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

[Dominik Langer]

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



-------------- next part --------------
A non-text attachment was scrubbed...
Name: 2009_09_11__14_26_33h__channel00.tif
Type: image/tiff
Size: 132907 bytes
Desc: not available
Url : http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20090911/5cdee687/attachment-0002.tif 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 2009_09_11__14_26_33h__channel01.tif
Type: image/tiff
Size: 132907 bytes
Desc: not available
Url : http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20090911/5cdee687/attachment-0003.tif