In partnership with Cancer Research UK - City of London Centre

Microscopy Facility

The Barts Cancer Institute Microscopy Facility at Queen Mary University of London brings together a range of cutting-edge imaging systems, enabling imaging across scales – from whole tissues to nanoscale structures.

Welcome to the Barts Cancer Institute Microscopy Facility at Queen Mary University of London. Our facility brings together a range of cutting-edge imaging systems, enabling imaging across scales – from whole tissues to nanoscale structures.

We provide expert support at every stage of the imaging workflow, including sample preparation, image acquisition and image analysis. Our capabilities include multiple forms of confocal microscopy, whole-slide imaging and digitisation, live-cell imaging, and brightfield and fluorescence microscopy.

Beyond image acquisition, the facility offers specialist expertise in image analysis, helping researchers generate meaningful, robust and reproducible quantitative data from their experiments.

Contact details

For general enquiries:

Manager: Dr Sam Wallis, s.wallis@qmul.ac.uk

Please contact the Facility Manager for financial requests, quotations, grant applications, new project discussion or any enquiries for external access.

Location

We are located on the ground floor of John Vane Science Centre.

Address

BCI Microscopy Facility
Ground Floor, John Vane Science Centre
Charterhouse Square
London
EC1M 6BQ

Opening Hours

  • Systems can be used 24/7
  • Core hours: 9:00-18:00 Monday – Friday

Microscopy Facility team

Sam Wallis profile picture

Dr Sam Wallis

Microscopy Facility Manager

Image Gallery

Below is a selection of images captured at the Barts Cancer Institute Microscopy Facility.


Getting Started

For all users:

We use iLab as our booking system. Please register for an account if you do not already have one. Training on system use can be requested either through iLab, or by emailing the facility directly.

For external users:

If you require assistance in setting up your iLab account or have further questions, please email the facility manager.

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Acknowledgements

The Microscopy Core Facility is funded by Cancer Research UK.  Please acknowledge the CRUK MICROSCOPY CORE SERVICE GRANT at Barts Cancer Institute (Core Award CTRQQR-2021\100004) in all presentations and publications.

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Prices

For internal users, please visit our iLab page

For external users, please contact the facility manager: s.wallis@qmul.ac.uk

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Services and support

We offer a wide range of support throughout a whole imaging experiment. From guidance and expertise on sample preparation, full training and assisted help on all systems, to development of image analysis methodologies and workflows. Please get in contact with the facility for any imaging-based questions.

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Equipment

Our facility is equipped with a wide range of advanced imaging systems including multiple forms of confocal microscopy, whole-slide imaging and digitisation, live-cell imaging, and brightfield and fluorescence microscopy.

Confocal microscopy

Evident FV4000 - Inverted laser scanning confocal microscope

Inverted laser scanning confocal microscope with 10 dedicated laser lines through to the near-infrared spectrum (405nm, 445nm, 488nm, 514nm, 561nm, 594nm, 647nm, 685nm, 730nm, 785nm) and 6 SilVIR photon-counting detectors for simultaneous multiplex acquisition. Objectives: 2x/0.08, 10x/0.45, 20x/0.8, 25x/0.85 (sil), 30x/1.05 (sil), 40x/1.4 (oil), 60x/1.3 (sil) 60x/1.5 (oil)

Suitable for:

  • Super-resolution fixed sample imaging
  • Multiplex immunofluoresence
  • Large 3D volumetric imaging of organoids
  • Multi-position tile-scans of tissue sections
  • Live cell imaging with full CO2, O2 and temperature control. Resonant scanner enables 200 frames per second imaging

Zeiss LSM880 with Airyscan Fast - Inverted laser scanning confocal microscope

Inverted laser scanning confocal microscope with 6 lasers (405nm, 457nm, 488nm, 514nm, 561nm, 633nm) two PMT detectors, a 32 channel GaAsP spectral detector and Airyscan Fast detector for super-resolution imaging. Objectives: 10x/0.45, 20x/0.80, 40x/0.55, 40x/1.30 (oil), 63x/1.40 (oil), 40x/1.20 (water)

Suitable for:

  • Super-resolution fixed and live sample imaging
  • Large tile-scans of tissue sections
  • Live cell imaging with full CO2 and temperature control. Airyscan Fast can be used to image at 30 fps

Nikon Spinning Disk Confocal – Inverted spinning disk confocal

Inverted spinning disk confocal (Yokogawa CSU-X1) with 4 laser lines (405nm, 488nm, 561nm, 640nm) and an Andor Zyla 4.2 Plus camera. A Piezo z-drive provides rapid 3D imaging capability. Objectives: 10x/0.45, 20x/0.45, 20x/0.8, 40x/1.3 (oil), 60x/1.42 (oil), 100x/1.45 (oil)

