Informatics, digital & computational pathology
Digital and whole slide imaging
WSI fundamentals
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Table of Contents
Definition / general | Essential features | Terminology | Images | History | Basics | Common methods of scanning | Techniques used in scanners with slide staining | Software | Categories of measurements | Pathologist's role in image analysis workflow | Clinical validation | Clinical applications | Nonclinical applications | Recent advances | Limitations | Videos | Board review style question #1 | Board review style answer #1Cite this page: Fathima S, Parwani A. WSI fundamentals. PathologyOutlines.com website. https://www.pathologyoutlines.com/topic/informaticswholeslidefund.html. Accessed April 19th, 2024.
Definition / general
- Whole slide imaging (WSI) or virtual microscopy involves the scanning (digitization) of glass slides to produce digital slides (Adv Anat Pathol 2012;19:152)
Essential features
- Whole slide imaging has 2 major components: hardware and software
- Hardware:
- Microscope with lens objectives
- Light source (bright field or fluorescent)
- Robotics to load and move glass slides around
- Digital cameras for image capture
- Computer
- Software to manipulate, manage and view digital slides
- Hardware:
Terminology
- Static digital image, virtual microscopy
Images
Contributed by Anil Parwani, M.D., Ph.D., M.B.A.
Omnyx whole slide imaging scanner
Tile based and line based scanning
History
- First scanners introduced in by Wetzel and Gilbertson in 1999 (Arch Pathol Lab Med 2019;143:222)
- Evolved from static digital images and robotic microscopy
- In 1997, Ferreira et al. used robot / microscope / computer combination to create a mosaic pattern of image tiles that produced a composite slide image (Path Lab Med Int 2015;7:23)
- A system capable of capturing entire slides at high resolution but in a time efficient fashion and with reasonable operating costs was produced by Interscope Technologies (Path Lab Med Int 2015;7:23)
Basics
- Traditional glass histology slide is digitized via a slide scanner and viewed on a computer screen or handheld device at a similar resolution as light microscopy
- Robotics are key to avoid breaking slides, for stage accuracy and for dependable objective switching
- Whole slide imaging instruments do batch scanning (i.e. scan one slide at a time) and continuous or random access processing (i.e. slides can be uploaded while another is being scanned)
- Entire glass slide or a preselected region of interest on the slide can be scanned
- Digital data are captured via the camera's charge coupled device (CCD) and then a computer employs specialized imaging software to generate a virtual slide
Common methods of scanning
- Tile based scanning
- Robotics controlled motorized slide stage obtains large numbers of square image frames and assembles them into a mosaic pattern
- Charge coupled device captured tiles are autocorrelated with each other to ensure proper alignment and stitched together in a single, massive seamless image
- Line based scanning
- Servomotor based slide stage moves in a jitter free linear fashion on a single axis of acquisition
- Group of images is produced in the form of long, uninterrupted strips or lines
Techniques used in scanners with slide staining
- Bright field
- Emulates standard bright field microscopy and is most common and cost effective
- Fluorescent
- Used to digitize fluorescently labeled slides (i.e. fluorescent immunohistochemistry, fluorescent in situ hybridization)
- Captures images as tiles
- Multispectral
- Captures spectral information across the spectrum of light
- Applied to both the bright field and fluorescent settings
Software
- Image viewer
- Software utilized to navigate digital slides
- Allows users to view and navigate (pan and zoom) virtual slides on a digital screen
- Image analysis
- Iterative process of adjusting the algorithm parameters, running the algorithm on a subset of images and evaluating the algorithm performance until sufficient algorithm performance is achieved
Categories of measurements
- Area based
- Basic assessments, for example, quantifying the areas (2 dimensional) of a certain stain (e.g. chemical or immunohistochemistry stain), the area of fat vacuoles or other events present on a slide
- Cell based
- Identifying and enumerating objects, e.g. cells
- Enables subsequent assessment of subcellular compartments
Pathologist's role in image analysis workflow
- To ensure the value and quality of generated data
- Value: technical knowledge of tissue handling, fixation, processing and staining, as well as the specialty expertise in biology, histology, pathology, pathophysiology, biomarker expression, comparative anatomy, etc.
- Quality: quality of the tissue, histology slide, stain and scan
- Validity of image analysis data can be greatly hampered by performing analysis on low quality tissue / histology slides or improperly optimized staining results
- Preanalytical variables such as interval between tissue harvest and fixation and total fixation time are often poorly controlled
Clinical validation
- Validation refers to the demonstration of equivalent diagnostic performance between digital slides and glass slides examined
- According to the College of American Pathologists (CAP), validation of the entire whole slide imaging system that involves trained pathologists should be performed in a manner that emulates the laboratory's actual clinical environment
- CAP recommends including at least 60 routine cases per application to assess interobserver diagnostic concordance between digitized and glass slides, viewed at least 2 weeks apart (Arch Pathol Lab Med 2013;137:1710)
Clinical applications
- Primary diagnosis
- Consultation (second opinions)
- Remotely interpreting frozen sections
- Remotely viewing immunostains
- Showcasing pathology slides at tumor boards
- Archiving and retrieval
- Performing image analysis
- Proficiency training
Nonclinical applications
- Education
- Clinical trials / research
- Customized reporting
- Digitization
- Data mining
Recent advances
- High definition hematoxylin and eosin test for digital pathology
- Color calibration slide to promote color standardization
- Vendor neutral viewers (e.g. OpenSlide)
- Usage of enhancement to avoid tissue folds interference with image analysis algorithms
Limitations
- Limiting technology and regulatory issues
- Image quality
- Cannot scan all materials (e.g. cytology, microbiology)
- Cost of the systems
- Digital slide storage
- Inability to handle high throughput routine work
- Regulatory barriers in certain countries
- User unfriendly ergonomics
- Increases viewing time
- Pathologists' reluctance to use whole slide imaging
Videos
Whole slide imaging overview
Scanning (MikroScan D2)
Board review style question #1
Tile based scanning is
- An iterative process of adjusting the algorithm parameters and running the algorithm on a subset of images
- Robotics controlled motorized slide stage that obtains large numbers of square image frames and assembles them into a mosaic pattern
- Servomotor based slide stage that moves in a jitter free linear fashion on a single axis of acquisition
- Software utilized to navigate digital slides
Board review style answer #1
B. Robotics controlled motorized slide stage that obtains large numbers of square image frames and assembles them into a mosaic pattern
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Reference: Whole slide imaging fundamentals
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Reference: Whole slide imaging fundamentals
