Update BioTek reader to allow brightfield-only plates by melissalinkert · Pull Request #303 · glencoesoftware/bioformats2raw

melissalinkert · 2026-03-11T23:07:18Z

Includes a test that should fail without the reader change.

Not super well-tested across a variety of real data yet, but shouldn't fail existing tests.

muhanadz

Using the original data without the PR given me a NullPointerException:

./bioformats2raw-0.11.0/bin/bioformats2raw Plate\ 1/Stitched_3\ -\ Copy/B3_1_Stitched\[A_Blue\]_3_001_1.tif ./pre_pr.zarr
java.lang.NullPointerException
	at com.glencoesoftware.bioformats2raw.BioTekReader$BioTekWell.getFile(BioTekReader.java:1021)
	at com.glencoesoftware.bioformats2raw.BioTekReader.initFile(BioTekReader.java:476)
	at loci.formats.FormatReader.setId(FormatReader.java:1480)
	at loci.formats.ImageReader.setId(ImageReader.java:864)
	at com.glencoesoftware.bioformats2raw.Converter.getBaseReaderClass(Converter.java:3094)
	at com.glencoesoftware.bioformats2raw.Converter.convert(Converter.java:1383)
	at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:1359)
	at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:106)
	at picocli.CommandLine.executeUserObject(CommandLine.java:2041)
	at picocli.CommandLine.access$1500(CommandLine.java:148)
	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2461)
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2453)
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2415)
	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2273)
	at picocli.CommandLine$RunLast.execute(CommandLine.java:2417)
	at picocli.CommandLine.execute(CommandLine.java:2170)
	at com.glencoesoftware.bioformats2raw.Converter.main(Converter.java:3315)

Running the same command with the build from this PR converts the file as expected:

./bioformats2raw-0.12.0-SNAPSHOT/bin/bioformats2raw Plate\ 1/Stitched_3\ -\ Copy/B3_1_Stitched\[A_Blue\]_3_001_1.tif ./post_pr.zarr

I was then able to import post_pr.zarr to OMERO Plus and display the plate without any issues.

erindiel

From @muhanadz 's test above, I agree that the data loads successfully, but it looks like the run name is still Fluorescence. Is it possible to fix that?

melissalinkert · 2026-03-27T21:52:43Z

I think 833cbaf will fix the plate acquisition name, but I now see a weird error when trying to test locally:

2026-03-27 16:45:59,329 [main] WARN  loci.formats.Memoizer - failed to save memo file: <REDACTED>.bfmemo
com.esotericsoftware.kryo.KryoException: java.lang.reflect.InaccessibleObjectException: Unable to make field private final java.lang.String java.io.File.path accessible: module java.base does not "opens java.io" to unnamed module @161b062a
Serialization trace:
file (loci.common.Location)
parent (com.glencoesoftware.bioformats2raw.BioTekReader)
	at com.esotericsoftware.kryo.serializers.ReflectField.write(ReflectField.java:101)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:108)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:642)
	at com.esotericsoftware.kryo.serializers.ReflectField.write(ReflectField.java:70)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:108)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:627)
	at loci.formats.Memoizer$KryoDeser.saveReader(Memoizer.java:212)
	at loci.formats.Memoizer.saveMemo(Memoizer.java:1004)
	at loci.formats.Memoizer.setId(Memoizer.java:733)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)
	at com.glencoesoftware.bioformats2raw.Converter.convert(Converter.java:1559)
	at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:1499)
	at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:123)
	at picocli.CommandLine.executeUserObject(CommandLine.java:2041)
	at picocli.CommandLine.access$1500(CommandLine.java:148)
	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2461)
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2453)
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2415)
	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2273)
	at picocli.CommandLine$RunLast.execute(CommandLine.java:2417)
	at picocli.CommandLine.execute(CommandLine.java:2170)
	at com.glencoesoftware.bioformats2raw.Converter.main(Converter.java:3652)
Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make field private final java.lang.String java.io.File.path accessible: module java.base does not "opens java.io" to unnamed module @161b062a
	at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
	at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
	at java.base/java.lang.reflect.Field.checkCanSetAccessible(Field.java:178)
	at java.base/java.lang.reflect.Field.setAccessible(Field.java:172)
	at com.esotericsoftware.kryo.serializers.CachedFields.addField(CachedFields.java:123)
	at com.esotericsoftware.kryo.serializers.CachedFields.rebuild(CachedFields.java:99)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:82)
	at com.esotericsoftware.kryo.SerializerFactory$FieldSerializerFactory.newSerializer(SerializerFactory.java:124)
	at com.esotericsoftware.kryo.SerializerFactory$FieldSerializerFactory.newSerializer(SerializerFactory.java:108)
	at com.esotericsoftware.kryo.Kryo.newDefaultSerializer(Kryo.java:469)
	at com.esotericsoftware.kryo.Kryo.getDefaultSerializer(Kryo.java:454)
	at com.esotericsoftware.kryo.util.DefaultClassResolver.registerImplicit(DefaultClassResolver.java:89)
	at com.esotericsoftware.kryo.Kryo.getRegistration(Kryo.java:581)
	at com.esotericsoftware.kryo.util.DefaultClassResolver.writeClass(DefaultClassResolver.java:112)
	at com.esotericsoftware.kryo.Kryo.writeClass(Kryo.java:613)
	at com.esotericsoftware.kryo.serializers.ReflectField.write(ReflectField.java:67)
	... 22 common frames omitted

That's with Java 17, which I was sure I had been using when originally working on this PR. Can investigate further next week.

melissalinkert · 2026-03-30T15:09:23Z

Upon further investigation, the error in #303 (comment) was present before, but does not block conversion. It only looked like a blocking issue at the end of Friday as I was testing with --no-tiles. I can now confirm that 833cbaf does fix the PlateAcquisition name to be Bright-field.

