Digital Pathology and analysis

Since 2008 the institute has been at the cutting edge of whole slide histology and works extremely closely with the Histology Facility. 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
  • Akoya 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 (10 licenses)
  • HALO AI for advanced segmentation and classification
  • QuPath, cross-platform, open source software for digital pathology and whole slide image analysis
  • Voloom, serial section reconstruction into a 3D model


CODEX image demonstrating part of a 12-component panel

pancK (red) Ki67 (green), CD3e (blue), CD20 (purple), CD8 (yellow), CD107a (teal)