Transcript www.julesberman.info

CaBig
February 6, 2007
Jules Berman, Ph.D., M.D.
Digital Imaging: How it relates to
Pathology
Pathologists who acquire images need to have be
able to convey annotations along with the image.
Identifiers (for patient, specimen and image)
Acquisition data (camera, microscope)
Information about the specimen
Clinical/diagnostic information
Image analysis information
DICOM is the image standard for radiology, and
there's an effort to migrate it to pathology.
DICOM is highly complex, few people outside of
radiology understand it, and it is nothing like
currently used Web (metadata) technologies.
If a medical image standard were developed
today, from scratch, it would probably not
resemble DICOM.
Some of the most important scientific uses of
DICOM cannot be pursued without infringing on
existing patents.
RDF is an XML dialect in which all statements are
triples consisting of a specified subject and a
metadata/data pair that bind to the subject.
You can do many many good things with RDF
1. Build ontologies that classify the subjects of the
triples.
2. Write software agents that infer knowledge from
RDF documents.
3. Retrieve and merge triples from heterogeneous
datasets (i.e., not just other images)
4 Fully specify ANYTHING.
5. Bind descriptive data with binary data (as in
images and annotative data)
At the APIII meeting (September 9-12, 2007,
Pittsburgh), the Association for Pathology
Informatics will freely discuss and distribute
resources or links to resources for the following:
1. An upper level RDF Schema for pathology
image annotation.
2. Method for creating RDF documents that
contain annotations for pathology images.
3. Method for including JPEG images within RDF
documents.
4. Method for including RDF documents in the
headers of JPEG images.
5. Method for pointing to JPEG or DICOM images
from RDF documents.
(Continued)
6. Method for composing multi-image, multi-RDF
image documents.
7. Method for parsing (one or more) RDF
documents and extracting the triples.
8. Method for stripping the header from DICOM
images and converting the header to RDF.
9. Method for converting JPEG to DICOM, DICOM
to JPEG.
The Association for Pathology Informatics is trying
to enhance data sharing, to complement on-going
DICOM activities, and to increase opportunities for
data-intensive translational efforts.
We do this by providing free, accessible methods
for encapsulating image binaries with image
annotations in a way that is portable (to/from
DICOM), that uses a Web specification (RDF),
that can merge image data with data collected by
biomedical researchers, and that can keep pace
with ever-changing technical properties of the
pathology image