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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>All,</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>A good example OS JAVA software package
that deals with these issues is JHOVE (<a href="http://hul.harvard.edu/jhove/">http://hul.harvard.edu/jhove/</a>
)</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>It will verify the internal file structure
to establish the type of file&image format</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>This is needed anyway since several completely
different image file foramts use the same (e.g. .img extension (NIFTI,
Analyse, …)</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>JHOVE is an extendable framework (we have
added several proprietary file format identifications to it)</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>JHOVE checks the well-formedness and the
validity of the files, even the value of the atrtribute fields (if you like)</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>So JHOVE could read the (OME- XML) ImageDescription
structure to decide on the “real” format.</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>See the attached png file</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Regards, frans</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal style='margin-left:36.0pt'><font size=2 face=Tahoma><span
style='font-size:10.0pt;font-family:Tahoma'>-----Original Message-----<br>
<b><span style='font-weight:bold'>From:</span></b> Ghislain Bonamy
[mailto:GBonamy@gnf.org] <br>
<b><span style='font-weight:bold'>Sent:</span></b> </span></font><font size=2 face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>Wednesday, 14
January 2009</span></font><font size=2 face=Tahoma><span style='font-size:
10.0pt;font-family:Tahoma'> </span></font><font size=2 face=Tahoma><span
style='font-size:10.0pt;font-family:Tahoma'>3:52 AM</span></font><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'><br>
<b><span style='font-weight:bold'>To:</span></b> Curtis Rueden<br>
<b><span style='font-weight:bold'>Cc:</span></b> </span></font><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>Cornelissen,
Frans [PRDBE]</span></font><font size=2 face=Tahoma><span style='font-size:
10.0pt;font-family:Tahoma'>; ome-devel@lists.openmicroscopy.org.uk<br>
<b><span style='font-weight:bold'>Subject:</span></b> RE: [ome-devel] ome-tiff
files: does it really needs to be namedxx.ome.tif ??</span></font></p>
<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'> </span></font></p>
<p class=MsoNormal style='margin-right:0cm;margin-bottom:12.0pt;margin-left:
36.0pt'><font size=3 color=black face="Times New Roman"><span style='font-size:
12.0pt;color:black'>Curtis,</span></font></p>
<div>
<blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;
margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt'>
<div>
<div>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'>I am glad that this is issue is raised as
.ext1.ext2 is in no way a standard extension.</span></font></p>
</div>
</div>
</blockquote>
<div>
<p class=MsoNormal style='margin-right:0cm;margin-bottom:12.0pt;margin-left:
36.0pt'><font size=3 face="Times New Roman"><span style='font-size:12.0pt'><br>
Not a common practice perhaps, but I am curious what you see as the practical
pitfalls of this compound extension. It seems to me that using .ome.tif gives
us the best of both worlds: 1) an unambiguous extension for the OME-TIFF
format, and 2) compatibility with existing TIFF software.</span></font></p>
<p class=MsoNormal style='margin-right:0cm;margin-bottom:12.0pt;margin-left:
36.0pt'><font size=2 color=red face=Arial><span style='font-size:11.0pt;
font-family:Arial;color:red'>I concede this, and my comment was more about the
form. In addition, I was more focused on whether or not the reader should
assume a file format based on the extension, and the fact that other tiff based
format may have a different extension than Tiff such as the .flex files from
evotech. This can be a problem since renaming the file would make it
inaccessible to other file systems etc. So perhaps, supposing than any unknown
extension is a Tiff based format and prioritizing tiffs to be first assumed to
me OME complient and then be a different flavor of it would make sense. For
instance a flex file with a flex extension is considered as such unless it has
a tag indicating that it is an OME compliant file (in which case it would be
handled by the OMETiffReader).</span></font></p>
</div>
<blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;
margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt'>
<div>
<div>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'>Perhaps, using simply a .tiff with a
format specific IFD would make more sense.</span></font></p>
</div>
</div>
</blockquote>
<div>
<p class=MsoNormal style='margin-right:0cm;margin-bottom:12.0pt;margin-left:
36.0pt'><font size=3 face="Times New Roman"><span style='font-size:12.0pt'><br>
We have discussed this idea in the past. Do you see any advantages to your
approach other than those you mention below?<font color=black><span
style='color:black'> </span></font></span></font></p>
<p class=MsoNormal style='margin-right:0cm;margin-bottom:12.0pt;margin-left:
36.0pt'><font size=2 color=red face=Arial><span style='font-size:11.0pt;
font-family:Arial;color:red'>No these are the advantages that I am referring
too.</span></font></p>
</div>
<blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;
margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt'>
<div>
<div>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'>In addition, this would allow for a
mechanism to transform Tiff based file formats more efficiently, and provide
backward compatibility with other readers.</span></font></p>
</div>
</div>
</blockquote>
<div>
<p class=MsoNormal style='margin-right:0cm;margin-bottom:12.0pt;margin-left:
36.0pt'><font size=3 face="Times New Roman"><span style='font-size:12.0pt'><br>
How would a custom IFD entry be more efficient than the current mechanism?
