[ome-users] bio-formats error on tf8 file import

[Kai Schleicher]

Hi,

The output on one of our microscopes is a tf8.

We have a user acquiring rather large datasets on it (multichannel + z-stack + time laps, about 7 GB per image), which worked fine in the past.

However, opening the tf8-files from his last acquisition fails with an error (see below).

The acquisition itself finished without error, but it is likely that the C drive of the acquisition machine was low on space at the end of the experiment.

Due to restrictions in the acquisition software (FEI Live Acquisition software) the data has to be recorded to the C drive.

Is there still something that could be done in order to save the data?

Thanks and cheers,
Kai

loci.formats.FormatException: loci.common.ReflectException: Cannot execute method: getNumPages
               at loci.formats.in.TiffJAIReader.initFile(TiffJAIReader.java:149)
               at loci.formats.FormatReader.setId(FormatReader.java:1426)
               at loci.formats.DelegateReader.setId(DelegateReader.java:298)
               at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505)
               at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)
               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:212)
               at ij.IJ.runPlugIn(IJ.java:176)
               at ij.Executer.runCommand(Executer.java:136)
               at ij.Executer.run(Executer.java:65)
               at ij.IJ.run(IJ.java:292)
               at ij.IJ.run(IJ.java:267)
               at ij.macro.Functions.doRun(Functions.java:603)
               at ij.macro.Functions.doFunction(Functions.java:96)
               at ij.macro.Interpreter.doStatement(Interpreter.java:230)
               at ij.macro.Interpreter.doStatements(Interpreter.java:218)
               at ij.macro.Interpreter.run(Interpreter.java:115)
               at ij.macro.Interpreter.run(Interpreter.java:85)
               at ij.macro.MacroRunner.run(MacroRunner.java:139)
               at java.lang.Thread.run(Thread.java:662)
Caused by: loci.common.ReflectException: Cannot execute method: getNumPages
               at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:316)
               at loci.formats.in.TiffJAIReader.initFile(TiffJAIReader.java:146)
               ... 21 more
Caused by: java.lang.reflect.InvocationTargetException
               at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
               at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
               at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
               at java.lang.reflect.Method.invoke(Method.java:597)
               at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:311)
               ... 22 more
Caused by: java.io.IOException: Bad magic number, should be 42.
               at com.sun.media.jai.codecimpl.CodecUtils.toIOException(CodecUtils.java:76)
               at com.sun.media.jai.codecimpl.TIFFImageDecoder.getNumPages(TIFFImageDecoder.java:98)
               ... 27 more
Caused by: java.lang.IllegalArgumentException: Bad magic number, should be 42.
               at com.sun.media.jai.codec.TIFFDirectory.getNumDirectories(TIFFDirectory.java:601)
               at com.sun.media.jai.codecimpl.TIFFImageDecoder.getNumPages(TIFFImageDecoder.java:96)
               ... 27 more




--
Kai Schleicher, PhD | Research Associate in Advanced Light Microscopy | Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel
Phone: +41 61 267 22 50 | kai.schleicher at unibas.ch<mailto:kai.schleicher at unibas.ch> | www.biozentrum.unibas.ch<http://www.biozentrum.unibas.ch/> | www.microscopynetwork.unibas.ch<http://www.microscopynetwork.unibas.ch/>

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