isyntax2raw-1/isyntax2raw/resources/ome_template.xml at 17c47850e31bc17d77d901275f60169a50e80ee3 · melissalinkert/isyntax2raw-1 · GitHub

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<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
  <Instrument ID="Instrument:0">
    <Objective ID="Objective:0:0" NominalMagnification="40.0"/>
  </Instrument>
  <Image ID="Image:0" Name="${image['name']}">
    <AcquisitionDate>${image['acquisitionDate']}</AcquisitionDate>
    <Description>${image['description']}</Description>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:0:0"/>
    <Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:0"
            Interleaved="false"
            PhysicalSizeX="${image['pixels']['physicalSizeX']}"
            PhysicalSizeXUnit="µm"
            PhysicalSizeY="${image['pixels']['physicalSizeY']}"
            PhysicalSizeYUnit="µm" SignificantBits="${image['pixels']['bits_stored']}"
            SizeC="3" SizeT="1"
            SizeX="${image['pixels']['sizeX']}"
            SizeY="${image['pixels']['sizeY']}"
            SizeZ="1" Type="${image['pixels']['type']}">
      <Channel ID="Channel:0:0" SamplesPerPixel="3">
        <LightPath/>
      </Channel>
      <MetadataOnly/>
    </Pixels>
  </Image>
  <Image ID="Image:1" Name="label image">
    <AcquisitionDate>${image['acquisitionDate']}</AcquisitionDate>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:0:0"/>
    <Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:1"
            Interleaved="false" SignificantBits="8" SizeC="3"
            SizeT="1" SizeX="${label['pixels']['sizeX']}" SizeY="${label['pixels']['sizeY']}"
            SizeZ="1" Type="uint8">
      <Channel ID="Channel:1:0" SamplesPerPixel="3">
        <LightPath/>
      </Channel>
      <MetadataOnly/>
    </Pixels>
  </Image>
  <Image ID="Image:2" Name="macro image">
    <AcquisitionDate>${image['acquisitionDate']}</AcquisitionDate>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:0:0"/>
    <Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:2"
            Interleaved="false" SignificantBits="8" SizeC="3"
            SizeT="1"
            SizeX="${macro['pixels']['sizeX']}"
            SizeY="${macro['pixels']['sizeY']}"
            SizeZ="1" Type="uint8">
      <Channel ID="Channel:2:0" SamplesPerPixel="3">
        <LightPath/>
      </Channel>
      <MetadataOnly/>
    </Pixels>
  </Image>
</OME>