Light Microscopy : Latest news

Things in the CALM STP nearly got back to normal in November and then… well, you know the story.

Despite the latest lockdown, there’s actually quite a bit going on:

Covid Rules

Our equipment is currently available to book with few or no additional restrictions due to Covid-19. We are offering equipment training in line with current Crick guidelines about essential work, meaning that if you request a training session we assume it is in order to perform essential work. Remote training is available on most systems and has been working quite well. Most remote training involves an on-line theory session followed by a hands-on session where the user is on the microscope and the trainer is connected remotely by Zoom. OUR BIGGEST PROBLEM continues to be multiple users crammed around the same instrument. Please don't do this; its bad social distancing. If you need help from a colleague while imaging, try using Zoom or remote desktop. LBNL please remember it's up to you to wipe down the equipment before using it; we don't wipe down systems between users.

What’s New?

A new set of 16x objectives has arrived for the Luxendo MuVi. It provides a slightly larger field of view than the 20x objectives while retaining cellular resolution. This makes it easier to take long-term time-lapse movies of zebrafish development without the embryo drifting out of view. Remember also that the MuVi has a pulsed IR laser for spatially confined photo-activation, bleaching, and ablation in living embryos. This is an amazing setup for live imaging!

The Brainsaw has been been ordered. This system will do 3-channel serial block-face sectioning of whole mouse organs. It was developed by Rob Campbell at the Sainsbury-Wellcome Center to image whole mouse brains, and is basically a home built one of these. Although it was developed for brain imaging it can also be used to image other organs, including tumours and lymph nodes. Dan Gunton will build the system down in LB4-3005 and we hope to have it running by late spring / early summer.

Our VisiTech iSIM microscope for live-cell super-resolution was installed in July and rapidly adopted (first data already accepted for publication!). Similar systems were installed in the Way and Beale labs, each one subtly different. Matt Renshaw has been working with VisiTech to optimise fast volume imaging on the CALM system. A 2-channel volume having 41 Z-steps (~70 x 45 x 4 µm) with 20 ms exposure now takes 2.5 seconds instead of 5, and Matt thinks we can get it down to under 2.

Our Nikon-Yokogawa Spinning Disk has become very popular, especially with the fly folk. As a result there is very little spare capacity on this system and the time to get a booking has become long. We are aware of the problem and Donald is developing a cunning plan for increasing our Spinning Disk capacity this year.

Do you want to segment nuclei? Have you seen StarDist? Its very cool, ask Todd.

Alex Palmer continues to do quality control checks on confocal microscopes in the facility and around the building. She can help with confocal issues on quadrant confocals, arrange for servicing, and if you ask her nicely she just might provide training on your system (when she’s not working on QUAREP-LiMi).

We are helping to set up SlideSeq, as part of a joint project with Advanced Sequencing, the Making Lab, BABS, and the Rodriguez Lab. Spatial transcriptomics, including SlideSeq, was Nature Methods' 2020 Method of the Year. The cooperation between Christina Dix and George Konstantinou in the Making Lab and Matt Renshaw in CALM is building our experience with complex microfluidic set ups. The hardware and software they’re developing have the potential to be adapted for other in situ sequencing projects.

Our OMERO server has gone live here. We’re offering our first training session on the new system to members of the Turajlic lab at the end of this week. OMERO is a place to store, share, and analyse image data. Our server is currently only visible from within the Crick or VPN, but we hope to have solution in place soon for sharing image data (especially big files) with external collaborators. Please contact Donald if you’d like to start using it.

Related to OMERO, we recently appointed Kenneth Ho to a joint position shared between CALM and Scientific Computing to help with the management of Big Image Data. Ken comes to the Crick from the Riken Quantitative Biology Institute in Kobe Japan, where (among other work) he built the Systems Science of Biological Dynamics database using OMERO. Ken will start at the Crick in early March.

Our PhaseFocus LiveCyte system was recently upgraded. This is a label-free imaging system for long-term live cell imaging with powerful software for cell tracking and lineage tracing. The environmental chamber offers improved stability, there’s now a filter cube to image far-red, and the analysis software now works on the fly. Contact Deb or Dave for more details. 

We are in the process of installing a new incubation chamber on our FV3000 multi-photon system, to enable long-term imaging of delicate samples like E6 - 7.5 mouse embryos. This system has also been fitted with a new anaesthetic unit for intravital microscopy.

You may recall that the image analysis workstations from SE4 were moved down to the LM facility last year. CP1, CP2, ZN1, and IM2 are in the main facility whereas IM1 and IM3 are located in SW302 next to the Carlton Lab. All of these workstations are available for remote access and getting heavy use. IM2 has just been replaced with a new machine (Dual Xeon Processors, 12 cores each 48 cores in total using hyperthreading, 256 GB RAM, 2 TB SSD, 8TB SATA hard drive, 2 NVIDIA RTX 4000 GPUs and a massive wrap-around monitor). The old IM2 is still available but will be blasted into outer space at the end of February, so if you have any data left on that machine please remove it soon.

