Aperio Digital Pathology Slide Scanner

The Aperio Digital Pathology Slide Scanner system is a whole slide, 20x or 40x brightfield imaging system that produces files compatible for viewing and analysis with the Aperio ImageScope software or other open source software like FIJI. This system is not available for self-service. The scanner is also capable of scanning large format slides (2×3).

For Aperio imaging questions, contact the TRIP Lab at trip@pathology.wisc.edu or 608-265-9168.

For pricing please see our TRIP Fee Schedule. To request imaging services, go to our iLab webpage.

Aperio ImageScope software – Free download


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Where should I drop off my slides for imaging?

For Aperio scanning, please contact the TRIP Lab at trip@pathology.wisc.edu or 608-265-9168 to arrange a drop off time.  The Aperio AT2 scanner is located in the TRIP Lab, 2214A WIMR.

What should I take into consideration when submitting an Aperio iLab request?

Please do the following:

  • Indicate the exact number of slides to scan.
  • Clean slides before giving them to TRIP.
  • By default, the scanner does scan the slide label, so if it has any information on it that needs to be covered up, do so beforehand. i.e.: de-identification of clinical slides. If you desire, the label scan can be omitted which will require you to provide a list of slide IDs and their corresponding coded IDs.

How can I obtain my image files and what software should I use to view my scanned images?

The software used to view the eSlides is called Aperio ImageScope and it is free and compatible only with Windows OS. You can install it on as many computers you want.

The files produced can be very large and the exact size depends on the magnification (20x or 40x) and the physical size of the specimen. A large specimen at 40x can be over 4GB (8GB for a 2×3 slide). An average sized specimen at 20x (1×3 slide) is usually around 500MB.

The scan files can be uploaded to a Google Drive folder and shared to your “wisc.edu” account (wisc.edu accounts only, no external accounts). The files will be shared to the original requestor, the PI and/or the collaborating pathologist. Files will be available for 30 days in which you should download and back up these files to your local storage. After 30 days, the files may be deleted from the Google Drive. An alternative is to provide a flash drive or external hard drive large enough to hold the images.

Our whole slide scanner can scan at either 20x or 40x and the resulting eSlides can be viewed at any magnification up to the magnification it was scanned at.

There is a price difference between 20x and 40x scanning because 40x takes significantly longer to scan.

If you’d like to see a sample eSlide, you can download it and the Aperio ImageScope software necessary to view it at this link https://uwmadison.box.com/v/SampleAperioSlide40x.