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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Arial","sans-serif";
color:black'>Curtis, Frans,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Arial","sans-serif";
color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Arial","sans-serif";
color:black'>I am glad that this is issue is raised as .ext1.ext2 is in no way
a standard extension.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Arial","sans-serif";
color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Arial","sans-serif";
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.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Arial","sans-serif";
color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Arial","sans-serif";
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.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Arial","sans-serif";
color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Arial","sans-serif";
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?<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Arial","sans-serif";
color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Arial","sans-serif";
color:black'>Best,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Arial","sans-serif";
color:black'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>Ghislain Bonamy, PhD<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>__________________________________________<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>Research Investigator I<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>Genomic Institute of the<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>Novartis Research<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>Foundation<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>Department of Molecular &
Cell Biology, room G214<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>10675 John Jay Hopkins Drive<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>San Diego CA 92121<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>USA<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>+1 (858) 812-1534 (W & F)<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>+1 (757) 941-4194 (H)<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>+1 (858) 354-7388 (M)<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'><a href="www.gnf.org">www.gnf.org</a><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'>Hudson-Alpha Institute for
Biotechnology<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Arial","sans-serif";color:black'><a href="www.haib.org">www.hudsonalpha.org</a><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Arial","sans-serif";
color:black'><o:p> </o:p></span></p>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
ome-devel-bounces@lists.openmicroscopy.org.uk
[mailto:ome-devel-bounces@lists.openmicroscopy.org.uk] <b>On Behalf Of </b>Curtis
Rueden<br>
<b>Sent:</b> Tuesday, January 13, 2009 1:00 PM<br>
<b>To:</b> Cornelissen, Frans [PRDBE]<br>
<b>Cc:</b> ome-devel@lists.openmicroscopy.org.uk<br>
<b>Subject:</b> Re: [ome-devel] ome-tiff files: does it really needs to be
namedxx.ome.tif ??<o:p></o:p></span></p>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal style='margin-bottom:12.0pt'>Hi Frans,<o:p></o:p></p>
<div>
<blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;
margin-left:4.8pt;margin-right:0cm'>
<p class=MsoNormal>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.<o:p></o:p></p>
</blockquote>
<div>
<p class=MsoNormal style='margin-bottom: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.<o:p></o:p></p>
</div>
<blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;
margin-left:4.8pt;margin-right:0cm'>
<p class=MsoNormal>Question: is it really a hard requirement that the .ome.
part is in the<br>
filename?<o:p></o:p></p>
</blockquote>
<div>
<p class=MsoNormal style='margin-bottom: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.<o:p></o:p></p>
</div>
<blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;
margin-left:4.8pt;margin-right:0cm'>
<p class=MsoNormal>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...<o:p></o:p></p>
</blockquote>
<div>
<p class=MsoNormal style='margin-bottom: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.<o:p></o:p></p>
</div>
<blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;
margin-left:4.8pt;margin-right:0cm'>
<p class=MsoNormal>Could the .ome. extension requirement be removed for
importing ome-tiff<br>
files into OMERO?<o:p></o:p></p>
</blockquote>
</div>
<p class=MsoNormal style='margin-bottom: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<o:p></o:p></p>
<div>
<p class=MsoNormal>On 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:<o:p></o:p></p>
<p class=MsoNormal>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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<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel"
target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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