The Bioimaging perspective; how our microscopy team locked-down and re-opened

March 2020 and the arrival of Covid-19 saw life in the UK change dramatically, and quickly.

Life and research here at the John Innes Centre, changed equally dramatically. Recently we spoke to John Lord about how these changes affected our Hort Services team and how they managed to ensure science didn’t grind to a halt.

Another core facility which needed to adapt quickly to ensure research could continue was our bioimaging and microscopy platform.

We spoke to Head of Bioimaging Kim Findlay about what happened and how she and her team have adapted to ensure scientists are once again able to peer down the lens.

“The first Covid-19 related death in the UK coincided with me returning from a BBSRC ALERT funding-review panel meeting in the first week of March 2020.

I had been following the news about the virus since early January, with growing concern as the numbers grew and cases spread to Europe.

On the train back from Bristol that week, I was acutely aware of the number of people I encountered and the many touchpoints, especially on the underground. Later that week, I felt uncomfortable not shaking hands with Baroness Natalie Bennett when our Director Professor Dale Sanders brought her to visit our Bioimaging facility.

The situation was developing quickly and because we have a lot of multi-user equipment, we are a high-risk area. The following Monday, I called a team meeting, where we instigated a new routine of daily cleaning of all equipment and tried to get hand sanitiser stations installed in Bioimaging.

We realised that that there is only one hand-washing sink in our lab, serving about 15 rooms. Others obviously found themselves in a similar situation, with a dearth of hand-washing facilities. On site supplies of hand-sanitiser had already gone and were sold-out online. A suggestion to buy supplies for every room from a supermarket was impossible due to rationing.

Later that week, the John Innes Centre’s Director, Dale Sanders announced that staff should not undertake any international travel, so we cancelled our imminent trip to Germany (Eva, Sergio and I were due to have microscope demos at Zeiss the following week) and I cancelled the technology seminar I had organised, to be given by a foreign visitor. These were rescheduled to take place online.

Fearing a full lockdown, I took the opportunity to visit my parents, both in their 80s, that weekend.

Returning to work on the Monday (16 March) we were notified that staff and students should work from home if possible, but that the Institute would remain open for now. The next morning, I called a team meeting that I will never forget.

As a team we stood, socially distanced, in the lab discussing what we could and should do next. The sombre tone,  rapid decisions and seriousness was matched by a great team-spirit. I vividly remember the feeling of increased weight on my shoulders.

We planned for home working, which for me meant ordering a laptop and ensuring all our team were set-up with VPN access.

Safety was paramount, and we wanted to keep the facility open for researchers. To do this we initiated a new routine of cleaning between every user, ceased all one-to-one training, limited people to one per microscope room and cancelled our microscopy training course in April. All training activities across the institute were cancelled the next day.

I emailed an update on the changes and put up notices in Bioimaging. I sent advice to other labs on site that I knew had microscopes, on how best to clean them, based on information distributed amongst light microscopy facility managers in the UK.

About this time, EuroBioimaging (based in Germany) issued a notice about Covid-19 safety in core facilities like ours, where we have lots of face to face interactions. It made sobering but welcome reading. I had been making all the decisions about the platform and welcomed this guidance.

On the Friday that week, Dale sent a mail to all platform managers, telling us we could switch to service mode only and provided guidance on what we might say to our teams. I welcomed this and found it enormously helpful and supportive.

At this point, the institute was not planning to close, so we were to try to minimise the impact on Science. That day I prepared a new policy document for the platform and switched to allowing only autonomous light microscope users and doing all EM as a service, to avoid having to go in the rooms with others to provide technical support.

On Monday 23 March, I finalised our contingency plans and documented what to do to keep all our equipment and services safe, in case of platform staff absences, institute closure, power loss to the building etc.

We couldn’t start to shut things down as closure had not been announced and we were experiencing a flurry of activity as scientists  tried to complete lots of imaging experiments  before any lockdown was enforced.

The following afternoon, Dale announced the John Innes Centre was to go into lockdown that night. Microscopes are complex pieces of equipment, so despite our planning it was then a race against time for the three of us who remained on-site to secure everything.

Eva turned off light microscopes. Elaine topped up the chillers and drained compressors and checked all the sample prep kit was empty of samples, clean and switched off. I put the scanning electron microscopes into standby mode but there was not enough time to put the TEM on full standby, as this requires two days. So, I burned off excess liquid nitrogen and turned off the electron source. After filling the liquid nitrogen dewar for storage of cryo-TEM samples and putting up a few notices for safety, I was the last one out of our lab. It felt strange and eerily quiet about the place.