Dr. Kurt I. Anderson
ALM Head - Crick Advanced Light Microscopy Facility
Interim Head of the Making Lab
The Francis Crick Institute
1 Midland Road
London
NW1 1AT

Dear users,

all users entering the Advanced Light Microscopy STP must respect our start-up guidelines:

The main points are: 

1. Work in line with Crick and Government guidelines.

2. Hand washing and social distancing are the most important things. People should not be closer than 2 meters for more than 15 minutes.

3. Extra measures are needed if you have to breach Social Distance rules. These measures include working back-to-back, working behind screens or curtains, wearing masks and visors, and wearing gloves. Use more than one approach if possible.

4. The occupancy of each room and the facility overall is restricted. This information is posted on the door of each room and the entrance to the facility. Please do not enter the facility without an actual booking.

5. We are enforcing a 30 minute gap between bookings to minimise user contact. During this time we ask each new user to wipe down the system  before use (keyboard, manual controls, eyepieces, desktop). Gloves and Distel wipes are provided at the entrance to the Facility.

6. Image analysis workstations should be used remotely where possible.

 

Staff on site and working remotely is available for assistance, this means  you can contact them all via email and Zoom.

Additionally every microscope has Zoom installed for desktop sharing.

Remember you can also use the general contact email calm@crick.ac.uk, which goes to everyone in the team.

Stay healthy,

Dr. Kurt I. Anderson

CALM Head

Crick Advanced Light Microscopy Facility

The Francis Crick Institute

1 Midland Road
London

NW1 1AT

New Confocal Arrivals: Installation of our new LSM 880 multi-photon system will begin the week of June 24th. The 880 MP will replace the 780 MP, which was moved to the 5th floor and remains open for general use as a CALM system. The new 880 MP is also inverted and will have a Ti:Saphire / OPO laser combination that expands imaging of multiple fluorophores through dual-line excitation and wavelength mixing. The following week we will take delivery on a new LSM 880 with AiryScan (also inverted). This workhorse will help take pressure of our existing 880 AiryScan system. Following the release of the new LSM 900 series in April (after we ordered our systems in December...) we are in discussion with Zeiss to upgrade the 880 Airyscan to a 980 in the near future. See Matt or Rocco for details.

Open Staff Positions: After 37 years working for the Crick, CRUK, and the ICRF, Trevor Duhig has moved on from his role as Senior Microscopist. We are currently advertising at the SLRS level for someone to fill Trevor’s position, which will involve a focus on confocal quality control. We also have approval now for a position at the LRS level to help with the management of confocal microscopes outwith the STP. This person will perform quality control checks, help manage repairs, and work closely with Trevor’s replacement to develop a QC strategy for confocal microscopes across the institute. See Kurt for details.

Data management: We now have a test version of OMERO running to evaluate this software for managing image data. Individual labs can use OMERO to facilitate the organisation, analysis, and sharing of image data. It has useful features for both researchers and lab heads. Our project to evaluate OMERO also has work packages dealing with Histopathology, High Throughput Screening, Long-term Time-lapse imaging, and analysis of STORM data using the high-performance cluster. See Kurt or Donald for details.

Huygens for AiryScan: SVI have released a Huygens module for deconvolution of AiryScan data which really improves on Zeiss’ own software. The Huygens software now accounts for the special geometry of the AiryScan detector. Anyone using the AiryScan for super-resolution should strongly consider processing their data using Huygens instead (for which we have a server license). See Dave or Matt for details.

Super-Resolution Demos: We currently have the OMX SR SIM system on extended demo. This system is suitable for imaging live and fixed tissue-culture cells and offers some advantages (as well as some disadvantages...) over the AiryScan. In July we will demo super-resolving spinning disk systems from Nikon and Olympus. See Matt or Donald for details.

Intravital Microscopy: Our new Olympus FV3000 multi-photon system has been installed in LB2-2681. This system offers several improvements over our LSM 700 MP system for intravital microscopy, including better correction for deep tissue imaging, extended laser tuning, and more sensitive detectors. The system is equipped with Olympus’ motorised 25x / 1.05 NA dipping objective which improves signal and resolution in tissue. It also has an Insight X3 laser with extended tuning range from 680 - 1300 nm for excitation of red fluorophores. Finally, the system is equipped with 4 non-descanned PMTs optimised for detection of scattered fluorescence, 2 of which are high-sensitivity GaAsP detectors. We are currently assembling the peripheral kit needed for intravital microscopy (temperature control, anaesthetic unit, dark box) and hope to start training users on this system soon. See Rocco or Donald for details.

Super-Resolution Microscopy: Many people have begun generating useful data with our Vutara STORM microscope. The system is proving easy to use for super-res newbies and has also received positive reviews from more experiences users. Todd Fallesen, our new image analyst, will provide specialised assistance for STORM data analysis. See Deb or Todd for details.

TIRF Microscopy: Our Olympus TIRF system is (finally!) operational. The system is equipped with 4 laser lines which can be individually adjusted for optimal evanescent field illumination (405, 488, 561, and 637 nm). See Donald or Kurt for details.

