CytometryML is an effort to produce a set of XML schemas to define Cytometry data. This is an open effort, and we appreciate your help.
As described below in the Abstract of CytometryML and other data formats, there are multiple organizations-groups working on cytometry and pathology imaging standards. These efforts are described in a spreadsheet. Summery of Existing and Proposed Standards and Specifications for Cytometry and Pathology Microscopy. The URLs, Abbreviations, and names of the societies and group involved in the creation of these specifications-standards and other relevant prganizations are given in Standards and Specifications,.
Ideally, all of the groups and societies, whose work is included in the spreadsheet and any others that have been missed should join together to produce one standard. Unfortunately, this may not be possible in the near future. However, these societies and groups should, at least, try to maximize interoperability by using the same data-types. It has been possible as shown in the CytometryML schemas to employ the same standard to describe Flow and Image Cytometry. In fact, both a flow cytometer and a digital microscope were derived by restriction from a generic cytometry instrument.
CytometryML has been divided into two groups of schemas. The first is specific to CytometryML; the second is a set of general utilities (XML_Utilities), which can be used for other applications.
Zip file of CytometryML XML Pages
Zip file of CytometryML Schemas
Zip file of XML_Utilities Schemas
R.C. Leif, S.H. Leif, S.B. Leif, CytometryML, An XML Format based on DICOM for Analytical Cytology Data Cytometry Vol. 54A pp. 56-65 (2003).
Abstract
Background:
Flow Cytometry Standard (FCS) was initially created to standardize software researchers use to analyze, transmit, and store data produced by flow cytometers and sorters. Because of the clinical utility of flow cytometry, it is necessary to have a standard consistent with the requirements of medical regulatory agencies.
Method:1) Extend the existing mapping of FCS to the Digital Imaging and Communications in Medicine (DICOM) standard to include list-mode data produced by flow, laser scanning cytometry, and microscopic image cytometry. FCS list-mode was mapped to the DICOM Waveform Information Object. 2) Create a collection of XML schemas to express the DICOM analytical cytology text based data-types except for large binary objects. 3) Accomplish this creation of a cytometry markup language, CytometryML, in an open environment that is subject to continuous peer review.
Results:The feasibility of expressing the data contained in FCS, including list-mode in DICOM, has been demonstrated; and a preliminary mapping for list-mode data in the form of XML Schemas and documents has been completed. DICOM permits the creation of indices that can be used to rapidly locate in a list-mode file the cells that are members of a subset. DICOM and its coding schemes for other medical standards can be represented by XML schemas, which can be combined with other relevant XML applications, such as Mathematical Markup Language (MathML).
Conclusions:The use of XML format based on DICOM for analytical cytology has met most of the previously specified requirements and appears capable of meeting the others; therefore, the present FCS should be retired and replaced by an open, XML based standard, CytometryML.
R.C. Leif CytometryML and other data formats to be published in Manipulation and Analysis of Biomolecules, Cells, and Tissues III, D. Farkas, D. V. Nicolau, and R. C. Leif, Editors, SPIE Proceeding Vol. 6088 (2006).
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.
R.C. Leif
CytometryML, Binary Data Standards
Manipulation and Analysis of Biomolecules, Cells, and Tissues
II, D. V. Nicolau, J. Enderlein, R. C. Leif, and D. Farkas,
Editors, SPIE Proceeding Vol. 5699, pp. 325-333 (2005).
Abstract
CytometryML is a proposed new Analytical
Cytology (Cytomics) data standard, which is based on a common
set of XML schemas for encoding flow cytometry and digital
microscopy text based data types (metadata). CytometryML
schemas reference both DICOM (Digital Imaging and
Communications in Medicine) codes and FCS keywords. Flow
Cytometry Standard (FCS) list-mode has been mapped to the
DICOM Waveform Information Object. The separation of the
large binary data objects (list mode and image data) from the
XML description of the metadata permits the metadata to be
directly displayed, analyzed, and reported with standard
commercial software packages; the direct use of XML
languages; and direct interfacing with clinical information
systems. The separation of the binary data into its own files
simplifies parsing because all extraneous header data has
been eliminated. The storage of images as two-dimensional
arrays without any extraneous data, such as in the
Adobe® Photoshop® RAW format, facilitates the
development by scientists of their own analysis and
visualization software. Adobe Photoshop provided the display
infrastructure and the translation facility to interconvert
between the image data from commercial formats and RAW
format. Similarly, the storage and parsing of list mode
binary data type with a group of parameters that are
specified at compilation time is straight forward. However
when the user is permitted at run-time to select a subset of
the parameters and/or specify results of mathematical
manipulations, the development of special software was
required. The use of CytometryML will permit investigators to
be able to create their own interoperable data analysis
software and to employ commercially available software to
disseminate their data.
