A whole slide image (WSI) is accomplished by digital scanning and allows online viewing of your entire stained section. The Aperio Scanscope CS is for brightfield scanning. The scanner automatically finds tissue then creates focus points across the entire section.
Slide scanning is an excellent way to archive and share slides, perform quantitative image analysis, and create publication quality images.
Several image analysis programs are available on a dedicated computer in D11-37.
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.
- 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.
- 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 UFHealth IT security policies for maintaining a secure password.
- Non-Pathology department users -Image server space is provided at no charge for 1 month for non-pathology users. You are responsible for image file transfers. Bring an external drive or DVD or purchase a DVD for image file transfers.
- You will receive an email when slides are ready for pickup. Pick up at D11-41 submissions counter.
Bookmark the link: http: https://apreslides.ahc.ufl.edu/Login.php
- Enter your username and password received from MPC. The 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 the box by each slide you want to open. Chose View Images from the specimen toolbar.
- Need assistance? Contact us or use Help in eSlide or ImageScope.
- 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.
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 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 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 quality scans. In some cases, we recommend sample recut or restaining.