[ome-devel] loading files saved using bio-formats exporter in Fiji/ImageJ

Thu Feb 23 15:21:39 GMT 2017

Hi all,

I am writing Python software that should be able to load data from various microscope manufacturers. I therefore went for the awesome OME / bioformats library. In order to access it from Python, I am using python-bioformats (https://github.com/CellProfiler/python-bioformats/tree/master/bioformats).
Now I ran into the following issue: In some cases, I would like to first preprocess the files in ImageJ (e.g. extract one series). So I do that and save using Plugins->Bio Formats->Bio Formats Exporter, as an .ome.tiff.
When I then load the file in my software, the number of slices in C and T are switched. Also, I can’t directly access metadata about channels. Apparently, the original metadata is encapsulated in a deeper layer. When I access the description of the first level of metadata, I get another omexml with approximately the original metadata - but it is rearranged in a way that makes me unable to access it the same way I access the original files (which are DeltaVision .dv files in this case). See below for example metadata of an original file and of a IJ-saved file.
However, when I load the .ome.tiff into ImageJ, the Bio-formats importer reads the correct metadata, so it should be possible to let bioformats do the work, I suspect.

Could anyone point me to a place where the Importer checks and finds the nested and correct metadata? Or tell me the solution?
I have tried to look here
https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats-plugins/src/loci/plugins/in/ImporterMetadata.java
and here
https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-bsd/utils/mipav/PlugInBioFormatsImporter.java
, didn’t find anything suspicious, and am slightly overwhelmed with the size of the project.

This is how python-bioformats gets metadata:
https://github.com/CellProfiler/python-bioformats/blob/master/bioformats/formatreader.py#L992

