[Fatal Error] :1:35: Character reference "�" is an invalid XML character.
Exception in thread "Thread-1" org.mozilla.javascript.WrappedException: Wrapped java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 35; Character reference "�" is an invalid XML character. (<java-python-bridge>#12)
at org.mozilla.javascript.Context.throwAsScriptRuntimeEx(Context.java:1754)
at org.mozilla.javascript.MemberBox.invoke(MemberBox.java:148)
at org.mozilla.javascript.NativeJavaMethod.call(NativeJavaMethod.java:225)
at org.mozilla.javascript.optimizer.OptRuntime.call1(OptRuntime.java:32)
at org.mozilla.javascript.gen._java_python_bridge__285._c_script_0(<java-python-bridge>:12)
at org.mozilla.javascript.gen._java_python_bridge__285.call(<java-python-bridge>)
at org.mozilla.javascript.ContextFactory.doTopCall(ContextFactory.java:394)
at org.mozilla.javascript.ScriptRuntime.doTopCall(ScriptRuntime.java:3091)
at org.mozilla.javascript.gen._java_python_bridge__285.call(<java-python-bridge>)
at org.mozilla.javascript.gen._java_python_bridge__285.exec(<java-python-bridge>)
at org.mozilla.javascript.Context.evaluateString(Context.java:1079)
Caused by: java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 35; Character reference "�" is an invalid XML character.
at ome.xml.model.XMLAnnotation.asXMLElement(XMLAnnotation.java:261)
at ome.xml.model.StructuredAnnotations.asXMLElement(StructuredAnnotations.java:679)
at ome.xml.model.OME.asXMLElement(OME.java:929)
at ome.xml.model.OME.asXMLElement(OME.java:769)
at ome.xml.meta.AbstractOMEXMLMetadata.dumpXML(AbstractOMEXMLMetadata.java:110)
at ome.xml.meta.OMEXMLMetadataImpl.dumpXML(OMEXMLMetadataImpl.java:105)
at loci.formats.services.OMEXMLServiceImpl.getOMEXML(OMEXMLServiceImpl.java:468)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.mozilla.javascript.MemberBox.invoke(MemberBox.java:126)
... 9 more
Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 35; Character reference "�" is an invalid XML character.
at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)
at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source)
at ome.xml.model.XMLAnnotation.asXMLElement(XMLAnnotation.java:257)
... 20 more
Metadata extraction failed for file:/Users/bcimini/Downloads/Spat-1-1.oir
OME-XML Metadata as extracted by Fiji (no weird characters present in the small cutoff bit- Fiji doesn't allow you to copy out the text of this as far as I can tell.
Metadata as extracted by Fiji-
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IsRGB false
LittleEndian true
PixelType uint16
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imageInfo width #1 640
imageSize height #1 640
imageSize height #2 512
imageSize width #1 640
imageSize width #2 512
imagingMainLaser forcedOff #01 false
imagingMainLaser forcedOff #02 false
imagingMainLaser forcedOff #03 false
imagingMainLaser forcedOff #04 false
imagingMainLaser forcedOff #05 false
imagingMainLaser forcedOff #06 false
imagingMainLaser forcedOff #07 false
imagingMainLaser forcedOff #08 false
imagingMainLaser forcedOff #09 false
imagingMainLaser forcedOff #10 false
imagingMainLaser forcedOff #11 false
imagingMainLaser forcedOff #12 false
imagingMainLaser forcedOff #13 false
imagingMainLaser forcedOff #14 false
imagingMainLaser forcedOff #15 false
imagingMainLaser wavelength #01 405
imagingMainLaser wavelength #02 445
imagingMainLaser wavelength #03 488
imagingMainLaser wavelength #04 514
imagingMainLaser wavelength #05 561
imagingMainLaser wavelength #06 594
imagingMainLaser wavelength #07 640
imagingMainLaser wavelength #08 730
imagingMainLaser wavelength #09 405
imagingMainLaser wavelength #10 445
imagingMainLaser wavelength #11 488
imagingMainLaser wavelength #12 514
imagingMainLaser wavelength #13 561
imagingMainLaser wavelength #14 594
imagingMainLaser wavelength #15 640
imagingMainLaser wavelength #16 730
imagingParam zDriveUnitType #1 Motor
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inTrigger enabled #3 false
