Informatics, digital & computational pathology

Digital and whole slide imaging

WSI implementation

Deputy Editors-in-Chief: Patricia Tsang, M.D., M.B.A., Andrey Bychkov, M.D., Ph.D.
Mark D. Zarella, Ph.D.

Last author update: 23 August 2021
Last staff update: 24 August 2021

Copyright: 2019-2024,, Inc.

PubMed Search: Whole slide imaging primary diagnosis [TIAB]

Mark D. Zarella, Ph.D.
Page views in 2023: 142
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Cite this page: Zarella MD. WSI implementation. website. Accessed May 19th, 2024.
Definition / general
  • Whole slide imaging (WSI) is a method for digitizing glass slides in their entirety
  • Implementation of WSI requires several technical and cost considerations
  • Pathology applications span multiple domains that can potentially improve efficiency, accessibility and quality
Essential features
  • Common clinical applications of WSI include:
    • Digital archival
    • Collaboration
    • Telepathology
    • Primary diagnosis (including remote signout)
    • Image quantification
  • Implementation of WSI benefits from oversight by pathologists and laboratorians
  • Input from others during planning is also important, as slides scanned for clinical purposes may have additional uses for research and education
  • College of American Pathologists guidelines should be followed to ensure the safe and effective use of WSI for clinical use (Arch Pathol Lab Med 2013;137:1710)
    • Recommendations center on validation and documentation, with a focus on interobserver and intraobserver concordance and understanding scope and limitations of the technology
    • Laboratory developed test (LDT) paradigm applies to many clinical use cases of WSI
    • FDA clearance is not itself a requirement for the clinical use of WSI
  • Considerations for implementation include:
    • Compatibility with downstream viewers and analytical tools
    • Informatics infrastructure, including file storage and bandwidth
    • Pathology workstations, e.g. the "pathologist cockpit" (J Pathol Inform 2010;1:19)
    • Workflow considerations for the intended use case(s), e.g. scanning pre versus post signout and their respective impacts on turnaround time (TAT)
    • Costs, not only for hardware but also ongoing costs, such as personnel
  • Compute the target scanning volume for the use cases
  • Craft a slide preparation strategy focused on slide cleaning, slide integrity checks (including trimming labels and coverslips) and quality control (QC)
  • Establish a prescan QC protocol to identify slides that may not be appropriate for scanning
    • Examples include slides that are not supported by the slide scanner (e.g., excessive slide thickness, plastic cover slips), slides that are damaged or slides that have excessive artifacts, such as air bubbles
    • This may need to be performed in coordination with the slide scanner selection process to understand the limitations of each scanner under consideration
  • Craft a post scan QC strategy that ensures that the images produced by the scanner are acceptable in quality
    • This may include automation such as digital image analysis if supported by your platform
    • If an automated procedure is adopted, it is generally best practice to adopt an ongoing validation procedure to ensure that the algorithm is working correctly; one approach is to visually analyze slides that fail the automated procedure as well as slides that pass the automated procedure
  • Craft a workflow blueprint that details how slides move through the pipeline
    • This should include slide preparation and QC strategy, selecting whether slides are rescanned if they fail QC (and how many rescan attempts) or returned to the lab
  • Allocate workforce based on the computed volume, taking the workflow envisioned into account
    • In addition to slide preparation and scanning, this may include efforts to pull or archive slides, manually associate slides with clinical (or research) cases in the system, data entry, selecting representative slides from cases, conducting image analysis, etc.
  • Identify slide scanners that have the speed, capacity and level of automation to reasonably achieve the calculated volume given the workforce available
    • For example, if the target volume is 500 slides per day, the workforce must be able to prepare and deliver 500 slides per day to the scanner and the scanner must be able to scan 500 slides daily
    • Note that speed scales with additional scanners operating in parallel, whereas larger capacity scanners do not necessarily add speed but may enable larger daily batches
  • When considering upgrades and enhancements, examine and identify bottlenecks in equipment and workforce planning; common bottlenecks include:
    • Not enough workforce devoted to all of the tasks necessary to scan slides
    • QC slowness creates a bottleneck in releasing slides to their ultimate destination
    • Automated slide scanning is not available (or fails); for example, automated tissue detection fails to reliably select tissue or automated focusing is insufficient to generate blur free images
    • Slide scanner is insufficient in speed to meet the target volume
  • Plan for the user experience and select platforms that meet those needs
    • Should the images be accessible over the local network so that they can be viewed at different workstations?
    • Should image management be deployed to aid with metadata collection, ease of viewing, searching and organization?
    • Will annotation be needed (e.g., drawing regions of interest)? If so, for what purpose?
    • Is integration with other systems necessary, such as the laboratory information system (LIS) / electronic health record (EHR)?
    • Is integration with image analysis and AI platforms desired?
    • Are the file types produced by the slide scanner(s) supported by the platform?