Training: We have just completed another lecture series on light microscopy, featuring weekly talks from CALM staff on topics including Intro to LM, Optical Sectioning, Confocal, Multi-photon, Light Sheet, and Live Cell Imaging. This series of talks is offered twice per year, and will be offered again starting in October. See Kurt or David Hudson for details.

Image Analysis: We have hired a second image analyst to work along side Dave Barry. Todd Fallesen is an alumni of the Surrey lab, and will start Monday, April 1st. Dave and Todd will be sitting in SW 302 along with Fabrice Prin (see below). They are available to work on any image analysis problems, not just light microscopy. See Dave for more info.

Dear users,

all users entering the Advanced Light Microscopy STP must respect our start-up guidelines reported below in the section "Full start-up guidelines" (see latest UPDATES).

The main points are: 

1. all of our equipment will be available for booking, but staff support will be limited during August because of roster in place in the institute.

2. maintain social distancing in the facility remains a must, but we have eased booking restrictions on most of our systems, while retaining a 30 minute buffer between bookings to (a) provide time to wipe the system down and (b) prevent overlap between subsequent users. You may also be asked to wear a mask on certain systems that are closely situated. The new rules will go into effect starting Monday, August 10th. 

3. we are developing new training procedures which maintain social distancing and reintroduced training from the second week of July.

4. image analysis will be done remotely by Dave and Todd working from home, which has generally worked pretty well thus far.

 

Staff on site and working remotely is available for assistance, this means  you can contact them all via email and Zoom.

Additionally every microscope has Zoom installed for desktop sharing.

Remember you can also use the general contact email calm@crick.ac.uk, which goes to everyone in the team.

Stay healthy,

Dr. Kurt I. Anderson

CALM Head

Crick Advanced Light Microscopy Facility

The Francis Crick Institute

1 Midland Road
London

NW1 1AT

Hey ho,

I hope you are coping with the covid. Here's a semi-normal CALM update about good stuff going on in the facility.

New Equipment Arrivals
Our new system for fluorescence lifetime imaging (Lambert Instruments Toggle https://www.lambertinstruments.com/toggel#toggel-introduction ) was installed just before lockdown and has been patiently waiting since then for users. The system is built around our workhorse platform comprising a Nikon Ti2 inverted scope, OkoLab incubator, and MicroManager. See Matt for details.

Our new VisiTech iSIM super-resolution microscope (http://www.visitech.co.uk/vt-isim.html) was finally installed last week. This system achieves ~170 nm lateral resolution at live imaging rates of 20 frames / second, which improves to ~120 nm following deconvolution. It has two cameras and can do simultaneous full-frame two-colour imaging, or 4-channel sequential imaging. Best results are achieved using the Olympus 150x/1.45 NA TIRF objective to image cells growing directly on glass coverslips. However we also have a 100x/1.35 NA silicon-immersion objective to image cells or tissue further from the coverslip. This system is ideal for imaging sub-cellular dynamics including golgi or ER, organelle traffic, actin, and microtubules. See Matt or Kurt for details.

Our new system for optical projection tomography (OPT, see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1571078/  ) has just moved from the French Lab, where it was designed and built, to the HREM Room (L3-2162, across the hall from the main facility). OPT has been extensively used by developmental biologists to make 3D reconstructions of large, thick samples such as mouse embryos. OPT is complimentary to HREM and light-sheet microscopy, and we think there will be interesting opportunities for correlative imaging using these methods. See Dan for details.

Methods on the (distant) Horizon
Sam Rodriguez, who developed the Slide-Seq (https://pubmed.ncbi.nlm.nih.gov/30923225/) approach to spatial transcriptomics, will be starting as a Junior Research Group Leader at the Crick this January. Along with advanced sequencing and bioinformatics, we will be helping to set up Slide-Seq at the Crick following Sam’s arrival.

Data Management
We have just completed procurement of a server license for OMERO.plus (https://www.glencoesoftware.com/products/omeroplus/), an image management platform from Glencoe Software based on the open-source OME package (Open Microscopy Environment). OMERO.plus includes proprietary modules for high-content screening and histopathology. We have also enlisted Glencoe to automate other aspects of the software including importing of data and meta-data. As well as helping researchers organise, view, and share image data, OMERO also integrates with software including Python and Fiji to serve as a platform for image analysis. OMERO will help to support work in the Light Microscopy, High Throughput Screening, and Histopathology STPs, and is being jointly implemented by CALM and Scientific Computing. See Kurt for details.

Image Analysis
The Image Analysis Helpdesk rides again! We held our first zoom helpdesk on July 15th and it went surprisingly well. Dave has now set it set up a recurring event on Cricknet https://intranet.crick.ac.uk/seminar/imaging-help-desk-2020-07-15 for the 3rd Wednesday of every month. Come and ask questions! See Dave or Todd for details.

Covid
You didn't think you were going to get away without being exposed to Covid-19 (news), did you? We are once again adapting our rules for working in the facility, based on government guidance and lessons learned over the past four months. The gist of it is that we have eased booking restrictions on most of our systems, while retaining a 30 minute buffer between bookings to (1) provide time to wipe it down and (2) prevent overlap between subsequent users. You may also be asked to wear a mask on certain systems that are closely situated. The new rules will be posted on our website https://www.crick.ac.uk/research/platforms-and-facilities/light-microscopy/news later this week and go into effect starting Monday, August 10th.

