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Can't get well plate information from OMEXML #167

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JKelle opened this issue Feb 19, 2024 · 0 comments
Open

Can't get well plate information from OMEXML #167

JKelle opened this issue Feb 19, 2024 · 0 comments

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@JKelle
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JKelle commented Feb 19, 2024

I'm not able to get plate or well information from the OMEXML object. I tried with a couple operetta format well plate images and an InCELL format image, both have this behavior. Here is a minimal example using one of the sample xml file downloaded from https://downloads.openmicroscopy.org/images/OME-XML/2016-06/one-screen-one-plate-four-wells.ome.xml

import bioformats
import javabridge

javabridge.start_vm(class_path=bioformats.JARS, run_headless=True)

# file downloaded from https://downloads.openmicroscopy.org/images/OME-XML/2016-06/one-screen-one-plate-four-wells.ome.xml
path = "one-screen-one-plate-four-wells.ome.xml"
with open(path) as f:
    raw_xml_string = f.read()
xml = bioformats.OMEXML(raw_xml_string)
print("number of plates:", len(xml.plates))
print(f"{xml.plates.ns=}")

javabridge.kill_vm()

The output of this script is

$ python plates_example.py
number of plates: 0
xml.plates.ns={'ome': 'http://www.openmicroscopy.org/Schemas/OME/2016-06', 'sa': None, 'spw': None}

I'm trying to iterate over the Wells to get each one's Row, Column, and Image IDs. Am I not using the xml object correctly, or is this a python-bioformats bug with parsing the tags from the xml?

Here is the content of the downloaded xml file mentioned above. It clearly has a Plate tag and several Well tags.

