We use cookies to track usage and preferences.
Here’s what’s new in the CALM STP:
Hey Ho, Lets Go!
We have added 2 new spinning disk confocals since last year, bringing the total in the facility to 3. Unlike our old system, both new systems are equipped for super-resolution. One system is based on an Olympus stand and runs CellSense whereas the other system is based on a Nikon stand and runs Elements. Spinning disk microscopy (as I'm sure you all know) is generally more gentle for live imaging than point-scanning microscopy. It also offers better sample penetration although not quite as good as lightsheet microscopy. To make space for both the new systems in room LM4, the old system has been moved down the hall into room SW3-2695.
We have added a new slide-scanner (an Olympus VS-200) and have begun to offer slide-scanning as a service. The system does conventional H&E and fluorescence, meaning it can also be used for basic immuno-fluorescence imaging. Data from the slide-scanner can be automatically imported into the Crick's OMERO database, which has a viewer with useful tools for pathology.
We had a few comments in the recent STP survey about delays in getting trained, so here's some info on how the process works. Last year we introduced a new approach to manage training. Requests, made via email, PPMS, or in person generate a Trello card on our Training board. Our team meets Mondays after lunch to triage the requests and assign them to the right member of staff. The initial request will often require further discussion with the trainee to decide which instrument is best. We strongly prefer to train people with their real samples so they can start using the microscope right away. This avoids people getting trained, then waiting so long for their samples to be ready that they need re-training. Waiting for the availability of a real sample is often the step which takes longest in the training process. Last year we ran 412 training sessions, which involves much more staff time than just the 1:1 session on the microscope. Because of the numbers involved, the final barrier to getting trained is often staff availability.
Registration is open for the next Crick BioImage Analysis Symposium (CBIAS):
https://www.crick.ac.uk/whats-on/crick-bioimage-analysis-symposium-2023
which will be held November 20-21. The symposium will bring together life scientists and leading developers of bioimage analysis methods to illustrate how such approaches can answer defined biological questions. Last year's event sold out, so register early if you want to guarantee your place.
Confocal microscope quality control: Harrison has left the confocal QC role to do an MSc in Medical Physics (sad for us, good for him). We have hired Lotanna Amazu to take over from Harrison. Lotanna will start in October, and should be trained up to resume testing confocal microscopes in November. Please bear with us during this interim period if some microscopes are a little messier than usual.
Congratulations to Cami, who is off on maternity leave until June 2024. Cami covers quite a few duties, including spatial transcriptomics, lightsheet, HREM, slide-scanning, and confocal microscopy, all of which have been shared out among the team for the time being. We hope to recruit maternity cover soon.
In the mean time, you may notice a new face sitting in Cami's spot. Vanessa Dao is a 2nd year MPhys sandwich student joining us from Bath University. Vanessa is working with Dave Barry on image processing pipelines for large, multi-dimensional data sets, especially using HPC tools. Ask Vanessa about astrophysics!
Equipment and Fees: After many requests, we have added a new CALM webpage
<https://www.crick.ac.uk/research/platforms-and-facilities/light-microscopy/equipment-and-fees>
listing our equipment fees.
Project work: We have recently begun offering more in-depth staff support for imaging and (especially) analysis projects. This has allowed us to bring down the hourly rates for general general microscope use. This approach is kind of an experiment for the STP, and we welcome your feedback.
Looking ahead... we will organise another round of light microscopy lectures beginning January 19th of 2024. The weekly series of talks will cover a wide range of topics, including: Introduction to Optics and Flourescence, Optical sectioning, Confocal and MP microscopy, How to design and implement an immunofluorescence experiment (together with Histopathology STP), Super-resolution microscopy, Lightsheet microscopy and friends, Image Analysis, and (LBNL) Data Management. These talks are a great opportunity to get into the details of light microscopy, especially for new students.
kurt
.
Dr. Kurt I. Anderson
CALM Head - Crick Advanced Light Microscopy Facility
The Francis Crick Institute
1 Midland Road
London
NW1 1AT
Here’s what’s new in the CALM STP:
COVID-19: CALM staff are primarily working in the building now, with some continued, selective, working from home. Some things, like remote training, are likely to continue as the new normal because we’ve found they work better. Social distancing rules are no longer in operation in the facility, in line with recent rule relaxations at the Crick.
