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Proceedings Paper

CytometryML and other data formats
Author(s): Robert C. Leif
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Paper Abstract

Cytology automation and research will be enhanced by the creation of a common data format. This data format would provide the pathology and research communities with a uniform way for annotating and exchanging images, flow cytometry, and associated data. This specification and/or standard will include descriptions of the acquisition device, staining, the binary representations of the image and list-mode data, the measurements derived from the image and/or the list-mode data, and descriptors for clinical/pathology and research. An international, vendor-supported, non-proprietary specification will allow pathologists, researchers, and companies to develop and use image capture/analysis software, as well as list-mode analysis software, without worrying about incompatibilities between proprietary vendor formats. Presently, efforts to create specifications and/or descriptions of these formats include the Laboratory Digital Imaging Project (LDIP) Data Exchange Specification; extensions to the Digital Imaging and Communications in Medicine (DICOM); Open Microscopy Environment (OME); Flowcyt, an extension to the present Flow Cytometry Standard (FCS); and CytometryML. The feasibility of creating a common data specification for digital microscopy and flow cytometry in a manner consistent with its use for medical devices and interoperability with both hospital information and picture archiving systems has been demonstrated by the creation of the CytometryML schemas. The feasibility of creating a software system for digital microscopy has been demonstrated by the OME. CytometryML consists of schemas that describe instruments and their measurements. These instruments include digital microscopes and flow cytometers. Optical components including the instruments' excitation and emission parts are described. The description of the measurements made by these instruments includes the tagged molecule, data acquisition subsystem, and the format of the list-mode and/or image data. Many of the CytometryML data-types are based on the Digital Imaging and Communications in Medicine (DICOM). Binary files for images and list-mode data have been created and read.

Paper Details

Date Published: 21 February 2006
PDF: 7 pages
Proc. SPIE 6088, Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues IV, 60880L (21 February 2006); doi: 10.1117/12.645295
Show Author Affiliations
Robert C. Leif, Newport Instruments (United States)


Published in SPIE Proceedings Vol. 6088:
Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues IV
Daniel L. Farkas; Dan V. Nicolau; Robert C. Leif, Editor(s)

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