Suitable for:

  • Rapid acquisition of multiple positions in 3D
  • Large tile-scans of tissue sections
  • Gentle live cell imaging with full CO2 and temperature control

 

Slide scanners

Zeiss Axioscan 7 – Multi-purpose slide scanner

Multi-purpose slide scanner with brightfield, fluorescence and polarised light imaging options. Multiplex fluorescence imaging can be used for 405nm, 488nm, 568nm, 647nm and 750nm simultaneously. Capable of running up to 100 slides at a time with different settings and modalities if required. Objectives: 5x/0.16, 10x/0.45, 20x/0.8, 20x/0.5 (polarised), 40x/0.95

Suitable for:

  • Multiplex immunofluorescene of tissues and cells
  • Polarised light imaging
  • Fast whole slide imaging and digitisation

Hamamatsu Nanozoomer S60 – User friendly multi-purpose slide scanner

User friendly multi-purpose slide scanner with brightfield and fluorescence imaging options. Fluorescence imaging can be used for 405nm, 445nm, 488nm, 568nm, 594nm, 647nm. Capable of running up to 60 slides at a time. Objectives: 20x/0.8, 40x/0.95

Suitable for:

  • Multiplex immunofluorescene of tissues
  • Whole slide imaging and digitisation

Hamamatsu Nanozoomer S210 – User friendly brightfield slide scanner

User friendly brightfield slide scanner. Capable of running up to 210 slides at a time. Objectives: 20x/0.8, 40x/0.95

Suitable for:

  • Fast whole slide imaging and digitisation

3D Histech Pannoramic 250HT – User friendly brightfield slide scanner.

User friendly brightfield slide scanner. Capable of running up to 250 slides at a time. Objective: 20x/0.8

Suitable for:

  • Fast whole slide imaging and digitisation

Live cell imaging

Sartorius Incucytes

We have 3 Incucytes (both S3 and SX5) available for long-term, high-content live cell imaging experiments. Cells are maintained in a regular incubator and do not move during imaging to minimise impact on cell viability. Capable of both label-free and multicolour fluorescence (488nm, 546nm and 647nm). Objectives: 4x/0.13, 10x/0.3, 20x/0.45

Modules include:

  • All standard confluency programmes
  • Cell by cell analysis
  • Spheroid
  • Organoid
  • Scratch Wound
  • Chemotaxis

DeltaVision Elite

We have 3 DeltaVision Elite widefield fluorescence systems with environmental controls for live cell imaging. Fluorescence imaging is available for 405nm, 445nm, 488nm, 514nm, 546nm, 647nm. High-sensitivity EMCCD cameras enable imaging of low expression fluorescent proteins and deconvolution improves resolution. Objectives: 20x/0.85 (oil), 40x/1.30 (oil), 60x/1.42 (oil), 100x/1.40 (oil)

Suitable for:

  • Gentle live cell imaging in multiple positions
  • Fast acquisition of z-stacks

Other systems and software

Additional Systems

Zeiss PALM Laser Capture Microdissection – LCM system to extract specific regions within fixed tissue samples. Using a UV laser and light-pulsed catapulting, user defined regions of tissues on slides can collected to perform downstream processing such as sequencing, transcriptomics and proteomics.

We also have a number of standard upright and inverted microscopes for both fluorescence and brightfield imaging to check slides.

Analysis software

Oxford Instruments IMARIS – 3D reconstruction and analysis

SVI Huygens – Deconvolution and image restoration

Indica Labs HALO AI – Complete histology analysis suite with advanced AI segmentation

Zeiss Zen Blue and Nikon Imaging Suite – Stand-alone versions of acquisition software

Open Access Tools – FIJI, CellProfiler, Napari, Cellpose, ilastik, ICY, QuPath


Training

Training on system use can be requested either through iLab, or by emailing the facility directly.

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Publications

  • The RNA-binding protein RSRC2 promotes mitotic fidelity by interacting with the lncRNA C1QTNF1-AS1. bioRxiv 2025.01.21.634161;  doi: 10.1101/2025.01.21.634161
  • Centrosome amplification fine tunes tubulin acetylation to differentially control intracellular organization. EMBO J. 2023 Aug 15;42(16):e112812.
    PMID: 37403793.
  • The ESCRT machinery counteracts Nesprin-2G-mediated mechanical forces during nuclear envelope repair. Dev Cell. 2021 Dec 6;56(23):3192-3202.e8.
    PMID: 34818527

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