Thanks very much
    Heinrich

————————————— Metadata of series 0 of original .dv(DeltaVision) file with 1 series————————————  
<?xml version="1.0" encoding="UTF-8" standalone="no"?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2015-01" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2015-01 http://www.openmicroscopy.org/Schemas/OME/2015-01/ome.xsd"><Instrument ID="Instrument:0"><Objective Correction="PlanApo" ID="Objective:10612" Immersion="Oil" LensNA="1.42" Manufacturer="Olympus" Model="1-U2B933" NominalMagnification="60.0" WorkingDistance="150.0" WorkingDistanceUnit="µm"/></Instrument><Image ID="Image:0" Name="DeltaVision_Test.dv"><InstrumentRef ID="Instrument:0"/><ObjectiveSettings ID="Objective:10612"/><Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:0" Interleaved="false" PhysicalSizeX="0.10829800367355347" PhysicalSizeXUnit="µm" PhysicalSizeY="0.10829800367355347" PhysicalSizeYUnit="µm" PhysicalSizeZ="0.20000000298023224" PhysicalSizeZUnit="µm" SignificantBits="16" SizeC="3" SizeT="1" SizeX="2048" SizeY="2048" SizeZ="1" Type="uint16"><Channel EmissionWavelength="676.0" EmissionWavelengthUnit="nm" ExcitationWavelength="632.0" ExcitationWavelengthUnit="nm" ID="Channel:0:0" NDFilter="0.0" SamplesPerPixel="1"><LightPath/></Channel><Channel EmissionWavelength="632.0" EmissionWavelengthUnit="nm" ExcitationWavelength="575.0" ExcitationWavelengthUnit="nm" ID="Channel:0:1" NDFilter="0.0" SamplesPerPixel="1"><LightPath/></Channel><Channel EmissionWavelength="523.0" EmissionWavelengthUnit="nm" ExcitationWavelength="475.0" ExcitationWavelengthUnit="nm" ID="Channel:0:2" NDFilter="0.0" SamplesPerPixel="1"><LightPath/></Channel><MetadataOnly/><Plane DeltaT="0.0" DeltaTUnit="s" ExposureTime="2.0" ExposureTimeUnit="s" PositionX="1688.268" PositionXUnit="reference frame" PositionY="-431.984" PositionYUnit="reference frame" PositionZ="0.0" PositionZUnit="reference frame" TheC="0" TheT="0" TheZ="0"/><Plane DeltaT="2.4860000610351562" DeltaTUnit="s" ExposureTime="5.0" ExposureTimeUnit="s" PositionX="1688.268" PositionXUnit="reference frame" PositionY="-431.984" PositionYUnit="reference frame" PositionZ="0.0" PositionZUnit="reference frame" TheC="1" TheT="0" TheZ="0"/><Plane DeltaT="7.808000087738037" DeltaTUnit="s" ExposureTime="10.0" ExposureTimeUnit="s" PositionX="1688.268" PositionXUnit="reference frame" PositionY="-431.984" PositionYUnit="reference frame" PositionZ="0.0" PositionZUnit="reference frame" TheC="2" TheT="0" TheZ="0"/></Pixels></Image><StructuredAnnotations xmlns="http://www.openmicroscopy.org/Schemas/SA/2015-01"><XMLAnnotation ID="Annotation:0" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Wavelength 3 min. intensity</Key><Value>1641.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:1" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W2 T0:photosensorReading</Key><Value>3809518.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:2" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W0 T0:ndFilter</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:3" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>X axis angle</Key><Value>90.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:4" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W0 T0:maxInten</Key><Value>7108.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:5" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W1 T0:energyConvFactor</Key><Value>1.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:6" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Z axis tilt angle</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:7" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W0 T0:minInten</Key><Value>247.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:8" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Lens ID Number</Key><Value>10612</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:9" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Wavelength 4 (in nm)</Key><Value>0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:10" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>ImageWidth</Key><Value>2048</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:11" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Column axis sequence</Key><Value>1</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:12" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Wavelength 2 (in nm)</Key><Value>632</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:13" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Sub-image starting point (Z)</Key><Value>0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:14" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Wavelength 3 max. intensity</Key><Value>11290.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:15" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Y axis tilt angle</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:16" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Image sequence</Key><Value>WZT</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:17" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Title</Key><Value>[???, þ(OiÆ	ÖA, ½ÊC,E]</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:18" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Wavelength 2 min. intensity</Key><Value>234.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:19" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>PixelType</Key><Value>16 bit unsigned integer</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:20" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>ImageHeight</Key><Value>2048</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:21" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W1 T0:timeStampSeconds</Key><Value>2.486</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:22" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Number of focal planes</Key><Value>1</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:23" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Z element length (in um)</Key><Value>0.2</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:24" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Number of Sub-resolution sets</Key><Value>1</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:25" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Y axis angle</Key><Value>90.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:26" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W0 T0:photosensorReading</Key><Value>3841243.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:27" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Sub-image starting point (Y)</Key><Value>0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:28" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W2 T0:emWavelen</Key><Value>523.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:29" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Wavelength 2 max. intensity</Key><Value>5509.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:30" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W0 T0:energyConvFactor</Key><Value>1.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:31" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>X axis tilt angle</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:32" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Section axis sequence</Key><Value>3</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:33" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Pixel sampling size (Z)</Key><Value>1</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:34" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Z origin (in um)</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:35" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Wavelength 1 min. intensity</Key><Value>247.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:36" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W0 T0:expTime</Key><Value>2.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:37" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Wavelength 1 max. intensity</Key><Value>7108.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:38" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W2 T0:exWavelen</Key><Value>475.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:39" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W1 T0:maxInten</Key><Value>5509.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:40" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Sub-image starting point (X)</Key><Value>0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:41" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Z axis reduction quotient</Key><Value>1</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:42" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W1 T0:minInten</Key><Value>234.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:43" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W0 T0:timeStampSeconds</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:44" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W1 T0:emWavelen</Key><Value>632.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:45" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Space group number</Key><Value>0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:46" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Pixel sampling size (Y)</Key><Value>1</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:47" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Number of wavelengths</Key><Value>3</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:48" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Z axis angle</Key><Value>90.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:49" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Y element length (in um)</Key><Value>0.108298</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:50" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W1 T0:ndFilter</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:51" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Y origin (in um)</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:52" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Wavelength 5 (in nm)</Key><Value>0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:53" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W2 T0:intenScaling</Key><Value>1.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:54" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W0 T0:emWavelen</Key><Value>676.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:55" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Wavelength 3 (in nm)</Key><Value>523</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:56" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W1 T0:expTime</Key><Value>5.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:57" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W1 T0:exWavelen</Key><Value>575.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:58" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W1 T0:photosensorReading</Key><Value>3850251.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:59" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Wavelength 1 (in nm)</Key><Value>676</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:60" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Pixel sampling size (X)</Key><Value>1</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:61" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Row axis sequence</Key><Value>2</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:62" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Wavelength 5 min. intensity</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:63" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W0 T0:exWavelen</Key><Value>632.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:64" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Wavelength 5 max. intensity</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:65" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>X origin (in um)</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:66" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W2 T0:energyConvFactor</Key><Value>1.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:67" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W1 T0:intenScaling</Key><Value>1.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:68" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>X element length (in um)</Key><Value>0.108298</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:69" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W2 T0:maxInten</Key><Value>11290.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:70" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W0 T0:intenScaling</Key><Value>1.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:71" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W2 T0:expTime</Key><Value>10.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:72" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W2 T0:minInten</Key><Value>1641.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:73" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Number of timepoints</Key><Value>1</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:74" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Wavelength 1 mean intensity</Key><Value>437.96347</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:75" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Wavelength 4 min. intensity</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:76" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W2 T0:timeStampSeconds</Key><Value>7.808</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:77" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Image Type</Key><Value>unknown</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:78" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>DeltaVision_Test.dv Extended header Z0 W2 T0:ndFilter</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:79" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>Wavelength 4 max. intensity</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:80" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>NumberOfImages</Key><Value>3</Value></OriginalMetadata></Value></XMLAnnotation></StructuredAnnotations></OME>

————————————— Metadata when opened with ImageJ saved using bio-formats exporter————————————  

