Microscopy facilities: resuming operations

after Covid-19
Published on the 1 June 2020

Some of the core facilities have started to resume work, gradually finding how to function in these specific circumstances of pandemic.  Many institutions and research groups have published guidelines and information to help facilities to adapt and find suited methods.

With the global Covid-19 crisis and the containment rule, many facilities had to reduce or cease institutional activities in the past few months. The return to normal operations will most probably be a gradual process, depending on countries’ regulations, institutions’ decisions, and specificities of each facility.

Fortunately, in those troubled times, the research community has stayed strongly implicated: many institutions and research groups have published guidelines and information to help core facilities resume operations in the best conditions. We strongly recommend reading:

1. Personal Protective Equipment for your staff and users

Staff should be equipped with Personal Protective Equipment (PPE), and the same precautions should be requested from users.

  • Wear gloves: this does not prevent washing hands, as gloves rarely stay sterile.
  • Wear a clean gown: do not share them.
  • Wear face masks at any time to reduce the chances of contamination by droplets. The World Health Organization is giving information to remind everyone how to efficiently wear a mask, how to put it on, and dispose of it. Good infographics to print and display!
Image by United Nations on Unsplash
  • Provide safety googles, disinfected before and after each use.
    • Some cores have wrapped up the eyepiece in plastic wrap to minimize COVID-19 transmission, but it may be hard to maintain with the increasing number of users getting back in.
    • Safety glasses offer the advantages of being easily disinfected, more sustainable. Some users have found it hard to use with the rubber eyecups (which can be removed), but this would be a more realistic and workable option. (See thread “Use of Safety Glasses at Scopes?” on the Confocal microscopy list)
  • Put sanitizing hand rub dispensers in prominent places around the workplace. Make sure these dispensers are regularly refilled.

2. Cleaning protocol

Needless to say, hygiene and disinfection will be key to get back to the facility in a safe and sanitary environment.

  • Request that users:
    • clean the oculars they have used with Ethanol on a disposable wiper before and after each use.
    • clean the computer parts (keyboard, mouse), microscope knobs, and any touchable surface with Ethanol on a disposable wiper before and after each use.
  • Include this time for cleaning in your schedule between two sessions.
  • Do not forget to make the cleaning products available in sufficient quantity and to refill it regularly.
Image by United Nations on Unsplash
  • Empty bins regularly: wipes and masks may pile up quickly, and bins could be contamination pools.
  • Use the right disinfectant product: of course, you do not want to harm rubber or optic coating. Neutralizing the SARS-CoV-2 virus is done by diluting its lipid layer[1]. 70% ethanol is recommended for disinfection purposes while being safe for cleaning equipment. Manufacturers have issued guides to sanitizing a microscope.
  •  Cleaning and disinfection of the whole facility (elevators buttons, telephones, desks, door handles, drawers, top of the chairs…) are to be regularly carried out.

3. Communicate with your users

Whether dealing with internal or external users, it is important to let them know when and under which conditions the facility will resume operations.

  • Inform your users of the reopening plan and measures taken by the facility by posting it on the facility website. Here are examples of Q&A on measures provided by core facilities: Georgia Tech and MSK Research Laboratory
  • Display information posters throughout the core, promoting handwashing and good practices.
  • Request that users warn you if they present any signs of sickness, even a mild cough or low-grade fever. Any suspected users should not be allowed to access the facility as prevention.
  • Ask the users to arrive with samples that have been wiped and are non-hazardous.

Download here our posters about general sanitary rules in the lab and microscope cleaning.

Download Posters

Download our free posters on Sanitary rules in the lab and Microscopes cleaning

 4. Change of behavior

The still-present risk of contamination requests us to change our habits, and rethink how we used to carry out some of our daily tasks.

  • Practice physical distancing. Stand 1.5m behind the user, allow only one person per microscope session, make sure to regulate the flow of people in the same room to limit room occupancy.
  • Assess the state of systems. Some microscopes may have not been used for some time. An assessment of their status would be good, to ensure they are performing as they used to do before the global lockdown. To guide you, you can read our selection of scientific publications about Quality Control or our article “Quality control on fluorescence microscopes: what is it and why should we perform it?”.
  • Prefer camera view over eyepieces for visualization of samples.
  • Train users. Authorized users (already trained) might not be a problem but letting untrained users operating systems may not be something you are comfortable with.
    • Training new users will definitely require some new methods to do it while respecting the recommended distances, as remote training does not seem suited for each case, depending on the necessary back-and-forth discussions.
    • Knobs on microscope and equipment can be labeled to give easier indications, or trainer can simply point them out with a basic laser pointer.
    • A double mouse can be plugged to the computer to help show on the screen where to click.
    • Alternatively, Teamviewer installed on the acquisition computer also allows trainers to fulfill that mission.
    • If not existent, it is the opportunity to produce self-help material: practical guides for each instrument, basics written procedures, simple tutorial videos… This might not replace training but could accompany trained users and be re-used post-Covid-19
    • This is also the opportunity to train users to cleaning and sanitary recommendations.

The following tips may not be comprehensive. If you feel that further details and precautions are missing, please do share them on our twitter @argolight, or LinkedIn – we will keep on updating this article to centralize pieces of information you may share.

We wish a safe ramp-up period to the whole microscopy community.

Have courage for the great sorrows of life and patience for the small ones; and when you have laboriously accomplished your daily task, go to sleep in peace. ”  Victor Hugo


[1] “Why does soap work so well on SARS-CoV-2?” by Prof. Palli Thordarson, Uni of New South Wales. https://virologydownunder.com/why-does-soap-work-so-well-on-sars-cov-2/


Header photo by Branimir Balogović on Unsplash
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