Transcript Pathology specimen module

DICOM INTERNATIONAL
CONFERENCE & SEMINAR
April 8-10, 2008
Chengdu, China
Pathology in DICOM – Progress
from Working Group 26 and IHE
Bruce BECKWITH(1), Christel Daniel LE BOZEC(2),
Marcial GARCIA-ROJO(3), John GILBERTSON(4), Harry SOLOMON (5)
1) Department of Pathology, North Shore Medical Center, Salem, MA. 2)
INSERM UMRS 872, Université René Descartes Paris, France. 3) Department
of Pathology, Hospital General de Ciudad Real, Spain. 4) Department of
Pathology, Massachusetts General Hospital, Boston, MA. 5) GE Healthcare
Integrated IT Solutions, Barrington, IL, USA
Presenter: Marcial García Rojo
Pathology
• Pathology (understanding the basis of
the disease) is a visually rich medical
specialty
– Led by Radiology it is quickly moving toward
extensive use of digital images.
– Important differences between the imaging
processes in the two specialties.
– Adapt current DICOM standard to
accommodate unique aspects of imaging in
Pathology.
Pathology Images
• Gross images:
– biopsies, surgical specimens, autopsy. Videos.
• Microscopic images:
– Histological sections (biopsies, cell blocks,
autopsies). Staining and special techniques.
– Cytology, dispersions.
• Molecular Pathology:
– FISH, CISH, SISH (microscopy).
– Agarose gels.
– Sequencing.
DICOM Service
Consistent Presentation
Acquired
Display
Print
Medical images web service
Tools in image viewer
Image Consistent
Presentation
What the Pathologist
sees:
What the Reviewing
Physician Sees:
Area Of
Interest
Area Of
Interest
Original Image
& Presentation State
Annotate
Annotate
The Pathologist’s
Transformations Are
Saved
Prepared Image
Zoom
Flip
Original Image
Window Level
Original Image
The Pathologist’s
Transformations Are
Lost
Original Image
DICOM and Pathology
• Specific DICOM objects (“Information Object
Definitions”) are defined for Pathology
• Modification and/or extension are necessary
for two main reasons:
– DICOM model did not provide a strong mechanism for
describing the specimen being imaged or associating
a particular specimen with a particular image.
– Some pathology-related image formats (whole-slide
images, multispectral images, flow cytometry, etc) do
not have applicable DICOM Information Object
Definitions.
Working Group 26
•
It was established in September 2005
with the two immediate aims:
1. Update and extend the data model used to
describe pathologic specimens which are
the subject of imaging procedures.
2. Create a mechanism to store, retrieve and
view microscope whole slide images within
the DICOM framework.
WG26. Participants
• Representatives from pathology
professional societies in Europe, Japan
and the US.
• Liaison with the HL7 Anatomic
Pathology, IHE-pathology and
Laboratory Special Interest Groups
(e.g. European COST IC0604).
DICOM Supplement 122
• Defines a specimen data model to
accommodate a wide variety of relevant
information needed to interpret
pathology images:
– type of specimen,
– procedure used to obtain specimen,
– physical and chemical processing,
– sampling and sub-sampling methods, etc.
Unifying concepts
• An important part of the Supplement is establishing
uniform definitions for the major concepts.
• Specimen is defined as a physical object considered
by the laboratory as a single discrete, uniquely
identified unit that is the subject of one or more
steps in the diagnostic workflow.
– Objects at all levels of processing (from fresh tissue to sections
made from embedded tissue, or dispersions).
• Container: Where specimens (1 or multiple) are
physically placed.
– Buckets, cassettes, vials, and slides.
DICOM Model for Specimens
Patient
1
1
Is
source
of
Has
n
Study
n
1
Contains
n
Equipment
1
Modality
n
Creates
Series
1
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
Compatibility
• The Supplement also addresses
compatibility between the new
Specimen Module and the Specimen
Identification Module currently defined
in the standard
• The decision was: To retire the old
DICOM specimen identification module
Whole Slide Imaging
• Unique challenges:
– In terms of size (they may contain billions or
even trillions of pixels)
• Over 1 GB compressed file / slide.
– Access functionality
• Mimic the experience of viewing a physical
microscope slide.
Viewing large images
• Sending small subsets of the image
data in response to interactive user
commands.
• Proposed solution for incorporating
these whole slide images into the
DICOM standard in a manner that will
enable interoperability and support
rapid and dynamic viewing.
Universidades de Tampere y
Helsinki
Universidades de Tampere y
Helsinki
Revised specimen module
• Supplement 122 provides for “Specimen Module and
Revised Pathology SOP Classes.”
• While DICOM Supplement 15 added the concept of
specimens, the location of specimens in the DICOM
information model had not been explicitly stated,
and current specimen identification is at the Patient
level.
• New Specimen Module at the level of the Image.
• Specimen that forms the immediate subject of the
image is identified, together with critical specimen
information, such as description, specimen ancestry
and processing, necessary to interpret the image.
Required changes in DICOM
• The Specimen Module has been harmonized with the
HL7 v2 SPM segment and the HL7 v3 draft Specimen
Domain Information Model.
• Existing Accession Number at the study level may
be reused.
• No changes to the information or real world models
in DICOM are required .
• An extension of the DICOM information model for
specimen-related information is provided.
• Old Specimen Identification Module is retired from
all IODs. Does it affect existing implementations?
Probably not, since there were few, if any, actual
implementations that used the old specimen
identification module. Minimal problems expected.
Modalities
• Modalities Worklist
– Modalities must obtain the specimen identification
and include it in the acquired images.
– Pathology information system provides the attributes
of the Specimen Module for each specimen being
imaged (IHE profile).
– In radiology, the imaging subject is the patient; in
pathology, the imaging subject is the specimen
derived from the patient.
• Modality Performed Procedure Step
– Laboratory Information System can obtain the list of
images created for each specimen (IHE Profile).
Virtual Slides in DICOM
• “As PACS vendor we see the WSI as one of
the major adventures of the next years.”
• “For Pathology it is of great importance that
images sent from the scanner are already
formatted for efficient distribution out of the
PACS.”
• “A Pathology PACS will have to manage the
"through-streaming" of the scanner device to
the viewing clients.”
(Ralf Zwönitzer. August, 2006. WG26 mailing list)
Advantages of DICOM in
Pathology
• Organization: Central repository of
medical images for all medical
specialties: PACS.
• Integration with e-Health Record.
• One viewer for all medical images.
• Independence of
– devices manufacturers.
– proprietary file formats.
Standards: IHE. Actors &
Transactions
An example of DICOM
implementation in Pathology
Conclusions
• Digital images and virtual slides are already
being commonly used in Pathology, mainly
for second opinion and continuing education.
• Virtual slides are a important challenge to
existing standards.
• DICOM standard in Pathology is needed for
interoperability and long term solutions.
• PACS should be able to manage over 50 TB
per year.
• JPEG 2000 (JPIP) has been considered as an
alternative by some groups.