Happy trails,

Kurt

Dr. Kurt I. Anderson
CALM Head - Crick Advanced Light Microscopy Facility
Interim Head of the Making Lab
The Francis Crick Institute
1 Midland Road
London
NW1 1AT

Basic Assumptions

The guiding principle of returning to work in CALM is to ensure that staff feel safe by introducing workflows that reduce viral transmission. We assume that COVID prevalence in London is below 0.2% (1 in 500), and that staff will self-isolate if they suspect they are ill. Therefore the risk of transmission among Crick staff is inherently low. However we cannot expect to absolutely prevent the spread of virus among staff, as this would require everyone working under CL3 conditions. Instead we must aim to strike a balance between minimising viral spread while enabling staff to return to work. Government guidelines for returning to work in a laboratory/research setting primarily rely on social distancing and hygiene, and discourage the use of PPE specifically to address COVID-19 risk (https://www.gov.uk/guidance/working-safely-during-coronavirus-covid-19/labs-andresearch-facilities); relevant points from these guidelines have been summarised at the end of this document.

Relevant Crick guidelines to date

Relevant Crick guidelines to date -Maintain social distancing -Crick will have staff testing in place by June 15th -Researchers are free to attend weekends although STP staff are not required to do so -Restrict occupancy of lab or write-up bays to 2 people per day -Consider the number of people working in shared work areas and the use of equipment to maintain social distancing. -Encourage people to share tasks or experiments -Use 1-way traffic circulation.

CALM Guidelines for working in the facility

1. Social Distancing

• Some STPs, especially those impacted by covid testing, may not allow direct user access to equipment or lab space in the short to mid-term. Our operational model is based on the sequential use of equipment by multiple users each day and as a result we are a high-traffic area.
• Our first general approach to COVID-19 safety will be to rely on social distancing by limiting the number of people allowed in small spaces, and the number of people allowed in the facility overall at one time. We will initially rely on reduced staff numbers within the institute to achieve social distancing within the facility, but we will introduce measures to reduce overall bookings if it becomes difficult to maintain this.
• Over half of our systems are in enclosed spaces which are not suitable for occupation by more than one person at a time under social distancing rules. All of our rooms will be posted with a limit for the maximum number of people allowed in the room at steady-state.
• We will manage bookings to ensure that no more than 10 users are present in the facility at one time and that certain additional spatial restrictions are maintained. In addition to spatial distancing we will introduce temporal distancing by enforcing 1 hour gaps between subsequent bookings of the same equipment. To facilitate management of equipment booking, users will have to book equipment at least 72 hours in advance and all bookings will require confirmation by a CALM member of staff. To allow researchers to plan their experiments, we will confirm bookings at least 48 hours before they occur (booking management will be performed by staff working from home).
• Facility access will be restricted to people who have a booking at that time.
• Training protocols previously involved close interaction between two people for over 2 hours per system. For the time being no new training sessions will be offered, we are updating our training protocols to account for social distancing; we aim to start confocal trainings in the second week of July and gradually include other systems. One approach to mitigate the consequences of this will be to encourage experienced lab members to image samples for their untrained fellow lab members. Remote training available from second week of July.
• 1:1 trouble shooting will be performed using strict social distancing, or make use of Zoom, phones, and other remote interactions (again, remote support will be provided by staff working from home).
• We will have a 1-way circulation system in place, and request users not to enter the facility through the write-up area unless accompanied by a member of staff.
• General user-staff discussions (eg experimental planning) will be conducted by zoom or in open common areas under social distancing rules.
• Image analysis will be performed following video consultation, by staff working from home.
• Image analysis workstations should be booked as usual but used remotely. Direct use of these machines will be allowed with specific permission.
• Staff will come to work under a rota system, which maintains social distancing in the write-up space, accordingly to Crick guidelines.
• These guidelines will be under constant review and updated as required.

2. PPE

• Microscope eyepiece use is probably the single greatest risk of transmission among users. We will provide plastic clingfilm to cover the eyepieces (and associated microscope parts located close to the users face when looking down the eyepieces). It will be the responsibility of those users wanting to use clingfilm to apply it when they arrive and and remove it at the end of their session.
• The second risk of viral transmission is through keyboard/computer/microscope use and contamination from the general area. Ordinarily we request that users do not wear gloves when using the microscope or other common equipment because we are concerned that dirty gloves coming into the facility from elsewhere will contaminate keyboards etc for non-glove wearers. We will now give users the option of putting on fresh gloves (provided by us) upon entering the facility (no gloves from outside). Disinfectant and wipes will also be provided for users and staff wanting to wipe-down any aspect of the equipment, including keyboards, monitors,and worktops.
• Different people may have different feelings about the relative level of safety they wish to have at work. We will try to be flexible in allowing people to work how they feel safe.

