1. Proposal for Storing Whole Slide Images for Pathology in DICOM
DICOM Working Group 26
1/17/07

2. Agenda Introduction Description of Problem
Characteristics of Whole Slide Images
DICOM Limitations and Characteristics
Description of Proposed Solution

3. Introduction Pathology is undergoing a transformation
Digital imaging is increasingly important
Driven by availability of instruments for digitizing microscope slides, resulting in whole-slide images (WSI)
WSI are different to other images stored in DICOM
Size - larger
Access patterns – pan, zoom, focus
It is desirable to support WSI for Pathology in DICOM
Will facilitate interoperability with other modalities
Will foster adoption of Digital Pathology

4. Description of Problem Characteristics of WSI
Image dimensions, data size
Typical: 20mm x .25mpp (“40X”) = 80,000 x 60,000 pixels = 4.8Gp = 15GB
Extreme: 50mm x .1mpp (“100X”) = 500,000 x 250,000 pixels = 125Gp = 375GB
x 10 Z-planes => 3.75TB

5. Description of Problem Characteristics of WSI
Access patterns
Pathologists cannot view entire microscope slide at diagnostic resolution
Pan around at low res (2.5mpp = “4X”), then zoom in at high res (.25mpp = “40X”)
Requires organization to support rapid panning & zooming
Multiple Z-planes may be captured
Requires organization to support rapid focusing

6. Description of Problem Characteristics of WSI
Simple image organization: Stripped
Does not support efficient panning
image strips
image pixels
region to be viewed
or processed
region (strips) to be loaded

7. Description of Problem Characteristics of WSI
More complex image organization: Tiled
Does support efficient panning
image pixels
region (tiles) to be loaded
region to be viewed
or processed
image tiles

8. Description of Problem Characteristics of WSI
Still have an issue with zooming
lower resolution,
larger image region
highest resolution,
small image region

9. Description of Problem Characteristics of WSI
Pyramid addresses zooming
Baseline Image Tile
Thumbnail Image (low resolution)
Intermediate Zoom Image Tile
Baseline Image (highest resolution)
Intermediate Zoom Image (intermediate resolution)
Retrieved image region

10. Description of Problem DICOM Limitations and Characteristics
16-bit signed integer for pixel dimensions: 32K x 32K
32-bit signed integer for image object size: 2GB
No subregion access to images

11. Description of Problem DICOM Limitations and Characteristics
DICOM Characteristics
Successful, widely adopted
An important reason why is extension process
DICOM extensions
Conservative – only extend standard when necessary, leverage existing standard
Encourage innovation – involve vendors in process, enable vendors to innovate within [extended] standard
Better products for market
Discourage proprietary solutions
Backward compatible – maximize compatibility with existing [non-extended] systems, degrade gracefully

12. Description of Proposed Solution Store WSI Pyramid as DICOM Series
Each “tile” of each level of each plane of WSI corresponds to image in series
DICOM Series
Thumbnail Image
Intermediate Image Tiles
Baseline Image Tiles

13. Description of Proposed Solution Store WSI Pyramid as DICOM Series
Tile size can vary (240 … 1K … 4K … 32K)
Each resolution level stored separately in the series (typically thumbnail is first)
Each Z-plane stored separately in the series
Each image in series identified by coordinates
X, Y offsets
Zoom (resolution)
Z offset (plane)

14. Description of Proposed Solution Characteristics of Proposed Solution
Works around DICOM limitations
16-bit pixel dimension: okay, tiles will be less than 32K x 32K
32-bit image size: okay, tiles will be smaller than 2GB
No subregion access: okay, each tile is individually addressible as an image
Encompasses storage of single image in a series by itself as proper subset

15. Description of Proposed Solution Characteristics of Proposed Solution
Will require little change by PACS vendors
They already handle images in series
Degrades gracefully for existing DICOM viewers
Thumbnails / low-level images display “as is”
High-res images display as pieces of entire image
(Pathologists will require purpose built viewer)
Rapid pan, zoom, etc.
Simple to implement for WSI vendors
Solution is similar to blocked TIFF, which most WSI vendors use for storing WSI now
Simple to export from DICOM to TIFF
For compatibility with existing viewers, image analysis tools, and other WSI applications

16. Description of Proposed Solution Characteristics of Proposed Solution
Issues not addressed by proposed solution
Compression type
Support uncompressed, lossless (e.g. LZW), and lossy (e.g. JPEG, JPEG2000)
As per current DICOM specification
Transport mechanism
Support image retrieval and JPIP
Multichannel / multispectral data
Solution addresses how to store images and pixels
Not composition / format of pixels
May need to extend DICOM specification to allow format and content of pixels to be defined for images in series