It feels like Bio-formats can read the metadata
<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">
<Plate Columns="6" ID="Plate:0" Name="test-plate" Rows="4">
<Well Column="0" ID="Well:0:0" Row="0"/>
<Well Column="1" ID="Well:0:1" Row="0"/>
<Well Column="2" ID="Well:0:2" Row="0"/>
<Well Column="3" ID="Well:0:3" Row="0"/>
<Well Column="4" ID="Well:0:4" Row="0"/>
<Well Column="5" ID="Well:0:5" Row="0"/>
<Well Column="0" ID="Well:0:6" Row="1"/>
<Well Column="1" ID="Well:0:7" Row="1"/>
<Well Column="2" ID="Well:0:8" Row="1"/>
<Well Column="3" ID="Well:0:9" Row="1"/>
<Well Column="4" ID="Well:0:10" Row="1"/>
<Well Column="5" ID="Well:0:11" Row="1"/>
<Well Column="0" ID="Well:0:12" Row="2"/>
<Well Column="1" ID="Well:0:13" Row="2"/>
<Well Column="2" ID="Well:0:14" Row="2"/>
<Well Column="3" ID="Well:0:15" Row="2">
<WellSample ID="WellSample:0:15:0" Index="0">
<ImageRef ID="Image:0"/>
<Well Column="4" ID="Well:0:16" Row="2">
<WellSample ID="WellSample:0:16:0" Index="1">
<ImageRef ID="Image:1"/>
<Well Column="5" ID="Well:0:17" Row="2"/>
<Well Column="0" ID="Well:0:18" Row="3"/>
<Well Column="1" ID="Well:0:19" Row="3"/>
<Well Column="2" ID="Well:0:20" Row="3"/>
<Well Column="3" ID="Well:0:21" Row="3"/>
<Well Column="4" ID="Well:0:22" Row="3"/>
<Well Column="5" ID="Well:0:23" Row="3"/>
<PlateAcquisition ID="PlateAcquisition:0:0" MaximumFieldCount="1">
<WellSampleRef ID="WellSample:0:15:0"/>
<WellSampleRef ID="WellSample:0:16:0"/>
<Instrument ID="Instrument:0">
<Detector ID="Detector:0:0" Type="Other"/>
<Objective ID="Objective:0:0" LensNA="0.45"/>
<Image ID="Image:0" Name="Well C04 Field #1">
<AcquisitionDate>2019-05-15T15:52:30.617</AcquisitionDate>
<Description/>
<InstrumentRef ID="Instrument:0"/>
<ObjectiveSettings ID="Objective:0:0" RefractiveIndex="1.0"/>
<ImagingEnvironment Temperature="-29.95" TemperatureUnit="°C"/>
<Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:0" Interleaved="false" PhysicalSizeX="0.325" PhysicalSizeXUnit="µm" PhysicalSizeY="0.325" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="2" SizeT="2" SizeX="1392" SizeY="1040" SizeZ="1" Type="uint16">
<Channel ID="Channel:0:0" Name="RFP" SamplesPerPixel="1">
<DetectorSettings Binning="1x1" ID="Detector:0:0"/>
<LightPath/>
<Channel ID="Channel:0:1" Name="GFP" SamplesPerPixel="1">
<LightPath/>
<MetadataOnly/>
<Plane DeltaT="0.0" DeltaTUnit="s" ExposureTime="0.01" ExposureTimeUnit="s" PositionX="41380.0" PositionXUnit="reference frame" PositionY="29240.0" PositionYUnit="reference frame" PositionZ="0.0" PositionZUnit="reference frame" TheC="0" TheT="0" TheZ="0"/>
<Image ID="Image:1" Name="Well C05 Field #1">
<AcquisitionDate>2019-05-15T15:52:30.617</AcquisitionDate>
<Description/>
<InstrumentRef ID="Instrument:0"/>
<ObjectiveSettings ID="Objective:0:0" RefractiveIndex="1.0"/>
<ImagingEnvironment Temperature="-29.95" TemperatureUnit="°C"/>
<Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:1" Interleaved="false" PhysicalSizeX="0.325" PhysicalSizeXUnit="µm" PhysicalSizeY="0.325" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="2" SizeT="2" SizeX="1392" SizeY="1040" SizeZ="1" Type="uint16">
<Channel ID="Channel:1:0" Name="RFP" SamplesPerPixel="1">
<DetectorSettings Binning="1x1" ID="Detector:0:0"/>
<LightPath/>
<Channel ID="Channel:1:1" Name="GFP" SamplesPerPixel="1">
<LightPath/>
<MetadataOnly/>
<Plane DeltaT="0.0" DeltaTUnit="s" ExposureTime="0.01" ExposureTimeUnit="s" PositionX="41380.0" PositionXUnit="reference frame" PositionY="29240.0" PositionYUnit="reference frame" PositionZ="0.0" PositionZUnit="reference frame" TheC="0" TheT="0" TheZ="0"/>
but there seems to be something wrong with the series, even the thumbnails for showing the different series don’t work somehow…
Here is the complete error I’m getting with Bio-formats 6.1.1, hope that helps.
Warning: Error loading thumbnail for series #1
Warning: Error loading thumbnail for series #2
loci.formats.FormatException: Invalid image number: 1 (series=0, imageCount=1)
at loci.formats.FormatTools.checkPlaneNumber(FormatTools.java:1012)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1000)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.MetamorphReader.openBytes(MetamorphReader.java:285)
at loci.formats.in.CellWorxReader.openBytes(CellWorxReader.java:224)
at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:156)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:233)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334)
at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:186)
at loci.plugins.in.ImagePlusReader.readProcessors(ImagePlusReader.java:422)
at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:387)
at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:282)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:243)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:221)
at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:116)
at loci.plugins.in.Importer.readPixels(Importer.java:149)
at loci.plugins.in.Importer.run(Importer.java:86)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:229)
at ij.IJ.runPlugIn(IJ.java:193)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at ij.IJ.run(IJ.java:309)
at ij.IJ.run(IJ.java:320)
at ij.macro.Functions.doRun(Functions.java:623)
at ij.macro.Functions.doFunction(Functions.java:97)
at ij.macro.Interpreter.doStatement(Interpreter.java:270)
at ij.macro.Interpreter.doStatements(Interpreter.java:256)
at ij.macro.Interpreter.run(Interpreter.java:152)
at ij.macro.Interpreter.run(Interpreter.java:91)
at ij.macro.MacroRunner.run(MacroRunner.java:139)
at java.lang.Thread.run(Thread.java:748)