Download LDIP Blog for Lab IntoTech Summit, December 7

Annotating and Integrating Pathology Images: Why Bother?!
Jules J. Berman Ph.D., M.D. and Bruce A. Friedman, M.D.
December 7, 2004
The Association for Pathology Informatics (API) has recently embarked on a project to develop a
data exchange specification for pathology images. The effort currently has 30 participants
working in12 task groups and is expected to take 3-5 years for completion [1]. The sole purpose
of the project is to provide the pathology community with a uniform way of annotating and
exchanging pathology images.
When undertaking a new technical project, it's worthwhile taking stock of reality and asking if
it's really worth the bother. After all, there are plenty of standard image formats (maybe, too
many), we all know how to send images around by email, and many of us have already figured
out how to include images in surgical pathology reports.
Basically, the impetus for the project relates to our expectations of the growing importance of
data annotation and date integration. In particular, it relates to a critical role for pathologists as
the only professionals who can unite research datasets with clinical datasets [related to pathology
specimens]. Despite the long-heralded arrival of a revolution in biomedical science, the pace
of medical progress has slowed in the past decade. This is the opinion of the FDA and of others,
based on counting new tests, therapies, and diagnostic devices [2-5]. There doesn't seem to be
any slowdown in fundamental scientific discoveries, but there is a real disconnect between
discovery and clinical implementation. What seems to be lacking is a way of quickly and
efficiently validating candidate markers and tests and their therapeutic effects using datasets of
pathology specimens.
When you start talking about connecting research data with clinical data, you're opening the big
issue of data integration. Data integration occurs when you can sensibly relate [e.g. retrieve,
compare, analyze, marge] data of one type type with data of another type. In order to do these
things, the data needs to be annotated. Data annotation involves making sure that every piece
of data in a record is provided with another set of information that describes the data (so-called
metadata or data about the data). Once data has been annotated, it can be associated with other,
related data [data integration], even when the other data is found in a seemingly unrelated
database. In the past few years, biomedical informatics has transformed into the science
that derives biomedical value from computations performed on annotated databases [6].
This brings us back to pathology image annotation. The data exchange specification will
conform to the same kind of data annotation/integration that biologists, rocket scientists and even
businessmen have come to trust - eXtensible Markup Language (XML). The Specification will
include descriptors for the specimen and the manner in which the specimen was prepared, the
image aquisition devices, the binary representations of the image, clinical/pathologic
information, and information related to confidentiality, intellectual property and authenticity of
the image [1]. When an image file describes itself completely [and that's really our goal], the
image becomes a database that is keyed to a particular specimen. Miraculously, this
image-data-object has properties that are of immense value to image vendors, pathologists,
students, and researchers.
Image vendors can keep their proprietary formats and still ensure their customers that the
captured images can be exported to collaborators who use different systems. All they need to do
is write a simple program that ports their image into the image exchange specification. Since
the image exchange specification will have well-defined descriptors for logical parts of any
image, including the binary, this should be easy. If the image exchange specification is widely
adopted, pathologists won't need to worry anymore about vendor "lock-in."
Pathologists can use the data exchange specification to strip relevant parts [i.e. the viewable
binary] from the file and insert it into a pathology report. The pathologist can also send the fully
annotated image file, or any part of the file, to other pathologists for the purpose of consultation
or collaboration. Real-time messaging of the image file can be used in telepathology.
Collections of image files can be merged into a teaching database. Clinical and pathologic
annotations will greatly enhance the didactic value of the images. Databases using the
specification can easily be merged into mega-image databases.
Perhaps most importantly, the image file can be integrated with biologic datasets, making it
possible to discover or validate relationships between genomic, proteomic or metabolomic
expression patterns against morphologic/pathologic/clinical features. The availability of large
numbers of annotated images keyed to specimens provides new opportunities for medical
advancement.
So, is it worth the bother? It depends on your view of the future.
References:
1. Laboratory Digital Imaging Project. [www.pathologyinformatics.org/ldip.html].
2. Innovation or Stagnation: Challenge and Opportunity on the Critical Path to New Medical
Products. U.S. Department of Health and Human Services, Food and Drug Administration
(2004).
3. Anderson NL, Anderson NG. The human plasma proteome: history, character and diagnostic
prospects. Mol. Cell. Proteomics 1, 845-867 (2002).
4. Benowitz S. Biomarker boom slowed by validation concerns. J. Natl. Cancer Inst. 96(18),
1356-1357 (2004).
5. Evans WE, Relling MV. Pharmacogenomics: translating functional genomics into rational
therapeutics. Science. 286, 487-491 (1999).
6. Berman JJ. Pathology data integration with XML. In press, Human Pathology
file: c:\ftp\jb_blog.rtf