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Color of each Channel

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Color of each Channel

Postby bhcho » Tue Nov 23, 2010 8:08 pm

Hi All,

I generated a ome.tif image with 3 different channel. But I wrote the ome-xml part directly by myself and overwrote. However, when I see the image from OMERO.insight after I import it to my server (4.2.1), the color of each channel is blue, green, blue for channel 0, 1, 2, respectively.
I thought it is usually ordered as red, green, and blue for ch 0, 1, 2.

the ome-xml part of theimage is something like this. could anyone tell me about this?

Code: Select all
<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2010-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2010-06  http://www.openmicroscopy.org/Schemas/OME/2010-06/ome.xsd">
   <Instrument ID="Instrument:In001">
   <Microscope Manufacturer="Beckman-Coulter" SerialNumber="S4SID479780"/><Detector ID="Detector:D004" Manufacturer="Orca" Model="C4742-80-12AG" SerialNumber="620280" Type="CCD"/><Objective ID="Objective:O005" LensNA="0.9" Manufacturer="Nikon" Model="S Fluor" NominalMagnification="40" SerialNumber="062364"/><Filter ID="Filter:0" Type="BandPass">
        <TransmittanceRange CutIn="477" CutOut="491"/>
     </Filter><Filter ID="Filter:1" Type="BandPass">
        <TransmittanceRange CutIn="502" CutOut="532"/>
     </Filter><Filter ID="Filter:2" Type="BandPass">
        <TransmittanceRange CutIn="437" CutOut="451"/>
     </Filter><Filter ID="Filter:3" Type="BandPass">
        <TransmittanceRange CutIn="351" CutOut="373"/>
     </Filter><Filter ID="Filter:4" Type="BandPass">
        <TransmittanceRange CutIn="321" CutOut="350"/>
     </Filter><Filter ID="Filter:5" Type="BandPass">
        <TransmittanceRange CutIn="200" CutOut="211"/>
   <Image ID="Image:I001">
      <InstrumentRef ID="Instrument:In001">
      <Pixels DimensionOrder="XYCZT" ID="Pixels:P001" SizeC="3" SizeT="1" SizeX="1344" SizeY="1024" SizeZ="1" Type="uint8">
      <Channel ID="Channel:0:0" Name="dna" SamplesPerPixel="1">
            <ExcitationFilterRef ID="Filter:2"/>
           <EmissionFilterRef ID="Filter:3"/>
      </Channel><Channel ID="Channel:0:1" Name="ATP_synthase" SamplesPerPixel="1">
            <ExcitationFilterRef ID="Filter:0"/>
           <EmissionFilterRef ID="Filter:1"/>
      </Channel><Channel ID="Channel:0:2" Name="autofluorescence" SamplesPerPixel="1">
            <ExcitationFilterRef ID="Filter:4"/>
           <EmissionFilterRef ID="Filter:5"/>
      </Channel><TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1"/><TiffData FirstC="1" FirstT="0" FirstZ="0" IFD="1" PlaneCount="1"/><TiffData FirstC="2" FirstT="0" FirstZ="0" IFD="2" PlaneCount="1"/><Plane ExposureTime="4" TheC="0" TheT="0" TheZ="0"/><Plane ExposureTime="5" TheC="1" TheT="0" TheZ="0"/><Plane ExposureTime="6" TheC="2" TheT="0" TheZ="0"/></Pixels>

And could you also tell me how to apply a manual color to each channel?
I know there is an attribute in the ome-xml where I can change the color for each channel.
which is /OME/Image/Pixels/Channel@Color.
the color value should be a signed 32 bit value.
then what is the 32bit signed number for Red, Green, and Blue color?
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Re: Color of each Channel

Postby jburel » Thu Nov 25, 2010 4:21 pm


Unless there is a color assigned to a channel, we try to determine the color by looking at the metadata in the following order:
* emission wavelength
* emission filter.
* excitation wavelength
* excitation filter
If it was not possible to determine the color, we then go for RED, GREEN, BLUE.

In your example, we use the transmittance range to determine the color

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Re: Color of each Channel

Postby bhcho » Thu Nov 25, 2010 4:32 pm

Hi jmarie,

that's really cool.
I put the transmittance ranges in the example just temporarily.

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