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Read our frequently asked questions here, along with tips on how to make the most out of our services

How will I receive my scanned slide files?

Slide Scanning, Automated Tissue Segmentation and Scoring

Dependent on your preference, and the size or number of files, we can transfer your files via:

  • OxFile: You will receive an email with a link to download your scan files.
  • A hard-drive: We will let you know how much space is required and you can provide a hard-drive onto which we will transfer your scan files.
  • HALO: If you are analysing your images in HALO we can transfer them in directly.

In what format will I receive scanned slide files?

Slide Scanning, Automated Tissue Segmentation and Scoring

The whole slide scans are saved as qptiff files which can be opened and viewed in Phenochart or QuPath, which can both be downloaded for free. Please note that Phenochart cannot be downloaded onto Mac computers.

How long will we store your files?

Multi-plex Immunofluorescence (IF) Imaging Slide Scanning, Automated Tissue Segmentation and Scoring

Due to the nature of the file sizes, we can only store data until the end of each project.

What factors affect the quality and consistency of brightfield images?

Single and Double Antibody Tissue Staining (Chromogenic IHC) Slide Scanning, Automated Tissue Segmentation and Scoring

  • Staining is dependent on antibody quality and epitope expression levels.
  • Endogenous pigment can interfere with analysis in bright field imaging (melanin, carbon, tattoo, haemosiderin). We recommend choosing an appropriate coloured chromogen.
  • Targets where there is a validated clinical grade antibody will show better results.
  • Cell localised targets, rather than connective tissue or stroma localised tissue, will often give better analysis results.

What factors affect the quality and consistency of multiplexed images?

Multi-plex Immunofluorescence (IF) Imaging Slide Scanning, Automated Tissue Segmentation and Scoring

  • Large tissue sections and TMAs show more variation than smaller sections. Sections no larger than 2cmx2cm are recommended.
  • We recommend the use of TOMO slides which preserve tissue substantially better than conventional coated slides.
  • Epitopes that share the same sub-cellular localisation (e.g.in the same receptor complex) may be prone to steric hindrance. Careful selection of panels is therefore recommended.

Please see the FAQ ‘What factors affect the quality and consistency of brightfield images?’ for further considerations.