inTrigger enabled #4 false
inTrigger enabled #5 false
inTrigger enabled #6 false
inTrigger mode #1 Once
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inTrigger timing #5 Start
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inTrigger triggerNo #5 0
inTrigger triggerNo #6 1
integration count #1 2
integration type #1 None
interlace enabled #1 false
interlace number #1 1
lambdaCellSettings resolution #1 20
lambdaCellSettings startWavelength #1 400
lambdaSeriesParam bandWitdh #1 20
lambdaSeriesParam endWaveLength #1 794
lambdaSeriesParam startWaveLength #1 414
lambdaSeriesParam stepSize #1 15
laser id #1 LD405_65792
laser id #2 LD445_65793
laser id #3 LD488_65794
laser id #4 LD514_65795
laser id #5 LD561_65796
laser id #6 LD594_65797
laser id #7 LD640_65798
laser id #8 AUXOUT_131328
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laser name #2 LD445
laser name #3 LD488
laser name #4 LD514
laser name #5 LD561
laser name #6 LD594
laser name #7 LD640
laser name #8 AUXOUT
laser optionalTransmissivity #01 20.0
laser optionalTransmissivity #02 21.2
laser optionalTransmissivity #03 20.0
laser optionalTransmissivity #04 19.9
laser optionalTransmissivity #05 20.1
laser optionalTransmissivity #06 20.0
laser optionalTransmissivity #07 20.0
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laser optionalTransmissivity #14 20.0
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laser optionalTransmissivity #16 0.0
laser power #01 100.0
laser power #02 100.0
laser power #03 100.0
laser power #04 100.0
laser power #05 100.0
laser power #06 100.0
laser power #07 100.0
laser power #08 100.0
laser power #09 100.0
laser power #10 100.0
laser power #11 100.0
laser power #12 100.0
laser power #13 100.0
laser power #14 100.0
laser power #15 100.0
laser power #16 100.0
laser transmissivity #01 2.0
laser transmissivity #02 2.12
laser transmissivity #03 2.0
laser transmissivity #04 1.99
laser transmissivity #05 2.01
laser transmissivity #06 2.0
laser transmissivity #07 2.0
laser transmissivity #08 1.5
laser transmissivity #09 0.0
laser transmissivity #10 1.5
laser transmissivity #11 0.0
laser transmissivity #12 2.0
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laser transmissivity #14 2.0
laser transmissivity #15 0.0
laser transmissivity #16 0.0
length x #1 2.485922277608955
length x #2 2.485922277608955
length x #3 2.485922277608955
length x #4 2.485922277608955
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length x #9 2.485922277608955
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length z #1 35.0
length z #2 35.0
length z #3 35.0
length z #4 35.0
length z #5 35.0
length z #6 35.0
length z #7 35.0
length z #8 35.0
length z #9 35.0
lightpath diaLampState #1 Off
lightpath diaLampState #2 Off
lightpath diaLampState #3 Off
lightpath diaLampValue #1 0.0
lightpath diaLampValue #2 50.0
lightpath diaLampValue #3 55.0
lightpath diaShutterState #1 Close
lightpath diaShutterState #2 Close
lightpath diaShutterState #3 Close
lightpath dicPrismContrast #1 0
lightpath dicPrismContrast #2 0
lightpath dicPrismContrast #3 0
lightpath dicPrismState #1 Out
lightpath dicPrismState #2 Out
lightpath dicPrismState #3 In
lightpath epiShutterState #1 Open
lightpath epiShutterState #2 Close
lightpath epiShutterState #3 Open
lightpath pinholeDiameter #1 140
lightpath pinholeDiameter #2 800
lightpath poralizerState #1 In
lightpath poralizerState #2 Out
lightpath poralizerState #3 In
lineAttribute style #1 SOLID
lineAttribute style #2 SOLID
lineAttribute style #3 SOLID
lineAttribute style #4 SOLID
lineAttribute style #5 SOLID
lineAttribute width #1 1
lineAttribute width #2 1
lineAttribute width #3 1
lineAttribute width #4 1
lineAttribute width #5 1
mainLaser optionalTransmissivity #01 0.0
mainLaser optionalTransmissivity #02 0.0
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mainLaser optionalTransmissivity #10 21.2
mainLaser optionalTransmissivity #11 20.0
mainLaser optionalTransmissivity #12 19.9
