Transcript No Slide Title

The Development of Imaging Standards for
Pathology
Lab Infotech Summit
March 2-4, 2005
Las Vegas, Nevada
Jules J. Berman, Ph.D., M.D.
Program Director, Pathology Informatics
Cancer Diagnosis Program, NCI, NIH
email: [email protected]
UFO Abductees
Lots of them
They often say about the same thing (independent
confirmations)
All walks of life
Minority are a little crazy
Mostly honest and rational people
One problem: no evidence
Researchers who don’t publish their primary data
Lots of them
They often say about the same thing (independent
confirmations)
All walks of life
Minority are a little crazy
Mostly honest and rational people
One problem: no evidence
After your research data reaches a certain size, the
data becomes the publication, and the journal
articles become tiny editorials that describe or
interpret the data
In a data-intensive world, the data is the center
of the universe. Manuscripts are satellites
revolving around a central large BLOB of data.
What are the tasks involved in data
sharing?
Legal tasks (ip rights, confidentiality, security,
encryption)
Data organization (annotation, ontologies,
classifications, taxonomies, data exchange
specifications)
Data Retrieval/Data analysis (algorithms,
statistics, deep thought)
What are the things that pathologists
share?
Text (reports, protocols, transaction data)
Images (includes annotations of images)
Tissues (35 million archived cases in U.S.
each year)
Standard ways of exchanging images
and the annotations that describe the
image.
Forget about concepts like:
Standard image file formats
Thumbnail inventories
Think about:
Self-describing image files
XML is the greatest information organizing
tool since the invention of the book.
Much more important than HTML
Takes advantage of:
Metadata
Namespaces
Internet
External links
Ontologies
Permits the integration of data held in different databases
Example: Tissue Microarray Data Exchange
Specification
The TMA Specification is an open access document that can
be used without any restriction.
Its development was sponsored by the NCI and by the
Association for Pathology Informatics
Basics of the Tissue MicroArray data exchange specification:
Jules J Berman, Mary Edgerton and Bruce Friedman. The tissue
microarray data exchange specification: a community-based, open source
tool for sharing tissue microarray data. BMC Med Inform Decis Mak. 2003
May 23;3:5
Real-world implementation example:
Jules J Berman, Milton Datta, Andre Kajdacsy-Balla, Jonathan Melamed,
Jan Orenstein, Kevin Dobbin, Ashok Patel, Rajiv Dhir, Michael J Becich.
The tissue microarray data exchange specification: implementation by the
Cooperative Prostate Cancer Tissue Resource. BMC Bioinformatics 2004
Feb 27, 5:19
LDIP (Laboratory Digital Imaging Project)
Association for Pathology Informatics
Pathology Image Data Exchange Specification
Information available at:
http://www.pathologyinformatics.org/ldip.htm
Minutes, charter, interim documents, all public and
downloadable
LDIP (Laboratory Digital Imaging Project)
First organizing conference call….. May 3, 2004
First public presentation of the LDIP data exchange
specification concept… Oct 6, 2004
Projected completion of first draft… Sometime in 2007
Thomas J. Barr
Bruce Beckwith
Ann Cecil
Alton D. Floyd
Jeffrey A. Beckstead
Jules Berman
Bill Beyer
Dave Billiter
Jack A. Zeineh
Mark Newberger
Tony C. Pan
Ulysses Balis
Andy Lowe
Walter Henricks
Mike Szymanski
Mark Tuthill
Kemp Watson
Bruce Friedman
Ole Eichhorn
Stan Schwartz
Keith Kaplan
Amitabh Deshpande
Bill Fester
James M. Crawford
Emily Burns
John Stinson
Mark E. Sobel
Steve Barbee
Bruce Williams
Ohio State University
Harvard
Interscope
NIH
Trestle
Apollo
dmetrix.com
Henry Ford Hospital
Cleveland Clinic
Bioimagene
U of Michigan
Aperio
Nikon
Walter Reed
Olympus
University of Florida
AFIP
Assoc Soc Investigative Pathologists
LDIP Task Groups
1. Communications task group
2. Workshop task group
3. Schema task group
4. File CDE task group
5. Binary object CDE task group
6. Image descriptor task group
7. Specimen CDE task/force
8. Clinical CDE task group
9. Usability task group
10. Messaging task group
11. Review task group
12. Publications/Public Relations task group
Ultimate Goals
Will allow anyone who uses pathology images to
exchange images and accompanying annotations
in a format that can be completely understood by
anyone
Vendors will be able to write simple software that will
be able to port their proprietary images into or out
of the data exchange standard
The standard will be portable to and from DICOM
The standard will permit the integration of
metadata/data pairs with related data in other
databases.
end