The Development of Imaging Standards for Pathology

Lab Infotech SummitMarch 2-4, 2005Las Vegas, Nevada

Jules J. Berman, Ph.D., M.D.Program Director, Pathology InformaticsCancer Diagnosis Program, NCI, NIHemail: bermanj@mail.nih.gov

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. BarrBruce BeckwithAnn CecilAlton D. FloydJeffrey A. BecksteadJules BermanBill BeyerDave BilliterJack A. ZeinehMark NewbergerTony C. PanUlysses BalisAndy LoweWalter HenricksMike Szymanski

Mark TuthillKemp WatsonBruce FriedmanOle EichhornStan SchwartzKeith KaplanAmitabh DeshpandeBill FesterJames M. CrawfordEmily BurnsJohn StinsonMark E. SobelSteve BarbeeBruce Williams

Ohio State UniversityHarvardInterscopeNIHTrestleApollodmetrix.comHenry Ford HospitalCleveland ClinicBioimageneU of MichiganAperioNikonWalter ReedOlympusUniversity of FloridaAFIPAssoc Soc Investigative Pathologists

LDIP Task Groups1. 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 GoalsWill 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.

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