Open Microscopy Environment

Dear all,

I'm sorry to report that Bitplane once again changed the Imaris file format without telling anyone (BF is not the only software suffering from this change). Trying to open the attached file (created with Imaris 7.6.4) with an up-to-date Fiji (including the Bioformats daily build repository), results in this error message:

Code: Select all

(Fiji Is Just) ImageJ 1.48f; Java 1.6.0_24 [64-bit]; Linux 3.11.0-13-generic; 22MB of 11103MB (<1%)

java.lang.IllegalStateException: MessageAttribute unknown version 72
   at ucar.nc2.iosp.hdf5.H5header$MessageAttribute.read(H5header.java:2566)
   at ucar.nc2.iosp.hdf5.H5header$DataObject.processAttributeInfoMessage(H5header.java:1502)
[...]
   at ij.macro.Interpreter.run(Interpreter.java:110)
   at ij.macro.Interpreter.run(Interpreter.java:80)
   at ij.macro.MacroRunner.run(MacroRunner.java:139)
   at java.lang.Thread.run(Thread.java:662)


Let me know if I can help you with anything here!

Thanks,
~Niko

Updated this morning to BF5 using the new update site announced by Curtis. Still doesn't work with this Imaris file, however the error message is slightly different:

Code: Select all

(Fiji Is Just) ImageJ 1.48f; Java 1.6.0_24 [64-bit]; Linux 3.11.0-13-generic; 28MB of 11103MB (<1%)

java.lang.NoClassDefFoundError: org/scijava/nativelib/NativeLibraryUtil
   at loci.formats.services.JPEGTurboServiceImpl.<init>(JPEGTurboServiceImpl.java:113)
   at loci.formats.in.HamamatsuVMSReader.<init>(HamamatsuVMSReader.java:79)
   at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
   at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
   at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
   at java.lang.Class.newInstance0(Class.java:355)
   at java.lang.Class.newInstance(Class.java:308)
   at loci.formats.ImageReader.<init>(ImageReader.java:134)
   at loci.plugins.util.LociPrefs.makeImageReader(LociPrefs.java:84)
   at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:594)
   at loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:472)
   at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)
   at loci.plugins.in.Importer.showDialogs(Importer.java:141)
   at loci.plugins.in.Importer.run(Importer.java:79)
   at loci.plugins.LociImporter.run(LociImporter.java:81)
   at ij.IJ.runUserPlugIn(IJ.java:196)
   at ij.IJ.runPlugIn(IJ.java:160)
   at ij.Executer.runCommand(Executer.java:131)
   at ij.Executer.run(Executer.java:64)
   at ij.IJ.run(IJ.java:266)
   at ij.IJ.run(IJ.java:244)
   at ij.macro.Functions.doRun(Functions.java:591)
   at ij.macro.Functions.doFunction(Functions.java:89)
   at ij.macro.Interpreter.doStatement(Interpreter.java:225)
   at ij.macro.Interpreter.doStatements(Interpreter.java:213)
   at ij.macro.Interpreter.run(Interpreter.java:110)
   at ij.macro.Interpreter.run(Interpreter.java:80)
   at ij.macro.MacroRunner.run(MacroRunner.java:139)
   at java.lang.Thread.run(Thread.java:662)


Hi Niko,

Thank you for the bug report. Is Imaris able to reopen this file? Initial investigation suggests that this file is subtly corrupted, but if Imaris can open it then we'll look into it further.

Regards,
-Melissa

Hi Melissa,

yes I double checked that Imaris can reopen the file. As I mentioned in my initial posting, we got confirmation from another company that the Imaris file format was indeed slightly changed with the last release. Maybe this only differs effectively in certain situation (like XYZCT, but not XYZC or something)?

Cheers
~Niko

Uh-oh. I just figured out that I can't open anything anymore using the BF importer since I enabled the BF5 update site. Tried an old Imaris file that worked before, tried a Zeiss LSM, even tried an OME-TIFF. Always results in the error message I posted in my second message.

I ran the updater again and made sure every required piece is there by checking the "uninstalled files" section.

Guess we should get that one sorted first?!

Thanks for the report, ehrenfeu. There were a couple of dependencies (notably joda and JWlz) missing from the BF 5 update site. I have remedied the situation. If you update again, you will get these JARs too.

However, the error you posted ("java.lang.NoClassDefFoundError: org/scijava/nativelib/NativeLibraryUtil") implies a missing native-lib-loader-2.0-SNAPSHOT.jar (or dependency thereof, but that library has none). The native-lib-loader JAR is definitely included on the update site. This is where I would normally tell you to check the updater's advanced mode in the "uninstalled files" section to see if the JAR still needs to be installed, but you said you already did that, so... can you verify that that JAR file is indeed present in your Fiji's jars folder?

My bad - Curtis, you're right, I didn't have the native-lib-loader JAR installed. I remember seeing it in the "uninstalled" list and thought I enabled it, but maybe I didn't as it was shown being located in the (default) LOCI update site, not the BF5 site. Would it be possible to mark it explicitly as a dependency, like you did with the two other missing JARs? Or does this only work on JARs from the same repo?

However, I'm now able to open my old test files again (so my generic BF5 issue is sorted). Still, the 7.6.4 file fails with the error message from my initial posting. Meanwhile I opened this file with a couple of older Imaris versions, firstly to see if it opens (yes), secondly to store them with the older versions for testing them with BF5. Current result is that BF5 opens the file saved with Imaris 7.5.2 (both 1T and 5T), whereas it already fails on the file created with 7.6.3.

I didn't have the time yet to create files with Imaris 7.6.2 and .1 - in case you'd be interested I could do that, just let me know.

Thanks
~Niko

Hi Niko,

We now have a fix under review for the 7.6.4 files:

https://github.com/openmicroscopy/bioformats/pull/790

Once that shows as being closed, you should hopefully be able to update Fiji and open the file (though it may take up to 24 hours for the new version to appear). I don't think we'll need 7.6.1 or 7.6.2 files at the moment; if anything doesn't work once that fix is in, though, then please let us know.

Regards,
-Melissa

Thank you Melissa, that's really great news! I'll test and report!

~Niko