Digital Pathology

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Q: How do I begin?

Steps:

  1. Know how to get the glass slides to us.
  2. Unless prior arrangements have been made, we require a filled-out scan request form prior to the glass slide drop-off. 
  3. Using the form, through the drop-down menus and the "comment" field at the bottom, communicate your intended purpose for the digital images and any additional needs to us.  Examples include:
    • Faculty member personal collection
    • Tumor Board
    • Whether copies should be publicly available for educational or collaborative purposes, and if so, via which interface (if you're not sure, we are happy to help).
  4. Know where to look for the digital images once the scanning request is complete.

 

Next Steps:

  1. Review the instructions for submitting slides, followed by filling out the online slide submission form & obtaining a printout.
  2. Dept of Pathology Administrative Assistants: 
    1. There are pickup spots for the slide and mail runners. They will drop off slides with us.
    2. You are also welcome to deliver slides to us personally at NCRC 35 G417. 
  3. For research requests originating at the NCRC: 
    1. Use the wall box located outside NCRC Building 60, room 1631-C. 
    2. You must email slidescanningserv@med.umich.edu so we know to come and pick the slides up.
  4. For research requests originating at the main medical campus:
    • Bring the appropriate form and your slides to the location designated in the Transport of Slides to/from NCRC link.
    • Slides will be packaged for courier shipment to NCRC. When the slide scan order is finished, slides will be returned to UH via courier. Please allow 3-4 hours after receiving an email notification before checking the designated pickup area in UH for your slides.
  5. Note for researchers:  if you are mounting slides personally, please make sure slides are clean and free of air bubbles trapped beneath the coverslip.  Slides must be granted proper conditions for the mounting medium to completely cure:  at least 10-18 hours in a well-ventilated space (not inside a small, sealed slide box).  Slides suspected of incomplete curing will be held or returned.  Avoid excess mounting medium and align the coverslip carefully. 

Q: How do I see my scanned slides?

First, consider:

  • Where do I look for my scanned slide images?
    The interface you will use for viewing slides partially depends upon what you communicate to us through the slide scan request form.  Michigan Medicine Pathology faculty, House Officers, and staff should consider the search engine within the "Tumor Boards" application inside the Pathology Clinical Lab Portal as their "go-to" interface for viewing scanned slides. 

 

Available Interfaces for Viewing Slides

  • The search engine within the Pathology Clinical Lab Portal
    • Searches the entirety of our scanned slide collection
    • Can open scanned slides directly using either ImageScope or WebScope
    • Copy of Path Lab report provided if available
    • Behind U-M firewall; access is limited to those Pathology faculty and staff with permission to access the "Tumor Boards" application within the Portal.
    • If a slide has been archived, it will be documented on the interface. If a copy of the image is on the Virtual Slide Box (a server separate from our main one), a link will be provided. 

  • The Pathology Virtual Slide Box
    • This is a separate set of cases intended for educational purposes.
    • The VSB consists of image copies that have been de-identified. A copy of the digital slide with the captured slide label image and any identifying information on it is maintained in the eSlide Manager database.
    • Indicate your interest in having de-identified slide copies pushed to the VSB by making use of the "radio button" on the slide scan request form.  In addition, please notify us in the comments which collection you wish them to be included in.

 

  • Research clients
    • Researchers will receive copies of their whole-slide images via Dropbox.
    • Please see "Research Lab" section below.

 

Examples of Specific Applications

Tumor Boards Main PageTumor Boards Main PageTumor Boards Main Page

I'm showing Pathology Images at a Michigan Medicine Tumor Board conference."

Slides scanned for tumor boards are assigned to a dated web page within the "Tumor Boards" section of the Pathology Clinical Lab Portal.  A screenshot from the main interface is shown below. Note: not all conferences have shown here.

Simply click the appropriate date and a list of cases will appear.  Each case will have a link to the Pathology report next to the last name. To open all case images at once, click the last name. To open a single slide, click the stain name.

You may select the modality for displaying the scanned images. "ImageScope" is the vendor's software and must be installed locally on the workstation. "WebScope" will open the images within your web browser.

 

I would like to show some scanned images for an educational conference, such as unknowns for Pathology residents.

This process is undergoing revision as of mid-2025. Trainees will be expected to mask slide labels and bring them to us "Case 01, Case 02," etc.

 

I need to share my images with a collaborator / colleague outside U-M.

Please contact Digital Pathology directly for these kinds of requests.  As of 2024 we are referring faculty to use of third-party company PathPresenter.  You may email slidescanningserv@med.umich.edu for more information.

 

I am with a research laboratory. 

When you indicate "Research" in the "Group" field, you will be required to indicate via the "radio button" icon your preference for viewing your slides. "MBox or Dropbox" is strongly recommended.

Very important: researchers submitting slides with human tissue will be required to provide an IRB HUM# before slides can be scanned. Copies of images provided back to you will be de-identified. You will receive a spreadsheet to allow matching of image files to slide-level metadata.

NOTE:

  • The scanning process results in ".svs" image files.  These image files are archived on a secure server, and copies may be given upon request. Currently, 40X scans result in image files that average 0.5 to 1.0 GB each.  The file size varies directly with the size of the tissue slice.  Image file sizes can range from 0.1 to 3.0 GB.  Please make sure you have a storage device of appropriate capacity prior to requesting copies of a group of image files.

 

Clients that elect to receive copies of their .svs files can open them using the freeware ImageScope.  With ImageScope, clients can extract jpg images suitable for PowerPoint presentations, posters, and publications.  Multiple images can be compared simultaneously.  Areas of interest can be annotated with arrows, shape tools, and labels for downstream presentation or teaching purposes.  Note: as of March 2022, there is no Mac-compatible version of ImageScope software. An alternative, Mac-compatible product is "QuPath."  Link here: https://qupath.github.io/

 

Q: How fast is the slide scanning service?

Our Service prioritizes tasks of importance to Pathology's clinical mission. For Tumor Board support, we routinely handle "last minute" slides prior to conferences. Other urgent requests (< 24 hrs turnaround time) are handled to the best of our ability and in keeping with both our prioritization policy and staff availability. Reasonable efforts will be made to accommodate these requests but guarantees cannot be given at this time.

 

Q: I use a Macintosh computer. 

At this time there is not a Macintosh-compatible version of ImageScope software available. There is, however, a Mac-compatible program on GitHub called "QuPath."  QuPath is designed for the analysis of whole-slide images. 

 

Q: How do I get my slides from Main Campus to NCRC? (For research clients)

There is no direct access to our actual scanning area for non-Pathology clients. 

For research clients based at the main medical campus: click one of the buttons below. 

Research clients based at NCRC: use the wall box located outside NCRC Building 60, 1631-C. After placing slides in the box (together with the filled-out scan request form), email slidescanningserv@med.umich.edu.

Research clients not part of Michigan Medicine: please contact slidescanningserv@med.umich.edu prior to placing slides in the drop box.  We will take your information and fill out a form on your behalf. 

Courier Service Instructions

Department Staff and Faculty  All Others

 

Driving and Parking Directions for our NCRC Location
Occasionally it will be necessary for a client to visit us in person. This can happen if the client is not part of Michigan Medicine and cannot access the slide scan request form, or for other reasons.  A map of our location is provided below. You may leave or pick up your slides from the box in the photo below the map. 

PLEASE NOTE: You must alert Digital Pathology that slides have been dropped off by sending an email to slidescanningserv@med.umich.edu.

NCRC satellite 2023-1.jpg

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