HMC Digital Pathology Facility: Research and Academic Services


The Harborview Medical Center Digital Pathology Facility provides whole slide imaging services for clinical, research, and academic use. The Digital Pathology Facility is part of UW Medicine Hospital Pathology Laboratories and is based at Harborview Medical Center.

Clinical Services

Please see this page if you are interested in digital pathology support of internal clinical workflows:

Whole Slide Scanning for Clinical Workflows  

Research and Academic Whole Slide Scanning


  • Brightfield whole slide scanning at 20X (0.50µm/pixel) or 40X (0.25µm/pixel) objectives of 1x3 inch glass slides
  • Images and associated metadata accessible in web-based UI
  • Online project and slide management
  • Account creation for sharing scanned slides
  • Support for creating publication/grant figures
  • Basic training for accessing, viewing, annotating, and capturing snapshots from whole slide images

The Harborview Digital Pathology Facility, a component of the UW Medicine Hospital Pathology Laboratories, is managed by Jonathan Henriksen, (, 206.221.5830).  The facility provides brightfield whole-slide histologic imaging suitable to prepare publication-quality figures or quantify image features using quantitative analysis tools.

Facilities and Equipment:  The Harborview Digital Pathology Facility is located at the Harborview Ninth and Jefferson Building. The facility is equipped with an Aperio ScanScope AT2 digital whole slide scanner which creates diagnostic quality brightfield whole slide image scans at high continuous throughput with a 400 slide capacity. The scanner instrument is networked to two dedicated Dell PowerEdge R510 servers equipped with Aperio eSlide Manager server applications and Aperio Brightfield Toolbox image analysis software.  These servers each contain 15TB of direct-attached storage, and are hosted in the University of Washington enterprise class data center with automated nightly backups to two secure geodiverse locations.

UW and Affiliated Fred Hutch Users

Slide scanning services for research and academic purposes are provided at a per-slide rate of $5 per slide for UW and Affiliated Fred Hutch users.

External Users

Slide scanning services are provided to external users through NWBioSpecimen, the Department of Pathology’s biospecimen annotation and research services core facility.

Services Detail

The Aperio ScanScope AT2 is used to prepare diagnostic quality brightfield whole slide image scans (WSI) at 20X (0.50µm/pixel) or 40X (0.25µm/pixel) magnification, performing at high continuous throughput with a 400 slide capacity.  Scanned slides may be viewed at any magnification up to the scanning resolution. The 20x and 40x scanning resolutions correspond to viewing cell sizes on a microscope through 20x or 40x objectives with 10x eyepieces.

Online access to your whole slide images is provided with Aperio eSlide Manager server software. This web-based software allows you to access your whole slide images on computer and iPad for viewing and capturing publication quality snapshots. You can optionally have multiple online accounts created to collaborate with co-investigators by sharing scanned slides and annotations securely. Slide images are immediately available on the server after scanning and assigning to your account. All slide scans are hosted on our secure servers with automated nightly backups.

Additional services can be provided. Please inquire for more detailed information.

Quantitative Image Analysis Services

Once slides are scanned, the whole slide images may be analyzed using image analysis software to quantify regions of interest for area-staining or cell-staining within nuclear, membrane, and cytoplasmic regions of any chromogen. These services are offered by NWBioSpecimen, the Department of Pathology’s biospecimen annotation and research services core facility. These services are billed at an hourly rate and require a signed Statement of Work. Please inquire with if you are interested in these services.


Digital Imaging Facility Service Rate Internal (UW/FH) Rate External

Slide Scanning
Whole slide images, includes server hosting

$5/slide Please inquire with NWBioSpecimen for latest pricing.

Billing/Fund Transfer

Internal Requestors (UW Budgets only)

The budget number you supply on the request form will be billed by way of a JV transfer process by Anatomic Pathology.

Affiliated Requestors (Fred Hutch)

You must supply an invoice address/email with each scanning request. You will receive an invoice from Anatomic Pathology with instructions on how to submit payment by check.

External Requestors

Please inquire with NWBioSpecimen for information on establishing a Goods & Services Agreement, the latest pricing, and billing process.

Requesting Slide Scanning Services

  1. Download and complete the appropriate Slide Scan Request Form.

      Slide Scan Request Form for Research

      Slide Scan Request Form for Academic

    For research slides, a project name, description, PI/contact name, and budget number (or invoice information for FH users) must be included with all requests. This information will be used to organize your slides into a project folder. Please indicate if you scanning additional slides for a project which was already created.

    For teaching slides, each slide/case must include clinical history (if relevant), body site, and diagnosis. If submitting many cases to scan at once, you may submit this information in an excel document. This information will be used to add the slides to a collective library available to UW Pathology Residents and Fellows.
  2. Submit the slides along with the request form.

    Please contact Jonathan Henriksen at for the best method of delivering the slides to the scanning location at Harborview. This page will be updated in the near future with more specific instructions for submitting slides for scanning from H arborview and UW Medical Center - Montlake's Health Sciences Building.
  3. You will be notified via email once the slides are scanned and the slides will be returned to the appropriate destination.

Accessing Slides on the UW Pathology Aperio Digital Slide Server

Aperio eSlide Manager is a digital pathology image server with a web based interface and slide information management component.

Research slides are organized into groups by your project and assigned metadata such as project name, slide set, tissue site, stain, and block number. eSlide Manager also stores digital slide annotations and image analysis data.

Teaching slides can be organized into individual interesting cases or slide collections. Metadata can be added for history, body site, diagnosis, pathologic process, and procedure. Additional images (gross, radiological, EM, etc.) can be added as JPG or TIFF images.

Secure access to slides and metadata is governed by user accounts, roles, and permissions within the system. You will only be able to see and edit those slides which are within your allowed access groups.

If you are requesting slides to be scanned for the first time, an account will be created for you and instructions for accessing the slides will be emailed to you.

You may also view guides on how to access, view, and search for scanned slides on our Aperio ePathology wiki page: