[ome-users] Cannot open Andor TIFF - Bio-Formats

Fri Jan 19 13:37:35 GMT 2018

Hi James,

it sounds like you are encountering the conflicting JARs issues described in this
thread [1].
Which update sites do you have currently enabled? If both Fiji-legacy and Java-8
are enabled, could you try to disable the Fiji-legacy update site and see if it
resolves the issue?

Best,
Sebastien

[1] http://forum.imagej.net/t/fiji-and-bioformats-conflicting-jars/5736/7

On 19 Jan 2018, at 12:53, James Wainwright <jimboesq at gmail.com<mailto:jimboesq at gmail.com>> wrote:

Hi Bio-Formats team!

I've just tried to load an Andor TIFF file into FIJI, but it produces a huge error message, which I will copy below.

I have uploaded a sample datatset - "1 - Stream Defaults.tif" on the QA website.

Could you let me know if this is a Bio-Formats problem or an install problem on my side? I've run FIJI updater.

Thanks as always!

James

(Apps Specialist, Andor Technology)

There was a problem with the class loci.common.RandomAccessInputStream which can be found here:
/C:/Fiji.app/jars/bio-formats/formats-common-5.1.10.jar
/C:/Fiji.app/jars/bio-formats/ome-common-5.3.3.jar

WARNING: multiple locations found!
java.lang.NoSuchMethodError: loci.common.RandomAccessInputStream.readUnsignedInt()J
at loci.formats.tiff.TiffParser.getNextOffset(TiffParser.java:1257)
at loci.formats.tiff.TiffParser.getFirstOffset(TiffParser.java:366)
at loci.formats.tiff.TiffParser.getFirstIFD(TiffParser.java:320)
at loci.formats.in.SEQReader.isThisType(SEQReader.java:73)
at loci.formats.FormatReader.isThisType(FormatReader.java:615)
at loci.formats.ImageReader.getReader(ImageReader.java:185)
at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:618)
at loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:484)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:137)
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:221)
at ij.IJ.runPlugIn(IJ.java:185)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at ij.IJ.run(IJ.java:301)
at ij.IJ.run(IJ.java:276)
at ij.macro.Functions.doRun(Functions.java:604)
at ij.macro.Functions.doFunction(Functions.java:96)
at ij.macro.Interpreter.doStatement(Interpreter.java:247)
at ij.macro.Interpreter.doBlock(Interpreter.java:630)
at ij.macro.Interpreter.runMacro(Interpreter.java:156)
at ij.macro.MacroRunner.run(MacroRunner.java:152)
at java.lang.Thread.run(Thread.java:745)

[ERROR] null
java.lang.NoSuchMethodException: Could not find method loci.common.RandomAccessInputStream.readUnsignedInt()J
There was a problem with the class loci.common.RandomAccessInputStream which can be found here:
/C:/Fiji.app/jars/bio-formats/formats-common-5.1.10.jar
/C:/Fiji.app/jars/bio-formats/ome-common-5.3.3.jar

WARNING: multiple locations found!
java.lang.NoSuchMethodError: loci.common.RandomAccessInputStream.readUnsignedInt()J
at loci.formats.tiff.TiffParser.getNextOffset(TiffParser.java:1257)
at loci.formats.tiff.TiffParser.getFirstOffset(TiffParser.java:366)
at loci.formats.tiff.TiffParser.getFirstIFD(TiffParser.java:320)
at loci.formats.in.SEQReader.isThisType(SEQReader.java:73)
at loci.formats.FormatReader.isThisType(FormatReader.java:615)
at loci.formats.ImageReader.getReader(ImageReader.java:185)
at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:618)
at loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:484)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:137)
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:221)
at ij.IJ.runPlugIn(IJ.java:185)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at ij.IJ.run(IJ.java:301)
at ij.IJ.run(IJ.java:276)
at ij.macro.Functions.doRun(Functions.java:604)
at ij.macro.Functions.doFunction(Functions.java:96)
at ij.macro.Interpreter.doStatement(Interpreter.java:247)
at ij.macro.Interpreter.doBlock(Interpreter.java:630)
at ij.macro.Interpreter.runMacro(Interpreter.java:156)
at ij.macro.MacroRunner.run(MacroRunner.java:152)
at java.lang.Thread.run(Thread.java:745)

at loci.formats.tiff.TiffParser.getNextOffset(TiffParser.java:1257)
at loci.formats.tiff.TiffParser.getFirstOffset(TiffParser.java:366)
at loci.formats.tiff.TiffParser.getFirstIFD(TiffParser.java:320)
at loci.formats.in.SEQReader.isThisType(SEQReader.java:73)
at loci.formats.FormatReader.isThisType(FormatReader.java:615)
at loci.formats.ImageReader.getReader(ImageReader.java:185)
at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:618)
at loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:484)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:137)
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:221)
at ij.IJ.runPlugIn(IJ.java:185)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at ij.IJ.run(IJ.java:301)
at ij.IJ.run(IJ.java:276)
at ij.macro.Functions.doRun(Functions.java:604)
at ij.macro.Functions.doFunction(Functions.java:96)
at ij.macro.Interpreter.doStatement(Interpreter.java:247)
at ij.macro.Interpreter.doBlock(Interpreter.java:630)
at ij.macro.Interpreter.runMacro(Interpreter.java:156)
at ij.macro.MacroRunner.run(MacroRunner.java:152)
at java.lang.Thread.run(Thread.java:745)

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