Connecting plant scientists with their data: Using Zegami, a Software-as-a-Service solution for the visualisation of time-course image data collected at the Australian Plant Phenomics Facility.

Mr George Sainsbury1

1Australian Plant Phenomics Facility, Adelaide, Australia

At the Australian Plant Phenomics Facility (APPF), we capture tens of thousands of images of individual plants a day. Analysis of these images is automated, and the general wisdom is that “if you take 10,000 photos a day, they’re not for looking at.” However, there are many reasons why researchers and operational staff might want to look at them; from quality control to determination of growth stages.

We partnered with Zegami; a company formed by Oxford University Innovation after humble beginnings in South Australia. The software-as-a-service (SaaS) they offer was originally inspired by Microsoft PivotViewer, but has expanded significantly, with major user experience improvements and Zegami is now integrating deep learning to help discover more about the images in the collections.

We developed an Export-Transform-Load (ETL) tool from the LemnaTec system at The Plant Accelerator (TPA) to Zegami’s service, hosted on Microsoft Azure. Data ingest and processing is fully automated, running in Docker on Pawsey’s Nimbus cloud. Images and data are updated daily. Our collections are some of the largest on Zegami and as such we have collaborated on service and API improvements.

Zegami allows researchers conducting experiments at TPA to view and share their experiments from the comfort of their own workspaces. Many experiments are publicly available and Zegami is one piece of a larger puzzle to make data at APPF more FAIR.


George Sainsbury is the Data Architect & Software Engineer at The Plant Accelerator (TPA), the lead node of the Australian Plant Phenomics Facility (APPF). George is responsible for “all things IT” at TPA and his role encompasses software development, research data management, systems administration and everything in between. 2020 will be George’s fifth year at eResearch Australasia.

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