Open Microscopy Environment

Hello,

I have a set of TIFF files taken from the same source, but half of the files are not being loaded into ImageJ or Bioformats. Opening in ImageJ does not do anything even after an hour of wait, and using Bioformats gives the following errors:

[ERROR] Error reading IFD type at: 213421728
Reading IFDs

then:

java.io.EOFException: Attempting to read beyond end of file.
at loci.common.NIOFileHandle.readInt(NIOFileHandle.java:378)
at loci.common.RandomAccessInputStream.readInt(RandomAccessInputStream.java:507)
at loci.common.RandomAccessInputStream.readUnsignedInt(RandomAccessInputStream.java:514)
at loci.formats.tiff.TiffParser.getNextOffset(TiffParser.java:1257)
at loci.formats.tiff.TiffParser.getIFDOffsets(TiffParser.java:303)
at loci.formats.tiff.TiffParser.getIFDs(TiffParser.java:217)
at loci.formats.in.MinimalTiffReader.initFile(MinimalTiffReader.java:448)
at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:583)
at loci.formats.FormatReader.setId(FormatReader.java:1397)
at loci.formats.DelegateReader.setId(DelegateReader.java:291)
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:228)
at ij.IJ.runPlugIn(IJ.java:192)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.nio.BufferUnderflowException: null
at java.nio.Buffer.nextGetIndex(Buffer.java:506)
at java.nio.HeapByteBuffer.getInt(HeapByteBuffer.java:361)
at loci.common.NIOFileHandle.readInt(NIOFileHandle.java:376)
... 19 common frames omitted
Checking for JAI
Reading movie dimensions

followed by a prompt saying there was an error during import and then in the ImageJ log:

loci.formats.FormatException: loci.common.ReflectException: Cannot execute method: decodeAsRenderedImage
at loci.formats.in.TiffJAIReader.openBufferedImage(TiffJAIReader.java:196)
at loci.formats.in.TiffJAIReader.initFile(TiffJAIReader.java:156)
at loci.formats.FormatReader.setId(FormatReader.java:1397)
at loci.formats.DelegateReader.setId(DelegateReader.java:300)
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:228)
at ij.IJ.runPlugIn(IJ.java:192)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:745)
Caused by: loci.common.ReflectException: Cannot execute method: decodeAsRenderedImage
at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:316)
at loci.formats.in.TiffJAIReader.openBufferedImage(TiffJAIReader.java:191)
... 13 more
Caused by: java.lang.reflect.InvocationTargetException
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:497)
at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:311)
... 14 more
Caused by: java.io.IOException: Illegal page requested from a TIFF file.
at com.sun.media.jai.codecimpl.TIFFImageDecoder.decodeAsRenderedImage(TIFFImageDecoder.java:104)
... 19 more


Again, this is only for half the files while the other half works fine. If anybody has had similar errors or possible solutions, help would be greatly appreciated. Thank you!

At least here at OME's end I am afraid that I don't think we recognize that particular issue. Which version of Bio-Formats are you using? If you send us a problem image via http://qa.openmicroscopy.org.uk/qa/upload/ we'd be happy to try your image with ImageJ here.

Cheers,
Mark

Further, I am kindly reminded to check: Have you managed to confirm in any other viewing software that the problem image files are actually fine as TIFFs, that those files aren't simply truncated or otherwise corrupted?

Cheers,
Mark