Core microscopy facilities provide many services to the research community: access to cutting edge equipment, sharing expert knowledge and training our future scientific leaders. Their staff advise students and group leaders on different techniques, maintain healthy relationships with the different vendors to know what is currently available and what is coming soon, and often work collaboratively with their peers in other facilities to provide technical advice and to run workshops together.
Recently, Nicholas Condon from the Institute of Molecular Bioscience at UQ attended Microscopy Australia’s Sydney University facility, Sydney Microscopy & Microanalysis (SMM) to explore how they are handling big data and applying their analysis tools. Carolina Chavez from the Florey Institute in Melbourne visited The University of Queensland’s, Queensland Brain Institute (QBI) to connect two leading neuroscience microscopy facilities.
Some of their comments are below:
“Thanks to this very generous award from Microscopy Australia, Microscopy New Zealand and the Australian Microscopy & Microanalysis society, I was able to spend a very successful week visiting SMM facility in late September, hosted by Neftali Flores Rodriguez and Eleanor Kable (and the other awesome members of the light microscopy team). Recently, Neftali had visited the University of Queensland Institute for Molecular Biosciences Microscopy to learn about how data is captured, processed and visualised on our 3i Lattice Light-Sheet microscope prior to SMM taking delivery of their own system.
This Knowledge Exchange award allowed me to better understand how big data is moved about their facility and how they are processing the many hundreds of gigabytes to terabytes of data produced by their camera-based optical microscopes.
Nick at Sydney Microscopy and Microanalysis
During the visit I experienced how the light optical team works across 3 different buildings. It was very enlightening to see how the staff move back and forth across campus to be at the right microscope at the right time with the right user. I was also lucky enough to be involved with the on-boarding of a new user to the facility, seeing how the team discusses the potential new project with both the PhD student and their supervisor, highlighting the need for controls, and to begin thinking about what analysis would need to be performed down the track. These thought stimulating questions will shortly be included in our own PPMS training request questionnaires here at the IMB!
While on this knowledge exchange it became clear how in many ways we are working on similar problems and facing similar issues. One commonality between our facilities is the push for 100 Gbp networks from scope to analysis computers being the current dream.
Despite this knowledge exchange formally taking a week, the discussions, emails, calls, sharing of ideas, contacts and experiences are ongoing and will remain into the future. I encourage anybody eligible for this wonderful scheme to apply in future rounds.”
SMM platform scientist Neftali at one of the confocal microscopes.
“Visiting the Advanced Microscopy Facility at QBI was a valuable experience both personally and professionally. This was a great opportunity to create a network between two neuroscience-focused microscopy facilities. The knowledge exchange program allowed me to gain insight into the daily operations of the facility and showed me how different microscopes are used in imaging projects, with a focus on spinning disk confocal microscopes and their applications.
Overall, this exchange provided me with an opportunity to discuss and share experiences with other facility managers and staff about user training, improving immunohistochemistry workflows, handling microscopy data, key instrumentation, and day-to-day running of a microscopy facility. Handy suggestions were also shared on what instrument specifications should be considered by users and what they should be aware of. This visit has assisted in preparing future infrastructure investment cases and has established an ongoing collaboration between our microscopy teams. A big thank-you to Rumelo, Andrew and Arnaud from the Advanced Microscopy Facility at QBI, plus the microscopy teams on campus for being generous with their time and knowledge!”
The scheme is still open so contact Lisa Yen at lisa.yen@sydney.edu.au for more information on how to apply.
Nick with the team at SMM including from left to right Michael Kuligowski, Pamela Young, Eleanor Kable, Susan (Ying Ying) Su, Nick Condon, and Neftali Flores Rodriguez.
January 18, 2023
