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Hi Heinrich,
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<div class="">Your workflow looks reasonable and it is true that the metadata of the generated OME-TIFF is surprising.</div>
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<div class="">An immediate thought: which version of Bio-Formats are you using? From the schema used at export</div>
<div class="">(2015-01), it looks like you are using BIo-Formats 5.1.x. Could you try upgrading to the latest version [1]</div>
<div class="">and see if the problem persists?</div>
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<div class="">If this is still the case, we might need to have access to a sample file to try and reproduce the issue.</div>
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<div class="">Best,</div>
<div class="">Sebastien</div>
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<div class=""> [1] <a href="http://downloads.openmicroscopy.org/bio-formats/" class="">http://downloads.openmicroscopy.org/bio-formats/</a></div>
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<div class="">On 23 Feb 2017, at 15:21, Heinrich Grabmayr <<a href="mailto:h.grabmayr@physik.uni-muenchen.de" class="">h.grabmayr@physik.uni-muenchen.de</a>> wrote:</div>
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Hi all,</div>
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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 (<a href="https://github.com/CellProfiler/python-bioformats/tree/master/bioformats" class="">https://github.com/CellProfiler/python-bioformats/tree/master/bioformats</a>).</div>
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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.</div>
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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.</div>
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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.</div>
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Could anyone point me to a place where the Importer checks and finds the nested and correct metadata? Or tell me the solution?</div>
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I have tried to look here</div>
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<a href="https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats-plugins/src/loci/plugins/in/ImporterMetadata.java" class="">https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats-plugins/src/loci/plugins/in/ImporterMetadata.java</a></div>
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and here</div>
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<a href="https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-bsd/utils/mipav/PlugInBioFormatsImporter.java" class="">https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-bsd/utils/mipav/PlugInBioFormatsImporter.java</a></div>
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, didn’t find anything suspicious, and am slightly overwhelmed with the size of the project.</div>
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This is how python-bioformats gets metadata:</div>
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<a href="https://github.com/CellProfiler/python-bioformats/blob/master/bioformats/formatreader.py#L992" class="">https://github.com/CellProfiler/python-bioformats/blob/master/bioformats/formatreader.py#L992</a></div>
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Thanks very much</div>
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Heinrich</div>
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————————————— Metadata of series 0 of original .dv(DeltaVision) file with 1 series———————————— </div>
<div class=""><?xml version="1.0" encoding="UTF-8" standalone="no"?><OME xmlns="<a href="http://www.openmicroscopy.org/Schemas/OME/2015-01" class="">http://www.openmicroscopy.org/Schemas/OME/2015-01</a>" xmlns:xsi="<a href="http://www.w3.org/2001/XMLSchema-instance" class="">http://www.w3.org/2001/XMLSchema-instance</a>"
xsi:schemaLocation="<a href="http://www.openmicroscopy.org/Schemas/OME/2015-01" class="">http://www.openmicroscopy.org/Schemas/OME/2015-01</a>
<a href="http://www.openmicroscopy.org/Schemas/OME/2015-01/ome.xsd" class="">http://www.openmicroscopy.org/Schemas/OME/2015-01/ome.xsd</a>"><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="<a href="http://www.openmicroscopy.org/Schemas/SA/2015-01" class="">http://www.openmicroscopy.org/Schemas/SA/2015-01</a>"><XMLAnnotation
ID="Annotation:0" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Wavelength 3 min. intensity</Key><Value>1641.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:1" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>X axis angle</Key><Value>90.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:4" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Z axis tilt angle</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:7" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Lens ID Number</Key><Value>10612</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:9" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Wavelength 4 (in nm)</Key><Value>0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:10" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>ImageWidth</Key><Value>2048</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:11" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Column axis sequence</Key><Value>1</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:12" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Wavelength 2 (in nm)</Key><Value>632</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:13" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Sub-image starting point (Z)</Key><Value>0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:14" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Wavelength 3 max. intensity</Key><Value>11290.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:15" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Y axis tilt angle</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:16" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Image sequence</Key><Value>WZT</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:17" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Title</Key><Value>[???, þ(OiÆ<span class="Apple-tab-span" style="white-space:pre">
</span>ÖA, ½ÊC,E]</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:18" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Wavelength
2 min. intensity</Key><Value>234.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:19" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>PixelType</Key><Value>16
bit unsigned integer</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:20" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>ImageHeight</Key><Value>2048</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:21" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Number of focal planes</Key><Value>1</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:23" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Z element length (in um)</Key><Value>0.2</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:24" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Number of Sub-resolution sets</Key><Value>1</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:25" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Y axis angle</Key><Value>90.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:26" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Sub-image starting point (Y)</Key><Value>0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:28" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Wavelength 2 max. intensity</Key><Value>5509.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:30" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>X axis tilt angle</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:32" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Section axis sequence</Key><Value>3</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:33" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Pixel sampling size (Z)</Key><Value>1</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:34" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Z origin (in um)</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:35" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Wavelength 1 min. intensity</Key><Value>247.