3. Room Occupation Limits

• HREM: 3 people providing they are working on system 2 meters apart
• LM1: 2 people providing they are working on system 2 meters apart
• LM2: 2 people providing they are working on system 2 meters apart
• LM3: 2 people providing they are working on system 2 meters apart
• LM4: 2 people providing they are working on system 2 meters apart
• BS1: 1 person
• BS2: 1 person
• BS3: 1 person
• Confocal Bays: 1 person per bay
• Workstations: Remote access in the first instance; 2 people per bay providing they are working on system 2 meters apart.
• Total occupancy within the STP will be limited to 10 people at a time. We will, however, consider the manner in which systems are used. For example, LTTL users may only be present in LM2 for the first 45-60 minutes of a much longer booking in order to set up their sample.

Stay healthy,

Dr. Kurt I. Anderson

CALM Head

Crick Advanced Light Microscopy Facility

The Francis Crick Institute

1 Midland Road
London

NW1 1AT

Extracted points from UK Govt guidelines on returning to work in a lab setting https://www.gov.uk/guidance/working-safely-during-coronavirus-covid-19/labs-andresearch-facilities

1.1 Managing Risk

-In every workplace, increasing the frequency of handwashing and surface cleaning.

-Businesses and workplaces should make every reasonable effort to enable working from home as a first option. Where working from home is not possible, workplaces should make every reasonable effort to comply with the social distancing guidelines set out by the government (keeping people 2m apart wherever possible).

3.0 Social Distancing at Work

-It will not always be possible to keep a distance of 2m in labs and R&D facilities that may be designed for close-proximity collaboration. Fixed equipment may mean that changing layouts to create more space may not be practical.

-Where the social distancing guidelines cannot be followed in full in relation to a particular activity, businesses should consider whether that activity needs to continue for the business to operate, and, if so, take all the mitigating actions possible to reduce the risk of transmission between their staff.

-Mitigating actions include:

-Keeping the activity time involved as short as possible

-Using screens or barriers to separate people from eachother

-Using back-to-back or side-to-side working (rather thanface-to-face) whenever possible

-Reducing the number of people each person has contactwith by using “fixed teams or partnering” (so each person works with only a few others)

-Increasing the frequency of hand washing and surface cleaning

3.3 Workplaces and workstations

-Using floor tape or paint to mark areas to help people keep to a 2m distance.

- Managing occupancy levels, to maintain social distancing in labs with restricted space, for example, by adapting booking systems to limit usage.

-Cleaning workstations and shared equipment and machinery, where it is feasible to do so.

5.2 Keeping the Workplace clean

-Frequent cleaning of work areas and equipment between uses, using your usual cleaning products.

-Determining the required cleaning process for expensive equipment that cannot be washed down, designing protection around machines and equipment. -Frequent cleaning of objects and surfaces that are touched regularly, such as door handles and testing surfaces andmaking sure there are adequate safe disposal arrangements.

-Clearing workspaces and removing waste and belongings from the work area at the end of a shift.

6.0 PPE

When managing the risk of COVID-19, additional PPE beyond what you usually wear is not beneficial. This is because COVID-19 is a different type of risk to the risks you normally face in a workplace, and needs to be managed through social distancing, hygiene and fixed teams or partnering, not through the use of PPE.

Workplaces should not encourage the precautionary use of extra PPE to protect against COVID-19 outside clinical settings or when responding to a suspected or confirmed case of COVID-19.

Unless you are in a situation where the risk of COVID-19 transmission is very high, your risk assessment should reflect the fact that the role of PPE in providing additional protection is extremely limited. However, if your risk assessment does show that PPE is required, then you must provide this PPE free of charge to workers who need it. Any PPE provided must fit properly.

Basic Assumptions

The guiding principle of returning to work in CALM is to ensure that staff feel safe by introducing workflows that reduce viral transmission. We assume that COVID prevalence in London is below 0.2% (1 in 500), and that staff will self-isolate if they suspect they are ill. Therefore the risk of transmission among Crick staff is inherently low. However we cannot expect to absolutely prevent the spread of virus among staff, as this would require everyone working under CL3 conditions. Instead we must aim to strike a balance between minimising viral spread while enabling staff to return to work. Government guidelines for returning to work in a laboratory/research setting primarily rely on social distancing and hygiene, and discourage the use of PPE specifically to address COVID-19 risk (https://www.gov.uk/guidance/working-safely-during-coronavirus-covid-19/labs-andresearch-facilities); relevant points from these guidelines have been summarised at the end of this document.

Relevant Crick guidelines to date

Relevant Crick guidelines to date -Maintain social distancing -Crick will have staff testing in place by June 15th -Researchers are free to attend weekends although STP staff are not required to do so -Restrict occupancy of lab or write-up bays to 2 people per day -Consider the number of people working in shared work areas and the use of equipment to maintain social distancing. -Encourage people to share tasks or experiments -Use 1-way traffic circulation.

