proposal for storing whole slide images for pathology in dicom dicom working group 26 1/17/07

Proposal for StoringWhole Slide Images for Pathology in DICOMDICOM Working Group 261/17/07

Agenda• Introduction• Description of Problem

• Characteristics of Whole Slide Images• DICOM Limitations and Characteristics

• Description of Proposed Solution

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

Description of ProblemCharacteristics of WSI

Image dimensions, data size• Typical: 20mm x 15mm @ .25mpp (“40X”) =

80,000 x 60,000 pixels = 4.8Gp = 15GB• Extreme: 50mm x 25mm @ .1mpp (“100X”) =

500,000 x 250,000 pixels = 125Gp = 375GB• x 10 Z-planes => 3.75TB


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


Simple image organization: Stripped

Does not support efficient panning

image strips

image pixels

region to be viewedor processed

region (strips) to be loaded


More complex image organization: Tiled

Does support efficient panning

image pixels

region (tiles) to be loaded

region to be viewedor processed

image tiles


Still have an issue with zooming

lower resolution,larger image region

highest resolution,small image region


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

Description of ProblemDICOM Limitations and Characteristics

DICOM Limitations• 16-bit signed integer for pixel dimensions: 32K x 32K• 32-bit signed integer for image object size: 2GB• No subregion access to images

Description of ProblemDICOM 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

Description of Proposed SolutionStore 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

Description of Proposed SolutionStore 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)

Description of Proposed SolutionCharacteristics 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


• 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


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• As per current DICOM specification

• 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

proposal for storing whole slide images for pathology in dicom dicom working group 26 1/17/07

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