EsotericSoftware/kryo#885 and EsotericSoftware/kryo#859 suggest this is expected behavior, so separately from this PR will need to investigate the workarounds described in those issues.

sbesson · 2026-03-31T07:47:47Z

@melissalinkert does BioRekReader need a similar change as in ome/bioformats#3815 i.e. the private Location internal fields should be replaced by primitive Java types?

melissalinkert · 2026-03-31T14:27:06Z

Good point - ea839e5 fixes the error above when testing locally.

sbesson

Running bioformats2raw from version 0.12.0rc2 or from a build against this PR against some of the BioTek fluorescence plate and running a recursive diff between the generated Zarr datasets, I see some minor differences in terms of the metadata e.g.

<     <PlateAcquisition ID="PlateAcquisition:0:0" MaximumFieldCount="3" Name="Fluorescence" StartTime="2023-07-10T10:46:28">
---
>     <PlateAcquisition ID="PlateAcquisition:0:0" MaximumFieldCount="3" Name="Fluorescence" StartTime="2023-07-10T10:47:41">
26c26
<     <AcquisitionDate>2023-07-10T10:46:28</AcquisitionDate>
---
>     <AcquisitionDate>2023-07-10T10:47:41</AcquisitionDate>
29c29
<     <ImagingEnvironment Temperature="25.9" TemperatureUnit="°C"/>
---
>     <ImagingEnvironment Temperature="26.0" TemperatureUnit="°C"/>
65c65
<     <AcquisitionDate>2023-07-10T10:46:28</AcquisitionDate>
---
>     <AcquisitionDate>2023-07-10T10:47:41</AcquisitionDate>
68c68
<     <ImagingEnvironment Temperature="25.9" TemperatureUnit="°C"/>
---
>     <ImagingEnvironment Temperature="26.0" TemperatureUnit="°C"/>
104c104
<     <AcquisitionDate>2023-07-10T10:46:28</AcquisitionDate>
---
>     <AcquisitionDate>2023-07-10T10:47:41</AcquisitionDate>
107c107
<     <ImagingEnvironment Temperature="25.9" TemperatureUnit="°C"/>
---
>     <ImagingEnvironment Temperature="26.0" TemperatureUnit="°C"/>

Is that related to a difference in file ordering?

melissalinkert · 2026-03-31T16:10:14Z

The behavior in #303 (review) is fixed by 13749b2 when testing locally.

erindiel · 2026-03-31T20:26:45Z

@muhanadz could you please re-run the conversion and confirm that the PlateAcquisition name is fixed?

sbesson

Retested the latest changes using a set of private customer BioTek plates including with 0.12.0-rc2 and with a build of this PR.

The diff between the Zarr datasets generated by different versions of the utility is now reduced to all .zattrs files as the version of Bio-Formats is 8.5.0 since #308. In particular the OME-XML metadata stored as OME/METADATA.ome.xml is identical with and without this PR for all converted fluorescence-only plates.

For the brightfield-only plate, conversion was failing with 0.12.0-rc2 and is successful with this PR. The generated metadata shows a brightfield plate with the RGB channels separated