CALM Guidelines for working in the facility

1. Social Distancing

• Some STPs, especially those impacted by covid testing, may not allow direct user access to equipment or lab space in the short to mid-term. Our operational model is based on the sequential use of equipment by multiple users each day and as a result we are a high-traffic area.
• Our first general approach to COVID-19 safety will be to rely on social distancing by limiting the number of people allowed in small spaces, and the number of people allowed in the facility overall at one time. We will initially rely on reduced staff numbers within the institute to achieve social distancing within the facility, but we will introduce measures to reduce overall bookings if it becomes difficult to maintain this.
• Over half of our systems are in enclosed spaces which are not suitable for occupation by more than one person at a time under social distancing rules. All of our rooms will be posted with a limit for the maximum number of people allowed in the room at steady-state.
• We will manage bookings to ensure that no more than 10 users are present in the facility at one time and that certain additional spatial restrictions are maintained. In addition to spatial distancing we will introduce temporal distancing by enforcing 1 hour gaps between subsequent bookings of the same equipment. To facilitate management of equipment booking, users will have to book equipment at least 72 hours in advance and all bookings will require confirmation by a CALM member of staff. To allow researchers to plan their experiments, we will confirm bookings at least 48 hours before they occur (booking management will be performed by staff working from home).
• Facility access will be restricted to people who have a booking at that time.
• Training protocols previously involved close interaction between two people for over 2 hours per system. For the time being no new training sessions will be offered, we are updating our training protocols to account for social distancing; we aim to start confocal trainings in the second week of July and gradually include other systems. One approach to mitigate the consequences of this will be to encourage experienced lab members to image samples for their untrained fellow lab members.
• 1:1 trouble shooting will be performed using strict social distancing, or make use of Zoom, phones, and other remote interactions (again, remote support will be provided by staff working from home).
• We will have a 1-way circulation system in place, and request users not to enter the facility through the write-up area unless accompanied by a member of staff.
• General user-staff discussions (eg experimental planning) will be conducted by zoom or in open common areas under social distancing rules.
• Image analysis will be performed following video consultation, by staff working from home.
• Image analysis workstations should be booked as usual but used remotely. Direct use of these machines will be allowed with specific permission.
• Staff will come to work under a rota system, which maintains social distancing in the write-up space, accordingly to Crick guidelines.
• These guidelines will be under constant review and updated as required.

2. PPE

• Microscope eyepiece use is probably the single greatest risk of transmission among users. We will provide plastic clingfilm to cover the eyepieces (and associated microscope parts located close to the users face when looking down the eyepieces). It will be the responsibility of those users wanting to use clingfilm to apply it when they arrive and and remove it at the end of their session.
• The second risk of viral transmission is through keyboard/computer/microscope use and contamination from the general area. Ordinarily we request that users do not wear gloves when using the microscope or other common equipment because we are concerned that dirty gloves coming into the facility from elsewhere will contaminate keyboards etc for non-glove wearers. We will now give users the option of putting on fresh gloves (provided by us) upon entering the facility (no gloves from outside). Disinfectant and wipes will also be provided for users and staff wanting to wipe-down any aspect of the equipment, including keyboards, monitors,and worktops.
• Different people may have different feelings about the relative level of safety they wish to have at work. We will try to be flexible in allowing people to work how they feel safe.

3. Room Occupation Limits

• HREM: 3 people providing they are working on system 2 meters apart
• LM1: 2 people providing they are working on system 2 meters apart
• LM2: 2 people providing they are working on system 2 meters apart
• LM3: 2 people providing they are working on system 2 meters apart
• LM4: 2 people providing they are working on system 2 meters apart
• BS1: 1 person
• BS2: 1 person
• BS3: 1 person
• Confocal Bays: 1 person per bay
• Workstations: Remote access in the first instance; 2 people per bay providing they are working on system 2 meters apart.
• Total occupancy within the STP will be limited to 10 people at a time. We will, however, consider the manner in which systems are used. For example, LTTL users may only be present in LM2 for the first 45-60 minutes of a much longer booking in order to set up their sample.

Stay healthy,

Dr. Kurt I. Anderson

CALM Head

Crick Advanced Light Microscopy Facility

The Francis Crick Institute

1 Midland Road
London

NW1 1AT

Extracted points from UK Govt guidelines on returning to work in a lab setting https://www.gov.uk/guidance/working-safely-during-coronavirus-covid-19/labs-andresearch-facilities

1.1 Managing Risk

-In every workplace, increasing the frequency of handwashing and surface cleaning.

-Businesses and workplaces should make every reasonable effort to enable working from home as a first option. Where working from home is not possible, workplaces should make every reasonable effort to comply with the social distancing guidelines set out by the government (keeping people 2m apart wherever possible).

3.0 Social Distancing at Work

-It will not always be possible to keep a distance of 2m in labs and R&D facilities that may be designed for close-proximity collaboration. Fixed equipment may mean that changing layouts to create more space may not be practical.

-Where the social distancing guidelines cannot be followed in full in relation to a particular activity, businesses should consider whether that activity needs to continue for the business to operate, and, if so, take all the mitigating actions possible to reduce the risk of transmission between their staff.

