Digital Pathology- Slide Scanning

Whole digital slide scanning allows online viewing of your entire tissue section for digital pathology reviews. The Aperio Scanscope CS is for brightfield scanning. The system automatically finds tissue then creates focus points across the entire section. Slide scanning is an excellent way to archive slides, annotate regions of interest, share, and create publication quality images. Several image analysis programs are also available.

Prepare Slides

Best results are obtained with tissues with even thickness (4-5um) (see Slide Quality Counts 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 (these edges are interpreted by software as tissue). These issues can be corrected by having a specimen re-cut, re-cover slipped, or re-stained.

Submit Slides

  • Clinical slides? Do not submit slides with private health information (PHI)- conceal with a opaque temporary label.
  • Complete and submit the Slide Scanning form.
  • Bring slides to D11-41 submissions counter.
  • Turnaround time is 0.5-2 work days depending on slide numbers and staff availability. Let staff know of any deadlines at sample submission. 
  • Non-Pathology department users- Bring an external drive or DVD or purchase a DVD from the Core for image file transfers. Image server space is provided at no charge for 1 month for users outside the Departments of Pathology and Oral Pathology then files are transferred by FTP or drive to you for storage.
  • 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 log in. Follow UFHealth IT security policies for maintaining a secure password.
  • Your will be emailed when slides are ready for pickup. Pick up in D11-41 right next to the drop off counter.

Log in to eSLIDE Image server

  • Web address: http://ahc-path-aperio11.ad.ufl.edu/. MPC home page has a link over Google search bar on the home page if you forget to bookmark.

  • Enter your username and password received from MPC. Username will generally be the text before “@” in your email address. Change your temporary password.
  • Find your Case (clinical) or Project (research)- These are listed by PI’s last name or group 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.
  • Click on box by each slide you want to open. Chose View Images from the specimen tool bar.
  • Need assistance? Contact us or use Help in eSlide or ImageScope.

Viewing Scans

  • Windows computers- install free Imagescope software from Aperio website –  ImageScope Download
    • 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.
    • ImageScope needs to be selected from Webviewer the first time then it will become the default image viewing program. Chose the link in the upper right of the Webview image border.
  • Mac computers- uses Webviewer.
  • iPAD ePathViewer from iTUNES- add MPC as a site to the navigation bar. Great for emailing snap-shots to colleagues.

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 cover slips, 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 a 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 back or the bottom of slide, double slides, or broken slides. The slide and coverslip should be free of finger prints, 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 quality scans. In some cases, we recommend sample recut or restaining.