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Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
https://www.openmicroscopy.org/bio-formats
GNU General Public License v2.0
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CZI (from AiryScan2) cannot be read in BioFormats 6.3.1 #3501

Closed sebi06 closed 4 years ago

sebi06 commented 4 years ago

Hi guys,

I tried to open the attached CZI (from AiryScan2) using BioFormats 6.3.1 and got an exception and we think it is releated to entries for the Zoom level like illustrated below. Let me know if you need more info to fix it.

Sebi

image

(Fiji Is Just) ImageJ 2.0.0-rc-71/1.52p; Java 1.8.0_172 [64-bit]; Windows 10 10.0; 207MB of 24433MB (<1%)

java.lang.NumberFormatException: For input string: "2.8,2.8"
    at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043)
    at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
    at java.lang.Double.parseDouble(Double.java:538)
    at java.lang.Double.<init>(Double.java:608)
    at loci.formats.in.ZeissCZIReader.translateInformation(ZeissCZIReader.java:2367)
    at loci.formats.in.ZeissCZIReader.translateMetadata(ZeissCZIReader.java:2002)
    at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:1131)
    at loci.formats.FormatReader.setId(FormatReader.java:1389)
    at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:499)
    at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)
    at loci.plugins.in.Importer.showDialogs(Importer.java:140)
    at loci.plugins.in.Importer.run(Importer.java:76)
    at loci.plugins.LociImporter.run(LociImporter.java:78)
    at ij.IJ.runUserPlugIn(IJ.java:230)
    at ij.IJ.runPlugIn(IJ.java:193)
    at ij.Executer.runCommand(Executer.java:137)
    at ij.Executer.run(Executer.java:66)
    at ij.IJ.run(IJ.java:312)
    at ij.IJ.run(IJ.java:323)
    at ij.macro.Functions.doRun(Functions.java:624)
    at ij.macro.Functions.doFunction(Functions.java:97)
    at ij.macro.Interpreter.doStatement(Interpreter.java:275)
    at ij.macro.Interpreter.doStatements(Interpreter.java:261)
    at ij.macro.Interpreter.run(Interpreter.java:157)
    at ij.macro.Interpreter.run(Interpreter.java:91)
    at ij.macro.MacroRunner.run(MacroRunner.java:139)
    at java.lang.Thread.run(Thread.java:748)

Fluocell_Airyscan.zip

dgault commented 4 years ago

Thanks @sebi06 for raising this. I have opened a PR which should fix this exception and improve some of the other Detector values.