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Use "Color mode" OME-XML field in guessRgb function #474
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@keller-mark Is this a part of the OMEXML data model? Could you provide the whole OMEXML? |
I am not sure if This is the full OME-XML:<?xml version="1.0" encoding="utf-8"?>
<!-- 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: https://docs.openmicroscopy.org/latest/ome-model/ome-tiff/. -->
<OME Creator="OME Bio-Formats 6.6.1" UUID="urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6"
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">
<Image ID="Image:0" Name="selected.tif">
<Description />
<Pixels BigEndian="true" DimensionOrder="XYCZT" ID="Pixels:0" Interleaved="false" PhysicalSizeX="1.0"
PhysicalSizeXUnit="µm" PhysicalSizeY="1.0" PhysicalSizeYUnit="µm" SignificantBits="8" SizeC="3" SizeT="1"
SizeX="5721" SizeY="9392" SizeZ="9" Type="uint8">
<Channel ID="Channel:0:0" Name="DAPI" SamplesPerPixel="1">
<LightPath />
</Channel>
<Channel ID="Channel:0:1" Name="Membrane" SamplesPerPixel="1">
<LightPath />
</Channel>
<Channel ID="Channel:0:2" Name="PolyA" SamplesPerPixel="1">
<LightPath />
</Channel>
<TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
<TiffData FirstC="1" FirstT="0" FirstZ="0" IFD="1" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
<TiffData FirstC="2" FirstT="0" FirstZ="0" IFD="2" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
<TiffData FirstC="0" FirstT="0" FirstZ="1" IFD="3" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
<TiffData FirstC="1" FirstT="0" FirstZ="1" IFD="4" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
<TiffData FirstC="2" FirstT="0" FirstZ="1" IFD="5" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
<TiffData FirstC="0" FirstT="0" FirstZ="2" IFD="6" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
<TiffData FirstC="1" FirstT="0" FirstZ="2" IFD="7" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
<TiffData FirstC="2" FirstT="0" FirstZ="2" IFD="8" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
<TiffData FirstC="0" FirstT="0" FirstZ="3" IFD="9" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
<TiffData FirstC="1" FirstT="0" FirstZ="3" IFD="10" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
<TiffData FirstC="2" FirstT="0" FirstZ="3" IFD="11" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
<TiffData FirstC="0" FirstT="0" FirstZ="4" IFD="12" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
<TiffData FirstC="1" FirstT="0" FirstZ="4" IFD="13" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
<TiffData FirstC="2" FirstT="0" FirstZ="4" IFD="14" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
<TiffData FirstC="0" FirstT="0" FirstZ="5" IFD="15" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
<TiffData FirstC="1" FirstT="0" FirstZ="5" IFD="16" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
<TiffData FirstC="2" FirstT="0" FirstZ="5" IFD="17" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
<TiffData FirstC="0" FirstT="0" FirstZ="6" IFD="18" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
<TiffData FirstC="1" FirstT="0" FirstZ="6" IFD="19" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
<TiffData FirstC="2" FirstT="0" FirstZ="6" IFD="20" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
<TiffData FirstC="0" FirstT="0" FirstZ="7" IFD="21" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
<TiffData FirstC="1" FirstT="0" FirstZ="7" IFD="22" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
<TiffData FirstC="2" FirstT="0" FirstZ="7" IFD="23" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
<TiffData FirstC="0" FirstT="0" FirstZ="8" IFD="24" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
<TiffData FirstC="1" FirstT="0" FirstZ="8" IFD="25" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
<TiffData FirstC="2" FirstT="0" FirstZ="8" IFD="26" PlaneCount="1">
<UUID FileName="selected.ome.tiff">urn:uuid:1ecf7448-56c5-45cb-ab2f-492b6e455ce6</UUID>
</TiffData>
</Pixels>
</Image>
<StructuredAnnotations>
<XMLAnnotation ID="Annotation:0" Namespace="openmicroscopy.org/OriginalMetadata">
<Value>
