UCL Queen Square Institute of Neurology


Digital Pathology

Slide scanning

Digital pathology starts with the digitisation of histological slides to produce whole slide images (WSI). With an appropriate WSI viewer, users can pan and zoom around the entire slide, providing spatial orientation that single field of view snapshot images cannot.

Our slide scanners

We have two slide scanners available for different services:

Hamamatsu NanoZoomer S360

  • Very high-throughput brightfield slide scanner.
  • Capable of rapidly scanning up to 360 slides in a batch.
  • Scanning speed of ~30 s for a 15 mm × 15 mm area at 40×.

Hamamatsu NanoZoomer S60

  • High-throughput brightfield and fluorescence slide scanner.
  • Filters for common fluorophores are available (see list below). Please enquire for specific fluorophores.
  • Capable of scanning up to 60 standard-sized slides (26 mm × 76 mm) or 30 double-sized slides (52 mm × 76 mm) in a batch.
  • Scanning speed of ~60 s (20×) or ~150 s (40×) for a 15 mm × 15 mm area per channel.

Common fluorophores that we can scan:

  • Alexa 405, 488, 514, 568, 594, 647, 680
  • Opal 520, 570, 620, 650, 690
  • Atto 490LS, 514/520, 550/565, 590/594, 633/635/647
  • Others: DAPI, EBFP2, FITC, eGFP, YFP, Rhodamine Red X, mCherry, Texas Red

Price for slide scanning

Whole slide image storage, annotation and viewing

WSI are stored on our server and can be accessed remotely through a web browser (example WSI). Users can be allocated private storage spaces with controlled user access.

Price for storage of WSI

Image analysis

The real value of digital slides can be unlocked with WSI analysis. For example, any desired analysis can be performed on the entire section instead of specific or random field of views, extracting more representative data from the tissue section. The data can be exported into a table format for further data processing. 

Price for image analysis

General workflow for digital pathology and image analysis

General Workflow Digital Imaging