<?xml version="1.0" encoding="UTF-8"?>
<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="3" ID="Plate:0" Name="Plate 1" Rows="2">
    <Well Column="2" ID="Well:0:0" Row="1">
      <WellSample ID="WellSample:0:0:0" Index="0">
        <ImageRef ID="Image:0"/>
      </WellSample>
      <WellSample ID="WellSample:0:0:1" Index="1">
        <ImageRef ID="Image:1"/>
      </WellSample>
      <WellSample ID="WellSample:0:0:2" Index="2">
        <ImageRef ID="Image:2"/>
      </WellSample>
      <WellSample ID="WellSample:0:0:3" Index="3">
        <ImageRef ID="Image:3"/>
      </WellSample>
      <WellSample ID="WellSample:0:0:4" Index="4">
        <ImageRef ID="Image:4"/>
      </WellSample>
      <WellSample ID="WellSample:0:0:5" Index="5">
        <ImageRef ID="Image:5"/>
      </WellSample>
      <WellSample ID="WellSample:0:0:6" Index="6">
        <ImageRef ID="Image:6"/>
      </WellSample>
      <WellSample ID="WellSample:0:0:7" Index="7">
        <ImageRef ID="Image:7"/>
      </WellSample>
      <WellSample ID="WellSample:0:0:8" Index="8">
        <ImageRef ID="Image:8"/>
      </WellSample>
      <WellSample ID="WellSample:0:0:9" Index="9">
        <ImageRef ID="Image:9"/>
      </WellSample>
      <WellSample ID="WellSample:0:0:10" Index="10">
        <ImageRef ID="Image:10"/>
      </WellSample>
      <WellSample ID="WellSample:0:0:11" Index="11">
        <ImageRef ID="Image:11"/>
      </WellSample>
      <WellSample ID="WellSample:0:0:12" Index="12">
        <ImageRef ID="Image:12"/>
      </WellSample>
      <WellSample ID="WellSample:0:0:13" Index="13">
        <ImageRef ID="Image:13"/>
      </WellSample>
      <WellSample ID="WellSample:0:0:14" Index="14">
        <ImageRef ID="Image:14"/>
      </WellSample>
      <WellSample ID="WellSample:0:0:15" Index="15">
        <ImageRef ID="Image:15"/>
      </WellSample>
    </Well>
    <PlateAcquisition ID="PlateAcquisition:0:0" MaximumFieldCount="16" Name="Bright-field" StartTime="2026-02-03T12:03:14">
      <WellSampleRef ID="WellSample:0:0:0"/>
      <WellSampleRef ID="WellSample:0:0:1"/>
      <WellSampleRef ID="WellSample:0:0:2"/>
      <WellSampleRef ID="WellSample:0:0:3"/>
      <WellSampleRef ID="WellSample:0:0:4"/>
      <WellSampleRef ID="WellSample:0:0:5"/>
      <WellSampleRef ID="WellSample:0:0:6"/>
      <WellSampleRef ID="WellSample:0:0:7"/>
      <WellSampleRef ID="WellSample:0:0:8"/>
      <WellSampleRef ID="WellSample:0:0:9"/>
      <WellSampleRef ID="WellSample:0:0:10"/>
      <WellSampleRef ID="WellSample:0:0:11"/>
      <WellSampleRef ID="WellSample:0:0:12"/>
      <WellSampleRef ID="WellSample:0:0:13"/>
      <WellSampleRef ID="WellSample:0:0:14"/>
      <WellSampleRef ID="WellSample:0:0:15"/>
    </PlateAcquisition>
  </Plate>
  <Instrument ID="Instrument:0">
    <Detector Gain="2.2" ID="Detector:0:0"/>
    <Objective ID="Objective:0:0" LensNA="0.45" Manufacturer="Olympus" Model="1220517" NominalMagnification="20.0"/>
  </Instrument>
  <Image ID="Image:0" Name="B03 #1">
    <AcquisitionDate>2026-02-03T12:03:14</AcquisitionDate>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:0:0"/>
    <ImagingEnvironment Temperature="36.5" TemperatureUnit="°C"/>
    <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" PhysicalSizeX="0.3488955823293173" PhysicalSizeXUnit="µm" PhysicalSizeY="0.3488955823293173" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="3" SizeT="1" SizeX="1992" SizeY="1992" SizeZ="1" Type="uint16">
      <Channel ID="Channel:0:0" Name="Red" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:0:1" Name="Green" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:0:2" Name="Blue" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <MetadataOnly/>
      <Plane TheC="0" TheT="0" TheZ="0"/>
      <Plane TheC="1" TheT="0" TheZ="0"/>
      <Plane TheC="2" TheT="0" TheZ="0"/>
    </Pixels>
  </Image>
  <Image ID="Image:1" Name="B03 #2">
    <AcquisitionDate>2026-02-03T12:03:14</AcquisitionDate>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:0:0"/>
    <ImagingEnvironment Temperature="36.5" TemperatureUnit="°C"/>
    <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:1" Interleaved="false" PhysicalSizeX="0.3488955823293173" PhysicalSizeXUnit="µm" PhysicalSizeY="0.3488955823293173" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="3" SizeT="1" SizeX="1992" SizeY="1992" SizeZ="1" Type="uint16">
      <Channel ID="Channel:1:0" Name="Red" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:1:1" Name="Green" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:1:2" Name="Blue" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <MetadataOnly/>
      <Plane TheC="0" TheT="0" TheZ="0"/>
      <Plane TheC="1" TheT="0" TheZ="0"/>
      <Plane TheC="2" TheT="0" TheZ="0"/>
    </Pixels>
  </Image>
  <Image ID="Image:2" Name="B03 #3">
    <AcquisitionDate>2026-02-03T12:03:14</AcquisitionDate>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:0:0"/>
    <ImagingEnvironment Temperature="36.5" TemperatureUnit="°C"/>
    <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:2" Interleaved="false" PhysicalSizeX="0.3488955823293173" PhysicalSizeXUnit="µm" PhysicalSizeY="0.3488955823293173" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="3" SizeT="1" SizeX="1992" SizeY="1992" SizeZ="1" Type="uint16">
      <Channel ID="Channel:2:0" Name="Red" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:2:1" Name="Green" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:2:2" Name="Blue" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <MetadataOnly/>
      <Plane TheC="0" TheT="0" TheZ="0"/>
      <Plane TheC="1" TheT="0" TheZ="0"/>
      <Plane TheC="2" TheT="0" TheZ="0"/>
    </Pixels>
  </Image>
  <Image ID="Image:3" Name="B03 #4">
    <AcquisitionDate>2026-02-03T12:03:14</AcquisitionDate>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:0:0"/>
    <ImagingEnvironment Temperature="36.5" TemperatureUnit="°C"/>
    <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:3" Interleaved="false" PhysicalSizeX="0.3488955823293173" PhysicalSizeXUnit="µm" PhysicalSizeY="0.3488955823293173" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="3" SizeT="1" SizeX="1992" SizeY="1992" SizeZ="1" Type="uint16">
