Hi Frans,<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">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>
</blockquote><div><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.<br>
<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Question: is it really a hard requirement that the .ome. part is in the<br>
filename?</blockquote><div><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.<br>
<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">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>
</blockquote><div><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.<br>
<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Could the .ome. extension requirement be removed for importing ome-tiff<br>
files into OMERO?<br>
</blockquote></div><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<br><br><div class="gmail_quote">On Mon, Jan 12, 2009 at 8:43 AM, Cornelissen, Frans [PRDBE] <span dir="ltr"><<a href="mailto:FCORNELI@its.jnj.com" target="_blank">FCORNELI@its.jnj.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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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</blockquote></div><br>