[ome-devel] ome-devel Digest, Vol 75, Issue 1

[Hans]

Dear Jason,
>
> Today, we are publishing a commentary on file formats in the Journal
> of Cell Biology.  The full text is available at:
>
> http://jcb.rupress.org/content/189/5/777

Excellent initiative! Fabulous!
I always hope that someday we can stop wasting our time writing, 
updating and patching all those crazy formats.
Is there a pdf to be found of the paper, somewhere? If I understand 
correctly, we can start linking to that pdf in 6 months, right?

Cheers, Hans

>
> The article represents OME's position on the continued explosion of
> file formats in biological imaging.  As we move towards more complex
> data, greater opportunities for data sharing and collaboration, and
> rapidly developing image repositories, we strongly contend  that the
> current situation must evolve.  New file formats should not be created
> with every new software release.  At the very least, the option of
> writing data to open, standardized file formats must be supported in
> all software, whether open or proprietary.  We understand that
> exceptional cases exists where specialized image data or metadata
> requires proprietary, custom formats.  However, our experience with
> OME-XML and Bio-Formats suggests that the great majority of metadata
> can be supported in open data formats.  For this reason, we believe
> that the option of writing image data to an open file format that
> includes support for image acquisition metadata should be mandatory in
> all imaging software.
>
> Our article contains a number of recommendations for driving use of
> standardized file formats.  Most importantly, we believe that those
> who decide on which platforms to invest in should use their purchasing
> power to demand support for open file formats.  Realistically, this is
> the only way these file formats will be universally used and supported.
>
> In this article, we have announced a new spec, the OME Compliant
> Specification.  This simply uses standard OME-XML, and requires that
> all components of the Image Element are filled in.  We see this as a
> first step towards a more complete set of metadata for imaging.  The
> documentation for the OME Compliant Specification is at:
>
>    http://ome-xml.org/wiki/CompliantSpecification
>
> A key point is that an 'OME Compliant' file is as complete as
> possible, but only contains metadata relevant to a specific imaging
> experiment.  The expectation is not that every field is filled out
> regardless of the experiment, but that all fields that are relevant to
> an experiment are completed.  As an example, PockelCellSetting would
> not be used in most wide-field microscopy experiments, but would be
> mandatory for many multi-photon imaging experiments.  The goal of that
> 'best-effort' should be to document an experiment as completely as
> possible, so another person could, with the same sample and
> microscope, reproduce the data recorded in the file.
>
> OME's own file formats, OME-XML and OME-TIFF are well exercised and
> supported by a number of commercial vendors (http://openmicroscopy.org/site/support/about/partners
> ).  We continue to work to develop and support these formats, and
> welcome any and all feedback on their design, use, and documentation.
> However, we recognize that OME-XML and OME-TIFF do not fulfill all
> requirements for all imaging experiments.  Many others (ICS, DICOM,
> NifTI) are available and will be more or less appropriate, depending
> on a specific experiment.  Individual scientists should decide which
> of these formats must be supported, and which they will use.  The
> critical point is that image data and metadata are complete and openly
> available for viewing and analysis.
>
> We appreciate any and all feedback on this issue.
>
> As always, thanks for your support.
>
> Cheers,
>
> Jason
>
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>
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> End of ome-devel Digest, Vol 75, Issue 1
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-- 
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dr. Hans T.M. van der Voort                           (hans at svi.nl)
Scientific Volume Imaging b.v.,             URL: http://www.svi.nl/