Digital Pathology

Contact: Amanda Koehne, Staff Scientist
Location: Thomas Building, DE-360
Contact phone: (206) 667-6166
Contact fax: (206) 667-6845
Contact e-mail:

New: HALO Link Collaborative Pathology Information System that takes image analysis and management to the web allowing anywhere, anytime access to study data, slides and analysis results from computer, tablet or smartphone. See details here.

If you are already a HALO Link user, log-in here

Experimental Histopathology provides a digitial pathology service using two powerful scanning systems for digitizing your slides. These systems provide many powerful and unique tools for analyzing your samples. Aperio ScanScope FL is a fluorescent slide scanner and the Aperio ScanScope AT is a brightfield system which can automatically digitally scan up to 400 brightfield slides at a time. (See the full specs for the Aperio AT and Aperio FL systems)








Characteristics of our Aperio service include:

  • Spectrum - A web-based digital pathology information management system
  • ImageScope - for visualizing samples at various magnifications, annotating samples, and more
  • Aperio image analysis software for many sophisticated analysis tasks (see below) including nuclear, cytoplasm, and membrane quantification, microvessel analysis, rare event detection, area quantification, and the Genie Histology Pattern Recognition software.
  • Tissue Microarray analysis tools that allow you to segment whole slide images, view spots in context of core, and automate image analysis.
  • Data Groups can be designed to facilitate collaboration between groups or add levels of security.
  • Long term, secured storage of histology data including special stains and immunofluorescence which fade over time.

Process at a Glance

Aperio FL Aperio AT
1. Request Spectrum account 1. Request Spectrum account
2. Exp Histo provides training 2. Deliver bright-field slides to Exp Histo
3. Schedule time on Instr Scheduler 3. Exp Histo scans slides and makes data group
4. Investigator scans slides and puts into data group 4. Investigator is contacted to pick up slides
5. Analyze images in Spectrum 5. Analyze images in Spectrum


Using the Aperio system

Spectrum: Your images will be stored and managed by the Spectrum information management system. Access to slides can be designated to several members in a data group.

When you request the digital pathology service from Experimental Histopathology, an account will be created for you in Spectrum. Go to to login (IP-restricted to Hutch - accessible only when on campus or via VPN). ImageScope is available after login.A quick-start guide is available for accessing and installing Spectrum, ImageScope and Second Slide softwares.

ImageScope. ImageScope is available after you login  to Spectrum. It allows you to visualize samples at various magnifications, annotate samples, rotate views and capture images. Several images can be viewed at once and synchronized for ease in viewing serial sections.

Image Analysis Suite.We now use the HALO image analysis modules. See the data analysis page on the HALO sofware.

Slide Quality

As with any technology, the better the input, the better the output. We will work with slides to achieve the highest quality image possible. Common problems that cause lower quality scans are air bubbles, cracks in the slide glass, and faint and/or scant tissue. In addition, very large tissues or tissues which are placed on the edges of the slide may be outside of the scanning area. Some slides that have these issues cannot be scanned, but these problems may be fixed by having a specimen re-cut, re-cover slipped, or re-stained.

The Aperio cannot scan slides that have wet mounting media, more than two slide labels, labels on back or the bottom of slide, double slides, or broken slides. The slides should be free of finger prints, dust, and dirt. Also, any pen markers on the slide or label may be removed by the prescanning cleaning.