BIG CHANGES: We have a number of new systems arriving and old systems retiring before the end of the year. Retiring systems include the Zeiss Invert 710 (CB2) and the Leica MPSP5 Upright (BS3). They will be replaced by an inverted Olympus CSU-W1 SoRa (super-resolution) spinning disk and an upright LSM 980 MP confocal microscope. The new 980 will simply occupy the place of the SP5 in BS3, but the SoRa system is too big to fit in CB2. So we have to play musical microscopes (like musical chairs, but with laser safety issues) by relocating our existing Nikon CSU-W1 spinning disk from LM4 into CB2 so the SoRa system can be installed in LM4. When the SoRa arrives, we intend to run that system at 37°C for live cell imaging and keep the existing Nikon spinning disk at room temperature for fish and flies. If that’s not enough to confuse the hell out of you, our Olympus IX83 system in LM1 will be incorporated into the new spinning disk in CB2 (because we had to save money to make the budget fit). There’s a lot going on here, so please talk to us if you have any concerns or questions.
Organoids and Spheroids: We are exploring options for 3D imaging of thicker samples like organoids, spheroids, and maybe early mouse embryos. Alessandro has had great results on the MuVi (lightsheet) with such samples, but throughput is low. This seems to be a bottle-neck for some experiments, so we are exploring options to address the issue. One possibility is to build an Oblique Plane Microscope (OPM) together with Chris Dunsby’s group. A big advantage of this approach would be the use of glass-bottom 96-well plates. Alternatives are the Luxendo TruLive3D and Viventis LS1 lightsheet systems. These can probably image slightly thicker samples, but rely on the use of specially fabricated chambers which can only image 4 - 6 samples at a time. We also had a quick look at the Zeiss Lattice Lighsheet 7, which can do multi-well plates but seems optimised for cells in culture. We are lining up demos in October and November, please see Camille if you would like more information.
Microscopy Training: The next round of microscopy training seminars will begin on Wednesday, October 13th, and run weekly through December 1st. This year we’re excited to add a new joint seminar with Mary Green from Experimental Histopathology on designing and imaging immunofluroescence experiments. Mary will discuss how to stain and Cami will discuss how to image your samples. All lectures are hybrid events, with coffee and pastries for people who show up in person. More information is available on the intranet for Crick internal users, and external users can find out more by emailing calm@crick.ac.uk.
Image Analysis Symposia: We have an embarrassment of riches with two image analysis symposia on the horizon: On November 8th and 9th we’ll host the AI-Powered Drug Discovery Symposium which is co-sponsored by the Society for Laboratory Automation and Screening (SLAS). Then we have the 2nd annual Crick BioImage Analysis Symposium (CBIAS), organised by Dave, Martin, and Todd, on November 22nd and 23rd. Registration is live now for both events.
Optical Tweezers: We recently installed a Lumics C-trap G2 optical tweezers in LB4-1485 (aka Imaging Room 3). Its a dual-trap system with a laser-scanning confocal microscope for imaging sample fluorescence. The system was validated by Ondrej Belan from the Boulton Lab, who performed DNA stretching experiments which yielded the expected force distance curves associated with helix melting. We will be scheduling some training sessions on October and/or November. Contact Kurt for details.
OMERO: Our OMERO server is now managing about 10 TB of data. Labs are using it for routine storage and to facilitate access to large data sets for external collaborators. A lot of people are finding it useful for histology data (we have a package for this called PathViewer). Please see Ken for more information, or to arrange an introduction for you or your lab.
Confocal Quality Control: Alex Palmer has left to pursue an MSc in Nuclear Imaging at Imperial College (Go Alex!). Until we are able to fill her position, confocal QC will be shared among the team. Please bear with us if everything is not quite as ship-shape as when Alex was in charge. Unfortunately we had a dismal response when we advertised her job in July. But we have tweaked the text to try again in October.
Brainsaw: The Brainsaw (photo below) is up and running! The system can image whole mouse organs (not just brains…) at cellular resolution. Dan has now trained a couple of people to use the system independently. It kicks out terabytes of data and we are working with Ken to automate the flow of reconstructed volumes into OMERO. We are lining up Adam Tyson and Rob Campbell from SWC to speak at the Advanced Imaging and Analysis Forum this fall. See Dan for more details about this system.