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:36" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Wavelength 1 max. intensity</Key><Value>7108.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:38" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Sub-image starting point (X)</Key><Value>0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:41" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Z axis reduction quotient</Key><Value>1</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:42" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Space group number</Key><Value>0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:46" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Pixel sampling size (Y)</Key><Value>1</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:47" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Number of wavelengths</Key><Value>3</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:48" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Z axis angle</Key><Value>90.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:49" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Y element length (in um)</Key><Value>0.108298</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:50" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Y origin (in um)</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:52" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Wavelength 5 (in nm)</Key><Value>0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:53" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Wavelength 3 (in nm)</Key><Value>523</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:56" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Wavelength 1 (in nm)</Key><Value>676</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:60" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Pixel sampling size (X)</Key><Value>1</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:61" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Row axis sequence</Key><Value>2</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:62" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Wavelength 5 min. intensity</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:63" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Wavelength 5 max. intensity</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:65" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>X origin (in um)</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:66" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>X element length (in um)</Key><Value>0.108298</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:69" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Number of timepoints</Key><Value>1</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:74" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Wavelength 1 mean intensity</Key><Value>437.96347</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:75" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Wavelength 4 min. intensity</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:76" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Image Type</Key><Value>unknown</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:78" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><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="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Wavelength 4 max. intensity</Key><Value>0.0</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:80" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>NumberOfImages</Key><Value>3</Value></OriginalMetadata></Value></XMLAnnotation></StructuredAnnotations></OME></div>
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————————————— Metadata when opened with ImageJ saved using bio-formats exporter———————————— </div>
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<div id="bloop_sign_1487859135194659072" class="bloop_sign"><?xml version="1.0" encoding="UTF-8" standalone="no"?><OME xmlns="<a href="http://www.openmicroscopy.org/Schemas/OME/2015-01" class="">http://www.openmicroscopy.org/Schemas/OME/2015-01</a>" xmlns:xsi="<a href="http://www.w3.org/2001/XMLSchema-instance" class="">http://www.w3.org/2001/XMLSchema-instance</a>"
xsi:schemaLocation="<a href="http://www.openmicroscopy.org/Schemas/OME/2015-01" class="">http://www.openmicroscopy.org/Schemas/OME/2015-01</a>
<a href="http://www.openmicroscopy.org/Schemas/OME/2015-01/ome.xsd" class="">http://www.openmicroscopy.org/Schemas/OME/2015-01/ome.xsd</a>"><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: <a href="http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/" class="">
http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/</a>. --><OME xmlns="<a href="http://www.openmicroscopy.org/Schemas/OME/2015-01" class="">http://www.openmicroscopy.org/Schemas/OME/2015-01</a>" xmlns:xsi="<a href="http://www.w3.org/2001/XMLSchema-instance" class="">http://www.w3.org/2001/XMLSchema-instance</a>"
UUID="urn:uuid:6b04671a-1994-49ad-a7dc-9db604cab07d" xsi:schemaLocation="<a href="http://www.openmicroscopy.org/Schemas/OME/2015-01" class="">http://www.openmicroscopy.org/Schemas/OME/2015-01</a>
<a href="http://www.openmicroscopy.org/Schemas/OME/2015-01/ome.xsd" class="">http://www.openmicroscopy.org/Schemas/OME/2015-01/ome.xsd</a>"><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="<a href="http://www.openmicroscopy.org/Schemas/SA/2015-01" class="">http://www.openmicroscopy.org/Schemas/SA/2015-01</a>"><XMLAnnotation
ID="Annotation:0" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>XResolution</Key><Value>92337</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:1" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>PhotometricInterpretation</Key><Value>Palette</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:2" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>PlanarConfiguration</Key><Value>Chunky</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:3" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>MetaDataPhotometricInterpretation</Key><Value>Monochrome</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:4" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>ImageLength</Key><Value>2048</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:5" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>BitsPerSample</Key><Value>16</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:6" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>ResolutionUnit</Key><Value>Centimeter</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:7" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>SamplesPerPixel</Key><Value>1</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:8" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Compression</Key><Value>Uncompressed</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:9" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>NumberOfChannels</Key><Value>3</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:10" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>Software</Key><Value>OME Bio-Formats</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation
ID="Annotation:11" Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>MetaMorph</Key><Value>no</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:12"
Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>ImageWidth</Key><Value>2048</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:13"
Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>SampleFormat</Key><Value>unsigned integer</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:14"
Namespace="<a href="http://openmicroscopy.org/OriginalMetadata" class="">openmicroscopy.org/OriginalMetadata</a>"><Value><OriginalMetadata><Key>YResolution</Key><Value>92337</Value></OriginalMetadata></Value></XMLAnnotation></StructuredAnnotations></OME></div>
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