RFE: Leica Channel Names from Detector

[wmoore]

Some LEI and LIF images don't have a "Stain" name to name a channel (Stain = "" or "None") and some Channels will never have a 'Stain' E.g. when detector is "PMT Trans".

In both these cases it would be nice to use the detector name for the Channel (instead of no Name). E.g. "PMT 1" or "PMT Trans" etc.

[mlinkert]

Should be working with ​https://github.com/melissalinkert/bioformats/commit/7d4345b72c16ad605ab8337937c6382986a2e684

The channel names for Image:0, Image:1, and Image:3 (in the XML for samples-SP2.lei) will need to be updated accordingly.

[wmoore]

Looks good

$ java -Xmx512m loci.formats.tools.ImageInfo -nopix -omexml-only -no-sas -xmlspaces 4 /Users/will/Documents/biology-data/Test-Import-Images/Martineica-SP2/samples-SP2/samples-SP2.lei | grep "Name="
    <Image ID="Image:0" Name="XYZ-Ch">
        <StageLabel Name="Position" Z="-2.2590361445783174"/>
            <Channel Color="-16776961" ID="Channel:0:0" Name="TRITC" PinholeSize="81.40681653372008" SamplesPerPixel="1">
            <Channel Color="-1" ID="Channel:0:1" Name="PMT Trans" PinholeSize="81.40681653372008" SamplesPerPixel="1">
    <Image ID="Image:1" Name="XY-Ch-trans">
        <StageLabel Name="Position" Z="-9.422826440898726"/>
            <Channel Color="16711935" ID="Channel:1:0" Name="PMT 1" PinholeSize="20.420594633792604" SamplesPerPixel="1">
            <Channel Color="-16776961" ID="Channel:1:1" Name="PMT 2" PinholeSize="20.420594633792604" SamplesPerPixel="1">
            <Channel Color="-1" ID="Channel:1:2" Name="PMT Trans" PinholeSize="20.420594633792604" SamplesPerPixel="1">
    <Image ID="Image:2" Name="XZY-Ch-trans">
        <StageLabel Name="Position" Z="0.38668186258547055"/>
            <Channel Color="-16776961" ID="Channel:2:0" Name="TEXAS RED" PinholeSize="243.3357505438723" SamplesPerPixel="1">
            <Channel Color="16711935" ID="Channel:2:1" Name="FITC" PinholeSize="243.3357505438723" SamplesPerPixel="1">
            <Channel Color="-1" ID="Channel:2:2" Name="PMT Trans" PinholeSize="243.3357505438723" SamplesPerPixel="1">
    <Image ID="Image:3" Name="XY-lambda">
        <StageLabel Name="Position" Z="-0.020351676978177666"/>
            <Channel Color="-1" ID="Channel:3:0" Name="PMT 3" PinholeSize="600.0" SamplesPerPixel="1">

omexml_repo updated accordingly: ​https://github.com/will-moore/openmicroscopy/commit/a9f7674e9234154d0190f103b8774d97e43aa261

Closing...