Instrumentation

High Content Screening 

Allowing the imaging and analysis of the phenotype of multiple cell populations so to study cellular responses, for applications such as drug discovery, RNAi, 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  (room RG105)
  • PerkinElmer Operetta CLS, a fluorescence wide-field based illumination system for screening system multi-well plates. (MCRC first floor middle lab)
  • ThermoScientific Cell-Insight, wide field illumination system with automated plate loader (room RG105)

 

Super Resolution Microscopy

The aim of this equipment is to achieve a resolution and clarity suitable for the task of visualising cancer cells at the molecular level.

  • Leica gated Stimulated Emission Depletion Microscopy (gSTED) with additional confocal and multi-photon illumination (room RG106). Under gSTED illumination and image deconvolution a resolution of 30nm can be attained. 

lasers going through an AOTF

The gSTED microscope in operation 

Confocal Microscopy

Imaging volumes of data via laser illumination so to examine the 3D nature and dynamics of cells and tissues.

  • Zeiss Airyscan (LSM880, invert stand), laser scanning confocal and fast super resolution. Fitted with an additional 355nm laser for induction of DNA damage (room RB112). Arrives late March 2017.
  • Leica (SP8 MP CSU, upright stand) confocal, two photon confocal microscope with second harmonic imaging for the visualisation of tissue and 3D cell culture (room RG105)
  • Leica (TCS SP8 inverted stand) confocal and two photon microscope with second harmonic imaging for the visualisation of tissue and 3D cell culture (room RG106)
  • Leica Macro-Confocal (TCS LSI) when imaging a large field of view is required such as primary tissue for translational studies (room RB112)

lasers going through an AOTF

Multiple lasers on an optical bench and controlled via an Acoustic Optical Tunable Filter for illumination to the spinning disk confocal microscope 

Flow Cytometry Sorters

Flexible cell sorters with environmental control that are standardised and calibrated by facility staff on a daily basis. All sorters are housed in class II cabinets and located in the main flow lab, room RG121

  • BD Aria III 6 lasers (355,405,445,488,561,640nm), 2-4 way sorting
  • BD Influx 5 lasers (355,405,488,595,640nm) 2-6 way sorting of cells
  • BD Aria II. 3 lasers (405,488,633nm) 2-4 way sorting

the sorting lab

The flow cytometry laboratory showing the newly installed Class II cabinets for the Aria III and Influx

Flow Cytometry Analysers

Multi-colour flow cytometry assays where the Institute's researchers are trained so that this equipment can be operated around the clock. All equipment, unless stated, is located in room RG112 

  • BD LSR Fortessa with high throughput sampler to process 96- and 384-well micrometer plates, 5 lasers (355,405,488,561,640nm)
  • BD LSRII, 4 lasers 355,405,488,633nm
  • BD Canto, 3 lasers 405,488,640nm with high throughput carousel
  • Amnis ImageStream II (room rb103)
  • Acea Novocyte 405, 488, 640nm (MCRC,1st floor mid.lab)

flow cell of the imagestream

The flow cell of the Amnis ImageStream II where up to 4,000 cells/sec can be imaged and assessed

Widefield Microscopy

Multidimensional imaging with multi-point time lapse, with advanced capabilities such as fluorescence recovery and FRET along with image reconstruction and analysis routines. All widefield instruments are located in the main imaging lab, room RB112

  • API Deltavision Core
  • Low light imaging system with an Andor iXon 888 camera 

Histology Scanning (virtual microscopy)

Automated digitisation of whole histology slides for the visualisation of multiplexed tissue (bright-field and fluorescence) at x400 total magnification. Image analysis and statistical analysis is provided offline via the Definiens (tissue studio and image miner) and the PekinElmer Inform (Vectra) software. All scanners are located in room RB112

  • Leica SCN400, bright-field illumination, able to batch up to 250 slides
  • PerkinElmer Vetra 3 automated multi-spectral imaging system, bright-field and fluorescence, able to batch process up to 150 slides
  • Leica Versa, bright-field and fluorescence illumination, with a range of objective lenses from x4-x63, allows automated oil immersion for high resolution imaging. Able to batch process up to 150 slides

setting up at the histology scanner

Setting up a large data run of histology slides which will then be taken through image analysis for mathematical modeling via Definiens Tissue Studio

3D Printshop

To allow the facility to respond to the changing research requirements of the users often laboratory, equipment is required to be designed and printed. Commonly customised sample holders and clamps are built anything up to a size of 25.2 L x 19.9 W x 15.0 H cm can be printed using PLA plastic filament which withstands being cleaned/autoclaved in a laboratory environment. Flow cytometry sample holders, microscopy stage components have been created in the laboratory (room RB111)

  • Makerbot Replicator. 3D desktop printer for building customised equipment
  • Matter and Form. 3D scanner for rendering real world objects into models for customisation

Radiation sources

  • X-ray source (controlled lab, basement), for x-ray irradiation of cells in a variety of vessels (misc.tubes, well plates, petri). The radiation quality of the output has a half-values layer of approximately 2.3mm Cu.​

Miscellaneous  Equipment 

  • The SeaHorse XFe Analyser (MCRC,1st floor, Marias lab), fast real time measuring of mitochondrial respiration and glycolysis in a microplate.

Software

A variety of image processing and analysis packages are available along with IT infrastructure (1 Linux and 1 windows multi-processor system, eight workstations, 200TB of temporary storage via the Scientific Computing department). All workstations are located in the imaging and flow IT room, rb106

  • FlowJo: viewing and analysis of flow cytometry data
  • Definiens Tissue Studio: image analysis of histological data sets
  • Definiens Image Miner: for drawing together measurement and statsitics from image analysis
  • Amnis IDEAS: analysis for the Amnis Imagestream
  • PerkinElmer Inform: multi-spectral defining and analysis for the PerkinElmer Vectra
  • PerkinElmer Phenochart: ROI definition and viewer for the PerkinElmer Vectra 
  • PerkinElmer Harmony: analysis of high content screening data
  • Columbus: for data storage and analysis of high content screening data
  • Bitplane Imaris: image processing and analysis of multi-dimensional data sets
  • SVI Huygens: image deconvolution software for multi-dimensional data from a variety of sources
  • Matlab: numerical processing and modeling of image analysis data
  • ImageJ/Fiji: open source image processing and analysis environment
  • CellProfiler: batch processor for analysis of images
  • Voloom: serial section alignment tool for 3D histology
  • Blender: for 3D print modelling