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To drop off – please leave samples at the ORCRB reception and call extension 617057 to let us know they are ready to collect.

To collect – we will email you to let you know they are ready to collect and arrange a date and time.

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.

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.

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

A multiplex panel can consist of up to 6 different antibodies, in addition to DAPI.

You can receive/view your multiplex slides in the following formats:

1. Spectrally mixed whole slide scan -qptiff (Phenochart/QuPath)

2. Spectrally unmixed tiles -tif

3. Spectrally unmixed whole slide scan -tif – (You can view these in HALO)

We will return your slides once they have been processed to the stage you require as above.

Trained users will need to book time slots on Calpendo. Users can then access HALO via remote desktop whilst connected to MSD IT Services VPN. Note that this is different to Oxford University VPN. We will provide the remote desktop IP address, username and password upon booking.

Samples must be provided already fixed, preferably in clearly labelled cassettes.

• Old tissue is often poorer quality than newer tissue. We recommend re-embedding in fresh wax prior to use.
• Tissue is better preserved in the block than on the slide, for example, historically cut slides often give poorer staining. We recommend sectioning close to the staining date.
• Optimal formalin fixation results in better IHC or multiplex staining.
• There should only be one tissue section per slide.
• Place tissue as centrally as possible on the slide.
• If intending to overlay images for analysis, tissue placement and orientation must be as similar as possible across each slide.
• Thick tissue sections give poorer quality staining. 5-micron sections are recommended.

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

We are only able to section FFPE blocks in standard-sized cassettes and scan standard-sized slides.

• 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.

• 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.

• Adipose (fat) rich areas, such as those within breast and pancreas tissue, can show poor staining and are prone to lifting off the slide. TOMO slides are always recommended in these tissues.
• Calcifications, which occur in tissues such as breast and serous tumours, can cause artefactual defects in tissue.
• Tissues rich in endogenous peroxidases such as muscle and liver often show more non-specific staining.