CytometryML, a markup language for analytical cytology

Proceedings of SPIE - The International Society for Optical Engineering

Volumn 4962, Issue , 2003, Pages 288-297

  Leif, Robert C ^a   Leif, Stephanie H ^a   Leif, Suzanne B ^a  

^a XML Med   (United States)

Author keywords

Cytometry Language; Cytometry Markup; CytometryML; DICOM; FCS; XML

Indexed keywords

INDEXING (OF INFORMATION); INTERFACES (COMPUTER); WAVEFORM ANALYSIS; XML;

CYTOMETRY LANGUAGE;

CYTOLOGY;

EID: 0242665664     PISSN: 0277786X     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1117/12.486320     Document Type: Conference Paper

References (19)

1. L. Seamer, B. Bagwell, L. Barden, M. Christofferson, L. E. Magruder, G. Malachowski, R. F. Murphy, D. Redelman, G. C. Salzman, and J. C. S. Wood. "Data File Standards Committee of the International Society for Analytical Cytology (ISAC), "Data File Standard for Flow Cytometry, Version FCS3.0," http://www.isac-net.org/1996.
2. L. C. Seamer, C. B. Bagwell, L. Barden, D. Redelman, G. C. Salzman, J. C. S. Wood, and R.F. Murphy, "Proposed New Data File Standard for Flow Cytometry, Version FCS 3.0.", Cytometry 28, 118-122, 1997.
3. R. C. Leif and S. B. Leif, "Evolution of Flow Cytometry Standard, FCS3.0, into a DICOM-Compatible Format". Optical Diagnostics of Biological Fluids and Advanced Techniques in Analytical Cytology, Ed. A. V. Priezzhev, T. Asakura, and R. C. Leif. A. Katzir Series Editor, Progress Biomedical Optics Series, SPIE Proceedings Series, Vol. 2982, pp. 354-366, 1997.
4. R. C. Leif and S. B. Leif, "A DICOM Compatible Format for Analytical Cytology Data", in Optical Investigations of Cells In Vitro and In Vivo, D. L. Farkas, R. C. Leif, B. J. Tromberg, Editors, A. Katzir Biomedical Optics Series Ed Proc. of SPIE Vol. 3260, ISBN 0-8194-2699-7 pp. 282-289, 1998.
5. R. C. Leif, and S. B. Leif, "A DICOM Compatible Format for Analytical Cytology Data, that can be Expressed in XML", Optical Diagnostics of Living Cells IV, D. L. Farkas and R. C. Leif, Editors, SPIE Proceedings Vol. 4260 pp. 238-48, 2001.
6. R. C. Leif, S. B. Leif, and S. H.Leif, "CytometryML, An XML Format based on DICOM and FCS for Analytical Cytology Data", submitted to Cytometry.
7. H. S. Thompson, D. Beech, M. Maloney, and N. Mendelsohn. XML Schema Part 1: Structures, W3C® (2001); www.w3.org/TR/2001/REC-xmlschema-1-20010502/2001.
8. P. V. Biron, A. Malhotra. XML Schema Part 2: Datatypes, W3C® (2001); www.w3.org/TR/2001/REC-xmlschema-2-20010502/2001.
9. Digital Imaging and Communications in Medicine (DICOM) PS 3.3 - 2001, A.34 Waveform Information Object Definitions, p. 112 and C.10.8 Waveform Identification Module pp. 489-499, National Electrical Manufacturers Association, VA, USA, 2001. http://medical.nema.org/dicom/2001/01_03PU.PDF.2001
10. T. Bray, J. Paoli, C. M. Sperberg-McQueen, E. Maler, Editors, Extensible Markup Language (XML) 1.0 (Second Edition) W3C Recommendation 6 October 2000. http://www.w3.org/TR/REC-xml/ 2000
11. N. G. Leveson, Safeware, System Safety and Computers, Addison-Wesley, ISBN 0-201-11972-2 p. 419, 1995.
12. Digital Imaging and Communications in Medicine (DICOM) PS 3.6 - 2001, Part 6: Data Dictionary, 6 Registry of DICOM data elements, pp. 5-60, 2001. http://medical.nema.org/dicom/2001/01_06PU.PDF
13. ECMA, Originally, European Computer Manufacturers Association. Now, ECMA International - European association for standardizing information and communication systems, http://www.ecma.ch/
14. Digital Imaging and Communications in Medicine (DICOM) PS 3.3 - 2001 Table C.10-8, Waveform Identification Module Attributes, Note: "The Acquisition Datetime (0008,002A) is the time of the original waveform data capture. Derived waveforms which are processed (e.g., averaged or filtered) and encoded subsequent to the waveform Acquisition Datetime have a Content Date (0008,0023) and Content Time (0008,0033) representing the time of the processing. In all cases the actual date and time of creation of the SOP (Service-Object Pair) Instance for transmission or storage may be recorded in the Instance Creation Date (0008,0012) and Instance Creation Time (0008,0013)". 2001
15. Redelman D, Coder DM. "Cell subset (CS) parameter to record the identities of individual cells in flow cytometric data." Cytometry: 18, pp. 95-102, 1994.
16. Mathematical Markup Language (MathML) Version 2.0, W3C Recommendation 21 February 2001. Carlisle D, Ion P, Miner R, Poppelier N, editors. http://www.w3.org/TR/2001/REC-MathML2-20010221/ 2001.
17. LOINC® and RELMA™ The Regenstrief Institute, http://www.regenstrief.org/loinc/loinc_information.html and LOINC® Database Version 2.05, Released: February 8, 2002 http://www.regenstrief.org/loinc/loincdb.pdf, 2002.
18. R. F. Murphy. International Society for Analytical Cytology, Data Standards Committee Meeting Minutes, Date: January 4-5, 2002. http://www.isac-net.org/ 2002.
19. G. Schadow, C. J. McDonald. The Unified Code for Units of Measure (UCUM), Version 1.4, April 27, 2000. Regenstriefinstitute for Health Care. http://aurora.rg.iupui.edu/UCUM/UCUM.pdf, 2000.