BUG: ROIs inside a CZI file are not read correctly from BioFormats 5.0

[crueden-x]

From Sebastian Rhode:

I just got aware of the following issue.-

• Create a CZI file in ZEN Blue and add a rectangular ROI

<GraphicElementCollection>
  <Rectangle Id="49">
    <Attributes>
      <UniqueName>a30d3f7d-88ee-4f66-aa06-e9953ea8ab6f</UniqueName>
      <FontSize>4</FontSize>
      <IsMeasurementVisible>true</IsMeasurementVisible>
    </Attributes>
    <TextElements>
      <TextElement Id="Annotation" Type="AlignPosition">
        <Position>59.319587628866,36.2268041237113</Position>
      </TextElement>
    </TextElements>
    <Geometry>
      <Left>57.319587628865975</Left>
      <Top>34.226804123711347</Top>
      <Width>58.969072164948471</Width>
      <Height>47.835051546391767</Height>
    </Geometry>
    <Features>
      <Feature>
        <Name>Area</Name>
        <IsDisplayEnabled>true</IsDisplayEnabled>
      </Feature>
      <Feature>
        <Name>IntensityMean</Name>
        <IsDisplayEnabled>true</IsDisplayEnabled>
      </Feature>
    </Features>
  </Rectangle>
</GraphicElementCollection>

This is the corresponding XML entry copied from ZEN.
When I use BioFormtas? 5.0 to read the file and display the ROI the position of the ROI is wrong. The XML shows a different Y-Coordinate. To me it looks like Y does not start on the upper left, but the lower left ...

Part of the XML looks like this

<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2013-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2013-06 http://www.openmicroscopy.org/Schemas/OME/2013-06/ome.xsd">
<Experimenter ID="Experimenter:0" UserName="M1SRH"/>
<Instrument ID="Instrument:0">
<Microscope Type="Inverted"/>
<Detector ID="Detector:Camera" Model="TestCam"/>
<Objective ID="Objective:1" Immersion="Air" LensNA="0.3" NominalMagnification="10.0" WorkingDistance="5580.0"/>
<FilterSet ID="FilterSet:1"/>
<FilterSet ID="FilterSet:2"/>
<Filter ID="Filter:1">
<TransmittanceRange CutIn="335" CutOut="383"/>
<Filter ID="Filter:2">
<TransmittanceRange CutIn="420" CutOut="470"/>
<Filter ID="Filter:3">
<TransmittanceRange CutIn="335" CutOut="383"/>
<Filter ID="Filter:4">
<TransmittanceRange CutIn="420" CutOut="470"/>
<Dichroic ID="Dichroic:1"/>
<Dichroic ID="Dichroic:2"/>
<Image ID="Image:0" Name="CZI_with_rectangular_ROI.czi #1">
<AcquisitionDate>2014-03-24T08:13:31.875</AcquisitionDate>
<ExperimenterRef ID="Experimenter:0"/>
<InstrumentRef ID="Instrument:0"/>
<ObjectiveSettings ID="Objective:1"/>
<Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:0" Interleaved="false" PhysicalSizeX="1.0" PhysicalSizeY="1.0" SignificantBits="16" SizeC="2" SizeT="1" SizeX="160" SizeY="120" SizeZ="1" Type="uint16">
<Channel AcquisitionMode="WideField" Color="-16776961" EmissionWavelength="515" ExcitationWavelength="366" Fluor="Dye1" ID="Channel:0:0" IlluminationType="Other" Name="Fura-2 in pH 7.2 Ca free" SamplesPerPixel="1">
<DetectorSettings Binning="1x1" ID="Detector:Camera"/>
<LightPath/>
<Channel AcquisitionMode="WideField" Color="16725759" EmissionWavelength="515" ExcitationWavelength="366" Fluor="Dye2" ID="Channel:0:1" IlluminationType="Other" Name="Fura-2 in pH 7.2 Ca free_2" SamplesPerPixel="1">
<DetectorSettings Binning="1x1" ID="Detector:Camera"/>
<LightPath/>
<MetadataOnly/>
<Plane DeltaT="0.9330000877380371" PositionX="0.0" PositionY="0.0" PositionZ="0.0" TheC="0" TheT="0" TheZ="0"/>
<Plane DeltaT="1.0450000762939453" PositionX="0.0" PositionY="0.0" PositionZ="0.0" TheC="1" TheT="0" TheZ="0"/>
<ROIRef ID="ROI:0" xmlns="http://www.openmicroscopy.org/Schemas/ROI/2013-06"/>
<StructuredAnnotations xmlns="http://www.openmicroscopy.org/Schemas/SA/2013-06"/>
<ROI ID="ROI:0" Name="Annotation" xmlns="http://www.openmicroscopy.org/Schemas/ROI/2013-06">
<Union>
<Shape ID="Shape:0:0">
<Rectangle Height="47.83505154639177" Width="58.96907216494847" X="57.319587628865975" Y="85.77319587628865"/>
<Description>Annotation</Description>

[crueden-x]

Migrated from the original bug report in the Fiji BugZilla?: ​http://fiji.sc/bugzilla/show_bug.cgi?id=721

[mlinkert]

Duplicate of #11367.