Whole Slide Imaging in DICOM

1
Whole Slide Imaging in DICOM

• Harry Solomon
• GE Healthcare

2
WSI Supplements

• Two DICOM Supplements developed by WG-26
  Anatomic Pathology
• Supplement 145 Whole Slide Imaging
• Adopted August 2010
• Supplement 122 Specimen Module
• Adopted June 2008

3
The Whole Slide Problem

• Need image resolution comparable to optical
  microscope
• Need image access as rapid as microscope (pan,
  zoom, focus)

Yukako Yagi UPMC
4
Digital slides are huge

• Sample size 20mm x 15mm
• Resolution of .25 µm/pixel (40X objective)
• 80,000 x 60,000 pixels 4.8 Gp
• 24-bit color 14.4 GB / slide
• 401 compression only 360 MB / typical slide
• Unless
• Larger specimen
• Higher resolution (100X objective)
• Multiple focal planes
• Multi-spectral imaging (16-bit / band)
• And
• A typical study may be 10 slides

5
Sup 145 Tiling and Multi-frame encoding

• Whole Slide Image divided into tiles
• Each tile encoded into a frame of multi-frame
  image object
• Per-frame header givesspatial location for each
  tile X, Y, and Z (focal plane)

Multiple focal planes
Multi-frame image object
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Z-planes (focal planes)

• Z-planes are identified as nominal physical
  height of image focal plane above reference
  surface (µm)
• Z-plane information is used for relative spatial
  positioning of image planes, and nominal
  inter-plane distance
• An image plane may track variable specimen
  thickness / surface contour, but only one Z-value
  used

? Z
Cover slip
? Z
Specimen
Slide substrate (glass)
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Z planes may track curved surface

• Z plane 1
• Z plane 2
• Z plane 3
• Z plane 4

Tile 1
Tile 2
Tile 3
Tile 4
Tile 5
Tile 6
Tile 7
Tile 8
Viktor Sebestyén Varga 3DHISTECH Ltd.
8
Total Pixel Matrix
Total Pixel Matrix Origin

• Total pixel matrix origin at top left hand corner
  of imaged volume
• Frame (tile) rows and columns align with total
  pixel matrix rows and columns
• Frames limited to 216 columns and rows each
• Total pixel matrix limited to 232 columns and
  rows

Columns ?
Rows
?
Frame Pixel Matrix Origin
Total pixel matrix coordinates used for frame
location and for annotation
9
Sparse tiling

• Slides may have substantial area with no specimen
• Empty tiles may be absent from multi-frame image

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Access Navigation and Zoom

• Need to rapidly access
• High resolution image of small areas
• Facilitated by tilling
• Low resolution image of whole slide
• For overview and navigation
• Intermediate resolutions
• Smooth zooming
• Lower resolution images may bepre-computed
• Hierarchical pyramid
• May add 33 to size of data

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Tiling and multi-frame at all hierarchical levels
Single frame image
Thumbnail Image
Multi-frame image (single object)
Intermediate Image
Multi-frame image (single object)may include
multipleZ-planes, color planes
Baseline Image
All image objects typically in 1 DICOM Series
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Localizer image flavor

• Thumbnail image (single frame) plus navigation
  links to each frame at each resolution
• Each tile of other resolution images has its
  corresponding area identified in thumbnail
• Full description of target tiles
• Object Unique ID and frame number
• Resolution
• Z-plane, color
• Multiple target frames can overlap
• Different resolution, Z-plane, color, etc.
• Presentation and any interactive behavior is not
  defined in standard

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Optical paths
Illumination Method
Illumination
Filters
Lens
Lens
Filters
Sensor

• Each combination of light source, lenses,
  illumination method, detected wavelengths, etc.
  used in a scan is an optical path
• Three primary mandatory attributes
• Illumination color or wavelength
• Illumination method (e.g., transmission,
  epifluorescence , darkfield, differential
  interference contrast)
• Detection color
• Additional optional attributes for lenses,
  filters, prisms, etc.
• Examples
• Full spectrum light, transmission, RGB color
  sensors
• UV excitation, epifluorescence, 535 nm emission
  filter, monochrome sensor

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Multi-spectral imaging

• Typical color image stored with RGB or YBR
  photometric interpretation
• 3 color values / pixel
• Multi-spectral image stored with MONOCHROME
  photometric interpretation
• 1 color value / pixel / color plane
• Multiple color planes may be stored in single
  image object
• Each frame references its optical path in
  per-frame header

3 x 8-bit RGB
n x 16-bit multi-spectral
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Standard DICOM mechanisms for annotation of WSI

• Color Presentation State
• Displayed Area Selection relative to WSI total
  matrix
• Graphic and text annotation with sub-pixel
  location resolution, even with 8M columns or rows
• Segmentation
• Can be created pixel-by-pixel against selected
  frames of original image
• 1-bit/source-pixel, or 8-bits/source-pixel
• Display of segmentation implicitly invokes
  blending with source image
• Structured Reporting
• Captures measurements, clinical observations,
  analyses, and findings
• Real World Value Mapping
• Specifies a mapping of the stored pixel values of
  images into some real world value in defined
  units
• Allows quantitative methods with monochrome
  images (original or derived)

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Anatomic Pathology Imaging Workflow
Slide preparation
Workstation
Gross specimen accessioning
Whole Slide Scanner
Surgical or biopsy procedure
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Sup 122 Specimen Module

• Support for pathology lab workflow,
  specimen-based imaging
• Gross specimens, blocks, vials, slides
• Image-guided biopsy samples
• Specimen Module at image level of hierarchy
• Identification, processing history (especially
  stains applied)
• Modality Worklist can convey Specimen Module
• Enables automated slide scanning devices to fully
  populate image header
• Processing history can be used to set up
  acquisition (based on stain)
• Modality Performed Procedure Step identifies
  imaged specimen
• Allows LIS/APLIS to track images for specimens

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Specimen Imaging Information Model
Disambiguates specimen and container Container is
target of image Container may have more than one
specimen Specimens have a physical derivation
(preparation) from parent specimens When more
than one specimen in an imaged container, each
specimen is distinguished (e.g., by position or
color-coding)
Basic DICOM Information Model
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Enabling Transformation to Digital Pathology

• Supplements 145 and 122 establish the foundation
  for a true market for digital imaging in anatomic
  pathology
• Comparable in importance to the introduction of
  DICOM to radiology in 1993
• Enables quantitation and collaboration
• In the next 5-10 years, we should expect a
  profound transformation of pathology from a
  highly manual process to a digital workflow
• The use of the DICOM Standard across radiology,
  pathology, surgery, and radiation therapy opens
  the door to truly integrated data from screening
  to biopsy to diagnosis to treatment