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Use "Color mode" OME-XML field in guessRgb function #474

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keller-mark opened this issue Jul 28, 2021 · 6 comments
Open

Use "Color mode" OME-XML field in guessRgb function #474

keller-mark opened this issue Jul 28, 2021 · 6 comments

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@keller-mark
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keller-mark commented Jul 28, 2021 •
edited

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.

Screen Shot 2021-07-28 at 2 33 47 PM
@ilan-gold
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@keller-mark Is this a part of the OMEXML data model? Could you provide the whole OMEXML?

@ilan-gold ilan-gold mentioned this issue Jul 28, 2021
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@keller-mark
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keller-mark commented Jul 28, 2021 •
edited

I am not sure if Color mode is part of the OME-XML data model. Alternatively, is there a way to explicitly prevent the RGB assumption for 3-channel 8-bit images (and available in Vitessce)? I tried specifying the channels and selections separately in spatialRasterLayers but it still renders as RGB.

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>

@keller-mark
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Maybe alternatively, if the 3 channels have Names, it should not be assumed to be RGB?

@keller-mark
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(I can also prevent the behavior by converting my image to 16-bit, but this makes the file much larger)

@ilan-gold
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ilan-gold commented Jul 29, 2021 •
edited

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.

@ilan-gold
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My concern about looking at the names is if people name things something like "red" or "g"

This was referenced Aug 4, 2021
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Add Expansion Button for Non-Interleaved RGB hms-dbmi/viv
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@keller-mark @ilan-gold