Wednesday 25 March was a strange one. I was at home and feeling rather exhausted after making so many rapid decisions and rushing around. I sent thanks to my team for their unwavering support and great team spirit. The rest of the week was going to be busy as we had virtual microscope demos with Zeiss for the next two full days, so I told them to take some time to rest and ensure they had what they needed.

The following week, I requested essential worker status and went back on-site to properly put the TEM on standby, double check everything and collect a few more things from my office and, fortunately, my new laptop.

Work continued from home for all my team throughout the closure, with an endless stream of virtual meetings, emails, requests for help with writing papers and grant costings, staff appraisals, preparation of equipment proposals, seminars, webinars, and various admin tasks including ordering a new stereo microscope.

We had several virtual team meetings, including some that were simply a coffee and chat, and one or two where we had fun, messed about with our video images, wore wigs or odd outfits, which was great to keep spirits up, and we celebrated Jake’s birthday virtually.

I’ve had three virtual imaging facility manager meetings through the Royal Microscopical Society between May and July, where it was really good to be able to share best practice across institutions and air any concerns. For example, many of us were concerned we would return to find our electron microscopes would not restart as these can be particularly difficult and temperamental beasts.

In total, the John Innes Centre was closed for six weeks, which passed surprisingly quickly for me.

Throughout the closure, along with the other platform managers, I was working on how we could safely re-open. To this end, I prepared an unwinding policy for the platform.

We re-opened on Monday 11 May, and on that first day I was very relieved to find the electron microscopes restarted OK. Thanks to the planning we had done ahead of time, we resumed performing electron microscopy (EM) as a service and were able to welcome eager light microscope users immediately.

Like many teams, throughout this time we’ve relied heavily on Computing. I know from my husband, who is Head of Computing, that this has been their busiest period as they have helped 500+ staff set up things like remote working. We could not have done it without them.

For example, we were able to offer microscopy support so quickly because Computing enabled remote working on our light microscopes so that we could help people with technical issues without going into the room. This has proved to be invaluable and is something we will keep as it is also proving useful when we run assisted sessions; letting the users dial in to see us operating the microscope.

Since re-opening we have been able to facilitate engineer visits and  installed a new stereo microscope.

Although we still spend some time working from home, this has become less and less as activity in the facility ramped up very quickly. We have also adapted how we work. Spreading out our computers from one small, shared office, to sharing rooms with equipment rather than people.

Having spent almost all our time cleaning equipment between every user before the closure, we realised this was impractical going forward and asked users to do it themselves between each other, with some top-up cleaning from us. This, along with not providing any training initially, freed up more of our time to do the additional service work, with a sample drop-off point at our lab door.

Another adaptation we have made was because of the nature of  air handling in the building which only recirculates air. Following a conversation with our Estates team, I decided we should leave a gap of one hour between bookings, to allow for sufficient exchange of air in the small rooms. We also had some rooms with multiple microscopes, but couldn’t have more than one person in there at a time. Both of these things meant that bookings had to be managed more carefully.

The difficulties of working from home had now given way to new kinds of stresses and there were many time-consuming emails to explain, justify or reassess our measures, to plan and coordinate efforts, and due to the limitations and restrictions we have had to impose, there have of course been frustrations. I admit, it was not easy. However, the kind words and appreciation from lots of our staff made all the difference.

We have tried to be as proactive as possible, reviewing the situation regularly, but we are a large facility with a lot of users, so the impact of any limitation on Science is obvious. I know we have not been able to satisfy all our users, which pains me, but the Bioimaging team are committed to helping as many as possible.

We have all been coping with increased anxiety, juggling new ways of working and added responsibilities, and the enormous pressure I felt on my own shoulders, to navigate us safely through an ever-changing landscape, was probably no less stressful for them. We all need support and guidance. But my team are outstanding and have all been willing to go the extra mile.

Yet another challenge is just around the corner, as the two equipment funding proposals I wrote during lockdown have just been approved by BBSRC. This means over £2M for a new SEM and high-end confocal.

The logistics of further demos, procurement, and getting old equipment out to make space for new installations will be more complex than usual under the cloud of Covid-19.

The virus is still out there and so we cannot return completely to the old ways of working without risk. This has given me pause for thought on the design for our platform in the future, thinking about the space we need to operate and house equipment, but more importantly to meet the needs of Science, adequately and safely”.