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

[Ghislain Bonamy]

Curtis, Frans,

 

I am glad that this is issue is raised as .ext1.ext2 is in no way a
standard extension.

 

Perhaps, using simply a .tiff with a format specific IFD would make more
sense. In addition, this would allow for a mechanism to transform Tiff
based file formats more efficiently, and provide backward compatibility
with other readers.

 

For instance the Opera .flex file is roughly a Tiff file with some
specific header (and in some cases a specific compression of the pixel
data). One could think that adding the OME-XML header under an OME
specific IFD would make the most sense. While the original IFD would
remain unchanged.

 

On another note and still about metadata. As the metadata can become
extremely large, would it make sense to provide a mechanism to compress
it using deflate for instance? Or is there a mechanism for this?

 

Best,

 

Ghislain Bonamy, PhD

__________________________________________

Research Investigator I

 

Genomic Institute of the

Novartis Research

Foundation

Department of Molecular & Cell Biology, room G214

10675 John Jay Hopkins Drive

San Diego CA 92121

USA

 

+1 (858) 812-1534 (W & F)

+1 (757) 941-4194 (H)

+1 (858) 354-7388 (M)

www.gnf.org

 

Hudson-Alpha Institute for Biotechnology

www.hudsonalpha.org

 

From: ome-devel-bounces at lists.openmicroscopy.org.uk
[mailto:ome-devel-bounces at lists.openmicroscopy.org.uk] On Behalf Of
Curtis Rueden
Sent: Tuesday, January 13, 2009 1:00 PM
To: Cornelissen, Frans [PRDBE]
Cc: ome-devel at lists.openmicroscopy.org.uk
Subject: Re: [ome-devel] ome-tiff files: does it really needs to be
namedxx.ome.tif ??

 

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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