-Mitigating actions include:

-Keeping the activity time involved as short as possible

-Using screens or barriers to separate people from eachother

-Using back-to-back or side-to-side working (rather thanface-to-face) whenever possible

-Reducing the number of people each person has contactwith by using “fixed teams or partnering” (so each person works with only a few others)

-Increasing the frequency of hand washing and surface cleaning

3.3 Workplaces and workstations

-Using floor tape or paint to mark areas to help people keep to a 2m distance.

- Managing occupancy levels, to maintain social distancing in labs with restricted space, for example, by adapting booking systems to limit usage.

-Cleaning workstations and shared equipment and machinery, where it is feasible to do so.

5.2 Keeping the Workplace clean

-Frequent cleaning of work areas and equipment between uses, using your usual cleaning products.

-Determining the required cleaning process for expensive equipment that cannot be washed down, designing protection around machines and equipment. -Frequent cleaning of objects and surfaces that are touched regularly, such as door handles and testing surfaces andmaking sure there are adequate safe disposal arrangements.

-Clearing workspaces and removing waste and belongings from the work area at the end of a shift.

6.0 PPE

When managing the risk of COVID-19, additional PPE beyond what you usually wear is not beneficial. This is because COVID-19 is a different type of risk to the risks you normally face in a workplace, and needs to be managed through social distancing, hygiene and fixed teams or partnering, not through the use of PPE.

Workplaces should not encourage the precautionary use of extra PPE to protect against COVID-19 outside clinical settings or when responding to a suspected or confirmed case of COVID-19.

Unless you are in a situation where the risk of COVID-19 transmission is very high, your risk assessment should reflect the fact that the role of PPE in providing additional protection is extremely limited. However, if your risk assessment does show that PPE is required, then you must provide this PPE free of charge to workers who need it. Any PPE provided must fit properly.

Basic Assumptions

The guiding principle of returning to work in CALM is to ensure that staff feel safe by introducing workflows that reduce viral transmission. We assume that COVID prevalence in London is below 0.2% (1 in 500), and that staff will self-isolate if they suspect they are ill. Therefore the risk of transmission among Crick staff is inherently low. However we cannot expect to absolutely prevent the spread of virus among staff, as this would require everyone working under CL3 conditions. Instead we must aim to strike a balance between minimising viral spread while enabling staff to return to work. Government guidelines for returning to work in a laboratory/research setting primarily rely on social distancing and hygiene, and discourage the use of PPE specifically to address COVID-19 risk (https://www.gov.uk/guidance/working-safely-during-coronavirus-covid-19/labs-andresearch-facilities); relevant points from these guidelines have been summarised at the end of this document.

Relevant Crick guidelines to date

Relevant Crick guidelines to date -Maintain social distancing -Crick will have staff testing in place by June 15th -Researchers are free to attend weekends although STP staff are not required to do so -Restrict occupancy of lab or write-up bays to 2 people per day -Consider the number of people working in shared work areas and the use of equipment to maintain social distancing. -Encourage people to share tasks or experiments -Use 1-way traffic circulation.

CALM Guidelines for working in the facility

1. Social Distancing

• Some STPs, especially those impacted by covid testing, may not allow direct user access to equipment or lab space in the short to mid-term. Our operational model is based on the sequential use of equipment by multiple users each day and as a result we are a high-traffic area.
• Our first general approach to COVID-19 safety will be to rely on social distancing by limiting the number of people allowed in small spaces, and the number of people allowed in the facility overall at one time. We will initially rely on reduced staff numbers within the institute to achieve social distancing within the facility, but we will introduce measures to reduce overall bookings if it becomes difficult to maintain this.
• Over half of our systems are in enclosed spaces which are not suitable for occupation by more than one person at a time under social distancing rules. All of our rooms will be posted with a limit for the maximum number of people allowed in the room at steady-state.
• We will manage bookings to ensure that no more than 10 users are present in the facility at one time and that certain additional spatial restrictions are maintained. In addition to spatial distancing we will introduce temporal distancing by enforcing 1 hour gaps between subsequent bookings of the same equipment. To facilitate management of equipment booking, users will have to book equipment at least 72 hours in advance and all bookings will require confirmation by a CALM member of staff. To allow researchers to plan their experiments, we will confirm bookings at least 48 hours before they occur (booking management will be performed by staff working from home).
• Facility access will be restricted to people who have a booking at that time.
• Training protocols currently involve close interaction between two people for over 2 hours per system. For the time being no new training sessions will be offered, until we can develop new training protocols. One approach to mitigating the consequences of this will be to encourage experienced lab members to image samples for their untrained fellow lab members.
• 1:1 trouble shooting will be performed using strict social distancing, or make use of Zoom, phones, and other remote interactions (again, remote support will be provided by staff working from home).
• We will have a 1-way circulation system in place, and request users not to enter the facility through the write-up area unless accompanied by a member of staff.
• General user-staff discussions (eg experimental planning) will be conducted by zoom or in open common areas under social distancing rules.
• Image analysis will be performed following video consultation, by staff working from home.
• Image analysis workstations should be booked as usual but used remotely. Direct use of these machines will be allowed with specific permission.
• Staff will come to work under a rota system, with no more than 2 people per write-up space in June.
• These guidelines will be under constant review and updated as required.

