Task #12124 (closed)
Opened 10 years ago
Closed 10 years ago
BUG: ROIs inside a CZI file are not read correctly from BioFormats 5.0
Reported by: | crueden-x | Owned by: | mlinkert |
---|---|---|---|
Priority: | minor | Milestone: | 5.0.2 |
Component: | Bio-Formats | Version: | 5.0.0 |
Keywords: | ZeissCZIReader | Cc: | sebrhode@… |
Resources: | n.a. | Referenced By: | n.a. |
References: | n.a. | Remaining Time: | n.a. |
Sprint: | n.a. |
Description
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>
Change History (3)
comment:1 Changed 10 years ago by crueden-x
comment:2 Changed 10 years ago by mlinkert
- Milestone changed from Unscheduled to 5.0.2
comment:3 Changed 10 years ago by mlinkert
- Resolution set to duplicate
- Status changed from new to closed
Duplicate of #11367.
Migrated from the original bug report in the Fiji BugZilla?: http://fiji.sc/bugzilla/show_bug.cgi?id=721