    • Is the user’s intended storage strategy supported by the platform?
  • Settle on a file storage strategy
    • If long term storage of the slide is necessary, expect the storage requirements to grow and plan accordingly
    • Calculate costs per scanned slide for storage; this requires an expectation of file size and target volume
    • Consider whether the intended storage strategy meets the needs of the user in terms of accessibility, rendering speed and byte level access
    • Consider issues surrounding personal health information (PHI), such as whether the intended storage supports PHI or whether PHI must first be separated from the whole slide image prior to storage
    • Determine a (preferably offsite) backup strategy; common methods are cold storage, such as tape backup and cloud services (particularly low cost ones that assume infrequent access)
    • Hybrid solutions are also possible, which may include a mixture of fast, highly accessible storage, slower storage with less frequent access and cold archival storage; if so, a strategy should be developed to determine which images should belong to which partition
Clinical use cases
  • Digital archival:
    • Slides can be scanned post signout to retain digital copies
    • Archived slides can be associated with the clinical case by integration into the laboratory information system or electronic health record, making them easily accessible for follow up
    • Has the potential to improve workflow efficiency and reduce costs associated with pulling archived glass slides (Arch Pathol Lab Med 2019;143:1545)
    • Can enable institutions to retain a digital copy of glass slides for consult cases that typically must be returned to the originating institution
  • Collaboration:
    • WSI eliminates the scarcity problem; images can simultaneously be viewed and navigated by different users and at potentially different locations
    • Useful for consultation without needing to ship and receive slides, particularly overseas where there can be legal barriers (J Pathol Inform 2015;6:63)
    • Tumor board, quality assurance and other conference-like settings can benefit, particularly if multiheaded microscopes aren't available or can't accommodate all participants
    • Screening and rapid evaluation (e.g. rapid onsite evaluation [ROSE], frozen sections) that may require remote reads at locations without on-site pathologists, reducing travel between sites
  • Telepathology:
    • Scanned slides can be made accessible remotely to users to enable remote consultation
    • Advantages compared with conventional telepathology systems include:
      • Local user does not necessarily have to be present at the time of slide review to load / unload slides in real time, establish connections and manipulate the slide
      • Remote user can have full control of the slide, including field of view and magnification
      • Permanent record of the entire slide can be retained
    • Drawbacks compared to conventional telepathology:
      • Requires extra time for whole slide scanning prior to review, which should be specifically validated if being considered for frozen section interpretation
      • Typically a larger investment than conventional telepathology systems
      • If using existing WSI equipment, telepathology may have to compete with other uses of the system, which can delay availability
      • Remote software still needs to be identified if a multiple user image management system is not used
  • Primary diagnosis:
  • Image quantification:
    • Digitization is a necessary step for digital image quantification
    • WSI enables digitization to be applied to the entire slide
      • WSI can also allow pathologists to more easily offload digital capture to technicians, as opposed to digital capture using microscope cameras
    • Quantification for clinical support commonly includes:
      • Immunohistochemistry scoring
        • There are some 510(k) cleared algorithms but many are research use only
        • Laboratory developed test mechanism can be applied to utilize algorithms clinically
        • For certain markers, such as HER2 scoring in breast cancer, additional reimbursement via CPT 88361 may be possible
      • Counting of cellular and subcellular structures
      • Area quantification
      • Emerging techniques, such as machine learning for tissue segmentation, tumor detection and grading have been demonstrated in a clinically relevant fashion and may be on the horizon (Nat Med 2019;25:1301, Lancet Digit Health 2020;2:e407, JAMA Netw Open 2020;3:e2023267, Mod Pathol 2021;34:660)
Board review style question #1
Which of the following considerations are unique to whole slide imaging (WSI) based telepathology and provide a potential advantage over most conventional telepathology systems?

  1. Slides can be viewed by users at remote locations
  2. Turnaround time is usually must faster using whole slide imaging versus microscope cameras or robotic microscopes
  3. WSI is typically less expensive than alternatives
  4. WSI does not necessarily require that a technician or resident is present during slide review
Board review style answer #1
D. Whole slide imaging (WSI) does not necessarily require that a technician or resident is present during slide review

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Reference: WSI implementation & primary diagnosis
Board review style question #2
Which of the following scenarios generally entails digital slide scanning prior to case signout?

  1. Digital slide archival
  2. Educational activities using whole slide imaging
  3. Primary diagnosis using whole slide imaging
  4. Retrospective research studies using whole slide imaging
Board review style answer #2
C. Primary diagnosis using whole slide imaging

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Reference: WSI implementation & primary diagnosis
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