      <Channel ID="Channel:3:0" Name="Red" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:3:1" Name="Green" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:3:2" Name="Blue" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <MetadataOnly/>
      <Plane TheC="0" TheT="0" TheZ="0"/>
      <Plane TheC="1" TheT="0" TheZ="0"/>
      <Plane TheC="2" TheT="0" TheZ="0"/>
    </Pixels>
  </Image>
  <Image ID="Image:4" Name="B03 #5">
    <AcquisitionDate>2026-02-03T12:03:14</AcquisitionDate>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:0:0"/>
    <ImagingEnvironment Temperature="36.5" TemperatureUnit="°C"/>
    <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:4" Interleaved="false" PhysicalSizeX="0.3488955823293173" PhysicalSizeXUnit="µm" PhysicalSizeY="0.3488955823293173" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="3" SizeT="1" SizeX="1992" SizeY="1992" SizeZ="1" Type="uint16">
      <Channel ID="Channel:4:0" Name="Red" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:4:1" Name="Green" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:4:2" Name="Blue" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <MetadataOnly/>
      <Plane TheC="0" TheT="0" TheZ="0"/>
      <Plane TheC="1" TheT="0" TheZ="0"/>
      <Plane TheC="2" TheT="0" TheZ="0"/>
    </Pixels>
  </Image>
  <Image ID="Image:5" Name="B03 #6">
    <AcquisitionDate>2026-02-03T12:03:14</AcquisitionDate>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:0:0"/>
    <ImagingEnvironment Temperature="36.5" TemperatureUnit="°C"/>
    <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:5" Interleaved="false" PhysicalSizeX="0.3488955823293173" PhysicalSizeXUnit="µm" PhysicalSizeY="0.3488955823293173" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="3" SizeT="1" SizeX="1992" SizeY="1992" SizeZ="1" Type="uint16">
      <Channel ID="Channel:5:0" Name="Red" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:5:1" Name="Green" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:5:2" Name="Blue" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <MetadataOnly/>
      <Plane TheC="0" TheT="0" TheZ="0"/>
      <Plane TheC="1" TheT="0" TheZ="0"/>
      <Plane TheC="2" TheT="0" TheZ="0"/>
    </Pixels>
  </Image>
  <Image ID="Image:6" Name="B03 #7">
    <AcquisitionDate>2026-02-03T12:03:14</AcquisitionDate>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:0:0"/>
    <ImagingEnvironment Temperature="36.5" TemperatureUnit="°C"/>
    <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:6" Interleaved="false" PhysicalSizeX="0.3488955823293173" PhysicalSizeXUnit="µm" PhysicalSizeY="0.3488955823293173" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="3" SizeT="1" SizeX="1992" SizeY="1992" SizeZ="1" Type="uint16">
      <Channel ID="Channel:6:0" Name="Red" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:6:1" Name="Green" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:6:2" Name="Blue" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <MetadataOnly/>
      <Plane TheC="0" TheT="0" TheZ="0"/>
      <Plane TheC="1" TheT="0" TheZ="0"/>
      <Plane TheC="2" TheT="0" TheZ="0"/>
    </Pixels>
  </Image>
  <Image ID="Image:7" Name="B03 #8">
    <AcquisitionDate>2026-02-03T12:03:14</AcquisitionDate>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:0:0"/>
    <ImagingEnvironment Temperature="36.5" TemperatureUnit="°C"/>
    <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:7" Interleaved="false" PhysicalSizeX="0.3488955823293173" PhysicalSizeXUnit="µm" PhysicalSizeY="0.3488955823293173" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="3" SizeT="1" SizeX="1992" SizeY="1992" SizeZ="1" Type="uint16">
      <Channel ID="Channel:7:0" Name="Red" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:7:1" Name="Green" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:7:2" Name="Blue" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <MetadataOnly/>
      <Plane TheC="0" TheT="0" TheZ="0"/>
      <Plane TheC="1" TheT="0" TheZ="0"/>
      <Plane TheC="2" TheT="0" TheZ="0"/>
    </Pixels>
  </Image>
  <Image ID="Image:8" Name="B03 #9">
    <AcquisitionDate>2026-02-03T12:03:14</AcquisitionDate>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:0:0"/>
    <ImagingEnvironment Temperature="36.5" TemperatureUnit="°C"/>
    <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:8" Interleaved="false" PhysicalSizeX="0.3488955823293173" PhysicalSizeXUnit="µm" PhysicalSizeY="0.3488955823293173" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="3" SizeT="1" SizeX="1992" SizeY="1992" SizeZ="1" Type="uint16">
      <Channel ID="Channel:8:0" Name="Red" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:8:1" Name="Green" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:8:2" Name="Blue" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <MetadataOnly/>
      <Plane TheC="0" TheT="0" TheZ="0"/>
      <Plane TheC="1" TheT="0" TheZ="0"/>
      <Plane TheC="2" TheT="0" TheZ="0"/>
    </Pixels>
  </Image>
  <Image ID="Image:9" Name="B03 #10">
    <AcquisitionDate>2026-02-03T12:03:14</AcquisitionDate>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:0:0"/>
    <ImagingEnvironment Temperature="36.5" TemperatureUnit="°C"/>
    <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:9" Interleaved="false" PhysicalSizeX="0.3488955823293173" PhysicalSizeXUnit="µm" PhysicalSizeY="0.3488955823293173" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="3" SizeT="1" SizeX="1992" SizeY="1992" SizeZ="1" Type="uint16">
      <Channel ID="Channel:9:0" Name="Red" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:9:1" Name="Green" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:9:2" Name="Blue" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <MetadataOnly/>
      <Plane TheC="0" TheT="0" TheZ="0"/>
      <Plane TheC="1" TheT="0" TheZ="0"/>
      <Plane TheC="2" TheT="0" TheZ="0"/>
    </Pixels>
  </Image>
  <Image ID="Image:10" Name="B03 #11">
    <AcquisitionDate>2026-02-03T12:03:14</AcquisitionDate>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:0:0"/>
    <ImagingEnvironment Temperature="36.5" TemperatureUnit="°C"/>
