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Task #11387 (closed)

Opened 11 years ago

Closed 10 years ago

Bug: ND2 OME-XML metadata for channels incorrect

Reported by:	omero-qa	Owned by:	mlinkert
Priority:	minor	Milestone:	5.0.3
Component:	Bio-Formats	Version:	4.4.8
Keywords:	ND2Reader	Cc:	jonas.ogaard@…
Resources:	n.a.	Referenced By:	https://trello.com/c/ArelsNBe/51-bug-nd2-bio-formats
References:	n.a.	Remaining Time:	n.a.
Sprint:	n.a.

Description

http://qa.openmicroscopy.org.uk/qa/feedback/7571/

The attached images (ND2/JP2) show a problem with channel colours when using ImageJ or imported into OMERO. These three colour/three-channel RGB images show as having "black/green/blue" channel colours rather than red/green/blue as expected.

The images show as having three samples per pixel (RGB), and there's a single associated colour value (0). Is this colour value correct?

Example metadata for one image:

<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2012-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLoc
ation="http://www.openmicroscopy.org/Schemas/OME/2012-06 http://www.openmicroscopy.org/Schemas/OME/2012-06/ome.xsd">
   <Instrument ID="Instrument:0">
      <Detector ID="Detector:0:0" Type="Other"/>
      <Objective CalibratedMagnification="1.0" Correction="Other" ID="Objective:0:0" Immersion="Other" LensNA="0.75"/>
   </Instrument>
   <Image ID="Image:0" Name="LinarKontrast-ManuellHvit-MaxKondens-IkkeFilterLys.jp2 (series 1)">
      <AcquisitionDate>2013-08-19T16:59:40</AcquisitionDate>
      <InstrumentRef ID="Instrument:0"/>
      <ObjectiveSettings ID="Objective:0:0" RefractiveIndex="1.0"/>
      <Pixels DimensionOrder="XYCZT" ID="Pixels:0" PhysicalSizeX="0.123893805309735" PhysicalSizeY="0.123893805309735" SizeC="3" S
izeT="1" SizeX="2560" SizeY="1920" SizeZ="1" Type="uint8">
         <Channel Color="0" ID="Channel:0:0" PinholeSize="0.0" SamplesPerPixel="3">
            <DetectorSettings Gain="1.0" ID="Detector:0:0" Voltage="0.0"/>
            <LightPath/>
         </Channel>
         <MetadataOnly/>
         <Plane TheC="0" TheT="0" TheZ="0"/>
      </Pixels>
   </Image>

References

Change History (5)

comment:1 Changed 11 years ago by rleigh

Component changed from from QA to Bio-Formats

comment:2 Changed 10 years ago by mlinkert

comment:3 Changed 10 years ago by mlinkert

Milestone changed from Unscheduled to 5.0.3

comment:4 Changed 10 years ago by jamoore

Referenced By set to https://trello.com/c/ArelsNBe/51-bug-nd2-bio-formats

comment:5 Changed 10 years ago by mlinkert

Resolution set to fixed
Status changed from new to closed

Current dev_5_0 does not set the channel color for these files - I suspect we fixed this in 5.0.2 (or possibly earlier).

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