Open Microscopy Environment

Hi all,

I inserted some meta info (NominalMagnification and LensNA of the Objective) to an ome-tiff file by manually parsing and editing the ome-xml header of the image file.
After I upload it via OMERO.importer (uploading was successful), I tried to see if the OMERO.insight will show me that meta info correctly. But I could not see any meta info. from the "Acqusition" tab of the OMERO.sight. (which is on the right panel)

Did I miss something when I manually insert the meta info?

here's the ome-xml meta info.

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<?xml version="1.0" encoding="UTF-8"?><!-- Warning: this comment is an OME-XML metadata block, which contains crucial dimensional parameters and other important metadata. Please edit cautiously (if at all), and back up the original data before doing so. For more information, see the OME-TIFF web site: http://ome-xml.org/wiki/OmeTiff. -->
<OME xmlns:AML="http://www.openmicroscopy.org/Schemas/AnalysisModule/2008-09" xmlns:Bin="http://www.openmicroscopy.org/Schemas/BinaryFile/2008-09" xmlns:MLI="http://www.openmicroscopy.org/Schemas/MLI/2008-09" xmlns:SA="http://www.openmicroscopy.org/Schemas/SA/2008-09" xmlns:OME="http://www.openmicroscopy.org/Schemas/OME/2008-09" xmlns:SPW="http://www.openmicroscopy.org/Schemas/SPW/2008-09" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:CA="http://www.openmicroscopy.org/Schemas/CA/2008-09" xmlns:STD="http://www.openmicroscopy.org/Schemas/STD/2008-09" xmlns:CLI="http://www.openmicroscopy.org/Schemas/CLI/2008-09" xmlns="http://www.openmicroscopy.org/Schemas/OME/2008-09" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2008-09 http://www.openmicroscopy.org/Schemas/OME/2008-09/ome.xsd http://www.openmicroscopy.org/Schemas/BinaryFile/2008-09 http://www.openmicroscopy.org/Schemas/BinaryFile/2008-09/BinaryFile.xsd http://www.openmicroscopy.org/Schemas/CA/2008-09 http://www.openmicroscopy.org/Schemas/CA/2008-09/CA.xsd http://www.openmicroscopy.org/Schemas/SPW/2008-09 http://www.openmicroscopy.org/Schemas/SPW/2008-09/SPW.xsd http://www.openmicroscopy.org/Schemas/STD/2008-09 http://www.openmicroscopy.org/Schemas/STD/2008-09/STD.xsd" UUID="urn:uuid:ce8e04a9-5d8a-4016-8a07-fcd212ec2553">
<Instrument ID="Instrument:0">
<Objective ID="Objective:0">
<LensNA>1.3</LensNA>
<NominalMagnification>100</NominalMagnification>
</Objective>
</Instrument>
<Image ID="Image:0">
<LogicalChannel ID="LogicalChannel:0" SamplesPerPixel="1"/>
<Pixels BigEndian="true" DimensionOrder="XYCZT" ID="Pixels:0" PixelType="uint8" SizeC="1" SizeT="1" SizeX="768" SizeY="512" SizeZ="1">
<TiffData>
<UUID FileName="img2.ome.tif">urn:uuid:ce8e04a9-5d8a-4016-8a07-fcd212ec2553</UUID>
</TiffData>
</Pixels>
</Image>
</OME>

Hi

The image is not linked to the instrument.
You will need to add something like:

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<Image ...>
<InstrumentRef ID="urn:lsid:-.-:Instrument:0"/>
</Image>


Jmarie

thank you so muh jburel.

after I inserted the following lines in my java code,

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      String inst= omexmlMeta.getInstrumentID(0); // omexmlMeta is IMetadata
      omexmlMeta.setImageInstrumentRef(inst,0);

Now I can see the inserted information (Nominal magnification and Lens NA of Objective) at the Microscope tab. But I still don't see anything in the Original Metadata (see attached image). when I downloaded, it's just

[GlobalMetadata]
[SeriesMetadata]

Is it common thing? or
Am I still missing something? the updated ome-xml part is below.

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<?xml version="1.0" encoding="UTF-8"?><!-- Warning: this comment is an OME-XML metadata block, which contains crucial dimensional parameters and other important metadata. Please edit cautiously (if at all), and back up the original data before doing so. For more information, see the OME-TIFF web site: http://ome-xml.org/wiki/OmeTiff. -->
<OME xmlns:AML="http://www.openmicroscopy.org/Schemas/AnalysisModule/2008-09" xmlns:Bin="http://www.openmicroscopy.org/Schemas/BinaryFile/2008-09" xmlns:MLI="http://www.openmicroscopy.org/Schemas/MLI/2008-09" xmlns:SA="http://www.openmicroscopy.org/Schemas/SA/2008-09" xmlns:OME="http://www.openmicroscopy.org/Schemas/OME/2008-09" xmlns:SPW="http://www.openmicroscopy.org/Schemas/SPW/2008-09" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:CA="http://www.openmicroscopy.org/Schemas/CA/2008-09" xmlns:STD="http://www.openmicroscopy.org/Schemas/STD/2008-09" xmlns:CLI="http://www.openmicroscopy.org/Schemas/CLI/2008-09" xmlns="http://www.openmicroscopy.org/Schemas/OME/2008-09" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2008-09 http://www.openmicroscopy.org/Schemas/OME/2008-09/ome.xsd http://www.openmicroscopy.org/Schemas/BinaryFile/2008-09 http://www.openmicroscopy.org/Schemas/BinaryFile/2008-09/BinaryFile.xsd http://www.openmicroscopy.org/Schemas/CA/2008-09 http://www.openmicroscopy.org/Schemas/CA/2008-09/CA.xsd http://www.openmicroscopy.org/Schemas/SPW/2008-09 http://www.openmicroscopy.org/Schemas/SPW/2008-09/SPW.xsd http://www.openmicroscopy.org/Schemas/STD/2008-09 http://www.openmicroscopy.org/Schemas/STD/2008-09/STD.xsd" UUID="urn:uuid:beb0d8e6-5dc1-47c1-8d05-ea50e1eb7f96">
<Instrument ID="Instrument:0">
<Objective ID="Objective:0">
<LensNA>1.3</LensNA>
<NominalMagnification>100</NominalMagnification>
</Objective>
</Instrument>
<Image ID="Image:0">
<InstrumentRef ID="Instrument:0"/>
<LogicalChannel ID="LogicalChannel:0" SamplesPerPixel="1"/>
<Pixels BigEndian="true" DimensionOrder="XYCZT" ID="Pixels:0" PixelType="uint8" SizeC="1" SizeT="1" SizeX="768" SizeY="512" SizeZ="1">
<TiffData>
<UUID FileName="img4.ome.tif">urn:uuid:beb0d8e6-5dc1-47c1-8d05-ea50e1eb7f96</UUID>
</TiffData>
</Pixels>
</Image>
</OME>

Hi
There is no guarantee that the info will be in the Original Metadata file created while importing the image and then displayed in the Original Metadata section.

If it is critical, we will have to review sections of the import process.
Thanks for your feedback

jmarie