proposal for storing whole slide images for pathology in dicom l.
Download
Skip this Video
Loading SlideShow in 5 Seconds..
Proposal for Storing Whole Slide Images for Pathology in DICOM PowerPoint Presentation
Download Presentation
Proposal for Storing Whole Slide Images for Pathology in DICOM

Loading in 2 Seconds...

play fullscreen
1 / 16

Proposal for Storing Whole Slide Images for Pathology in DICOM - PowerPoint PPT Presentation


  • 139 Views
  • Uploaded on

Proposal for Storing Whole Slide Images for Pathology in DICOM. DICOM Working Group 26 1/17/07. Agenda. Introduction Description of Problem Characteristics of Whole Slide Images DICOM Limitations and Characteristics Description of Proposed Solution. Introduction.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about 'Proposal for Storing Whole Slide Images for Pathology in DICOM' - nola


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
agenda
Agenda
  • Introduction
  • Description of Problem
    • Characteristics of Whole Slide Images
    • DICOM Limitations and Characteristics
  • Description of Proposed Solution
introduction
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 problem characteristics of wsi
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
description of problem characteristics of wsi5
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
description of problem characteristics of wsi6

image strips

image pixels

region (strips) to be loaded

region to be viewed

or processed

Description of ProblemCharacteristics of WSI

Simple image organization: Stripped

Does not support efficient panning

description of problem characteristics of wsi7

image pixels

image tiles

region (tiles) to be loaded

region to be viewed

or processed

Description of ProblemCharacteristics of WSI

More complex image organization: Tiled

Does support efficient panning

description of problem characteristics of wsi8

lower resolution,

larger image region

highest resolution,

small image region

Description of ProblemCharacteristics of WSI

Still have an issue with zooming

description of problem characteristics of wsi9

Thumbnail Image (low resolution)

Intermediate Zoom Image Tile

Intermediate Zoom Image (intermediate resolution)

Retrieved image region

Baseline Image (highest resolution)

Baseline Image Tile

Description of ProblemCharacteristics of WSI

Pyramid addresses zooming

description of problem dicom limitations and characteristics
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 problem dicom limitations and characteristics11
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 solution store wsi pyramid as dicom series

Thumbnail Image

Intermediate Image Tiles

Baseline Image Tiles

DICOM Series

Description of Proposed SolutionStore WSI Pyramid as DICOM Series

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

description of proposed solution store wsi pyramid as dicom series13
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 solution characteristics of proposed solution
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
description of proposed solution characteristics of proposed solution15
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
description of proposed solution characteristics of proposed solution16
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