mainLaser optionalTransmissivity #13 20.1
mainLaser optionalTransmissivity #14 20.0
mainLaser optionalTransmissivity #15 20.0
mainLaser optionalTransmissivity #16 15.0
mainLaser optionalTransmissivity #17 0.0
mainLaser optionalTransmissivity #18 15.0
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mainLaser optionalTransmissivity #20 20.0
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mainLaser optionalTransmissivity #22 20.0
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mainLaser power #01 100.0
mainLaser power #02 100.0
mainLaser power #03 100.0
mainLaser power #04 100.0
mainLaser power #05 100.0
mainLaser power #06 100.0
mainLaser power #07 100.0
mainLaser power #08 100.0
mainLaser power #09 100.0
mainLaser power #10 100.0
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mainLaser power #14 100.0
mainLaser power #15 100.0
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mainLaser power #19 100.0
mainLaser power #20 100.0
mainLaser power #21 100.0
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mainLaser power #23 100.0
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mainLaser transmissivity #15 2.0
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mainLaser transmissivity #19 0.0
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mainLaser transmissivity #21 0.0
mainLaser transmissivity #22 2.0
mainLaser transmissivity #23 0.0
mainLaser transmissivity #24 0.0
mainLaserNDFilter name #1 ND1
mainLaserNDFilter name #2 ND1
mainLaserNDFilter transmissivity #1 10.0
mainLaserNDFilter transmissivity #2 10.0
method sequentialType #1 Line
microscope name #1 IX83P2ZF
middleLayer objectId #1 d0ce0ebe-e734-4446-9b7e-7f8b3f2537e3
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middleLayer objectId #5 94e5b065-cd68-4e07-8126-f9b127f5d2d6
middleLayer overlayType #1 ROI
middleLayer overlayType #2 ROI
middleLayer overlayType #3 ROI
middleLayer overlayType #4 ROI
middleLayer overlayType #5 ROI
objectiveLens afContinuous #1 false
objectiveLens afContinuousForPlastic #1 false
objectiveLens afOneShot #1 false
objectiveLens afOneShotForPlastic #1 false
objectiveLens displayName #1 UPLSAPO 4X
objectiveLens immersion #1 DRY
objectiveLens magnification #1 4.0
objectiveLens naValue #1 0.16
objectiveLens name #1 UPLSAPO 4X
objectiveLens refraction #1 1.0
objectiveLens wdValue #1 13.0
opticalResolution x #1 1.659553209144471
opticalResolution x #2 1.659553209144471
opticalResolution x #3 1.659553209144471
opticalResolution x #4 1.659553209144471
opticalResolution x #5 1.254689350771814
opticalResolution x #6 1.659553209144471
opticalResolution x #7 1.659553209144471
opticalResolution x #8 1.659553209144471
opticalResolution x #9 1.659553209144471
opticalResolution y #1 1.659553209144471
opticalResolution y #2 1.659553209144471
opticalResolution y #3 1.659553209144471
opticalResolution y #4 1.659553209144471
opticalResolution y #5 1.254689350771814
opticalResolution y #6 1.659553209144471
opticalResolution y #7 1.659553209144471
opticalResolution y #8 1.659553209144471
opticalResolution y #9 1.659553209144471
opticalResolution z #1 213.19249727146874
opticalResolution z #2 213.19249727146874
opticalResolution z #3 213.19249727146874
opticalResolution z #4 213.19249727146874
opticalResolution z #5 46.75188170920429
opticalResolution z #6 213.19249727146874
opticalResolution z #7 213.19249727146874
opticalResolution z #8 213.19249727146874
opticalResolution z #9 213.19249727146874
outTrigger enabled #1 false
outTrigger enabled #2 false
outTrigger enabled #3 false
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outTrigger enabled #5 false
outTrigger enabled #6 false
outTrigger timing #1 Start
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outTrigger timing #3 Start
outTrigger timing #4 End
outTrigger timing #5 Start
outTrigger timing #6 End
outTrigger triggerNo #1 2
outTrigger triggerNo #2 3
outTrigger triggerNo #3 0
outTrigger triggerNo #4 1
