Proposal for Storing Whole Slide Images for Pathology in DICOM

1
Proposal for StoringWhole 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

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Description of ProblemCharacteristics of WSI

• Image dimensions, data size
• Typical 20mm x 15mm _at_ .25mpp (40X) 80,000 x
  60,000 pixels 4.8Gp 15GB
• Extreme 50mm x 25mm _at_ .1mpp (100X) 500,000 x
  250,000 pixels 125Gp 375GB
• x 10 Z-planes gt 3.75TB

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Description of ProblemCharacteristics 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

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Description of ProblemCharacteristics of WSI

• Simple image organization Stripped
• Does not support efficient panning

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Description of ProblemCharacteristics of WSI

• More complex image organization Tiled
• Does support efficient panning

8
Description of ProblemCharacteristics of WSI

• Still have an issue with zooming

9
Description of ProblemCharacteristics of WSI

• Pyramid addresses zooming

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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

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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

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Description of Proposed SolutionStore WSI
Pyramid as DICOM Series

• Each tile of each level of each plane of WSI
  corresponds to image in series

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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)

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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

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Description of Proposed SolutionCharacteristics
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

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Description of Proposed SolutionCharacteristics
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
• 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