FAQ
Frequently Asked Questions
Scanning options, slide preparation, ethics clearance, storage and costs. If your question is not answered here, contact us.
What magnifications are available?
Slides can be scanned at 10x, 20x or 40x. 10x suits low-power morphology and gives the smallest files; 20x is the general-purpose choice for most histology and teaching sets; 40x is for cytological detail, nuclear features, mitotic counts and small organisms. If you need more than one magnification, say so in the comments on the request form.
What is the difference between Flat, EFI and Z-stack?
Flat is a single focal plane: fast, standard use, roughly 2 to 4 GB per slide. EFI (extended focus imaging) combines several focal planes into one sharp image for uneven or thick sections: slower, roughly 4 to 12 GB per slide. Z-stack preserves multiple focal planes as separate layers for special cases: very slow, 12 GB or more per slide. If you are unsure, choose Flat and describe your tissue in the comments.
What file format do I receive?
Whole slide images are produced in .vsi format. Tell us on the request form if your analysis pipeline requires something specific and we will advise on what is possible.
How should slides be prepared and labelled?
Glass slides must be 75 x 25 x 1 mm with a coverslip of 55 x 24 x 0.13 to 0.16 mm, allowing for the mounting medium layer. Every slide must be labelled with the slide ID or lab number, the stain, the tissue type, and the project name. Slides that are not labelled appropriately will not be accepted.
Which slides cannot be scanned?
Cracked or broken slides, and slides with loose, lifting, slanted, thickly glued or missing coverslips, cannot be processed: they jam the autoloader and can damage the scanner. Excessive scratches, dirt, fingerprints, air bubbles under the coverslip or surplus mounting medium will degrade the digital image even where the slide can be scanned.
Is there a charge for cleaning slides?
Yes. A surcharge of R6.50 per slide applies where slides require cleaning before scanning, for example removing dust, oil or marker pen, or trimming excess mounting medium and labels from the slide edges.
How long are my images stored?
Scanned data is held on a non-internet-accessible drive for a default period of 30 days. Longer online access can be arranged for 3 months, 6 months or 1 year, and storage costs are incurred for the period selected.
Do you keep a backup of my images?
No. No backup copy is retained by the Hub, and digital slides are not stored beyond 30 days without a storage agreement in place. Backing up your images is your responsibility. Download and archive your data as soon as you receive it.
Do I need ethics clearance?
Yes, for human and animal tissue. Human tissue requires HREC clearance, or evidence that clearance has been applied for, and NHLS AARMS approval where applicable. Animal tissue requires an Animal Ethics Committee protocol or clearance certificate. The clearance certificate number is a required field on the request form.
How much will it cost?
Cost depends on the number of slides, the magnification, the imaging mode and the storage period selected, so every job is quoted individually. Complete the request form with those details, and we will return a quotation against your cost center.
Who delivers and collects the slides?
Delivery and collection are the requester’s responsibility. Submit slides in a clearly labelled slide box with correct contact and project information, stating the total number of slides enclosed. You will be notified by email when scanning is complete, with collection and image transfer details
Can researchers from other institutions use the facility?
Yes, by arrangement. Complete the request form with your institution and billing details and we will advise on logistics and costs
Still Have a Question?
Email the Hub and we will get back to you, or go straight to the request form if you are ready to submit slides.