<OriginalMetadata>
<Key>BitsPerSample</Key>
<Value>8</Value>
</OriginalMetadata>
</Value>
</XMLAnnotation>
<XMLAnnotation ID="Annotation:1" Namespace="openmicroscopy.org/OriginalMetadata">
<Value>
<OriginalMetadata>
<Key>XResolution</Key>
<Value>1.0</Value>
</OriginalMetadata>
</Value>
</XMLAnnotation>
<XMLAnnotation ID="Annotation:2" Namespace="openmicroscopy.org/OriginalMetadata">
<Value>
<OriginalMetadata>
<Key>hyperstack</Key>
<Value>true</Value>
</OriginalMetadata>
</Value>
</XMLAnnotation>
<XMLAnnotation ID="Annotation:3" Namespace="openmicroscopy.org/OriginalMetadata">
<Value>
<OriginalMetadata>
<Key>ImageJ</Key>
<Value>1.53c</Value>
</OriginalMetadata>
</Value>
</XMLAnnotation>
<XMLAnnotation ID="Annotation:4" Namespace="openmicroscopy.org/OriginalMetadata">
<Value>
<OriginalMetadata>
<Key>MetaDataPhotometricInterpretation</Key>
<Value>Monochrome</Value>
</OriginalMetadata>
</Value>
</XMLAnnotation>
<XMLAnnotation ID="Annotation:5" Namespace="openmicroscopy.org/OriginalMetadata">
<Value>
<OriginalMetadata>
<Key>SamplesPerPixel</Key>
<Value>1</Value>
</OriginalMetadata>
</Value>
</XMLAnnotation>
<XMLAnnotation ID="Annotation:6" Namespace="openmicroscopy.org/OriginalMetadata">
<Value>
<OriginalMetadata>
<Key>NewSubfileType</Key>
<Value>0</Value>
</OriginalMetadata>
</Value>
</XMLAnnotation>
<XMLAnnotation ID="Annotation:7" Namespace="openmicroscopy.org/OriginalMetadata">
<Value>
<OriginalMetadata>
<Key>ImageWidth</Key>
<Value>5721</Value>
</OriginalMetadata>
</Value>
</XMLAnnotation>
<XMLAnnotation ID="Annotation:8" Namespace="openmicroscopy.org/OriginalMetadata">
<Value>
<OriginalMetadata>
<Key>NumberOfChannels</Key>
<Value>1</Value>
</OriginalMetadata>
</Value>
</XMLAnnotation>
<XMLAnnotation ID="Annotation:9" Namespace="openmicroscopy.org/OriginalMetadata">
<Value>
<OriginalMetadata>
<Key>ResolutionUnit</Key>
<Value>None</Value>
</OriginalMetadata>
</Value>
</XMLAnnotation>
<XMLAnnotation ID="Annotation:10" Namespace="openmicroscopy.org/OriginalMetadata">
<Value>
<OriginalMetadata>
<Key>ImageLength</Key>
<Value>9392</Value>
</OriginalMetadata>
</Value>
</XMLAnnotation>
<XMLAnnotation ID="Annotation:11" Namespace="openmicroscopy.org/OriginalMetadata">
<Value>
<OriginalMetadata>
<Key>PhotometricInterpretation</Key>
<Value>BlackIsZero</Value>
</OriginalMetadata>
</Value>
</XMLAnnotation>
<XMLAnnotation ID="Annotation:12" Namespace="openmicroscopy.org/OriginalMetadata">
<Value>
<OriginalMetadata>
<Key>Color mode</Key>
<Value>grayscale</Value>
</OriginalMetadata>
</Value>
</XMLAnnotation>
<XMLAnnotation ID="Annotation:13" Namespace="openmicroscopy.org/OriginalMetadata">
<Value>
<OriginalMetadata>
<Key>YResolution</Key>
<Value>1.0</Value>
</OriginalMetadata>
</Value>
</XMLAnnotation>
<XMLAnnotation ID="Annotation:14" Namespace="openmicroscopy.org/OriginalMetadata">
<Value>
<OriginalMetadata>
<Key>MetaMorph</Key>
<Value>no</Value>
</OriginalMetadata>
</Value>
</XMLAnnotation>
<XMLAnnotation ID="Annotation:15" Namespace="openmicroscopy.org/OriginalMetadata">
<Value>
<OriginalMetadata>
<Key>loop</Key>
<Value>false</Value>
</OriginalMetadata>
</Value>
</XMLAnnotation>
<XMLAnnotation ID="Annotation:16" Namespace="openmicroscopy.org/OriginalMetadata">
<Value>
<OriginalMetadata>
<Key>Compression</Key>
<Value>Uncompressed</Value>
</OriginalMetadata>
</Value>
</XMLAnnotation>
</StructuredAnnotations>
</OME> |
Maybe alternatively, if the 3 channels have |
(I can also prevent the behavior by converting my image to 16-bit, but this makes the file much larger) |
No I think it's time to create some sort of option for showing or hiding the controls if the data is not interleaved but 3 channels/8bit. You're not the first person to bring this up. |
My concern about looking at the names is if people name things something like "red" or "g" |
User story
I created a 3-channel 8-bit Tiff using ImageJ and selected "Grayscale" as the color mode when I created the hyperstack. However Viv (via Vitessce) thinks it is an RGB image due to the 3 channels.
Preferred solution
Use the "Color mode" OME-XML field in the guessRgb function if it is available.
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