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Confocal microscopy and live cell imaging facilities

Confocal microscopy and live cell imaging is available at both the Chelsea and Sutton sites and provides researchers with confocal microscopy, high content imaging and time-lapse microscopy. All the microscopes have temperature control, CO2 control and motorised stages, and can perform multi-position time-lapse experiments.

Chelsea facility

Equipment available:

Three wide field microscopes for wide field imaging of samples and for long time lapse experiments of live cells:

  • Marianna’s wide field microscope: This is the newest system.
  • Nikon eclipse Ti: Capable of hypoxia incubation.
  • Nikon TE 2000.

Three confocal microscopes for different confocal imaging and for time lapse experiments of live cells:

  • Basic spinning disk confocal microscope.
  • Advanced spinning disk confocal microscope: For advanced live cell microscopy and photo manipulation.
  • Zeiss 710 point scanning confocal microscope

Three plate based high through put microscopes:

  • Celigo S: Wide field system that can scan plates very fast.
  • Operetta: High content spinning disc microscope.
  • ImageXpress: High content spinning disc microscope.

Two light sheet microscopes:

  • Lattice light sheet microscope: The lattice light sheet utilises extremely thin lattices (0.5 μm) made from Bessel beams to illuminate the sample. The thin sheet makes it possible to sub-section through a cell but still collecting all the light. The main benefits are extremely low photo toxicity and extremely fast imaging. The system does support one super resolution method, structured illumination microscopy (SIM).
  • DiSPIM (dual inverted single plain illumination microscopy): The DiSPIM uses a Gaussian light sheet. Because it is possible to image from two sides this microscope can provide images with iso-tropic resolution. It is very useful for larger structures such as organoids as well as for single cells.

One total internal reflection fluorescence (TIRF) microscope which is also capable of super resolution imaging (STORM and PALM):

  • Total internal reflection fluorescence (TIRF).


Software available:

The microscopy facility in Chelsea has licenses for a number of image analysis packages, along with experience in using many different programs.

Commercial software:

  • SlideBook: Image acquisition and analysis software from 3i.
  • Arivis: A single license (owned by 3i) is available in the facility for this software. Particularly useful for rendering of very large images (e.g. lightsheet).
  • MetaXpress: Operates the ImageXpress system, and can also be used for image analysis. 
  • Harmony: Similar to MetaXpress, Harmony is the software used to run the Operetta system, and can be used for analysis.
  • Columbus: Separate analysis software from Perkin Elmer to analysis data from the Operetta, which can also be used for data from other systems. This belongs to Chris Bakals group but can be used by the users of the facility.
  • Celigo: Operates the Celigo plate-based imager and can be used to analyse the data.
  • Zen2009: Used to operate the Zeiss 710 point-scanning confocal.
  • Volocity: Flexible image analysis software for visualisation and analysis of data from any system.

Open-source software:

  • FIJI (ImageJ): Perhaps the most popular image analysis software, with hundreds of plugins to carry out nearly every kind of image analysis. Fairly easy to use (with no prior experience needed), but requires some trial and error.
  • Cell Profiler and Cell Profiler Analyst: Complementary to FIJI in that Cell Profiler allows automatic analysis of thousands or even millions of images, particularly from high-content, plate-based systems. Cell profiler analyst is designed to work with data processed with Cell Profiler and can be used for automatic, machine-learning based image classification.
  • Vaa3D: Less flexible than FIJI, and lower throughput than Cell Profiler, but designed for 3D (and above) datasets. Particularly useful for visualisation of 3D images and for tracing of projections, but a number of other plugins are available.
  • Ilastik: Has a number of features, but the unique feature is pixel-based classification. This is a machine learning approach which is useful when features of interest cannot be detected using intensity alone (such as brightfield images).

Other resources:

  • Custom scripting (e.g. MATLAB): For any image analysis that is not well catered to by existing software packages, custom programs can be written to perform image processing, image analysis and statistical analysis.
  • High performance computing (HPC): For any analysis that is impractical to run on desktop PCs such as huge screening experiments, or light sheet imaging with large individual file sizes, HPC can be used to greatly speed up parallelisable computational problems.
  • ICR research data storage (RDS): Data storage in the facility is temporary and so scientific computing provides high capacity storage when the needs of a lab outgrow local solutions (e.g. external hard drives).


Sutton facility

Equipment available:

  • Zeiss LSM700: Point scanning confocal microscope
  • Zeiss/Metasystems: Automated fluorescence and brightfield scanning system
  • Zeiss Axio Scan.Z1: Automated brightfield and fluorescence slide scanner with 100 slide capacity.
  • Nikon TE-2000-s: Time Lapse microscope.
  • Zeiss Axioskop 2: Upright light microscope with image capture capability.
  • Dedicated image analysis computer

Software available:

  • Zen 2009 software: For Zeiss LSM700 machine control and image analysis.
  • Metacyte: Finds and identifies nuclei or cells based on morphologic criteria, automatically stores position data, acquires fluorescence signals within objects from different focal planes and in up to 6 colour channels.
  • In Situ Imaging System software: For manual capture, processing, archiving and analysis of single plane or Z-stacked fluorescence images.
  • Tissue FISH module: For automated analysis of cell signal in tissue sections. Includes optional pre-marking of regions of interest and dedicated tools for interactive and automated separation of cells.
  • V-slide software and VSViewer: Digitises slides in brightfield and/or fluorescence. VMD – Virtua
  • Microscope Database: Server software module for database management of virtual slide images created by the Metafer-Vslide.
  • Zen 2.3: For editing and viewing virtual slides from the Zeiss Axio Scan Z1 slide scanner.
  • Definiens Tissue Studio software: Advanced image analysis software for brightfield and immunofluorescent images of tissue and cells.
  • PathXL software: A comprehensive image and data management platform for digital slide management, analysis, sharing and archiving requirements.
  • Axiovision software version 4.1: Image capture software.
  • Image J: Open source imaging software.
  • Duolink Image Tool: Image analysis software to quantify Duolink (proximity ligation assay) signals and cell nuclei.
  • HCIimage live: Operates the Nikon time lapse microscope.


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