    <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:10" Interleaved="false" PhysicalSizeX="0.3488955823293173" PhysicalSizeXUnit="µm" PhysicalSizeY="0.3488955823293173" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="3" SizeT="1" SizeX="1992" SizeY="1992" SizeZ="1" Type="uint16">
      <Channel ID="Channel:10:0" Name="Red" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:10:1" Name="Green" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:10:2" Name="Blue" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <MetadataOnly/>
      <Plane TheC="0" TheT="0" TheZ="0"/>
      <Plane TheC="1" TheT="0" TheZ="0"/>
      <Plane TheC="2" TheT="0" TheZ="0"/>
    </Pixels>
  </Image>
  <Image ID="Image:11" Name="B03 #12">
    <AcquisitionDate>2026-02-03T12:03:14</AcquisitionDate>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:0:0"/>
    <ImagingEnvironment Temperature="36.5" TemperatureUnit="°C"/>
    <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:11" Interleaved="false" PhysicalSizeX="0.3488955823293173" PhysicalSizeXUnit="µm" PhysicalSizeY="0.3488955823293173" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="3" SizeT="1" SizeX="1992" SizeY="1992" SizeZ="1" Type="uint16">
      <Channel ID="Channel:11:0" Name="Red" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:11:1" Name="Green" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:11:2" Name="Blue" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <MetadataOnly/>
      <Plane TheC="0" TheT="0" TheZ="0"/>
      <Plane TheC="1" TheT="0" TheZ="0"/>
      <Plane TheC="2" TheT="0" TheZ="0"/>
    </Pixels>
  </Image>
  <Image ID="Image:12" Name="B03 #13">
    <AcquisitionDate>2026-02-03T12:03:14</AcquisitionDate>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:0:0"/>
    <ImagingEnvironment Temperature="36.5" TemperatureUnit="°C"/>
    <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:12" Interleaved="false" PhysicalSizeX="0.3488955823293173" PhysicalSizeXUnit="µm" PhysicalSizeY="0.3488955823293173" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="3" SizeT="1" SizeX="1992" SizeY="1992" SizeZ="1" Type="uint16">
      <Channel ID="Channel:12:0" Name="Red" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:12:1" Name="Green" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:12:2" Name="Blue" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <MetadataOnly/>
      <Plane TheC="0" TheT="0" TheZ="0"/>
      <Plane TheC="1" TheT="0" TheZ="0"/>
      <Plane TheC="2" TheT="0" TheZ="0"/>
    </Pixels>
  </Image>
  <Image ID="Image:13" Name="B03 #14">
    <AcquisitionDate>2026-02-03T12:03:14</AcquisitionDate>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:0:0"/>
    <ImagingEnvironment Temperature="36.5" TemperatureUnit="°C"/>
    <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:13" Interleaved="false" PhysicalSizeX="0.3488955823293173" PhysicalSizeXUnit="µm" PhysicalSizeY="0.3488955823293173" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="3" SizeT="1" SizeX="1992" SizeY="1992" SizeZ="1" Type="uint16">
      <Channel ID="Channel:13:0" Name="Red" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:13:1" Name="Green" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:13:2" Name="Blue" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <MetadataOnly/>
      <Plane TheC="0" TheT="0" TheZ="0"/>
      <Plane TheC="1" TheT="0" TheZ="0"/>
      <Plane TheC="2" TheT="0" TheZ="0"/>
    </Pixels>
  </Image>
  <Image ID="Image:14" Name="B03 #15">
    <AcquisitionDate>2026-02-03T12:03:14</AcquisitionDate>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:0:0"/>
    <ImagingEnvironment Temperature="36.5" TemperatureUnit="°C"/>
    <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:14" Interleaved="false" PhysicalSizeX="0.3488955823293173" PhysicalSizeXUnit="µm" PhysicalSizeY="0.3488955823293173" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="3" SizeT="1" SizeX="1992" SizeY="1992" SizeZ="1" Type="uint16">
      <Channel ID="Channel:14:0" Name="Red" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:14:1" Name="Green" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:14:2" Name="Blue" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <MetadataOnly/>
      <Plane TheC="0" TheT="0" TheZ="0"/>
      <Plane TheC="1" TheT="0" TheZ="0"/>
      <Plane TheC="2" TheT="0" TheZ="0"/>
    </Pixels>
  </Image>
  <Image ID="Image:15" Name="B03 #16">
    <AcquisitionDate>2026-02-03T12:03:14</AcquisitionDate>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:0:0"/>
    <ImagingEnvironment Temperature="36.5" TemperatureUnit="°C"/>
    <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:15" Interleaved="false" PhysicalSizeX="0.3488955823293173" PhysicalSizeXUnit="µm" PhysicalSizeY="0.3488955823293173" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="3" SizeT="1" SizeX="1992" SizeY="1992" SizeZ="1" Type="uint16">
      <Channel ID="Channel:15:0" Name="Red" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:15:1" Name="Green" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <Channel ID="Channel:15:2" Name="Blue" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0"/>
        <LightPath/>
      </Channel>
      <MetadataOnly/>
      <Plane TheC="0" TheT="0" TheZ="0"/>
      <Plane TheC="1" TheT="0" TheZ="0"/>
      <Plane TheC="2" TheT="0" TheZ="0"/>
    </Pixels>
  </Image>
  <StructuredAnnotations>
    <XMLAnnotation ID="Annotation:0" Namespace="openmicroscopy.org/OriginalMetadata">
      <Value>
        <OriginalMetadata>
          <Key>Y fields</Key>
          <Value>4</Value>
        </OriginalMetadata>
      </Value>
    </XMLAnnotation>
    <XMLAnnotation ID="Annotation:1" Namespace="openmicroscopy.org/OriginalMetadata">
      <Value>
        <OriginalMetadata>
          <Key>X fields</Key>
          <Value>4</Value>
        </OriginalMetadata>
      </Value>
    </XMLAnnotation>
    <XMLAnnotation ID="Annotation:2" Namespace="openmicroscopy.org/OriginalMetadata">
      <Value>
        <OriginalMetadata>
          <Key>Reverse plate orientation</Key>
          <Value>FALSE</Value>
        </OriginalMetadata>
      </Value>
    </XMLAnnotation>
  </StructuredAnnotations>
</OME>

