Whole Slide Scanning

A whole slide image (WSI) is accomplished by digital scanning and allows online viewing of your entire stained section.

Please note! The Aperio Scanscope CS is available until 10/15/23 and will be replaced with an Olympus VS200 scanner by 11/1/23.

Slide scanning is an excellent way to archive and share slides, perform quantitative image analysis, and create publication-quality images.

Image analysis programs are available on a dedicated analysis workstation in D11-37.

Submit Slides

Clinical slides? Do not submit slides with private health information (PHI)- conceal with an opaque temporary label.
  • Submit the online Slide Scanning form.
  • Bring slides to D11-41 submissions counter.
  • Turnaround time is 0.5-2 work days depending on slide numbers. Let staff know of any deadlines by email at the time of slide submission. 
  • First-time UF submitters – request an individual user account on the Slide Scanning form. You will receive an email containing your username (Gatorlink ID or other provided email name) and a temporary password. The temporary password must be changed on first login. Follow UF Health IT security policies for maintaining a secure account system.
  • Non-Pathology department users – Image server space is provided at no charge for up to 3 months for non-pathology users. Users are responsible for providing a secure file transfer system or an external device to transfer image files.  
  • You will receive an email when the slides are ready for pickup at D11-41 submissions counter.

Prepare Slides

Best results are obtained with tissues with even thickness (4-5um) (more about Slide Quality below). Slides with air bubbles, cracks, marks, extra or wet mounting media, plastic coverslips, or thick slide labels may require additional efforts to obtain a quality scan. Sections placed close to slide edges or small coverslips will affect quality and image analysis as these edges can be interpreted by software as tissue. These issues can be corrected by having a specimen re-cut, re-cover slipped, or re-stained.

Slide Quality

Best scanning results will be obtained from glass slides with tissues of regular thickness (4-5 microns) and coverslipped. Slides with marks (such as ink dots), extra mounting medium, non-glass slides, plastic coverslips, thick labels, and labels that are going around the slide present challenges for proper imaging, and may need to be removed in order to obtain an optimal scan. Images are individually reviewed once the scanning is completed. Scans with poor quality will be rescanned manually to achieve the maximum quality possible. The equipment can not scan slides with wet mounting media, more than two slide labels, labels on the back or the bottom of the slide, double slides, or broken slides. The slide and coverslip should be free of fingerprints, dust, and dirt. Any pen markers on the slide also need to be removed as the scanner will consider such marks as tissue. Faint stains, air bubbles, thick sections, or marks on the glass surface can cause lower scan quality. In some cases, sample recut or restaining may be recommended.

Login to eSLIDE Image Server– inactive after 10/15/23

  • The online eSLIDE LIMS will no longer be available after October 15, 2023, due to the retirement of the image server with OS WIN10.
  • Login: https://apreslides.ahc.ufl.edu/Login.php
  • Enter your username and password received from MPC.
  • Find your Case (clinical) or Project (research) folder listed by PI’s last name.
  • Open your folder and look for the images in the lower panel. If there has been more than one subfolder, each is a separate “specimen”. Open the specimen for the images using the “+” sign of the icon or click on the brain icon.
  • View all slides by clicking on the “eyeball”. To view individual slides, click on the box by each slide and choose “View Images” from the specimen toolbar. If you are using a PC, you can select View images in ImageScope then the program will default to that image viewer.
  • Need assistance? Contact us or check out Help in eSlide or ImageScope.

Viewing Scans

  • Windows computers- Install free ImageScope software from the Aperio website.
    • Highly recommended- allows snapshots for publication-quality images (TIFF, JPEG), annotating, distance measurements, positive pixel count, and many other features. Will open any .jpg and .tif image. Manual
    • ImageScope needs to be selected from the default viewer. Choose the link in the upper right of the Webview image border.

Fees and Invoicing

Please visit the Fee page for information on costs and billing.