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outTrigger triggerNo #6 1
param autoPinhole #1 false
param autoPinhole #2 false
phase name #1 Phase 1
pinAssign pattern #01 1
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pinAssign pattern #03 4
pinAssign pattern #04 8
pinAssign pattern #05 16
pinAssign pattern #06 32
pinAssign pattern #07 1
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pinAssign pattern #11 16
pinAssign type #1 In
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pixelCalibration x #1 1.0
pixelCalibration y #1 1.0
pixelCalibration z #1 1.0
pixelUnit x #1 MICRO_METER
pixelUnit x #2 MICRO_METER
pixelUnit x #3 MICRO_METER
pixelUnit x #4 MICRO_METER
pixelUnit x #5 MICRO_METER
pixelUnit x #6 MICRO_METER
pixelUnit x #7 MICRO_METER
pixelUnit x #8 MICRO_METER
pixelUnit x #9 MICRO_METER
pixelUnit y #1 MICRO_METER
pixelUnit y #2 MICRO_METER
pixelUnit y #3 MICRO_METER
pixelUnit y #4 MICRO_METER
pixelUnit y #5 MICRO_METER
pixelUnit y #6 MICRO_METER
pixelUnit y #7 MICRO_METER
pixelUnit y #8 MICRO_METER
pixelUnit y #9 MICRO_METER
pixelUnit z #1 MICRO_METER
pixelUnit z #2 MICRO_METER
pixelUnit z #3 MICRO_METER
pixelUnit z #4 MICRO_METER
pixelUnit z #5 MICRO_METER
pixelUnit z #6 MICRO_METER
pixelUnit z #7 MICRO_METER
pixelUnit z #8 MICRO_METER
pixelUnit z #9 MICRO_METER
pmt gain #01 1.0
pmt gain #02 1.0
pmt gain #03 1.0
pmt gain #04 1.0
pmt gain #05 1.0
pmt gain #06 1.0
pmt gain #07 1.0
pmt gain #08 1.0
pmt gain #09 1.0
pmt gain #10 1.0
pmt offset #01 0
pmt offset #02 9
pmt offset #03 9
pmt offset #04 6
pmt offset #05 0
pmt offset #06 0
pmt offset #07 9
pmt offset #08 9
pmt offset #09 6
pmt offset #10 0
pmt voltage #01 500
pmt voltage #02 575
pmt voltage #03 539
pmt voltage #04 468
pmt voltage #05 188
pmt voltage #06 500
pmt voltage #07 575
pmt voltage #08 539
pmt voltage #09 468
pmt voltage #10 188
pmtCommon autoHV #1 true
productData asFullOpen #1 false
productData diaAs #1 80
productData fptEnabled #1 false
productData lightpathPrismState #1 Camera
productData observation #1 LSM
productData pinholeDiameter #1 800.0
productData pinholeDiameter #2 800.0
productData pinholeDiameter #3 800.0
productData pinholeDiameter #4 800.0
productData pmtProtection #1 true
productData referencePhaseId #1 3bc410bb-1dae-4a5d-9836-51ad7bdf8000
productData scanUnitType #1 Main
productData topLens #1 Out
productData zdcDmState #1 Out
red contrast #01 0.0
red contrast #02 1.0
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reflectWaveRange endWavelength #12 645
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reflectWaveRange startWavelength #02 483
reflectWaveRange startWavelength #03 556
reflectWaveRange startWavelength #04 635
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reflectWaveRange startWavelength #11 556
reflectWaveRange startWavelength #12 635
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reflectWaveRange startWavelength #14 400
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reflectWaveRange startWavelength #16 0
region roiType #1 BackgroundROI
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rrcm mode #1 STANDARD
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rrcm quality #1 4
rrcm strength #1 10.0
speed focus #1 0
speed focus #2 0
speed roundtrip #1 false
speed roundtrip #2 false
speed roundtrip #3 false
speed speed #1 2.0
speed speed #2 2.0
speed speed #3 0.067
speedInformation frameSpeed #1 1520.452
speedInformation frameSpeed #2 4556.612
speedInformation frameSpeed #3 65.77946768060836
speedInformation lineSpeed #1 2.372
speedInformation lineSpeed #2 2.372
speedInformation lineSpeed #3 0.1267427122940431
speedInformation pixelSpeed #1 0.002
speedInformation pixelSpeed #2 0.002
speedInformation pixelSpeed #3 6.7E-5
speedInformation seriesInterval #1 46847.468
speedInformation seriesInterval #2 8966.058301647656
stimulationMainLaser wavelength #1 405
stimulationMainLaser wavelength #2 445
stimulationMainLaser wavelength #3 488
stimulationMainLaser wavelength #4 514