Finally the four examples of mixed fluorescence/brightfield plates have slight differences in terms of the metadata which boils down to difference start/acquisition times, different detector gain and temperatures and additional Pixels metadata like PhysicalSizeZ/PhysicalSizeZUnit e.g.

72c72
<     <PlateAcquisition ID="PlateAcquisition:0:0" MaximumFieldCount="4" Name="Fluorescence" StartTime="2020-04-10T18:09:47">
---
>     <PlateAcquisition ID="PlateAcquisition:0:0" MaximumFieldCount="4" Name="Fluorescence" StartTime="2020-04-10T18:06:12">
98c98
<     <Detector Gain="22.325" ID="Detector:0:0"/>
---
>     <Detector Gain="15.6" ID="Detector:0:0"/>
102c102
<     <AcquisitionDate>2020-04-10T18:09:47</AcquisitionDate>
---
>     <AcquisitionDate>2020-04-10T18:06:12</AcquisitionDate>
105,106c105,106
<     <ImagingEnvironment Temperature="37.1" TemperatureUnit="°C"/>
<     <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" PhysicalSizeX="1.6119281045751634" PhysicalSizeXUnit="µm" PhysicalSizeY="1.6117256637168142" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="6" SizeT="3" SizeX="1224" SizeY="904" SizeZ="6" Type="uint16">
---
>     <ImagingEnvironment Temperature="37.0" TemperatureUnit="°C"/>
>     <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" PhysicalSizeX="1.6119281045751634" PhysicalSizeXUnit="µm" PhysicalSizeY="1.6117256637168142" PhysicalSizeYUnit="µm" PhysicalSizeZ="53.8" PhysicalSizeZUnit="µm" SignificantBits="16" SizeC="6" SizeT="3" SizeX="1224" SizeY="904" SizeZ="6" Type="uint16">
243c243
<     <AcquisitionDate>2020-04-10T18:09:47</AcquisitionDate>
---
>     <AcquisitionDate>2020-04-10T18:06:12</AcquisitionDate>
246,247c246,247
<     <ImagingEnvironment Temperature="37.1" TemperatureUnit="°C"/>
<     <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:1" Interleaved="false" PhysicalSizeX="1.6119281045751634" PhysicalSizeXUnit="µm" PhysicalSizeY="1.6117256637168142" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="6" SizeT="3" SizeX="1224" SizeY="904" SizeZ="6" Type="uint16">
---
>     <ImagingEnvironment Temperature="37.0" TemperatureUnit="°C"/>
>     <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:1" Interleaved="false" PhysicalSizeX="1.6119281045751634" PhysicalSizeXUnit="µm" PhysicalSizeY="1.6117256637168142" PhysicalSizeYUnit="µm" PhysicalSizeZ="53.8" PhysicalSizeZUnit="µm" SignificantBits="16" SizeC="6" SizeT="3" SizeX="1224" SizeY="904" SizeZ="6" Type="uint16">
384c384
<     <AcquisitionDate>2020-04-10T18:09:47</AcquisitionDate>
---
>     <AcquisitionDate>2020-04-10T18:06:12</AcquisitionDate>
387,388c387,388
<     <ImagingEnvironment Temperature="37.1" TemperatureUnit="°C"/>
<     <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:2" Interleaved="false" PhysicalSizeX="1.6119281045751634" PhysicalSizeXUnit="µm" PhysicalSizeY="1.6117256637168142" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="6" SizeT="3" SizeX="1224" SizeY="904" SizeZ="6" Type="uint16">
---
>     <ImagingEnvironment Temperature="37.0" TemperatureUnit="°C"/>
>     <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:2" Interleaved="false" PhysicalSizeX="1.6119281045751634" PhysicalSizeXUnit="µm" PhysicalSizeY="1.6117256637168142" PhysicalSizeYUnit="µm" PhysicalSizeZ="53.8" PhysicalSizeZUnit="µm" SignificantBits="16" SizeC="6" SizeT="3" SizeX="1224" SizeY="904" SizeZ="6" Type="uint16">
525c525
<     <AcquisitionDate>2020-04-10T18:09:47</AcquisitionDate>
---
>     <AcquisitionDate>2020-04-10T18:06:12</AcquisitionDate>
528,529c528,529
<     <ImagingEnvironment Temperature="37.1" TemperatureUnit="°C"/>
<     <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:3" Interleaved="false" PhysicalSizeX="1.6119281045751634" PhysicalSizeXUnit="µm" PhysicalSizeY="1.6117256637168142" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="6" SizeT="3" SizeX="1224" SizeY="904" SizeZ="6" Type="uint16">
---
>     <ImagingEnvironment Temperature="37.0" TemperatureUnit="°C"/>
>     <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:3" Interleaved="false" PhysicalSizeX="1.6119281045751634" PhysicalSizeXUnit="µm" PhysicalSizeY="1.6117256637168142" PhysicalSizeYUnit="µm" PhysicalSizeZ="53.8" PhysicalSizeZUnit="µm" SignificantBits="16" SizeC="6" SizeT="3" SizeX="1224" SizeY="904" SizeZ="6" Type="uint16">
666c666
<     <AcquisitionDate>2020-04-10T18:09:47</AcquisitionDate>
---
>     <AcquisitionDate>2020-04-10T18:06:12</AcquisitionDate>
669,670c669,670
<     <ImagingEnvironment Temperature="37.1" TemperatureUnit="°C"/>
<     <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:4" Interleaved="false" PhysicalSizeX="1.6119281045751634" PhysicalSizeXUnit="µm" PhysicalSizeY="1.6117256637168142" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="6" SizeT="3" SizeX="1224" SizeY="904" SizeZ="6" Type="uint16">
---
>     <ImagingEnvironment Temperature="37.0" TemperatureUnit="°C"/>
>     <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:4" Interleaved="false" PhysicalSizeX="1.6119281045751634" PhysicalSizeXUnit="µm" PhysicalSizeY="1.6117256637168142" PhysicalSizeYUnit="µm" PhysicalSizeZ="53.8" PhysicalSizeZUnit="µm" SignificantBits="16" SizeC="6" SizeT="3" SizeX="1224" SizeY="904" SizeZ="6" Type="uint16">
807c807
<     <AcquisitionDate>2020-04-10T18:09:47</AcquisitionDate>
---
>     <AcquisitionDate>2020-04-10T18:06:12</AcquisitionDate>
810,811c810,811
<     <ImagingEnvironment Temperature="37.1" TemperatureUnit="°C"/>
<     <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:5" Interleaved="false" PhysicalSizeX="1.6119281045751634" PhysicalSizeXUnit="µm" PhysicalSizeY="1.6117256637168142" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="6" SizeT="3" SizeX="1224" SizeY="904" SizeZ="6" Type="uint16">
---
>     <ImagingEnvironment Temperature="37.0" TemperatureUnit="°C"/>
>     <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:5" Interleaved="false" PhysicalSizeX="1.6119281045751634" PhysicalSizeXUnit="µm" PhysicalSizeY="1.6117256637168142" PhysicalSizeYUnit="µm" PhysicalSizeZ="53.8" PhysicalSizeZUnit="µm" SignificantBits="16" SizeC="6" SizeT="3" SizeX="1224" SizeY="904" SizeZ="6" Type="uint16">