<?xml version="1.0" encoding="UTF-8" standalone="no"?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2015-01" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2015-01 http://www.openmicroscopy.org/Schemas/OME/2015-01/ome.xsd"><Image ID="Image:0" Name="DeltaVisionTest_bioformatsIJexport.ome.tif"><Description><?xml version="1.0" encoding="UTF-8" standalone="no"?><!-- 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://www.openmicroscopy.org/site/support/ome-model/ome-tiff/. --><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2015-01" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" UUID="urn:uuid:6b04671a-1994-49ad-a7dc-9db604cab07d" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2015-01 http://www.openmicroscopy.org/Schemas/OME/2015-01/ome.xsd"><Instrument ID="Instrument:0"><Objective Correction="PlanApo" ID="Objective:10612" Immersion="Oil" LensNA="1.42" Manufacturer="Olympus" Model="1-U2B933" NominalMagnification="60.0" WorkingDistance="0.15" WorkingDistanceUnit="mm"/></Instrument><Image ID="Image:0" Name="DeltaVision_Test.dv"><InstrumentRef ID="Instrument:0"/><ObjectiveSettings ID="Objective:10612"/><Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:0" Interleaved="false" PhysicalSizeX="0.10829800367355347" PhysicalSizeXUnit="µm" PhysicalSizeY="0.10829800367355347" PhysicalSizeYUnit="µm" PhysicalSizeZ="0.20000000298023224" PhysicalSizeZUnit="µm" SignificantBits="16" SizeC="3" SizeT="1" SizeX="2048" SizeY="2048" SizeZ="1" TimeIncrement="0.0" TimeIncrementUnit="s" Type="uint16"><Channel EmissionWavelength="676.0" EmissionWavelengthUnit="nm" ExcitationWavelength="632.0" ExcitationWavelengthUnit="nm" ID="Channel:0:0" NDFilter="0.0" SamplesPerPixel="1"><LightPath/></Channel><Channel EmissionWavelength="632.0" EmissionWavelengthUnit="nm" ExcitationWavelength="575.0" ExcitationWavelengthUnit="nm" ID="Channel:0:1" NDFilter="0.0" SamplesPerPixel="1"><LightPath/></Channel><Channel EmissionWavelength="523.0" EmissionWavelengthUnit="nm" ExcitationWavelength="475.0" ExcitationWavelengthUnit="nm" ID="Channel:0:2" NDFilter="0.0" SamplesPerPixel="1"><LightPath/></Channel><TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1"><UUID FileName="DeltaVisionTest_bioformatsIJexport.ome.tif">urn:uuid:6b04671a-1994-49ad-a7dc-9db604cab07d</UUID></TiffData><TiffData FirstC="1" FirstT="0" FirstZ="0" IFD="1" PlaneCount="1"><UUID FileName="DeltaVisionTest_bioformatsIJexport.ome.tif">urn:uuid:6b04671a-1994-49ad-a7dc-9db604cab07d</UUID></TiffData><TiffData FirstC="2" FirstT="0" FirstZ="0" IFD="2" PlaneCount="1"><UUID FileName="DeltaVisionTest_bioformatsIJexport.ome.tif">urn:uuid:6b04671a-1994-49ad-a7dc-9db604cab07d</UUID></TiffData><Plane DeltaT="0.0" DeltaTUnit="s" ExposureTime="2.0" ExposureTimeUnit="s" PositionX="1688.268" PositionXUnit="reference frame" PositionY="-431.984" PositionYUnit="reference frame" PositionZ="0.0" PositionZUnit="reference frame" TheC="0" TheT="0" TheZ="0"/><Plane DeltaT="2.4860000610351562" DeltaTUnit="s" ExposureTime="5.0" ExposureTimeUnit="s" PositionX="1688.268" PositionXUnit="reference frame" PositionY="-431.984" PositionYUnit="reference frame" PositionZ="0.0" PositionZUnit="reference frame" TheC="1" TheT="0" TheZ="0"/><Plane DeltaT="7.808000087738037" DeltaTUnit="s" ExposureTime="10.0" ExposureTimeUnit="s" PositionX="1688.268" PositionXUnit="reference frame" PositionY="-431.984" PositionYUnit="reference frame" PositionZ="0.0" PositionZUnit="reference frame" TheC="2" TheT="0" TheZ="0"/></Pixels></Image></OME></Description><Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:0" Interleaved="false" PhysicalSizeX="0.10829800426813266" PhysicalSizeXUnit="µm" PhysicalSizeY="0.10829800426813266" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="1" SizeT="3" SizeX="2048" SizeY="2048" SizeZ="1" Type="uint16"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><MetadataOnly/></Pixels></Image><StructuredAnnotations xmlns="http://www.openmicroscopy.org/Schemas/SA/2015-01"><XMLAnnotation ID="Annotation:0" Namespace="openmicroscopy.org/OriginalMetadata"><Value><OriginalMetadata><Key>XResolution</Key><Value>92337</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:1" 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