DICOM and the Pathology Community Experience Bruce Beckwith, MD
Jan 03, 2016
DICOM and the Pathology Community Experience
Bruce Beckwith, MD
Whole Slide Imaging (WSI)
Scanner
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.
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
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
Comparison of Digital ImagingRadiology
• Digital acquisition
• Manageable file size
• Many clinician interpretable
• Cost savings compared to analog
• Computer aided detection for mammograms
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
Resolution Challenge
The Image Size Challenge
1 focal plane24 bit color40x magnification15 Gigabytes
10 focal planes24 bit color40x magnification3.75 Terabytes
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”
Slide Navigation Device
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
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
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
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
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
SpecimenPhysical object
ContainerBox, Block, Slide, etc.
Is child of
n
PreparationStep
Collect, Sample, Stain, Process
Image
Isacquired
on
1
Series
1
Contains
n
1
CreatesEquipment
Modality
1 n
Study
Contains
Patient
1
Has
n
1
n
Issource
of
1
Contains
Contains1 n
n
Has1 n
1
Has
1ComponentBase, Coverslip
n
Pathology Imaging in DICOM
Base Std
Supp 122
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
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
Tiling and Multi-frame encoding
• Whole Slide Image divided into tiles• Each tile encoded into a frame of multi-frame image
object• Per-frame header gives
spatial location for each tile: X, Y, and Z (focal plane)
Pixel dataDimension dataPer-frame headerFixed Header
Multi-frame image object
H Solomon GE
Image Pyramid
All image objectstypically in 1 DICOM Series
Thumbnail Image
Intermediate Image
BaselineImage
Multi-frame image(single object)
Multi-frame image(single object)may include multipleZ-planes, color planes
Single frame image
H Solomon GE
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
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
Pathology Imaging Workflow
Slide prep data
Whole Slide Scanner
Images w/slide prep data
PathologyWorkstation
Images
Gross specimen
accessioning
Specimen Images
Surgical or biopsy
procedure
Images – X-ray, U/S, optical, etc.
Slide preparationCase info
PathologyOrder & Specimeninfo
Slide ID
Scanning orders
Adapted from H Solomon GE
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
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
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
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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/