stimulationMainLaser wavelength #5 561
stimulationMainLaser wavelength #6 594
stimulationMainLaser wavelength #7 640
stimulationMainLaser wavelength #8 730
stimulationParam scanUnitType #1 Main
syncWaitTime time #1 0.0
synchronizationParam baseMethod #1 LSM_STIMULATION
synchronizationParam restInStimulation #1 false
synchronizedAcquisitionParamList enabled #1 true
synchronizedAcquisitionParamList enabled #2 true
synchronizedAcquisitionParamList imagingFrameCount #1 10
synchronizedAcquisitionParamList preFrameCount #1 0
synchronizedAcquisitionParamList restTime #1 0.0
synchronizedAcquisitionParamList stimulationFrameCount #1 2
synchronizedAcquisitionParamList type #1 LSM_IMAGING
synchronizedAcquisitionParamList type #2 LSM_STIMULATION
system deviceName #1 LSM
system systemName #1 FV3000
system systemVersion #1 2.4.1.198
textAttribute facename #1 Arial
textAttribute facename #2 Arial
textAttribute facename #3 Arial
textAttribute facename #4 Arial
textAttribute facename #5 Arial
textAttribute fillBackground #1 false
textAttribute fillBackground #2 false
textAttribute fillBackground #3 false
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textAttribute fillBackground #5 false
textAttribute size #1 11
textAttribute size #2 11
textAttribute size #3 11
textAttribute size #4 11
textAttribute size #5 11
textAttribute style #1 Bold
textAttribute style #2 Bold
textAttribute style #3 Bold
textAttribute style #4 Bold
textAttribute style #5 Bold
transmittedWaveRange endWavelength #01 470
transmittedWaveRange endWavelength #02 541
transmittedWaveRange endWavelength #03 620
transmittedWaveRange endWavelength #04 900
transmittedWaveRange endWavelength #05 470
transmittedWaveRange endWavelength #06 541
transmittedWaveRange endWavelength #07 620
transmittedWaveRange endWavelength #08 900
transmittedWaveRange endWavelength #09 900
transmittedWaveRange endWavelength #10 900
transmittedWaveRange startWavelength #01 425
transmittedWaveRange startWavelength #02 500
transmittedWaveRange startWavelength #03 570
transmittedWaveRange startWavelength #04 650
transmittedWaveRange startWavelength #05 425
transmittedWaveRange startWavelength #06 500
transmittedWaveRange startWavelength #07 570
transmittedWaveRange startWavelength #08 650
transmittedWaveRange startWavelength #09 610
transmittedWaveRange startWavelength #10 500
userPixelCalibration x #1 1.0
userPixelCalibration y #1 1.0
userPixelCalibration z #1 1.0
wavelengthRange endWavelength #01 470
wavelengthRange endWavelength #02 600
wavelengthRange endWavelength #03 750
wavelengthRange endWavelength #04 434
wavelengthRange endWavelength #05 760
wavelengthRange endWavelength #06 595
wavelengthRange endWavelength #07 658
wavelengthRange endWavelength #08 470
wavelengthRange endWavelength #09 600
wavelengthRange endWavelength #10 750
wavelengthRange endWavelength #11 750
wavelengthRange startWavelength #01 430
wavelengthRange startWavelength #02 500
wavelengthRange startWavelength #03 650
wavelengthRange startWavelength #04 414
wavelengthRange startWavelength #05 740
wavelengthRange startWavelength #06 575
wavelengthRange startWavelength #07 638
wavelengthRange startWavelength #08 430
wavelengthRange startWavelength #09 500
wavelengthRange startWavelength #10 650
wavelengthRange startWavelength #11 650
zPosition zStagePosition #1 6430.0
zdcLimit lower #1 -200.0
zdcLimit upper #1 570.0
zdcParam coverSlipPosition #1 0.0
zdcParam coverSlipType #1 Glass
zdcParam driftEnabled #1 false
zdcParam isUndefinedCoverslipPosition #1 true
zdcParam lowerLimit #1 499.0
zdcParam offset #1 0.0
zdcParam upperLimit #1 500.0
In an image from the forum (image attached here as well). Fails to open in CellProfiler with the error below, metadata etc posted underneath.
Spat-1-1.oir.zip
OME-XML Metadata as extracted by Fiji (no weird characters present in the small cutoff bit- Fiji doesn't allow you to copy out the text of this as far as I can tell.
Metadata as extracted by Fiji-