[ome-devel] Omero export

[Melissa Linkert]

Hi Roland,

> I have a question about the omero OME-TIFF export funktion. Martin Spitaler
> gave me your email adress for more technical questions on this topic.

I am copying this mail to the OME developer mailing list
(see http://openmicroscopy.org/site/community/mailing-lists), in case
anyone else is interested in this problem.

> We had problems to import OME-TIFF's produced by Martin, which he exported
> with Omero. Reason was that we read the "TiffData" tag in the meta data of
> the OME-TIFF image. The entry there was __omero_export__446776638494397324.ome.tiff
> but the physical file name was indeed different. We read this info because the
> image data for a 3D or time series can be spread over several physical files.
> For now if it's just one file and the name is different in the "TiffData" then
> we sue simply the same file name. But do you know why there is a different
> name and how is the naming in case that really several physical files are used.

The file name is incorrect because the OME-TIFF file is renamed after it
has been created.  The recommended solution is to use the "UUID" values
instead of the "FileName" values to determine which file contains the image
data for a particular "TiffData".

OME-TIFF files should have a "UUID" element in the "OME" tag - this
uniquely identifies each file, even if you rename the file.  The
"TiffData" tag should then have a "UUID" element; each "UUID" element
under "TiffData" matches one of the top-level "UUID" elements.

For example, suppose we have an OME-TIFF dataset with two timepoints,
where each timepoint is stored in its' own file.  The OME-XML data for
the first file would look something like this:

<OME>
  <!-- top level UUID element that identifies this file -->
  <UUID FileName="1.ome.tiff">
    urn:uuid:f139aef6-be53-4694-b5a5-3e95fff7ddf9
  </UUID>
  <Image>
    <Pixels SizeX="512" SizeY="512" SizeZ="1" SizeT="2" SizeC="1" PixelType="uint8">
      <TiffData FirstT="0">
        <!-- reference to this file -->
        <UUID FileName="1.ome.tiff">
          urn:uuid:f139aef6-be53-4694-b5a5-3e95fff7ddf9
        </UUID>
      </TiffData>
      <TiffData FirstT="1">
        <!-- reference to the other file -->
        <UUID FileName="2.ome.tiff">
          urn:uuid:6dd975be-587e-4f06-864a-54b0ec5ab2a0
        </UUID>
      </TiffData>
    </Pixels>
  </Image>
</OME>

And the second file's OME-XML data would look like this:

<OME>
  <!-- top level UUID element that identifies this file -->
  <UUID FileName="2.ome.tiff">
    urn:uuid:6dd975be-587e-4f06-864a-54b0ec5ab2a0
  </UUID>
  <Image>
    <Pixels SizeX="512" SizeY="512" SizeZ="1" SizeT="2" SizeC="1" PixelType="uint8">
      <TiffData FirstT="0">
        <!-- reference to the other file -->
        <UUID FileName="1.ome.tiff">
          urn:uuid:f139aef6-be53-4694-b5a5-3e95fff7ddf9
        </UUID>
      </TiffData>
      <TiffData FirstT="1">
        <!-- reference to this file -->
        <UUID FileName="2.ome.tiff">
          urn:uuid:6dd975be-587e-4f06-864a-54b0ec5ab2a0
        </UUID>
      </TiffData>
    </Pixels>
  </Image>
</OME>

So each file is referenced by both it's file name (which the user can
change), and it's UUID (which the user can't easily change). You can
certainly use the file name as a hint for where to look first, but the
UUIDs are the authoritative way of determining how multi-file datasets
are stored.

Please let me know if any of this is unclear, or if you have any other
questions.

Regards,
-Melissa

On Thu, Jul 01, 2010 at 03:31:48PM +0200, Winkler, Roland wrote:
> Hi Melissa,
>  
> I have a question about the omero OME-TIFF export funktion. Martin Spitaler gave me your email adress for more technical questions on this topic. 
>  
> We had problems to import OME-TIFF's produced by Martin, which he exported with Omero. Reason was that we read the "TiffData" tag in the meta data of the OME-TIFF image. The entry there was __omero_export__446776638494397324.ome.tiff but the physical file name was indeed different. We read this info because the image data for a 3D or time series can be spread over several physical files. For now if it's just one file and the name is different in the "TiffData" then we sue simply the same file name. But do you know why there is a different name and how is the naming in case that really several physical files are used.
>  
> Best Regards,
> Roland   
>  
>  
>  
> 
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