Imaging & Scanning

Scanning in Pathology

Pathology offers several options for digital imaging and scanning:

• WSI - Aperio whole slide scans (see section below for details)
• Digital Microscopy
• Nikon Coolscan for 35mm slides or prepared glass slides with adapter 
• Flatbed scans for gels, art work, radiology film, transparencies (12in x 17in max.)

The Epson flatbed and Nikon CoolScan scanners are available to the Pathology Department as self service or through Pathology Digital Imaging. Self-service must check in at Path ITS BML B50.

NOTE: Path Digital scanners are intended for high resolution uses. For basic scanning needs, use the office scanners. The larger business suites are equipped with searchable pdf options.

Aperio Whole Slide Scanning (Virtual Microscopy)

Note price change effective Dec. 1st, 2018

20x slides - $10.00 ea
40x slides-  $20.00 ea
Files are .svs format and can be read using QuPath software (github) or ImageScope (PC only) from Leica Biosystems.

  • All files are de-identified. 
  • Medical school teaching slides will be available on the image server.
  • Researchers must provide a storage drive to transfer files. 
  • All trays and boxes of slides submitted for scanning must be labeled with Name, Email address, and full COA number.
  • You must have your slides ready to scan. Cleaning is very important - there will be an extra charge for poorly cleaned or poorly processed slides.

For research use: Use Aperio Form A and drop off slide to Path Digital BML B50 Path ITS.

For Pathology clinical slides, teaching cases, or Radiology Resident conferences:
Use Aperio Form B and place the slides and forms in the slide box located in Surgpath/Report Generation and address to Path ITS. 
Slides will be returned to Surgical Pathology for filing unless otherwise directed.

NOTE: For all Radiology Resident scans please see the Pathology Chief Resident.

Informatics Information and Technology Services (ITS)

Director of Informatics: 
Peter Gershkovich, M.D., M.H.A.

Clinical ITS Emergencies: 203.370.1780 

ITS HelpDesk
Hours: M-F 8:30-5:00
Helpdesk: 203.785.3691 
Urgent during work hours: 203-623-4861 
Fax: 203.75.2403 
Email: pathITS@yale.edu

Yale School of Medicine
Department of Pathology 
PO Box 208023 
310 Cedar St. BML BB50  
New Haven, CT 06520