<?xml version="1.0" encoding="UTF-8"?>
<OME 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">
  <Plate ID="Plate:1">
    <Description>Plate 1 description.</Description>
    <Well ID="Well:1.1.1" Column="1" Row="1">
      <WellSample ID="WellSample:1.1.1.1" Index="1">
        <ImageRef ID="Image:0"/>
      </WellSample>
      <WellSample ID="WellSample:1.1.1.2" Index="5">
        <ImageRef ID="Image:1"/>
      </WellSample>
      <ReagentRef ID="Reagent:1"/>
    </Well>
    <Well ID="Well:1.2.1" Column="2" Row="1">
      <WellSample ID="WellSample:1.2.1.1" Index="2">
        <ImageRef ID="Image:2"/>
      </WellSample>
      <WellSample ID="WellSample:1.2.1.2" Index="6">
        <ImageRef ID="Image:3"/>
      </WellSample>
      <ReagentRef ID="Reagent:1"/>
    </Well>
    <Well ID="Well:1.1.2" Column="1" Row="2">
      <WellSample ID="WellSample:1.1.2.1" Index="3">
        <ImageRef ID="Image:4"/>
      </WellSample>
      <WellSample ID="WellSample:1.1.2.2" Index="7">
        <ImageRef ID="Image:5"/>
      </WellSample>
      <WellSample ID="WellSample:1.1.2.3" Index="11">
        <ImageRef ID="Image:6"/>
      </WellSample>
      <WellSample ID="WellSample:1.1.2.4" Index="15">
        <ImageRef ID="Image:7"/>
      </WellSample>
      <WellSample ID="WellSample:1.1.2.5" Index="19">
        <ImageRef ID="Image:8"/>
      </WellSample>
      <ReagentRef ID="Reagent:1"/>
    </Well>
    <Well ID="Well:1.2.2" Column="2" Row="2">
      <WellSample ID="WellSample:1.2.2.1" Index="4">
        <ImageRef ID="Image:9"/>
      </WellSample>
      <WellSample ID="WellSample:1.2.2.2" Index="8">
        <ImageRef ID="Image:10"/>
      </WellSample>
      <ReagentRef ID="Reagent:1"/>
    </Well>
    <PlateAcquisition ID="PlateAcquisition:Plate:1:ScreenAcquisition:1"
                          StartTime="2010-02-23T12:49:30" EndTime="2010-02-23T12:50:30">
      <WellSampleRef ID="WellSample:1.1.1.1"/>
      <WellSampleRef ID="WellSample:1.2.1.1"/>
      <WellSampleRef ID="WellSample:1.1.2.1"/>
      <WellSampleRef ID="WellSample:1.2.2.1"/>
    </PlateAcquisition>
    <PlateAcquisition ID="PlateAcquisition:Plate:1:ScreenAcquisition:2"
                          StartTime="2010-02-23T12:50:30" EndTime="2010-02-23T12:51:29">
      <WellSampleRef ID="WellSample:1.1.1.2"/>
      <WellSampleRef ID="WellSample:1.2.1.2"/>
      <WellSampleRef ID="WellSample:1.1.2.2"/>
      <WellSampleRef ID="WellSample:1.2.2.2"/>
    </PlateAcquisition>
  </Plate>
  <Screen ID="Screen:1" ProtocolDescription="" ProtocolIdentifier="" ReagentSetDescription=""
              ReagentSetIdentifier="" Name="" Type="">
    <Description/>
    <Reagent ID="Reagent:1" Name="" ReagentIdentifier="">
      <Description/>
    </Reagent>
    <PlateRef ID="Plate:1"/>
  </Screen>
  <Image ID="Image:0" Name="6x6x1x8-swatch.tif">
    <AcquisitionDate>2010-02-23T12:51:30</AcquisitionDate>
    <Pixels DimensionOrder="XYCZT" ID="Pixels:0:0" PhysicalSizeX="10000.0"
                PhysicalSizeY="10000.0" Type="uint8" SizeC="1" SizeT="1" SizeX="6" SizeY="4" SizeZ="1">
      <Channel Color="-2147483648" ID="Channel:0"/>
      <BinData BigEndian="false" Length="32"
                   >/wCrzur//wB5oMPi/wBIbJO3AP8ePGCF</BinData>
    </Pixels>
  </Image>
  <Image ID="Image:1" Name="6x6x1x8-swatch.tif-1">
    <AcquisitionDate>2010-02-23T12:51:30</AcquisitionDate>
    <Pixels DimensionOrder="XYCZT" ID="Pixels:1:0" PhysicalSizeX="10000.0"
                PhysicalSizeY="10000.0" Type="uint8" SizeC="1" SizeT="1" SizeX="6" SizeY="4" SizeZ="1">
      <Channel Color="-2147483648" ID="Channel:1"/>
      <BinData BigEndian="false" Length="32"
                   >/wCrzur//wB5oMPi/wBIbJO3AP8ePGCF</BinData>
    </Pixels>
  </Image>
  <Image ID="Image:2" Name="6x6x1x8-swatch.tif-2">
    <AcquisitionDate>2010-02-23T12:51:30</AcquisitionDate>
    <Pixels DimensionOrder="XYCZT" ID="Pixels:2:0" PhysicalSizeX="10000.0"
                PhysicalSizeY="10000.0" Type="uint8" SizeC="1" SizeT="1" SizeX="6" SizeY="4" SizeZ="1">
