[ome-devel] ome-tiff files: does it really needs to be named xx.ome.tif ??

[Curtis Rueden]

Hi Frans,

When using Tiff files, we would like to convert them to OME-tiff so that
> they do contain the OME-XML metadata.
>
> Currently the new files have to contain the .ome.tiff as extension
> In our analysis processes, the altered name causes a disruption.
>

Originally, the specification did not require the .ome.tif extension, but we
decided it would reduce ambiguity to prefer a more specific extension -- and
the .ome.tif extension allows non-OME-aware TIFF programs to continue seeing
the files as regular TIFFs.

Question: is it really a hard requirement that the .ome. part is in the
> filename?


At the moment, for Bio-Formats and hence OMERO, yes it is a hard
requirement. We are not necessarily opposed to parsing OME-TIFF metadata out
of files without the .ome.tif extension, but at the moment there are some
technical barriers to doing so efficiently.

This in itself is no proof of the fact that the file *really* contains a
> valid OME-xml structure, so an application is probably going the check
> internally to decide whether it is an OME file anyway...
>

True. The same is true for every file extension -- the only way to verify
that the file *really* contains correctly structured data of the indicated
type is to attempt to fully parse it. However, file extension is an
extremely useful hint that greatly improves performance. In some cases
(e.g., certain raw data formats) it might even be impossible to completely
determine the file format without the filename extension.

Could the .ome. extension requirement be removed for importing ome-tiff
> files into OMERO?
>

Yes, we always parse a TIFF file's ImageDescription block. Ideally, we
should be properly parsing any OME-XML we find there. However, as I said,
there are some performance challenges we need to sort out. The fix shouldn't
be too bad. We'll file a ticket to keep you posted.

-Curtis

On Mon, Jan 12, 2009 at 8:43 AM, Cornelissen, Frans [PRDBE] <
FCORNELI at its.jnj.com> wrote:

> Hi,
>
> When using Tiff files, we would like to convert them to OME-tiff so that
> they do contain the OME-XML metadata.
>
> Currently the new files have to contain the .ome.tiff as extension
> In our analysis processes, the altered name causes a disruption.
>
> Question: is it really a hard requirement that the .ome. part is in the
> filename?
> This in itself is no proof of the fact that the file *really* contains a
> valid OME-xml structure, so an application is probably going the check
> internally to decide whether it is an OME file anyway...
>
> Could the .ome. extension requirement be removed for importing ome-tiff
> files into OMERO?
>
> Best regards, frans cornelissen
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> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
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