[ome-devel] OMERO.importer: producing orphaned images depending on Image ID

Wed Sep 16 17:01:05 BST 2009

Hi Dominik,

I apologize for the delay, it has been a bit tricky tracking this down.

The reason for what you are seeing is a limitation in the reference  
handling scope of the Importer in 4.0.3. Without going too deeply into  
the details, it does not support references to more than one object  
with the same target and as you're also specifying an Image -->  
Instrument reference there's a possibility of the implicit Dataset -->  
Image reference being overwritten. This is fixed in the latest code  
base and will be fixed in our next OMERO release.

As I'm sure you're aware now, your XML is semantically valid. If you'd  
like to try a work-around, prefix the generated portion of your Image  
LSID string (now "BAYCLKPSJPAFWN" and "VWNEEVSRSELHMW") with "AAA".  
This should give you an LSID that looks like:

urn:lsid:hifo.uzh.ch:Image:AAABAYCLKPSJPAFWN:0

Let us know if that solves the import problem.

Thanks for your patience and interest.

-Chris

On 11 Sep 2009, at 13:54, Dominik Langer wrote:

> Dear ome-devel list members
>
> I am currently implementing the OME-TIFF file format into our two- 
> photon microscopy control software. When trying to import files  
> generated by the software into OMERO Beta 4.0.3 using OME.importer,  
> only some of the files are correctly imported, whereas others are  
> not. "Correctly" means that after import, they are assigned to a  
> Project/DataSet in OMERO.insight or OMERO.web, whereas "not  
> correctly" means that they only appear as "Orphaned Images" on  
> OMERO.web ("My Data" > "Orphaned Items").
>
> The only thing the files differ (apart from the actual image data)  
> are the IDs of the Image and of the Pixels tag in the OME header. As  
> it seems, the crucial point is the Image ID: if I replace the Image  
> ID in a file which could not be correctly imported previously with  
> one that can, then it can be imported as well afterwards. I have to  
> mention that all files are valid according to http://validator.openmicroscopy.org.uk/ 
> .
>
> Attached you find two files, where  
> 2009_09_11__14_26_33h__channel00.tif can be imported correctly,  
> whereas 2009_09_11__14_26_33h__channel01.tif leads to an orphaned  
> image.
>
> Their OME headers are as follows:
>
> 2009_09_11__14_26_33h__channel00.tif:
>
> <OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2008-09"  
> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"  
> xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2008-09/ome.xsd 
> "><Instrument ID="urn:lsid:hifo.uzh.ch:Instrument: 
> 135034851807:0"><Microscope Type="Upright" Manufacturer="Brain  
> Research Institute, University of Zurich, Switzerland" Model=""  
> SerialNumber=""></Microscope><LightSource ID="urn:lsid:hifo.uzh.ch:LightSource:650703004653:2 
> " Manufacturer="Spectra-Physics" Model="Mai Tai"  
> SerialNumber="1578"><Laser Type="SolidState"  
> LaserMedium="TiSapphire" FrequencyMultiplication="1" Tuneable="true"  
> Pulse="ModeLocked" RepetitionRate="80000000"></Laser></ 
> LightSource><Objective ID="urn:lsid:hifo.uzh.ch:Objective:291101115584:5 
> " Manufacturer="Olympus" Model="XLUMPlanFl 20x"  
> SerialNumber=""><Correction>PlanFluor</Correction><Immersion>Water</ 
> Immersion><LensNA>0.950000</LensNA><NominalMagnification>20</ 
> NominalMagnification><CalibratedMagnification>20.000000</ 
> CalibratedMagnification><WorkingDistance>0.000000</WorkingDistance></ 
> Objective></Instrument><Image ID="urn:lsid:hifo.uzh.ch:Image:BAYCLKPSJPAFWN:0 
> " DefaultPixels="urn:lsid:hifo.uzh.ch:Pixels:EJINIYBEEGZNJB: 
> 0"><CreationDate>2009-09-11T14:26:34</CreationDate><InstrumentRef  
> ID="urn:lsid:hifo.uzh.ch:Instrument:135034851807:0"></ 
> InstrumentRef><ObjectiveRef ID="urn:lsid:hifo.uzh.ch:Objective:291101115584:5 
> "></ObjectiveRef><Pixels ID="urn:lsid:hifo.uzh.ch:Pixels:EJINIYBEEGZNJB:0 
> " BigEndian="false" PixelType="uint16" DimensionOrder="XYZTC"  
> SizeC="1" SizeX="256" SizeY="256" SizeZ="1" SizeT="1"  
> PhysicalSizeZ="0.000000" PhysicalSizeX ="0.064935"  
> PhysicalSizeY="0.078125"><TiffData></TiffData></Pixels></Image></OME>
>
>
> 2009_09_11__14_26_33h__channel01.tif
>
> <OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2008-09"  
> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"  
> xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2008-09/ome.xsd 
> "><Instrument ID="urn:lsid:hifo.uzh.ch:Instrument: 
> 135034851807:0"><Microscope Type="Upright" Manufacturer="Brain  
> Research Institute, University of Zurich, Switzerland" Model=""  
> SerialNumber=""></Microscope><LightSource ID="urn:lsid:hifo.uzh.ch:LightSource:650703004653:2 
> " Manufacturer="Spectra-Physics" Model="Mai Tai"  
> SerialNumber="1578"><Laser Type="SolidState"  
> LaserMedium="TiSapphire" FrequencyMultiplication="1" Tuneable="true"  
> Pulse="ModeLocked" RepetitionRate="80000000"></Laser></ 
> LightSource><Objective ID="urn:lsid:hifo.uzh.ch:Objective:291101115584:5 
> " Manufacturer="Olympus" Model="XLUMPlanFl 20x"  
> SerialNumber=""><Correction>PlanFluor</Correction><Immersion>Water</ 
> Immersion><LensNA>0.950000</LensNA><NominalMagnification>20</ 
> NominalMagnification><CalibratedMagnification>20.000000</ 
> CalibratedMagnification><WorkingDistance>0.000000</WorkingDistance></ 
> Objective></Instrument><Image ID="urn:lsid:hifo.uzh.ch:Image:VWNEEVSRSELHMW:0 
> " DefaultPixels="urn:lsid:hifo.uzh.ch:Pixels:DLSRGGTGOKEXIV: 
> 0"><CreationDate>2009-09-11T14:26:36</CreationDate><InstrumentRef  
> ID="urn:lsid:hifo.uzh.ch:Instrument:135034851807:0"></ 
> InstrumentRef><ObjectiveRef ID="urn:lsid:hifo.uzh.ch:Objective:291101115584:5 
> "></ObjectiveRef><Pixels ID="urn:lsid:hifo.uzh.ch:Pixels:DLSRGGTGOKEXIV:0 
> " BigEndian="false" PixelType="uint16" DimensionOrder="XYZTC"  
> SizeC="1" SizeX="256" SizeY="256" SizeZ="1" SizeT="1"  
> PhysicalSizeZ="0.000000" PhysicalSizeX ="0.064935"  
> PhysicalSizeY="0.078125"><TiffData></TiffData></Pixels></Image></OME>
>
>
>
> I would appreciate any hints helping to solve this problem.
>
> Best regards,
> Dominik
>
>
>
> < 
> 2009_09_11__14_26_33h__channel00 
> .tif 
> > 
> < 
> 2009_09_11__14_26_33h__channel01 
> .tif>_______________________________________________
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