Dr. Kurt I. Anderson
CALM Head - Crick Advanced Light Microscopy Facility
The Francis Crick Institute
1 Midland Road
London
NW1 1AT
Here’s an update on what’s going on in the Light Microscopy STP:
CALM User’s Secret Symposium (CUSS): 3D Imaging Across Scales
The CALM User’s Symposium will be held online from 2:00 to 5:00 on June 7th and 8th, with the theme of 3D Imaging Across Scales. There will be an open forum for discussion about future directions for the STP at 4:00 on Tuesday, followed by an actual beer session in the Cafe starting at 5:00. The full program is available on CrickNet and registration is available here. Please contact Ale, Dan, or Rocco for more details.
Light Sheet imaging of Mouse Development
Congratulations to Clara Collart from the Smith lab and our very own Alessandro Ciccarelli for publishing a technically demanding study of vascular development in mouse. Clara and Ale adapted our Luxendo MuVi for extended time-lapse imaging to track the migratory pathways of cells during development of E8 - 9.5 embryos. Contact Ale for more details if you are interested in light sheet microscopy.
Brainsaw
Dan Gunton has started assembling our block-face serial-sectioning two-photon microscope (the Brainsaw, photo below). The system can acquire high-resolution fluorescence volume data of large tissue samples such as whole mouse brains and organs (tumours, lymph nodes, etc). The Brainsaw should be ready for testing next month, and we will start recruiting test samples soon. Please contact Dan if you are interested.
OMERO
Our OMERO server is available for general use. Ken Ho, our Big Image Data guru, has been working on streamlining OMERO workflows to import, organise, analyse, and share image data. We have started a number of projects using OMERO, including one with Experimental Histopathology to share images for 500 antibodies in their database across a range of tissue types. We have also started introducing individual labs to OMERO, and Ken will offer a general introductory seminar to image data management as part of the biannual CALM training seminars. Please contact Ken if you would like any further info, including access to OMERO.
Confocal Microscope Quality Control
Would you like help looking after your confocal microscope? Alex Palmer cleans and performs monthly quality control tests on confocal microscopes around the building, for both CALM and non-CALM systems. Alex can also arrange service visits from company engineers, and in some cases help to provide training. Contact (you guessed it) Alex for more information.
SlideSeq
We are working with Sam Rodriques, ASF, BABS, and the Making Lab to set up SlideSeq, and approach developed by Sam for spatial transcriptomics. This will be an in-house, cross-STP service similar to what is offered by 10x Genomics but with better spatial resolution and much lower cost. Contact Sam for more details.
Cell Profiler
Todd Fallesen is developing a training workshop for Cell Profiler, along the lines of Dave Barry’s popular Fiji training course. More details to follow soon… please contact Todd if you are interested.
FLIM
Fluorescence lifetime imaging is a powerful approach to analysing FRET, which can tease apart the relative amounts of FRETing and non-FRETing species. We have two systems for FLIM in the facility: the Leica TCS-SP8 FALCON, a confocal microscope which uses time-correlated single-photon counting to measure lifetime, and our new Lambert Instruments Toggle, which uses the frequency domain approach. The systems offer different spatial and temporal resolution, and suitability for live-cell or fixed imaging applications. Contact Rocco or Matt if you are FRETing about FRET.
Ongoing SPD demos…
There are currently two spinning disk demos running in the building through the end of next week. There is an Andor Dragonfly system set up in the facility and a Nikon Yokogawa SoRa system set up in SW5. Please contact Kurt or Matt if you would like to have a look at either of these systems next week.
Dr. Kurt I. Anderson
CALM Head - Crick Advanced Light Microscopy Facility
The Francis Crick Institute
1 Midland Road
London
NW1 1AT
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:
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.
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
Website
Our website is quite up to date with the latest information about our equipment and services (thanks Rocco). Start with the Overview page for a list of upcoming events and the News page to find the latest version of this newsletter. (Note that we only use the intranet site to point to the external site, where all the info sits.)
Imaging Thick Specimens
We have a mind-bending array of methods for imaging thicker samples. Our conventional point-scanning confocals from Zeiss, Leica, Olympus, and Nikon will get you about 20 µm into a fixed or living sample depending on the type of tissue. Our Yokogawa spinning disk confocal will get you a bit further (maybe 75 µm, popular with fly folk) and our multi-photon systems from Olympus, Zeiss, and Leica will potentially get you up to a few hundred µm into a fixed or living sample (especially useful for imaging living mice). Our Zeiss Apotome (structured illumination) also works around this depth (50 - 100 µm) but is possibly a bit more gentle for live imaging of tissue slices (and cheaper). Our two light-sheet systems are optimised for thinner (eg: live zebrafish embryos) and thicker (eg: adult mouse organs) samples. We are also expecting the arrival of a new OPT system, built by Sunil Kumar in Paul French’s lab, which is suitable for cleared specimens up to 1 cm in diameter. Bear in mind that thicker samples, especially mouse organs, will require clearing, which will extend the imaging depth for all of the systems mentioned above. Finally there is our world-famous HREM system, which does not require clearing (or even fluorescence) and can be used to image cm thick specimens such as adult mouse organs and various sized embryos.
