CaBig February 6, 2007 Jules Berman, Ph.D., M.D.

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Presentation transcript:

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