The facility offers a wide range of equipment to assist in visualising the macro to the nano, covering tissues to down to single molecule, in a standardised and validated manner. The facility in addition to providing training and support also works between the CRUK MI facilities’ to deliver novel workflows. Equipment broadly comes under the following areas;

  • High Content Screening
  • Histological imaging and analysis
  • Confocal & super resolution microscopy
  • Irradiation


High Content Screening

Permitting the imaging and analysis of the phenotype of multiple cell populations so to study cellular responses, for applications such as drug discovery and 3D culture (spheroids and organoids).

  • PerkinElmer Opera Phenix, a spinning disk based confocal screening system with a dedicated sCMOS camera per detection channel (4). Magnification from 1.25-x60 (water). Automation allows loading of multi-well plates at room temperature or from an incubator.
  • PerkinElmer Operetta CLS, a fluorescence wide-field based illumination system for screening system multi-well plates
  • Columbus, analysis via a webpage interface to permit complex phenotypic analysis

3D organoid acquired on the Opera Phenix using plastic bottomed 96-well plate with the 20x water objective in confocal mode. The organoid is stained with DAPI in blue and an membrane marker in green.

3D nuclear detection using PerkinElmer Harmony is demonstrated.

Data from Christopher Below and Claus Jorgensen (Systems Oncology).


Digital Pathology and analysis

Automated digitisation of whole histology slides for the visualisation of multiplexed tissue (bright-field and fluorescence) at x400 total magnification.

  • Olympus VS120, brightfield, polarised and fluorescence (5 colour) on standard slides, able to batch up to 150 slides
  • Olympus VS200, brightfield, phase, polarised and fluorescence on standard and mega slides, able to batch up to 200 slides
  • PerkinElmer Vectra 3, multi-spectral imaging system, bright-field and fluorescence, able to batch process up to 150 standard slides
  • Akoyan CODEX, to achieve high dimensionality by visualising up to 50 fluorescent labels on a 22x22mm coverslip
  • HALO server, analysis software to permit single cell phenotypic analysis
  • QuPath, cross-platform, open source software for digital pathology and whole slide image analysis
  • Voloom, serial section reconstruction into a 3D model

Benign Prostatic Hyperplasia - DAPI panCK, RunX1, RunX2.

Using RNAscope, whole slide imaging and HALO detection of localized mRNA in intact cells. Using these technologies a study of the molecular mechanisms of the cell is possible.

Data by Renaud Mevel and Georges Lacaud (Stem Cell Biology).

Confocal and super resolution microscopy

The confocal systems available have been designed to offer multiple imaging modes at a range of magnifications and working distance

  • Zeiss LSM880 Airyscan (LSM880, invert stand), laser scanning confocal and fast super resolution. Fitted with an additional 355nm laser for induction of DNA damage.
  • Leica (SP8 MP CSU, upright stand) confocal, two photon confocal microscope with second harmonic imaging for the visualisation of tissue and 3D cell culture
  • Leica (TCS SP8 inverted stand) confocal and two photon microscope with second harmonic imaging for the visualisation of tissue and 3D cell culture
  • Bitplane Imaris, visualisation and analysis of large data setsf large data sets
  • Fiji, open source software for data processing and analysis
  • CellProfiler, open source software for screening images

Irradiation sources

To permit the irradiation of samples such as 2D ad 3D cell culture, electronically derived irradiators are employed rather than radioisotope irradiators, thus offering a simpler and safer technique. The equipment can be utilised for the study of, for example, tumour microenvironment, radiobiological studies, DNA repair mechanisms and hypoxia research.

  • Xstrahl CIX3, 320kV metal ceramic x-ray tube with a variety of beam conditioning filters

Miscellaneous Equipment

  • The SeaHorse XFe Analyser, fast real time measuring of mitochondrial respiration and glycolysis in a microplate
  • Ultimaker S3, 3D desktop printer for building customised equipment and pre-production manufacture.