Currently you could inject the OME-XML metadata extremely efficiently by
surgically overwriting the ImageDescription tag. The only downside is that a
TIFF cannot simultaneously be an OME-TIFF and some other flavor of TIFF that
also uses the ImageDescription tag for its metadata. A custom IFD entry would
alleviate that issue.<br>
</span></font><font size=2 color=red face=Arial><span style='font-size:11.0pt;
font-family:Arial;color:red'>This is precisely my point.</span></font></p>
<p class=MsoNormal style='margin-right:0cm;margin-bottom:12.0pt;margin-left:
36.0pt'><font size=3 face="Times New Roman"><span style='font-size:12.0pt'><br>
How is the current specification not backwardly compatible with other readers?
The only way I can think of is if those other readers are also expecting custom
metadata from the same ImageDescription tag.</span></font></p>
<p class=MsoNormal style='margin-right:0cm;margin-bottom:12.0pt;margin-left:
36.0pt'><font size=2 color=black face=Arial><span style='font-size:11.0pt;
font-family:Arial;color:black'>I meant that the custom IFD being conserved, a
TIFF format could still be read by the other readers.</span></font></p>
</div>
<blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;
margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt'>
<div>
<div>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'>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.</span></font></p>
</div>
</div>
</blockquote>
<div>
<p class=MsoNormal style='margin-right:0cm;margin-bottom:12.0pt;margin-left:
36.0pt'><font size=3 face="Times New Roman"><span style='font-size:12.0pt'><br>
Is your concern that you do not wish to overwrite the Flex file's existing
ImageDescription tag? I checked a bunch of our sample Flex files, and none of
them have an existing ImageDescription tag. Are you using this field?<font
color=black><span style='color:black'> </span></font><br>
</span></font><font size=2 color=red face=Arial><span style='font-size:11.0pt;
font-family:Arial;color:red'>Perhaps, I am getting confused between IFDs and
ImageDescription tags. The Opera Flex file contains an IFD= 65200, which points
to an XML file containing the proprietary metadata. My idea would be to do the
same for OME-Tiff so that the metadata can be read by OME complient or
proprietary readers.</span></font></p>
<p class=MsoNormal style='margin-right:0cm;margin-bottom:12.0pt;margin-left:
36.0pt'><font size=3 face="Times New Roman"><span style='font-size:12.0pt'><br>
The rationale thus far has been that any actual "image description"
-- i.e., comment -- can go in the OME-XML block's Description tag. But I
understand that there are cases where this solution is undesirable: like I
said, if the same field holds metadata in some other structure, it could be a
problem. Examples include TIFFs saved by ImageJ, and Leica TCS TIFFs.<br>
<br>
Being able to combine these forms of metadata within a single TIFF is of potential
benefit. Is there anyone out there who wants to do this, and wants to see the
OME-TIFF specification changed?</span></font></p>
</div>
<blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;
margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt'>
<div>
<div>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'>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?</span></font></p>
</div>
</div>
</blockquote>
</div>
<p class=MsoNormal style='margin-right:0cm;margin-bottom:12.0pt;margin-left:
36.0pt'><font size=3 face="Times New Roman"><span style='font-size:12.0pt'><br>
For OME-TIFF, there is no mechanism to compress the XML at the moment. You can
do it with the OME-XML file format, using extension .omez, with zlib. However,
the metadata is a tiny fraction of the total data size, even when represented
in a rather inefficient XML format.<br>
</span></font><font size=2 color=red face=Arial><span style='font-size:11.0pt;
font-family:Arial;color:red'>I agree with this, which is why Tiff format might
be bit easier to implement this. One could compress the pixel data using an
optimized algorithm such as the JPEG2000, LZW… and compress the Metadata
contained in the ImageDescription tag (or in an IFD) using his preferred
algorithm. Although compressing this kind of data takes some time decompressing
it is extremely fast (cf. using GZIp compression). The easiest solution would be
to use an extra IFD to indicate if the metadata is compressed or not! </span></font></p>
<div>
<p class=MsoNormal style='margin-right:0cm;margin-bottom:12.0pt;margin-left:
36.0pt'><font size=3 face="Times New Roman"><span style='font-size:12.0pt'><br>
The major goals of OME-TIFF are performance and compatibility. Uncompressed
TIFF planes are essentially raw, and storing the metadata in the first ImageDescription
tag allows quick access (not to say that a custom tag wouldn't be just as
quick). Compressing the XML block would increase the amount of time necessary
to parse the metadata, though that is no reason not to allow it as an option.
