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<p>Dear OME team,</p>
<p>we recently had the opportunity to test Andors new Spinning-disk
confocal ("Dragonfly") together with its new acquisition software
"Fusion".</p>
<p>The default file format in which Fusion save the data is *.ims,
since Andor also owns Bitplane Imaris.</p>
<p>As expected <a moz-do-not-send="true"
href="https://filesender.switch.ch/filesender/?vid=03e9a405-643f-8229-0aa3-00000e50b3a6">these
images</a> open nicely in Imaris - but not when using Fiji with
the latest Bio-formats:</p>
<p>"Sorry, there was an I/O problem during import". See console and
log output at the end of this email.</p>
<p>I received this error both when opening files from a remote or
local destination.<br>
</p>
<p>The "regular" *.ims 5.5 images saved by Imaris still open fine in
Fiji.</p>
<p>Do you maybe have an idea whats the problem/difference in the
*.ims saved by the fusion software?</p>
<p>Thanks and cheers,<br>
Kai<br>
</p>
<p>
<blockquote type="cite">[ERROR] bad version 0 at filePos 862756381
<br>
[ERROR] bad version 0 at filePos 862756593 <br>
[ERROR] bad version 0 at filePos 862756603 <br>
[ERROR] bad version 53 at filePos 862756551 <br>
[ERROR] bad version 0 at filePos 862756429 <br>
[ERROR] bad version 111 at filePos 862756454 </blockquote>
<br>
</p>
<p>
<blockquote type="cite">java.io.IOException:
java.lang.IllegalStateException: MessageDataspace: unknown
version= 0 <br>
at ucar.nc2.NetcdfFile.open(NetcdfFile.java:425) <br>
at ucar.nc2.NetcdfFile.open(NetcdfFile.java:392) <br>
at ucar.nc2.NetcdfFile.open(NetcdfFile.java:379) <br>
at ucar.nc2.NetcdfFile.open(NetcdfFile.java:367) <br>
at
loci.formats.services.NetCDFServiceImpl.init(NetCDFServiceImpl.java:310)
<br>
at
loci.formats.services.NetCDFServiceImpl.setFile(NetCDFServiceImpl.java:103)
<br>
at
loci.formats.in.ImarisHDFReader.initFile(ImarisHDFReader.java:246)
<br>
at loci.formats.FormatReader.setId(FormatReader.java:1397) <br>
at
loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)
<br>
at
loci.plugins.in.ImportProcess.execute(ImportProcess.java:141) <br>
at loci.plugins.in.Importer.showDialogs(Importer.java:140) <br>
at loci.plugins.in.Importer.run(Importer.java:76) <br>
at loci.plugins.LociImporter.run(LociImporter.java:78) <br>
at ij.IJ.runUserPlugIn(IJ.java:217) <br>
at ij.IJ.runPlugIn(IJ.java:181) <br>
at ij.Executer.runCommand(Executer.java:137) <br>
at ij.Executer.run(Executer.java:66) <br>
at ij.IJ.run(IJ.java:297) <br>
at ij.IJ.run(IJ.java:272) <br>
at ij.macro.Functions.doRun(Functions.java:603) <br>
at ij.macro.Functions.doFunction(Functions.java:96) <br>
at ij.macro.Interpreter.doStatement(Interpreter.java:230) <br>
at ij.macro.Interpreter.doStatements(Interpreter.java:218) <br>
at ij.macro.Interpreter.run(Interpreter.java:115) <br>
at ij.macro.Interpreter.run(Interpreter.java:85) <br>
at ij.macro.MacroRunner.run(MacroRunner.java:139) <br>
at java.lang.Thread.run(Thread.java:745) <br>
Caused by: java.lang.IllegalStateException: MessageDataspace:
unknown version= 0 <br>
at
ucar.nc2.iosp.hdf5.H5header$MessageDataspace.read(H5header.java:2826)
<br>
at
ucar.nc2.iosp.hdf5.H5header$MessageAttribute.read(H5header.java:3683)
<br>
at
ucar.nc2.iosp.hdf5.H5header$DataObject.processAttributeInfoMessage(H5header.java:2364)
<br>
at
ucar.nc2.iosp.hdf5.H5header$DataObject.<init>(H5header.java:2332)
<br>
at
ucar.nc2.iosp.hdf5.H5header$DataObject.<init>(H5header.java:2180)
<br>
at
ucar.nc2.iosp.hdf5.H5header.getDataObject(H5header.java:2027) <br>
at ucar.nc2.iosp.hdf5.H5header.access$600(H5header.java:70)
<br>
at
ucar.nc2.iosp.hdf5.H5header$DataObjectFacade.<init>(H5header.java:2073)
<br>
at
ucar.nc2.iosp.hdf5.H5header.readGroupNew(H5header.java:3911) <br>
at ucar.nc2.iosp.hdf5.H5header.access$900(H5header.java:70)
<br>
at
ucar.nc2.iosp.hdf5.H5header$H5Group.<init>(H5header.java:2153)
<br>
at
ucar.nc2.iosp.hdf5.H5header$H5Group.<init>(H5header.java:2118)
<br>
at
ucar.nc2.iosp.hdf5.H5header.makeNetcdfGroup(H5header.java:472) <br>
at ucar.nc2.iosp.hdf5.H5header.read(H5header.java:215) <br>
at ucar.nc2.iosp.hdf5.H5iosp.open(H5iosp.java:128) <br>
at ucar.nc2.NetcdfFile.<init>(NetcdfFile.java:1521) <br>
at ucar.nc2.NetcdfFile.open(NetcdfFile.java:813) <br>
at ucar.nc2.NetcdfFile.open(NetcdfFile.java:422) <br>
... 26 more <br>
</blockquote>
<br>
</p>
<p><br>
</p>
<pre class="moz-signature" cols="72">--
>>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) | <a class="moz-txt-link-abbreviated" href="mailto:kai.schleicher@unibas.ch">kai.schleicher@unibas.ch</a> | <a class="moz-txt-link-abbreviated" href="http://www.biozentrum.unibas.ch">www.biozentrum.unibas.ch</a> | <a class="moz-txt-link-abbreviated" href="http://www.microscopynetwork.unibas.ch">www.microscopynetwork.unibas.ch</a></pre>
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