Images produced by the light microscopy team at The Crick.

Light Microscopy : Latest news

News and updates about Crick Advanced Light Microscopy STP

Work in CALM STP (2 February 2021)

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

Work in CALM STP (3 September 2020 UPDATES)

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, which goes to everyone in the team.

Stay healthy,


Dr. Kurt I. Anderson


Crick Advanced Light Microscopy Facility

The Francis Crick Institute

1 Midland Road


Full start-up guidelines - 10 August 2020 and UPDATES

Previous Virus updates

Previous CALM updates:

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