Posted by
Mark Cannell on
URL: http://confocal-microscopy-list.275.s1.nabble.com/OME-Compliant-Specification-tp5122114p5123428.html
Jason Swedlow wrote:
> 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.
Hi Jason,
With respect, isn't this also introducing yet another "non-standard"
format? I don't think your "specification" fits some of the new imaging
modalities and contains no validation information (to help stop data
fabrication). I think this is a weakness of your suggested standard
-let alone security issues.
I can't help wonder why you did not consider pushing/using an existing
_scientific image_ format, such as FITS -just look at the huge amount
of work by the IAS to establish that scientific image data format? Since
FITS is established, tightly controlled and can hold (as far as I know)
all the data necessary to define machine/modality/processing why did you
pick the 'XML bandwagon'?
Please don't get me wrong, I'm not saying that your effort in trying to
establish a standard for scientific imaging files is not worthwhile and
needed but the specification just seems too focussed on some current
confocal modalities...
Many regards Mark