Light Sheet Photo-manipulation
Ale has been working with the Hill lab to develop the use of a newly installed 980 nm pulsed laser on our Luxendo MuVi for photo-conversion of Kikume Green in live zebrafish embryos. Thus far he has been able to convert groups of around 10 - 20 cells from green to red and follow their migration overnight in a developing embryo. Its freaking gorgeous.
Calcium Imaging
Matt has put together an inverted microscope for Calcium imaging using dyes such as Fura-2. Drop by and ask him about it!
New System Arrival in March
We are eagerly awaiting delivery on a Lambert Instruments Toggle camera for frequency domain fluorescence lifetime imaging. This will extend our capabilities for live-cell imaging of FRET biosensors, and complement use of the Leica FALCON SP8, which uses a different approach (time-correlated single-photon counting) to measure fluorescence lifetime (see Matt or Kurt for details).
Confocal Microscope Quality Control
Alex Palmer started with us in December to work on confocal microscope quality control in the STP and for all instruments across the Crick. Confocal QC has been an important topic within the imaging community for many years, and is now being taken seriously by confocal manufacturers. Alex has started out using Trevor’s old QC protocol, but will work with Dan on developing a new protocol to take advantage of recent developments in test samples and metrology. Long-term we have initiated partnerships with Zeiss and with the Royal Microscopical Society to work on standardised protocols for use across the community.
Super-Resolution
We’ve just wrapped up a week-long workshop on STORM microscopy using our Bruker Vutara microscope. We heard from great speakers, including Susan Cox, Hylkje Geertsema, Janosch Heller, and Ricardo Henriques (inventor of pumpy mcpumpface and SRRF, and a visiting group leader at the Crick). Among Crick scientists there seems to be particular interest in using STORM to visualised the 3D structure of chromosomes.
Image Analysis Helpdesk
There is an image analysis help desk every 2nd and 4th Wednesday of the month in the Cafe, where EM and LM staff are available to discuss any aspect of image acquisition and analysis. Whether you have a major problem or just want to chat, please drop by.
Image Analysis Training
Dave and Co. run a monthly introductory workshop on image analysis using Fiji, as well as advanced courses on topics including Tracking, Segmentation, and Colocalization. You can register through your MyLearning tab on People Zone (Core HR)
Optics for Biologists Workshop
We recently advertised a new practical workshop on geometric optics called “Optics for Biologists” and were overwhelmed by the response. Since then we have run the course 3 times and will keep at it monthly until we work through the backlog of interested people. Contact Kurt for more details.
STP Reviews
Following the “Omics” STPs went well last year and there will be two more groups of STP reviews between now and the middle of this year. The next group (BRF, Histo, Cell Services, Fermentation and Flow) has been confirmed for the 2nd and 3rd of April 2020. Light microscopy will be part of the final review expected in May/June.
And Finally…
A popular 80’s imaging technique (Astley et al., 1987) has been making a comeback.
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.
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.
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.
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,
as you may have noticed, most of our equipment remains available for booking.
However, in line with government advice, we are implementing a rota in order to reduce the number of staff in the STP at any one time.
Barring holiday and sick leave, people who are not in the lab are working from home; this means you can contact them all via email and Zoom.
The scheme below will help you plan your work around staff presence:
Mon: Alexandra, Matt, Kurt, Alessandro
Tue: Camille, Dan, Kurt, Fabrice
Wed: Alexandra, Rocco, Kurt, Todd
Thu: Camille, Matt, Fabrice
Fri: Dan, Rocco, Alessandro
this is not really an ideal time to be trained on a new piece of equipment. However, in case of urgent need training will be coordinated around the rota.
Remember you can also use the general contact email calm@crick.ac.uk, which goes to everyone in the team.
Stay healthy,
Dear users,
Join our mailing lists to receive updates about our latest research and to hear about our free public events and exhibitions. If you would like to find out more about how we manage your personal information please see our privacy policy.