      <Channel Color="-2147483648" ID="Channel:2"/>
      <BinData BigEndian="false" Length="32"
                   >/wCrzur//wB5oMPi/wBIbJO3AP8ePGCF</BinData>
    </Pixels>
  </Image>
  <Image ID="Image:3" Name="6x6x1x8-swatch.tif-3">
    <AcquisitionDate>2010-02-23T12:51:30</AcquisitionDate>
    <Pixels DimensionOrder="XYCZT" ID="Pixels:3:0" PhysicalSizeX="10000.0"
                PhysicalSizeY="10000.0" Type="uint8" SizeC="1" SizeT="1" SizeX="6" SizeY="4" SizeZ="1">
      <Channel Color="-2147483648" ID="Channel:3"/>
      <BinData BigEndian="false" Length="32"
                   >/wCrzur//wB5oMPi/wBIbJO3AP8ePGCF</BinData>
    </Pixels>
  </Image>
  <Image ID="Image:4" Name="6x6x1x8-swatch.tif-4">
    <AcquisitionDate>2010-02-23T12:51:30</AcquisitionDate>
    <Pixels DimensionOrder="XYCZT" ID="Pixels:4:0" PhysicalSizeX="10000.0"
                PhysicalSizeY="10000.0" Type="uint8" SizeC="1" SizeT="1" SizeX="6" SizeY="4" SizeZ="1">
      <Channel Color="-2147483648" ID="Channel:4"/>
      <BinData BigEndian="false" Length="32"
                   >/wCrzur//wB5oMPi/wBIbJO3AP8ePGCF</BinData>
    </Pixels>
  </Image>
  <Image ID="Image:5" Name="6x6x1x8-swatch.tif-5">
    <AcquisitionDate>2010-02-23T12:51:30</AcquisitionDate>
    <Pixels DimensionOrder="XYCZT" ID="Pixels:5:0" PhysicalSizeX="10000.0"
                PhysicalSizeY="10000.0" Type="uint8" SizeC="1" SizeT="1" SizeX="6" SizeY="4" SizeZ="1">
      <Channel Color="-2147483648" ID="Channel:5"/>
      <BinData BigEndian="false" Length="32"
                   >/wCrzur//wB5oMPi/wBIbJO3AP8ePGCF</BinData>
    </Pixels>
  </Image>
  <Image ID="Image:6" Name="6x6x1x8-swatch.tif-6">
    <AcquisitionDate>2010-02-23T12:51:30</AcquisitionDate>
    <Pixels DimensionOrder="XYCZT" ID="Pixels:6:0" PhysicalSizeX="10000.0"
                PhysicalSizeY="10000.0" Type="uint8" SizeC="1" SizeT="1" SizeX="6" SizeY="4" SizeZ="1">
      <Channel Color="-2147483648" ID="Channel:6"/>
      <BinData BigEndian="false" Length="32"
                   >/wCrzur//wB5oMPi/wBIbJO3AP8ePGCF</BinData>
    </Pixels>
  </Image>
  <Image ID="Image:7" Name="6x6x1x8-swatch.tif-7">
    <AcquisitionDate>2010-02-23T12:51:30</AcquisitionDate>
    <Pixels DimensionOrder="XYCZT" ID="Pixels:7:0" PhysicalSizeX="10000.0"
                PhysicalSizeY="10000.0" Type="uint8" SizeC="1" SizeT="1" SizeX="6" SizeY="4" SizeZ="1">
      <Channel Color="-2147483648" ID="Channel:7"/>
      <BinData BigEndian="false" Length="32"
                   >/wCrzur//wB5oMPi/wBIbJO3AP8ePGCF</BinData>
    </Pixels>
  </Image>
  <Image ID="Image:8" Name="6x6x1x8-swatch.tif-8">
    <AcquisitionDate>2010-02-23T12:51:30</AcquisitionDate>
    <Pixels DimensionOrder="XYCZT" ID="Pixels:8:0" PhysicalSizeX="10000.0"
                PhysicalSizeY="10000.0" Type="uint8" SizeC="1" SizeT="1" SizeX="6" SizeY="4" SizeZ="1">
      <Channel Color="-2147483648" ID="Channel:8"/>
      <BinData BigEndian="false" Length="32"
                   >/wCrzur//wB5oMPi/wBIbJO3AP8ePGCF</BinData>
    </Pixels>
  </Image>
  <Image ID="Image:9" Name="6x6x1x8-swatch.tif-9">
    <AcquisitionDate>2010-02-23T12:51:30</AcquisitionDate>
    <Pixels DimensionOrder="XYCZT" ID="Pixels:9:0" PhysicalSizeX="10000.0"
                PhysicalSizeY="10000.0" Type="uint8" SizeC="1" SizeT="1" SizeX="6" SizeY="4" SizeZ="1">
      <Channel Color="-2147483648" ID="Channel:9"/>
      <BinData BigEndian="false" Length="32"
                   >/wCrzur//wB5oMPi/wBIbJO3AP8ePGCF</BinData>
    </Pixels>
  </Image>
  <Image ID="Image:10" Name="6x6x1x8-swatch.tif-10">
    <AcquisitionDate>2010-02-23T12:51:30</AcquisitionDate>
    <Pixels DimensionOrder="XYCZT" ID="Pixels:10:0" PhysicalSizeX="10000.0"
                PhysicalSizeY="10000.0" Type="uint8" SizeC="1" SizeT="1" SizeX="6" SizeY="4" SizeZ="1">
      <Channel Color="-2147483648" ID="Channel:10"/>
      <BinData BigEndian="false" Length="32"
                   >/wCrzur//wB5oMPi/wBIbJO3AP8ePGCF</BinData>
    </Pixels>
  </Image>
</OME>
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@JKelle