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
Spend most of this talk on Sup 145, but a brief discussion of Sup 122

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
40:1 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 gives spatial location for each tile: X, Y, and Z (focal plane)
Multiple focal planes
Multi-frame image object
Fixed Header
Per-frame header
Dimension data
Pixel data

6. 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)

7. Z planes may track curved surface
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

10. 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 be pre-computed
Hierarchical pyramid
May add ~ 33% to size of data

11. 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 multiple Z-planes, color planes
Baseline
Image
All image objects
typically in 1 DICOM Series

12. 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

13. 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

14. 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

15. 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)

16. Anatomic Pathology Imaging Workflow
Interpretation Worklist
by accession
Pathology order
Slide preparation
history data
LIS /
APLIS
Slide preparation
Imaging task
completion w/
list of images and specimen IDs
Specimen accessioning data
Modality Worklist Query
by slide barcode
Imaging task w/
slide preparation
history data
Workstation
Gross
specimen
accessioning
Images
Images
Whole Slide
Scanner
Our attention up to now has been on the WSI image itself, the output from a whole slide scanner modality. However, that scan process must be seen as just one step in the entire anatomic pathology workflow, which begins with collection of the specimen in a surgical or biopsy procedure, or even earlier with the original diagnostic exam. Detailed discussion of this workflow is not within the scope of this presentation, but I will briefly address specimen management in DICOM as specified in Supplement 122.
Surgical or
biopsy
procedure
Images w/ slide prep history
Images – X-ray, U/S, optical, etc.
PACS

17. 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

18. Specimen Imaging Information Model
Basic DICOM 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)

19. 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