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

[David Gault (Staff)]

Hi James,

The issue you are seeing is caused by a conflict between the newer ome-common jar and the older formats-common jar. When running the FIJI updater the formats-common jar should be marked as obsolete and suggest that it be uninstalled. If you do this that will remove the conflict and you should be able to import the file without problems.

With Thanks,
David Gault


> On 19 Jan 2018, at 12:53, James Wainwright <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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