If this option would really significantly reduce the size of your data, we can
discuss how best to add such a facility.<br>
</span></font><font size=2 color=red face=Arial><span style='font-size:11.0pt;
font-family:Arial;color:red'>Again allowing compression using for instance GZIP
is slow for the compression step but almost instantaneous when reading. In
addition, right now metadata are manageably small, but with ROI and other
flavor of metdata it may become more and more consequent. I am merely
mentioning something which I foresee could be useful in the future, while
remaining optional depending on the users need.</span></font><br>
In conclusion, I am resistant to changing the OME-TIFF specification without a
compelling practical benefit. The spec has already seen some breaking changes
that have made it difficult to maintain compatibility within Bio-Formats, and I
would prefer to avoid any further complications in the implementation. But it
would be foolish not to discuss and evaluate any potential benefits to such
changes.<br>
<br>
In this case, unless someone in the community would directly benefit from the
custom IFD entry approach, I think the advantages are mostly theoretical and
would not warrant the disruption caused by changing the specification again.
Please feel free to argue if you disagree. :-)<br>
<font size=2 color=red face=Arial><span style='font-size:11.0pt;font-family:
Arial;color:red'>Yes, this is still theoretical and it really depends on
everyone’s need. Obviously this would be most useful to us and other
people who do high-throughput imaging and collect millions of images for a
screen and where metadata becomes larger and larger. Perhaps, this would be
nice to keep in mind if an HTF format flavor is ever implemented. But once again,
perhaps, am I the only one in this situation… so far ;)</span></font></p>
<p class=MsoNormal style='margin-right:0cm;margin-bottom:12.0pt;margin-left:
36.0pt'><font size=2 color=black face=Arial><span style='font-size:11.0pt;
font-family:Arial;color:black'> </span></font></p>
<p class=MsoNormal style='margin-right:0cm;margin-bottom:12.0pt;margin-left:
36.0pt'><font size=2 color=red face=Arial><span style='font-size:11.0pt;
font-family:Arial;color:red'>-Ghislain</span></font></p>
<p class=MsoNormal style='margin-right:0cm;margin-bottom:12.0pt;margin-left:
36.0pt'><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>On </span></font>Tue, Jan 13, 2009 at 3:09 PM, Ghislain Bonamy <<a href="mailto:GBonamy@gnf.org">GBonamy@gnf.org</a>>
wrote:</p>
<div>
<div>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'>Curtis, Frans,</span></font></p>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'> </span></font></p>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'>I am glad that this is issue is raised as
.ext1.ext2 is in no way a standard extension.</span></font></p>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'> </span></font></p>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'>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.</span></font></p>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'> </span></font></p>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'>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.</span></font></p>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'> </span></font></p>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'>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?</span></font></p>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'> </span></font></p>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'>Best,</span></font></p>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'> </span></font></p>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'>Ghislain Bonamy, PhD</span></font></p>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'>__________________________________________</span></font></p>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'>Research Investigator I</span></font></p>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'> </span></font></p>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'>Genomic Institute of the</span></font></p>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'>Novartis Research</span></font></p>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'>Foundation</span></font></p>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'>Department of Molecular & Cell
Biology, room G214</span></font></p>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'>10675 John Jay Hopkins Drive</span></font></p>
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<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
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<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
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<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'>Hudson-Alpha Institute for Biotechnology</span></font></p>
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target="_blank">www.hudsonalpha.org</a></span></font></p>
<p style='margin-left:36.0pt'><font size=2 color=black face="Times New Roman"><span
style='font-size:11.0pt;color:black'> </span></font></p>
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<p style='margin-left:36.0pt'><b><font size=2 face="Times New Roman"><span
style='font-size:10.0pt;font-weight:bold'>From:</span></font></b><font size=2><span
