Transcript DICOM-for-Pathology

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
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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 Imaging
Radiology
• 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 plane
24 bit color
40x magnification
15 Gigabytes
10 focal planes
24 bit color
40x magnification
3.75 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
Pathology Imaging in DICOM
Patient
1
1
Is
source
of
Has
n
Study
n
1
Base Std
Contains
n
Equipment
1
Modality
n
Creates
Series
1
Supp 122
Contains
n
Image
1
Is
acquired
on
1
Component
Base, Coverslip
1
n
Has
Container
Box, Block, Slide, etc.
1
n
Specimen
Contains
Physical object
n
Is child of
1
1
n
Has
Preparation
Step
Collect, Sample,
Stain, Process
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
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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
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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)
Multi-frame image object
Fixed Header
Per-frame header
Dimension data
Pixel data
H Solomon GE
Image Pyramid
Single frame image
Thumbnail
Image
Multi-frame image
(single object)
Intermediate
Image
Baseline
Image
Multi-frame image
(single object)
may include multiple
Z-planes, color planes
All image objects
typically in 1 DICOM Series
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
Case info
Slide preparation
Slide prep data
LIS /
APLIS
Pathology
Order &
Specimen
info
Slide ID
Scanning orders
Gross
specimen
accessioning
Surgical or
biopsy
procedure
Specimen
Images
Pathology
Workstation
Whole Slide
Scanner
Images
Images w/
slide prep data
Images – X-ray, U/S,
optical, etc.
PACS
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
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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/