948c948
<     <AcquisitionDate>2020-04-10T18:09:47</AcquisitionDate>
---
>     <AcquisitionDate>2020-04-10T18:06:12</AcquisitionDate>
951,952c951,952
<     <ImagingEnvironment Temperature="37.1" TemperatureUnit="°C"/>
<     <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:6" Interleaved="false" PhysicalSizeX="1.6119281045751634" PhysicalSizeXUnit="µm" PhysicalSizeY="1.6117256637168142" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="6" SizeT="3" SizeX="1224" SizeY="904" SizeZ="6" Type="uint16">
---
>     <ImagingEnvironment Temperature="37.0" TemperatureUnit="°C"/>
>     <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:6" Interleaved="false" PhysicalSizeX="1.6119281045751634" PhysicalSizeXUnit="µm" PhysicalSizeY="1.6117256637168142" PhysicalSizeYUnit="µm" PhysicalSizeZ="53.8" PhysicalSizeZUnit="µm" SignificantBits="16" SizeC="6" SizeT="3" SizeX="1224" SizeY="904" SizeZ="6" Type="uint16">
1089c1089
<     <AcquisitionDate>2020-04-10T18:09:47</AcquisitionDate>
---
>     <AcquisitionDate>2020-04-10T18:06:12</AcquisitionDate>
1092,1093c1092,1093
<     <ImagingEnvironment Temperature="37.1" TemperatureUnit="°C"/>
<     <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:7" Interleaved="false" PhysicalSizeX="1.6119281045751634" PhysicalSizeXUnit="µm" PhysicalSizeY="1.6117256637168142" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="6" SizeT="3" SizeX="1224" SizeY="904" SizeZ="6" Type="uint16">
---
>     <ImagingEnvironment Temperature="37.0" TemperatureUnit="°C"/>
>     <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:7" Interleaved="false" PhysicalSizeX="1.6119281045751634" PhysicalSizeXUnit="µm" PhysicalSizeY="1.6117256637168142" PhysicalSizeYUnit="µm" PhysicalSizeZ="53.8" PhysicalSizeZUnit="µm" SignificantBits="16" SizeC="6" SizeT="3" SizeX="1224" SizeY="904" SizeZ="6" Type="uint16">
1230c1230
<     <AcquisitionDate>2020-04-10T18:09:47</AcquisitionDate>
---
>     <AcquisitionDate>2020-04-10T18:06:12</AcquisitionDate>
1233,1234c1233,1234
<     <ImagingEnvironment Temperature="37.1" TemperatureUnit="°C"/>
<     <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:8" Interleaved="false" PhysicalSizeX="1.6119281045751634" PhysicalSizeXUnit="µm" PhysicalSizeY="1.6117256637168142" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="6" SizeT="3" SizeX="1224" SizeY="904" SizeZ="6" Type="uint16">
---
>     <ImagingEnvironment Temperature="37.0" TemperatureUnit="°C"/>
>     <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:8" Interleaved="false" PhysicalSizeX="1.6119281045751634" PhysicalSizeXUnit="µm" PhysicalSizeY="1.6117256637168142" PhysicalSizeYUnit="µm" PhysicalSizeZ="53.8" PhysicalSizeZUnit="µm" SignificantBits="16" SizeC="6" SizeT="3" SizeX="1224" SizeY="904" SizeZ="6" Type="uint16">
1371c1371
<     <AcquisitionDate>2020-04-10T18:09:47</AcquisitionDate>
---
>     <AcquisitionDate>2020-04-10T18:06:12</AcquisitionDate>
1374,1375c1374,1375
<     <ImagingEnvironment Temperature="37.1" TemperatureUnit="°C"/>
<     <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:9" Interleaved="false" PhysicalSizeX="1.6119281045751634" PhysicalSizeXUnit="µm" PhysicalSizeY="1.6117256637168142" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="6" SizeT="3" SizeX="1224" SizeY="904" SizeZ="6" Type="uint16">
---
>     <ImagingEnvironment Temperature="37.0" TemperatureUnit="°C"/>
>     <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:9" Interleaved="false" PhysicalSizeX="1.6119281045751634" PhysicalSizeXUnit="µm" PhysicalSizeY="1.6117256637168142" PhysicalSizeYUnit="µm" PhysicalSizeZ="53.8" PhysicalSizeZUnit="µm" SignificantBits="16" SizeC="6" SizeT="3" SizeX="1224" SizeY="904" SizeZ="6" Type="uint16">
1512c1512
<     <AcquisitionDate>2020-04-10T18:09:47</AcquisitionDate>
---
>     <AcquisitionDate>2020-04-10T18:06:12</AcquisitionDate>
1515,1516c1515,1516
<     <ImagingEnvironment Temperature="37.1" TemperatureUnit="°C"/>
<     <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:10" Interleaved="false" PhysicalSizeX="1.6119281045751634" PhysicalSizeXUnit="µm" PhysicalSizeY="1.6117256637168142" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="6" SizeT="3" SizeX="1224" SizeY="904" SizeZ="6" Type="uint16">
---
>     <ImagingEnvironment Temperature="37.0" TemperatureUnit="°C"/>
>     <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:10" Interleaved="false" PhysicalSizeX="1.6119281045751634" PhysicalSizeXUnit="µm" PhysicalSizeY="1.6117256637168142" PhysicalSizeYUnit="µm" PhysicalSizeZ="53.8" PhysicalSizeZUnit="µm" SignificantBits="16" SizeC="6" SizeT="3" SizeX="1224" SizeY="904" SizeZ="6" Type="uint16">
1653c1653
<     <AcquisitionDate>2020-04-10T18:09:47</AcquisitionDate>
---
>     <AcquisitionDate>2020-04-10T18:06:12</AcquisitionDate>
1656,1657c1656,1657
<     <ImagingEnvironment Temperature="37.1" TemperatureUnit="°C"/>
<     <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:11" Interleaved="false" PhysicalSizeX="1.6119281045751634" PhysicalSizeXUnit="µm" PhysicalSizeY="1.6117256637168142" PhysicalSizeYUnit="µm" SignificantBits="16" SizeC="6" SizeT="3" SizeX="1224" SizeY="904" SizeZ="6" Type="uint16">
---
>     <ImagingEnvironment Temperature="37.0" TemperatureUnit="°C"/>
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2382c2382
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2406c2406
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2430c2430
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2433,2434c2433,2434
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This change is likely to be related to with the plane index sorting in 13749b2. The population of the physical size in Z in particular looks relevant as one of the channels is imaged across multiple Z sections but I could certainly use a second opinion to make sure this is the expectation.

