[ome-users] Can't read Andor Dragonfly/Fusion *.ims with Bioformats

[Kai Schleicher]

Dear OME team,

we recently had the opportunity to test Andors new Spinning-disk 
confocal ("Dragonfly") together with its new acquisition software "Fusion".

The default file format in which Fusion save the data is *.ims, since 
Andor also owns Bitplane Imaris.

As expected these images 
<https://filesender.switch.ch/filesender/?vid=03e9a405-643f-8229-0aa3-00000e50b3a6> 
open nicely in Imaris - but not when using Fiji with the latest Bio-formats:

"Sorry, there was an I/O problem during import". See console and log 
output at the end of this email.

I received this error both when opening files from a remote or local 
destination.

The "regular" *.ims 5.5 images saved by Imaris still open fine in Fiji.

Do you maybe have an idea whats the problem/difference in the *.ims 
saved by the fusion software?

Thanks and cheers,
Kai

> [ERROR] bad version 0 at filePos 862756381
> [ERROR] bad version 0 at filePos 862756593
> [ERROR] bad version 0 at filePos 862756603
> [ERROR] bad version 53 at filePos 862756551
> [ERROR] bad version 0 at filePos 862756429
> [ERROR] bad version 111 at filePos 862756454 

> java.io.IOException: java.lang.IllegalStateException: 
> MessageDataspace: unknown version= 0
>     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:310)
>     at 
> loci.formats.services.NetCDFServiceImpl.setFile(NetCDFServiceImpl.java:103) 
>
>     at loci.formats.in.ImarisHDFReader.initFile(ImarisHDFReader.java:246)
>     at loci.formats.FormatReader.setId(FormatReader.java:1397)
>     at 
> loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)
>     at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)
>     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:217)
>     at ij.IJ.runPlugIn(IJ.java:181)
>     at ij.Executer.runCommand(Executer.java:137)
>     at ij.Executer.run(Executer.java:66)
>     at ij.IJ.run(IJ.java:297)
>     at ij.IJ.run(IJ.java:272)
>     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:745)
> Caused by: java.lang.IllegalStateException: MessageDataspace: unknown 
> version= 0
>     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)
>     ... 26 more


-- 
>>Please note my NEW PHONE NUMBERS: +41 61 207 57 31 (direct) +41 61 207 22 50 (central)<<
Kai Schleicher, PhD | Research Associate in Advanced Light Microscopy | Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel |
Phone: +41 61 207 57 31 (direct) +41 61 207 22 50 (central) | kai.schleicher at unibas.ch | www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch

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