R.C. Leif, S.H. Leif, S.B. Leif,
CytometryML, a Markup
Language for Analytical Cytology in Manipulation
and Analysis of Biomolecules, Cells and Tissues, D. V.
Nicolau, J. Enderlein, and R. C. Leif, Editors, SPIE
Proceedings Vol. 4962 pp 288-297 (2003).
Abstract
Cytometry Markup Language, CytometryML, is a proposed new analytical cytology data standard. CytometryML is a set of XML schemas for encoding both flow cytometry and digital microscopy text based data types. CytometryML schemas reference both DICOM (Digital Imaging and Communications in Medicine) codes and FCS keywords. These schemas provide representations for the keywords in FCS 3.0 and will soon include DICOM microscopic image data. Flow Cytometry Standard (FCS) list-mode has been mapped to the DICOM Waveform Information Object. A preliminary version of a list mode binary data type, which does not presently exist in DICOM, has been designed. This binary type is required to enhance the storage and transmission of flow cytometry and digital microscopy data. Index files based on Waveform indices will be used to rapidly locate the cells present in individual subsets. DICOM has the advantage of employing standard file types, TIF and JPEG, for Digital Microscopy.
Using an XML schema based representation
means that standard commercial software packages such as
Excel and MathCad can be used to analyze, display, and store
analytical cytometry data. Furthermore, by providing one
standard for both DICOM data and analytical cytology data, it
eliminates the need to create and maintain special purpose
interfaces for analytical cytology data thereby integrating
the data into the larger DICOM and other clinical
communities. A draft version of CytometryML is available at
www.newportinstruments.com.
R.C. Leif and S.B. Leif,
A DICOM Compatible
Format for Analytical Cytology Data, that can be Expressed in
XML in Optical Diagnostics of Living Cells IV, D. L.
Farkas and R. C. Leif, Editors, SPIE Proceedings Vol. 4260
pp. 238-48 (2001).
Abstract
Flow Cytometry data can be directly mapped to the Digital Imaging and Communications in Medicine, DICOM standard. A preliminary mapping of list-mode data to the DICOM Waveform information Object will be presented. This mapping encompasses both flow and image list-mode data. Since list-mode data is also produced by digital slide microscopy, which has already been standardized under DICOM, both branches of Analytical Cytology can be united under the DICOM standard. This will result in the functionality of the present International Society for Analytical Cytology Flow Cytometry Standard, FCS, being significantly extended and the elimination of the previously reported FCS design deficiencies. Thus, The present Flow Cytometry Standard can and should be replaced by a Digital Imaging and Communications in Medicine, DICOM, standard. Expression of Analytical Cytology data in any other format, such as XML, can be made interoperable with DICOM by employing the DICOM data types. A fragment of an XML Schema has been created, which demonstrates the feasibility of expressing DICOM data types in XML syntax. The extension of DICOM to include Flow Cytometry will have the benefits of 1) retiring the present FCS, 2) providing a standard that is ubiquitous, internationally accepted, and backed by the medical profession,and 3) interoperating with the existing medical informatics infrastructure.
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).
Abstract
The addition of a list mode data type to the
Digital Imaging and Communications in Medicine standard,
DICOM will enhance the storage and transmission of digital
microscopy data and extend DICOM to include flow cytometry
data. This would permit the present International Society for
Analytical Cytology Flow Cytometry Standard to be retired.
DICOM includes: image graphics objects, specifications for
describing: studies, reports, the acquisition of the data,
work list management, and the individuals involved
(physician, patient, etc.). The glossary of terms (objects)
suitable for use with DICOM has been extended to include the
collaborative effort of Logical Observation Identifier Names
and Codes (LOINC) and Systematized Nomenclature of Human and
Veterinary Medicine (SNOMED) to create a consistent,
unambiguous clinical reference terminology. It also appears
that DICOM will be a significant part of the Common Object
Request Broker Architecture, CORBA.
R.C. Leif and S.B. Leif,
The Evolution of Flow
Cytometry Standard, FCS3.0, into a DICOM Compatible
Format, in 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).
Abstract
The International Society for Analytical
Cytology, ISAC,has developed a Flow Cytometry Standard (FCS)
to permit data interchange. ISAC will soon replace Flow
Cytometry Standard 2.0 (FCS2.0) with FCS3.0.
Unfortunately,the proposed FCS3.0 is still fraught with
problems, which are of sufficient magnitude as to warrant its
early replacement. The most reasonable replacement is as a
supplement to the Digital Imaging and Communications in
Medicine, DICOM 3.0, standard. The recent digital microscopy
extension of DICOM can be extended and modified to include
flow cytometry data. DICOM includes: image graphics objects,
specifications for describing: studies, reports,the
acquisition of the data and the individuals involved,
physician, patient, etc. Storing the present FCS data in a
database, which has already been accomplished with the QC
Tracker software, will facilitate the transition of FCS to
DICOM.