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DICOM and the Pathology Community Experience

DICOM and the Pathology Community Experience. Bruce Beckwith, MD. Scanner. Whole Slide Imaging (WSI). Pathology Disciplines. Tissue (Surgical) Pathology Tissue from biopsies, resections & autopsies Cytology Individual cells from smears/scrapings or fluids Clinical laboratory

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DICOM and the Pathology Community Experience

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  1. DICOM and the Pathology Community Experience Bruce Beckwith, MD

  2. Scanner Whole Slide Imaging (WSI)

  3. Pathology Disciplines • Tissue (Surgical) Pathology • Tissue from biopsies, resections & autopsies • Cytology • Individual cells from smears/scrapings or fluids • Clinical laboratory • Blood smears, protein electrophoresis, etc.

  4. Surgical Pathology Workflow • Pathology workflow starts with a specimen • Dissection • Chemical processing • Cut thin sections and place on glass slides • Stain with a variety of techniques • Chemical • Immunochemical • in-situ hybridization

  5. Why Move To Digital Imaging? • Location independence • Sharing of images with clinicians • Enables new analysis techniques • Computerized screening of pap smears • Image analysis for quantitation of special stains • ? Computer aided diagnosis for other specimens

  6. Comparison of Digital Imaging Radiology Digital acquisition Manageable file size Many clinician interpretable Cost savings compared to analog Computer aided detection formammograms Pathology Mainly analog data which is digitized Very large file size in pathology Some clinician interpretable Incremental costs in addition to analog Computer assisted screening for pap smears

  7. Resolution Challenge

  8. The Image Size Challenge 1 focal plane 24 bit color 40x magnification 15 Gigabytes 10 focal planes 24 bit color 40x magnification 3.75 Terabytes

  9. Navigation Challenge • Main challenge is rapid pan, zoom, focus, advancing to next slide • Intuitive “driving” of the slide will help transition • Some equipment is trying to recreate microscope “feel”

  10. Slide Navigation Device

  11. DICOM Digital Imaging and Communications in Medicine Voluntary standards organization Image exchange standard for CLINICAL images 27 working groups Anyone with a material interest may participate Version 3 of standard released 1992

  12. DICOM Overview Communication standard High level standard, conceptual Facilitates interchange, doesn’t mandate internal storage formats within PACS Image object definitions are central Widely adopted in radiology Addresses workflow as well as images

  13. Pathology in DICOM • Visible light supplement approved 1999 • Incomplete and rarely used • Doesn’t support the complexity of Pathology practice • Pathology WG needed • Created WG-26 Fall 2005 • Has met about 20 times • Representatives from most major pathology imaging vendors • Also pathologists, consultants and researchers • 90+ subscribers to email listserve • 60+ organizations • >10 countries

  14. WG-26 Goals • Initial goals: • Extend minimal capabilities to describe specimens in DICOM • Create a mechanism to allow exchange and use of whole slide microscopic images within DICOM • Long term goals: • Other imaging modalities, such as multi-spectral images, electron microscopy, flow cytometry, clinical lab images

  15. Supplement 122 • Specifies a specimen description model which allows description of: • Type of specimen • Procurement and processing steps • Sampling methods • Physical attributes of slides • Final text approved June 2008

  16. Pathology Imaging in DICOM Base Std Supp 122

  17. Implementation Issues • Supp 122 has the needed data elements, BUT most AP LIS Systems don’t have these data at the SPECIMEN level, if at all • Unique slide ID may not be explicitly present • No ability to identify subregions of a slide/block • Staining and fixation information often co-mingled • Specimen descriptions difficult to parse out from large text blocks • Dictionaries may be poorly implemented

  18. Supplement 145 – Whole Slide Images • Need a new DICOM Image Object Definition • Challenges • Vast size • Need for intuitive and fast viewing interface • DICOM specific issues • Image pixel dimensions limited to 64k x 64k • Image size description limited to 4GB • Desirable to be backwards compatible • Efficient sub-region access • Most DICOM services assume entire image transmission

  19. Tiling and Multi-frame encoding Fixed Header Dimension data Pixel data Per-frame header Multi-frame image object Whole Slide Image divided into tiles Each tile encoded into a frame of multi-frame image object Per-frame header givesspatial location for each tile: X, Y, and Z (focal plane) H Solomon GE

  20. Image Pyramid Single frame image Thumbnail Image Multi-frame image (single object) Intermediate Image Multi-frame image (single object)may include multipleZ-planes, color planes Baseline Image All image objects typically in 1 DICOM Series H Solomon GE

  21. 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 H Solomon GE

  22. Supplement 145 - Next Steps Supplement approved August 2010 DICOM is now able to handle most pathology and lab images Most slide scanner vendors have been involved, along with some PACS vendors Need to engage LIS vendors and publicize these changes

  23. Pathology Imaging Workflow Caseinfo Slide prep data LIS / APLIS Slide preparation Pathology Order & Specimen info Slide ID Scanning orders Images Specimen Images Images w/slide prep data PACS Images – X-ray, U/S, optical, etc. Pathology Workstation Gross specimen accessioning Whole Slide Scanner Surgical or biopsy procedure Adapted from H Solomon GE

  24. Image Sharing • Currently some pathologists include snapshots in reports • Tumors, specimen margins, unusual findings, etc • WSI allows ability to review slides remotely with clinicians • The ability to correlate slides with other images would be useful • Gross specimen images • Endoscopy images • Radiology images

  25. Challenges to Wider Adoption • Storage and bandwidth • PACS storage is relatively expensive • Don’t want to transfer entire huge files • Pathology systems need to become more image centric (as opposed to report centric) • EMR’s need to be able to accept or connect to images and display correctly • Security, credentialing, optimized viewers, etc

  26. Summary WG-26 has created supplements to incorporate modern digital pathology within DICOM The collaboration of DICOM, IHE and HL7 has led to a broad based standards effort for digital pathology The availability of a digital workflow for images will enable major changes in the practice of pathology DICOM support for radiology, pathology, surgery, and radiation therapy opens the door for true integration of data from these areas 26

  27. Acknowledgements • Members of DICOM WG-26 • Harry Solomon, mentor to WG-26 • IHE Anatomic Pathology WG • HL7 Anatomic Pathology WG • DICOM Website: http://medical.nema.org/

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