CZI: Reader does not handle plate wells with multiple fields

[dgault]

This issue was raised on imagesc thread https://forum.image.sc/t/importing-a-multi-position-plate-czi-file-in-omero/72250 When imported into OMERO the plate is displayed but each well only contains a single field and the remaining images are located in the orphaned section.

When tested with Bio-Formats 6.10.1 I could see only a single field for each well sample. In the sample image there are 99 images, Image:0-98, the first 50 are present are assigned to the plate which matches with the TemplateShapeId fields in the metadata which are currently used to parse plate positions.

<Plate Columns="12" ID="Plate:0" Rows="8">
    <Well Column="1" ID="Well:0:0" Row="1">
        <WellSample ID="WellSample:0:0:0" Index="0">
            <ImageRef ID="Image:0"/>
    <Well Column="2" ID="Well:0:1" Row="1">
        <WellSample ID="WellSample:0:1:0" Index="1">
            <ImageRef ID="Image:1"/>
    <Well Column="3" ID="Well:0:2" Row="1">
        <WellSample ID="WellSample:0:2:0" Index="2">
            <ImageRef ID="Image:2"/>
    <Well Column="4" ID="Well:0:3" Row="1">
        <WellSample ID="WellSample:0:3:0" Index="3">
            <ImageRef ID="Image:3"/>

    .....................................................................................

    <Well Column="7" ID="Well:0:46" Row="5">
        <WellSample ID="WellSample:0:46:0" Index="46">
            <ImageRef ID="Image:46"/>
    <Well Column="8" ID="Well:0:47" Row="5">
        <WellSample ID="WellSample:0:47:0" Index="47">
            <ImageRef ID="Image:47"/>
    <Well Column="9" ID="Well:0:48" Row="5">
        <WellSample ID="WellSample:0:48:0" Index="48">
            <ImageRef ID="Image:48"/>
    <Well Column="10" ID="Well:0:49" Row="5">
        <WellSample ID="WellSample:0:49:0" Index="49">
            <ImageRef ID="Image:49"/>

Looking at the reader and it appears that the well sample index and ref are always hardcoded to 0, only allowing a single field in each well (https://github.com/ome/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java#L1291)

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/importing-a-multi-position-plate-czi-file-in-omero/72250/6

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/importing-a-multi-position-plate-czi-file-in-omero/72250/13