style='font-size:10.0pt'> <a
href="mailto:ome-devel-bounces@lists.openmicroscopy.org.uk" target="_blank">ome-devel-bounces@lists.openmicroscopy.org.uk</a>
[mailto:<a href="mailto:ome-devel-bounces@lists.openmicroscopy.org.uk"
target="_blank">ome-devel-bounces@lists.openmicroscopy.org.uk</a>] <b><span
style='font-weight:bold'>On Behalf Of </span></b>Curtis Rueden<br>
<b><span style='font-weight:bold'>Sent:</span></b> </span></font><font size=2><span style='font-size:10.0pt'>Tuesday, January 13, 2009</span></font><font
size=2><span style='font-size:10.0pt'> </span></font><font
size=2><span style='font-size:10.0pt'>1:00 PM</span></font><font size=2><span
style='font-size:10.0pt'><br>
<b><span style='font-weight:bold'>To:</span></b> </span></font><font size=2><span
style='font-size:10.0pt'>Cornelissen, Frans [PRDBE]</span></font><font size=2><span
style='font-size:10.0pt'><br>
<b><span style='font-weight:bold'>Cc:</span></b> <a
href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank">ome-devel@lists.openmicroscopy.org.uk</a><br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [ome-devel] ome-tiff
files: does it really needs to be namedxx.ome.tif ??</span></font></p>
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<p style='margin-left:36.0pt'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> </span></font></p>
<p style='margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>Hi Frans,</span></font></p>
<div>
<blockquote style='border:none;border-left:solid windowtext 1.0pt;padding:0cm 0cm 0cm 6.0pt;
margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt;
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<p style='margin-left:36.0pt'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>When using Tiff files, we would like to convert them
to OME-tiff so that<br>
they do contain the OME-XML metadata.<br>
<br>
Currently the new files have to contain the .ome.tiff as extension<br>
In our analysis processes, the altered name causes a disruption.</span></font></p>
</blockquote>
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<p style='margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'><br>
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.</span></font></p>
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<blockquote style='border:none;border-left:solid windowtext 1.0pt;padding:0cm 0cm 0cm 6.0pt;
margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt;
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<p style='margin-left:36.0pt'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Question: is it really a hard requirement that the
.ome. part is in the<br>
filename?</span></font></p>
</blockquote>
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<p style='margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'><br>
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.</span></font></p>
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<blockquote style='border:none;border-left:solid windowtext 1.0pt;padding:0cm 0cm 0cm 6.0pt;
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<p style='margin-left:36.0pt'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>This in itself is no proof of the fact that the file
*really* contains a<br>
valid OME-xml structure, so an application is probably going the check<br>
internally to decide whether it is an OME file anyway...</span></font></p>
</blockquote>
<div>
<p style='margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'><br>
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.</span></font></p>
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<blockquote style='border:none;border-left:solid windowtext 1.0pt;padding:0cm 0cm 0cm 6.0pt;
margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt;
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<p style='margin-left:36.0pt'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Could the .ome. extension requirement be removed for
importing ome-tiff<br>
files into OMERO?</span></font></p>
</blockquote>
</div>
<p style='margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'><br>
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.<br>
<br>
-Curtis</span></font></p>
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<p style='margin-left:36.0pt'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>On </span></font>Mon, Jan 12, 2009 at 8:43 AM, Cornelissen, Frans [PRDBE] <<a href="mailto:FCORNELI@its.jnj.com"
target="_blank">FCORNELI@its.jnj.com</a>> wrote:</p>
<p style='margin-left:36.0pt'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Hi,<br>
<br>
When using Tiff files, we would like to convert them to OME-tiff so that<br>
they do contain the OME-XML metadata.<br>
<br>
Currently the new files have to contain the .ome.tiff as extension<br>
In our analysis processes, the altered name causes a disruption.<br>
<br>
Question: is it really a hard requirement that the .ome. part is in the<br>
filename?<br>
This in itself is no proof of the fact that the file *really* contains a<br>
valid OME-xml structure, so an application is probably going the check<br>
internally to decide whether it is an OME file anyway...<br>
<br>
Could the .ome. extension requirement be removed for importing ome-tiff<br>
files into OMERO?<br>
<br>
Best regards, frans cornelissen<br>
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