2. PPE

• Microscope eyepiece use is probably the single greatest risk of transmission among users. We will provide plastic clingfilm to cover the eyepieces (and associated microscope parts located close to the users face when looking down the eyepieces). It will be the responsibility of those users wanting to use clingfilm to apply it when they arrive and and remove it at the end of their session.
• The second risk of viral transmission is through keyboard/computer/microscope use and contamination from the general area. Ordinarily we request that users do not wear gloves when using the microscope or other common equipment because we are concerned that dirty gloves coming into the facility from elsewhere will contaminate keyboards etc for non-glove wearers. We will now give users the option of putting on fresh gloves (provided by us) upon entering the facility. Disinfectant and wipes will also be provided for users and staff wanting to wipe-down any aspect of the equipment. Keyboards, monitors, and worktops will be wiped down daily by staff.
• Different people may have different feelings about the relative level of safety they wish to have at work. We will try to be flexible in allowing people to work how they feel safe.

3. Room Occupation Limits

• HREM: 2 people providing they are working on system 2 meters apart
• LM1: 2 people providing they are working on system 2 meters apart
• LM2: 2 people providing they are working on system 2 meters apart
• LM3: 2 people providing they are working on system 2 meters apart
• LM4: 2 people providing they are working on system 2 meters apart
• BS1: 1 person
• BS2: 1 person
• BS3: 1 person
• Confocal Bays: 1 person per bay
• Workstations: Remote access in the first instance; 2 people per bay providing they are working on system 2 meters apart.
• Total occupancy within the STP will be limited to 10 people at a time. We will, however, consider the manner in which systems are used. For example, LTTL users may only be present in LM2 for the first 45-60 minutes of a much longer booking in order to set up their sample.

Stay healthy,

Dr. Kurt I. Anderson

CALM Head

Crick Advanced Light Microscopy Facility

The Francis Crick Institute

1 Midland Road
London

NW1 1AT

Extracted points from UK Govt guidelines on returning to work in a lab setting https://www.gov.uk/guidance/working-safely-during-coronavirus-covid-19/labs-andresearch-facilities

1.1 Managing Risk

-In every workplace, increasing the frequency of handwashing and surface cleaning.

-Businesses and workplaces should make every reasonable effort to enable working from home as a first option. Where working from home is not possible, workplaces should make every reasonable effort to comply with the social distancing guidelines set out by the government (keeping people 2m apart wherever possible).

3.0 Social Distancing at Work

-It will not always be possible to keep a distance of 2m in labs and R&D facilities that may be designed for close-proximity collaboration. Fixed equipment may mean that changing layouts to create more space may not be practical.

-Where the social distancing guidelines cannot be followed in full in relation to a particular activity, businesses should consider whether that activity needs to continue for the business to operate, and, if so, take all the mitigating actions possible to reduce the risk of transmission between their staff.

-Mitigating actions include:

-Keeping the activity time involved as short as possible

-Using screens or barriers to separate people from eachother

-Using back-to-back or side-to-side working (rather thanface-to-face) whenever possible

-Reducing the number of people each person has contactwith by using “fixed teams or partnering” (so each person works with only a few others)

-Increasing the frequency of hand washing and surface cleaning

3.3 Workplaces and workstations

-Using floor tape or paint to mark areas to help people keep to a 2m distance.

- Managing occupancy levels, to maintain social distancing in labs with restricted space, for example, by adapting booking systems to limit usage.

-Cleaning workstations and shared equipment and machinery, where it is feasible to do so.

5.2 Keeping the Workplace clean

-Frequent cleaning of work areas and equipment between uses, using your usual cleaning products.

-Determining the required cleaning process for expensive equipment that cannot be washed down, designing protection around machines and equipment. -Frequent cleaning of objects and surfaces that are touched regularly, such as door handles and testing surfaces andmaking sure there are adequate safe disposal arrangements.

-Clearing workspaces and removing waste and belongings from the work area at the end of a shift.

6.0 PPE

When managing the risk of COVID-19, additional PPE beyond what you usually wear is not beneficial. This is because COVID-19 is a different type of risk to the risks you normally face in a workplace, and needs to be managed through social distancing, hygiene and fixed teams or partnering, not through the use of PPE.

Workplaces should not encourage the precautionary use of extra PPE to protect against COVID-19 outside clinical settings or when responding to a suspected or confirmed case of COVID-19.

Unless you are in a situation where the risk of COVID-19 transmission is very high, your risk assessment should reflect the fact that the role of PPE in providing additional protection is extremely limited. However, if your risk assessment does show that PPE is required, then you must provide this PPE free of charge to workers who need it. Any PPE provided must fit properly.

Dear users,

for the moment all staff are working from home, and we will update you with further info as the situation changes.

This means you can contact them all via email and Zoom.

Remember you can also use the general contact email calm@crick.ac.uk, which goes to everyone in the team.

Stay healthy,

Dr. Kurt I. Anderson

CALM Head

Crick Advanced Light Microscopy Facility

The Francis Crick Institute

1 Midland Road
London

NW1 1AT

Dear users,

Dear users,