[ome-users] I/O problem during file import using Bio-Formats Importer in Fiji

Sebastien Besson (Staff) s.besson at dundee.ac.uk
Thu May 26 09:59:24 BST 2016

Hi Robert,

Many thanks for the detailed report, the file sharing and the investigation. We could indeed reproduce
the issue you described.

So far the netcdf dependency upgrade has been blocked by Java 6 which we will drop for
Bio-Formats 5.2.0. We will be looking into upgrading this HDF library as well as part of the next

Also, is it possible for us to use your attached .ims file as a public sample?


On 24 May 2016, at 16:34, CHODKOWSKI Robert <r.chodkowski at andor.com<mailto:r.chodkowski at andor.com>> wrote:


My name is Robert and I’m a senior software engineer working in Andor Technology. I was trying to use Bio-Formats importer in Fiji to open files (Files->Import->Bio Formats) created in Imaris format (*.ims) and I was getting I/O error when trying to open multi-channel image. It seems to be a problem with metadata block being too big to open by NetcdfFile.open() method. I use the latest Bio-Formats plugin (v5.1.10) which uses netcdf-4.3.19.jar to open Imaris files. When I updated the netcdf library in Fiji\jars folder to the latest version (netcdfAll-4.6.5.jar) the problem with opening the Imaris files seems to be fixed. Would be possible to update netcdf library in the next Fiji release to fix this problem?

I also attached the ims file that causing the I/O error in Fiji.

Many Thanks,
Robert Chodkowski
Senior Software Engineer

Andor Technology
Springvale Business Park
7 Millennium Way,
Co. Antrim
BT12 7AL
Tel: +44 (0)28 9023 7126
mailto:r.chodkowski at andor.com
skype: andor.r.chodkowski


Error details:


Stack trace log:
java.io.IOException: java.lang.IllegalStateException: MessageDataspace: unknown version= 117
                at ucar.nc2.NetcdfFile.open(NetcdfFile.java:425)
                at ucar.nc2.NetcdfFile.open(NetcdfFile.java:392)
                at ucar.nc2.NetcdfFile.open(NetcdfFile.java:379)
                at ucar.nc2.NetcdfFile.open(NetcdfFile.java:367)
                at loci.formats.services.NetCDFServiceImpl.init(NetCDFServiceImpl.java:307)
                at loci.formats.services.NetCDFServiceImpl.setFile(NetCDFServiceImpl.java:100)
                at loci.formats.in.ImarisHDFReader.initFile(ImarisHDFReader.java:247)
                at loci.formats.FormatReader.setId(FormatReader.java:1426)
                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:216)
                at ij.IJ.runPlugIn(IJ.java:180)
                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.lang.IllegalStateException: MessageDataspace: unknown version= 117
                at ucar.nc2.iosp.hdf5.H5header$MessageDataspace.read(H5header.java:2826)
                at ucar.nc2.iosp.hdf5.H5header$MessageAttribute.read(H5header.java:3683)
                at ucar.nc2.iosp.hdf5.H5header$DataObject.processAttributeInfoMessage(H5header.java:2364)
                at ucar.nc2.iosp.hdf5.H5header$DataObject.<init>(H5header.java:2332)
                at ucar.nc2.iosp.hdf5.H5header$DataObject.<init>(H5header.java:2180)
                at ucar.nc2.iosp.hdf5.H5header.getDataObject(H5header.java:2027)
                at ucar.nc2.iosp.hdf5.H5header.access$600(H5header.java:70)
                at ucar.nc2.iosp.hdf5.H5header$DataObjectFacade.<init>(H5header.java:2073)
                at ucar.nc2.iosp.hdf5.H5header.readGroupNew(H5header.java:3911)
                at ucar.nc2.iosp.hdf5.H5header.access$900(H5header.java:70)
                at ucar.nc2.iosp.hdf5.H5header$H5Group.<init>(H5header.java:2153)
                at ucar.nc2.iosp.hdf5.H5header$H5Group.<init>(H5header.java:2118)
                at ucar.nc2.iosp.hdf5.H5header.makeNetcdfGroup(H5header.java:472)
                at ucar.nc2.iosp.hdf5.H5header.read(H5header.java:215)
                at ucar.nc2.iosp.hdf5.H5iosp.open(H5iosp.java:128)
                at ucar.nc2.NetcdfFile.<init>(NetcdfFile.java:1521)
                at ucar.nc2.NetcdfFile.open(NetcdfFile.java:813)
                at ucar.nc2.NetcdfFile.open(NetcdfFile.java:422)
                ... 17 more

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.8.0_66
  java.vendor => Oracle Corporation
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.8.0_66-b18
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 25.66-b18
  java.vm.vendor => Oracle Corporation
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.8
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\Tools\Fiji.app/java/win64/jdk1.8.0_66//jre
  imagej.dir => C:\Tools\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20160504193521)
Fiji: http://update.fiji.sc/ (last check:20160509090721)
Java-8: http://sites.imagej.net/Java-8/ (last check:20160518185210)

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