Open Microscopy Environment

Hi,

When I export images with Omero.insight (on windows), I don't find into the Ome metadata (extracted by ImageJ, loci) the id of the image.

When I make some modification into my image, I would like to keep the information of the raw data. (ID raw data).
But I don"t have

How can I manage my images for keeping the ID ?

Marie Laure

The OMERO Image ID?

p

Yes the OMERO ID or something else to identify raw image uniquely

To keep raw image and do not mismatch our images, I would like to follow my image during their workflow :

Acquisition | | 3D view | | Image Analysis
| -> | | -> |
raw images | | | | image with the edge of objects underlined
id : 1.2.3 | | id: 2.3 | | id: 2.3


I hope to be more clear ...
Marie Laure

When you export an OME-TIFF from OMERO the <Image...> tag present in the TIFF description is laid out like this:

Code: Select all

...
<Image ID="urn:lsid:export.openmicroscopy.org:Image:[UNIQUE_OMERO_DATABASE_IDENTIFIER]:[IMAGE.ID]" Name="[IMAGE.NAME]">
...


Escuse me for my obstinacy .... I certainly make or understand something wrong ...
But when I export an image with Export as OME.TIFF, and when I open the image with loci on imageJ.
I have those metadata without an ID ...

Code: Select all

<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2011-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2011-06 http://www.openmicroscopy.org/Schemas/OME/2011-06/ome.xsd">
<Image ID="Image:0" Name="Y:/IP3D/MarieLaureB/data/Multiphoton/IP3D/Annaick/ECadherine/Sph20-22/20111216_HCT116HcR_ECadh_Sph20-22_lame2_C1M1-1.lsm">
<AcquiredDate>2012-05-22T05:00:01</AcquiredDate>
<Description/>
<Pixels DimensionOrder="XYZCT" ID="Pixels:0" PhysicalSizeX="0.08058922512704243" PhysicalSizeY="0.08058922512704243" PhysicalSizeZ="1.0E-13" SizeC="2" SizeT="1" SizeX="512" SizeY="512" SizeZ="1" TimeIncrement="1.0" Type="uint8">
<Channel Color="16711935" ID="Channel:0:0" Name="Ch2" PinholeSize="144.0" SamplesPerPixel="1">
<LightPath/>
<Channel Color="65535" ID="Channel:0:1" Name="Ch2" PinholeSize="896.0" SamplesPerPixel="1">
<LightPath/>
<BinData BigEndian="true" Length="0" xmlns="http://www.openmicroscopy.org/Schemas/BinaryFile/2011-06"/>
<TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1">
<UUID FileName="__omero_export__6787857773098101143.ome.tiff">urn:uuid:286ed49f-2889-454a-a30d-7ee6b086ee6f</UUID>
<TiffData FirstC="1" FirstT="0" FirstZ="0" IFD="1" PlaneCount="1">
<UUID FileName="__omero_export__6787857773098101143.ome.tiff">urn:uuid:286ed49f-2889-454a-a30d-7ee6b086ee6f</UUID>
<Plane DeltaT="0.0" ExposureTime="0.0" PositionX="-9.144481149225193" PositionY="-17.173781670495178" PositionZ="0.0" TheC="0" TheT="0" TheZ="0"/>
<Plane DeltaT="0.0" ExposureTime="0.0" PositionX="-9.144481149225193" PositionY="-17.173781670495178" PositionZ="0.0" TheC="1" TheT="0" TheZ="0"/>
<AnnotationRef ID="urn:lsid:export.openmicroscopy.org:Annotation:5841cf42-3665-4dae-b68e-257a46802553_1358:28557" xmlns="http://www.openmicroscopy.org/Schemas/SA/2011-06"/>
<StructuredAnnotations xmlns="http://www.openmicroscopy.org/Schemas/SA/2011-06">
<TagAnnotation ID="urn:lsid:export.openmicroscopy.org:Annotation:5841cf42-3665-4dae-b68e-257a46802553_1358:28557">
<Value>typdemanip-ELISA</Value>

Thank you for your help !
Marie Laure

That's because Bio-Formats rewrites those IDs during import into ImageJ. If you examine the TIFF description you will see the IDs laid out exactly as I described above.