[ome-users] OME Compliant Specification

[Jason Swedlow]

Dear All-

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

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

**************************
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

phone (01382) 385819
Intl phone:  44 1382 385819
FAX   (01382) 388072
email: jason at lifesci.dundee.ac.uk

Lab Page: http://gre.lifesci.dundee.ac.uk/staff/jason_swedlow.html
Open Microscopy Environment: http://openmicroscopy.org
**************************

The University of Dundee is a Scottish Registered Charity, No. SC015096.



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