To: cyto-inbox
flow cytometry file and software standardization and clinical
cytometry
One of the primary goals of a file standard in flow cytometry
should be to provide:
1.) general interchange of list mode files amongst different software
platforms.
2.) standardized interfaces for the import and export of sample (patient)
and result information e.g. from general information management
systems into list mode files or from list mode files into such
data management systems.
To achieve these goals, rigorous simplicity and conformity with
existing regulations in the biomedical health and research areas
are mandatory.
FCS1.0 and FCS2.0 standards have been *very helpful* for many
purposes and it was an *excellent* idea in retrospect to have introduced
a file standard relatively early in the history of ISAC. Both standards
have clearly favoured the interchange of list mode files and thus e.g.
greatly facilitated the efforts for standardized multiparameter data
classification
(http://www.biochem.mpg.de/valet/cellclas.html) in medicine.
On the other hands *both* standards have been in practice *quite difficult*
for the *automated* evaluation of even very *simple* things in files from
different flow cytometers and cell sorters like:
- which fluorescence or light scatter is associated with which photomultiplier,
- where is the patient identification located,
- where is the assay information
- which parameter is linear and which logarithmically measured,
- how can the computer clock time scale be converted into an obvious
time scale in sec
With FCS2.0 but even more with FCS3.0 we are thrown into the orcus
of bit compressed and multiexperiment information within single list mode files,
furthermore into non standardized areas for gate and result storage.
This development is *clearly* the *wrong* direction to go. Already FCS1.0
and FCS2.0 were only *frame standards* i.e. they left a much *too high* degree
of freedom for coding the *generally relevant information*. Since flow cytometry
has a strong biomedical bias and is used for diagnostic purposes in medicine,
it seems mandatory that file standards are produced which conform to
the required clarity for medical but also for research purposes. There is no
objection that there are reserved areas for the storage of proprietory
information
for certain algorithms of manufacturer software but the *generally* used
information must be *rigorously* standardized in future FCS standards !
It seems therefore important to reconsider the FCS3.0 standard. We all
apreciate the excellent work of the FCS3.0 standardization committee in
addressing the many relevant issues. The practical implementation of the
FCS3.0 file standard will, however, atomize and explode the efforts to process
each others files totally because these files will have in a *general sense* the
tendency to become *illegible* to third party software.
I believe that both Mario's and Bob's comments are *very relevant* and all
those involved in flow cytometric software should make efforts and reconsider
the FCS3.0 issue very seriously in the near future.
It *cannot* be the goal of all of us to favor *complications* in this
fundamentally
essential area of file formats and software standardization especially
in times were important developments from the side of ISAC/CCD/CCS as
well as from the European Working Group for Clinical Cell Analysis (EWGCCA,
http://www.biochem.mpg.de/valet/eurocel1.html) are under way. They promote
international harmonization e.g. of flow cytometric immunophenotyping and
cell function assays. By this, fascinating new developments in the area of
individualized patient therapy and Cellular Medicine
(http://www.biochem.mpg.de/valet/keyvirt1.html)
will be greatly favored. They will substantially enhance the use and importance
of flow cytometry in the clinical laboratory and in medicine in general.
My *suggestion* is that the FCS3.0 issue be officially readdressed at
Phil Dean's upcoming workshop in Asilomar.
Best regards
G.Valet
E-mail: valet@biochem.mpg.de
Internet: http://www.biochem.mpg.de/valet/cellbio.html
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