muhanadz

Running the same command with the latest build of this PR:

./bioformats2raw-0.12.0-SNAPSHOT/bin/bioformats2raw Plate\ 1/Stitched_3\ -\ Copy/B3_1_Stitched\[A_Blue\]_3_001_1.tif ./post_pr_2.zarr

Convert correctly and could then be imported with omero-importer-ngff:

Run name is now corrected. LGTM

erindiel

Thanks for the latest name change and re-test!

Update BioTek reader to allow brightfield-only plates

0a9af09

melissalinkert added this to the 0.12.0 milestone Mar 11, 2026

melissalinkert requested review from erindiel, muhanadz and sbesson March 11, 2026 23:07

muhanadz approved these changes Mar 23, 2026

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erindiel requested changes Mar 27, 2026

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Fix plate acquisition naming for brightfield-only

833cbaf

melissalinkert requested a review from erindiel March 30, 2026 15:09

Keep Location out of memo file

ea839e5

sbesson reviewed Mar 31, 2026

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Fix PlaneIndex sorting

13749b2

sbesson self-requested a review March 31, 2026 19:37

erindiel requested a review from muhanadz March 31, 2026 20:26

sbesson reviewed Apr 1, 2026

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sbesson approved these changes Apr 1, 2026

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muhanadz approved these changes Apr 2, 2026

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erindiel approved these changes Apr 2, 2026

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sbesson merged commit 5382161 into glencoesoftware:master Apr 3, 2026
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Update BioTek reader to allow brightfield-only plates#303

Update BioTek reader to allow brightfield-only plates#303
sbesson merged 4 commits intoglencoesoftware:masterfrom
melissalinkert:biotek-brightfield-only

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