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Proceedings Paper

A shared standard for cytometry and pathology
Author(s): Robert C. Leif; Stephanie H. Leif
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Paper Abstract

Introduction: The development of cytometry standards is complicated by their being relevant to pathology and biological science, which already have standards. CytometryML, the cytometry markup language, is an XML standard for flow and image cytometry, which includes both objects and their relationships, and is based upon existing standards: the International Society for Advancement of Cytometry ( ISAC) FCS, Digital Imaging and Communication in Medicine ( DICOM), and International Digital Publishing Forum (EPUB). Methods: The CytometryML schemas are written in XML Schema Definition (XSD1.1). Object-oriented methodology was employed to create the CytometryML schemas, which were tested by translating specific XSD elements into XML and filling in the values. The attribute based syntax description of relationships in the Resource Description Framework (RDF) has been replaced by an XSD element based implementation. The ISAC Archival Cytometry Standard (ACS) concept of a zipped data container file was further refined to be a EPUB file. Since Table of Contents information is present in an EPUB container, it was minimized in the Relations schema, which replaced the ToC schema of the ACS and includes a modified and extended version of the ToC RDF capabilities. Results: An XML based system that includes the DICOM specified separation of series and instances and includes relationships has been created. Conclusions: CytometryML and EPUB could be used for the transmission of research and medical data and be extension some of the pathology part of DICOM. The CytometryML version of RDF in XSD could be extended to provide XSD with full RDF capabilities.

Paper Details

Date Published: 22 February 2013
PDF: 13 pages
Proc. SPIE 8587, Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XI, 85871L (22 February 2013); doi: 10.1117/12.2006131
Show Author Affiliations
Robert C. Leif, Newport Instruments (United States)
Stephanie H. Leif, Newport Instruments (United States)

Published in SPIE Proceedings Vol. 8587:
Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XI
Daniel L. Farkas; Dan V. Nicolau; Robert C. Leif, Editor(s)

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