Bio-imaging & Flow Cytometry Facility – University of Leeds

Located within the Biological Sciences Faculty, the bio-imaging and flow cytometry facility at Leeds is a central resource for both internal and external (academic or commercial) users and provide access to state-of-the-art light microscopes, cytometry equipment and analysis software. We offer training, technical assistance and advice on a range of interdisciplinary projects and welcome enquiries from anyone interested in using our facility.

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Imaging Platforms

Keywords - Light Microscopy: Confocal microscopy | Superresolution microscopy | Widefield microscopy | Live cell imaging | PALM | STORM | FCS/FCCS | Structured Illumination Microsocpy | Airyscan | FRET/FRAP

Our facility is home to one widefield and three laser scanning confocal microscopes, as well as dedicated image analysis computers. We have two new additions in the form of our super resolution microscopes. Our microscopes are listed below: 

Zeiss LSM 880 (upright) with Airyscan
Zeiss LSM700 (inverted)
Zeiss LSM 880 (inverted) with Airyscan
DeltaVision widefield deconvolution

In addition, the facility has an InverterScope (LSM Tech) for imaging of vertical samples. 
For further super resolution (beyond the airyscan), we have a home built 3D PALM/STORM system and a home built instant SIM. Our flow cytometry area is home to a Becton-Dickinson analyser and cell sorter:

BD LSRFortessa

For more information on all of our equipment, please visit the Leeds facilities website.


Keywords - Biological: Cell Biology | Neurobiology | Developmental Biology | Immunobiology | Plant Biology | Zebrafish | C.elegans | Drosophila | Microbiology | Bio-materials | Histology/pathology
Keywords - Physical Sciences: Bioengineering and biomaterials | Electron Optics | Plasmonics | Metallurgy / alloy development | Corrosion / oxidation | Functional oxides | Nanomaterials (nanoparticles, 2D nanomaterials, nanowires and nanotubes) | Geology / mineralogy | Planetary sciences | Optical and photonic materials and devices | Magnetics, magnetic materials and spintronics | Polymers and organic electronics | Ionic conductors, fuel cells and batteries

Our microscopes can be used for a range of applications including both fixed and live cell imaging, FRAP and FRET imaging (and also FCS/FCCS in the case of the LSM880). The Zeiss microscopes are equipped with laser lines across the spectral range from 405 to 639 nm. The Deltavision has a mercury lamp and selection of standard filters. All microscopes are equipped as standard with objectives from 10x to 63x magnification, with additional objectives from 2.5x to 100x.
Flow cytometry allows the rapid measurement of fluorescently labelled samples. Common applications include cell cycle, ploidy analysis, proliferation, apoptosis, immunophenotyping, live/dead assays and expression analysis. This technology can also be used to separate out individual cells to either improve transfection efficiencies or create stable cell lines. Both our cytometers are equipped with a range of filters that allow analysis across the entire spectrum.

Sample Preparation

Keywords - Biological: Immunolabelling | Immunofluorescence | Live Cell

The bio-imaging and flow cytometry facility is used by molecular, cell, plant and medical biologists, but we have a growing number of users from a wide range of departments including chemistry, physics, material sciences and engineering. We aim to assist all users with their imaging and analysis needs - with such a broad range of applications required the microscopes and cytometers are geared up for flexibility and training is on an individual basis in order to tailor it towards specific users and research questions.

Our facilities have limited capacity for sample preparation and the majority of sample preparation is carried out in individuals own research laboratories. However, we do have a CO2 incubator for short-term storage of live cell samples and can offer advice on appropriate sample preparation for use with each of our microscopes and for flow cytometry.

For users of the STORM/PALM microscope, we can provide materials, reagents and help with sample preparation.

Data Analysis

Keywords - Software: ImageJ | FIJI | Imaris | Zen | Cell Profiler | BD FACSDiva | FlowJo | Modfit

A number of dedicated offline image analysis workstations are available to process and analyse images obtained on our imaging equipment. Help and guidance on the best analysis approaches, plus the development of analysis protocols are available and arranged through discussion with the facility manager.

Shared Access

The facility is open-access with no precedence given to internal users. However, please contact the facility manager in the first instance to discuss requirements and training. Training is compulsory to use the microscopes and the LSRFortessa cytometer and access to the online booking system requires sign off post-training session. Use of the FACSAria II cell sorter is by the facility manager only, with full consultation with the individual users.

The microscopes and cytometers are charged at an hourly rate for non-assisted sessions. Fully assisted sessions are not charged extra. Use of the image analysis computers is free of charge. 

For a limited time, use of our 3D PALM/STORM and iSIM systems is free of charge whilst they’re still in development.


The facility was established with support from The Wellcome Trust, BBSRC, Yorkshire Cancer Research and the University of Leeds. The build and development of the 3D PALM/STORM microscope was funded by kind donation from Michael Beverley – Alumnus (Economics & Politics 1973) and campaign board member for the University’s Making a World of Difference campaign.

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Point of Contact

Bio-imaging & Flow Cytometry Facility – University of Leeds
Bio-imaging & Flow Cytometry Facility, Faculty of Biological Sciences
Clarendon Way
University of Leeds
Leeds, LS2 9JT, United Kingdom

Dr Sally Boxall (Facility Manager), 0113 34 37270

Staff List

Dr Alistair Curd
Dr Alexa Cleasby