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

Tue Jun 1 22:59:00 BST 2010

Hi Hans-

Thanks much.  SVI was one of the first commercial entities to adopt  
and embrace OME-XML, and we very much appreciate your continued support.

The link for the PDF is on the page:

http://jcb.rupress.org/content/189/5/777.full.pdf+html

It's available to me from home, without VPN, so am pretty sure it is  
publicly available (also, it's now marked 'free access').  You can put  
that link anywhere, and anyone should be able to download the PDF.   
Alternatively, send them to the abstract page and they can decide what  
the want to do (http://jcb.rupress.org/content/189/5/777.abstract).

You can link to it, you just can't mirror for the first 6 months.   
After that, you can mirror, but you just need to attribute the  
original source.

Thanks again.

Cheers,

Jason

On 1 Jun 2010, at 17:43, Hans wrote:

> 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
>>
>> **************************
>> 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.
>>
>>
>>
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL:<http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20100531/8f40cdae/attachment-0001.html 
>> >
>>
>> ------------------------------
>>
>> _______________________________________________
>> ome-devel mailing list
>> ome-devel at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>>
>>
>> End of ome-devel Digest, Vol 75, Issue 1
>> ****************************************
>
>
> -- 
> -------------------------------------------------------------------
> dr. Hans T.M. van der Voort                           (hans at svi.nl)
> Scientific Volume Imaging b.v.,             URL: http://www.svi.nl/
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel

**************************
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.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20100601/c82bc53f/attachment-0001.html>