA 2019. (Photo: Dr Nick Hamilton, RCC.)
Dr Nick Hamilton speaking at the BioImage Analysis Satellite Symposium as part of LMA 2019. (Photo: Ian Harper.)
