Aperio ScanScope slide scanner

This instrument will be retired January 31,  2019. The Biorepository and Tissue Research Facility provides a  slide scanning service (core operated) which researchers can request through iLab (uva.corefacilities.org)

The ScanScope scans microscope slides at 20X, 40X or 63X to a digital image that can be viewed with software that simulates the use of a light microscope.

ScanscopeVirtual microscopy

Converting a glass slide to a virtual slide is the basis of digital histology and pathology. The advantages of a virtual slide include:

  • viewing by multiple people simultaneously either locally or elsewhere
  • easy sharing of a slide with others for consultation or analysis
  • ability to view a slide at different magnifications
  • easy assembly of collections of related slides
  • reduced storage space and easy duplication for backup
  • easy retrieval

The scanning process

For 20X and 40X scans, up to 5 slides can be scanned in one batch in an automatic mode. Scans can take from a few minutes to over three quarters of an hour, depending on tissue size and magnification.

Scanning at 63X with oil uses a dedicated lens and slide tray, and is slow and requires special setup and only used in limited circumstances.

Thick tissue sections as well as non-standard slide thickness can create special challenges.

Data output

A mechanical stage move the slide underneath a lens to generate a series of overlapping scanned strips which are assembled into an image file with .svs (ScanScope Virtual Slide) format, using JPEG compression. Large, high resolution images can have 1 GB file size.

Scans at 20X, 40X or 63X (with oil immersion lens), have resolutions of 0.5, 0.25, 0.17 micron/pixel respectively.

The files are moved from the ScanScope computer using a flash drive, a DVD, portable hard drive or electronic transfer over the network.

Viewing options

The image files can be converted to JPEG or TIFF format with Digital Slide Studio on the ScanScope computer.

The .svs files can be viewed and manipulated using a free software program called ImageScope which runs on Windows. ImageScope can extract parts of an image and save it in JPEG or TIFF format (similar to a screen capture).

Download ImageScope from the Aperio web site:


The same page can also take you to ePath Viewer which allows you to view Virtual Slides on an iPad or iPhone. The download may require you to supply identifying information. There is a charge to allow the app to upload slides from any source.

Catalogs of Virtual Slides

Click here for links to catalogs of Virtual Slides

Slide preparation

Link to notes on preparing slides


The ScanScope is located in Pinn Hall, room 1074.  Users can access the instrument at any time with appropriate entrance permissions on their identity card and the entry code for the room. Sign up for use on iLab (https://uva.corefacilities.org)