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 organizations 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 Schemas
Zip file of XML_Utilities Schemas
Zip file of CytometryML XML Pages
The page image.xml contains an abbreviated description of an image.
R.C. Leif, CytometryML, a data standard, which has been designed to interface with other standards. SPIE BiOS, 2007.
R.C. Leif, The Creation of Multiple Standards with Common Data-Types, Clinical Cytometry, in absentia, (2006).
R.C. Leif, The Creation of Multiple Standards With Common Data-Types, Advancing Practice, Instruction, and Innovation through Informatics (APIII), Poster 117 (2006).
R.C. Leif, Development of an Intersociety Laboratory Flow & Imaging Data Exchange Standard, ISAC XXIII, Poster 139 (2006).
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, a data standard, which has been designed to interface with other standards (preprint) to be in Manipulation and Analysis of Biomolecules, Cells, and Tissues V, D. Farkas, R. C. Leif, and D. V. Nicolau, Editors, SPIE Proceeding Vol. 6441(2007).
Abstract
Because of the differences in the requirements, needs, and past histories including existing standards of the creating organizations, a single encompassing cytology-pathology standard will not, in the near future, replace the multiple existing or under development standards. Except for DICOM and FCS, these standardization efforts are all based on XML. CytometryML is a collection of XML schemas, which are based on the Digital Imaging and Communications in Medicine (DICOM) and Flow Cytometry Standard (FCS) datatypes. The CytometryML schemas contain attributes that link them to the DICOM standard and FCS. Interoperability with DICOM has been facilitated by, wherever reasonable, limiting the difference between CytometryML and the previous standards to syntax. In order to permit the Resource Description Framework, RDF, to reference the CytometryML datatypes, id attributes have been added to many CytometryML elements. The Laboratory Digital Imaging Project (LDIP) Data Exchange Specification and the Flowcyt standards development effort employ RDF syntax. Documentation from DICOM has been reused in CytometryML. The unity of analytical cytology was demonstrated by deriving a microscope type and a flow cytometer type from a generic cytometry instrument type. The feasibility of incorporating the Flowcyt gating schemas into CytometryML has been demonstrated. CytometryML is being extended to include many of the new DICOM Working Group 26 datatypes, which describe patients, specimens, and analytes. In situations where multiple standards are being created, interoperability can be facilitated by employing datatypes based on a common set of semantics and building in links to standards that employ different syntax.
R.C. Leif CytometryML and other data formats in Manipulation and Analysis of Biomolecules, Cells, and Tissues III, D. Farkas, D. V. Nicolau, and R. C. Leif, Editors, SPIE Proceeding Vol. 6088-0L pp. 1-7 (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.