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<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Hi David,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">I did this while using netcdfAll-4.6.11.jar.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">The one supplied with FIJI is not present in the jars directory (I have deleted it).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Thanks – output below:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">ID is D:\FusionImages\2018-07-25\2018-07-25_08.45.37_Sample Prefix_Protocol.ims<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">File format is: Bitplane Imaris 5.5 (HDF)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">java.lang.reflect.InvocationTargetException<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at java.lang.reflect.Method.invoke(Method.java:497)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at loci.plugins.macro.MacroFunctions.handleExtension(MacroFunctions.java:82)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ij.macro.ExtensionDescriptor.dispatch(ExtensionDescriptor.java:288)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ij.macro.Functions.doExt(Functions.java:4702)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ij.macro.Functions.getStringFunction(Functions.java:275)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ij.macro.Interpreter.getStringTerm(Interpreter.java:1360)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ij.macro.Interpreter.getString(Interpreter.java:1338)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ij.macro.Interpreter.doStatement(Interpreter.java:303)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ij.macro.Interpreter.doStatements(Interpreter.java:235)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ij.macro.Interpreter.run(Interpreter.java:118)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ij.macro.Interpreter.run(Interpreter.java:89)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ij.macro.Interpreter.run(Interpreter.java:100)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:161)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ij.plugin.Macro_Runner.runMacroFile(Macro_Runner.java:145)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ij.plugin.Macro_Runner.run(Macro_Runner.java:39)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ij.IJ.runPlugIn(IJ.java:198)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ij.Executer.runCommand(Executer.java:137)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ij.Executer.run(Executer.java:66)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at java.lang.Thread.run(Thread.java:745)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Caused by: java.io.IOException: java.io.EOFException: Reading D:/FusionImages/2018-07-25/2018-07-25_08.45.37_Sample Prefix_Protocol.ims at 4776428346718162991 file length = 4776428346718162991<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ucar.nc2.NetcdfFile.open(NetcdfFile.java:427)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ucar.nc2.NetcdfFile.open(NetcdfFile.java:394)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ucar.nc2.NetcdfFile.open(NetcdfFile.java:381)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ucar.nc2.NetcdfFile.open(NetcdfFile.java:369)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at loci.formats.services.NetCDFServiceImpl.init(NetCDFServiceImpl.java:310)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at loci.formats.services.NetCDFServiceImpl.setFile(NetCDFServiceImpl.java:103)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at loci.formats.in.ImarisHDFReader.initFile(ImarisHDFReader.java:246)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at loci.formats.FormatReader.setId(FormatReader.java:1397)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at loci.formats.ImageReader.setId(ImageReader.java:842)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:291)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at loci.plugins.macro.LociFunctions.setId(LociFunctions.java:427)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> ... 22 more<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Caused by: java.io.EOFException: Reading D:/FusionImages/2018-07-25/2018-07-25_08.45.37_Sample Prefix_Protocol.ims at 4776428346718162991 file length = 4776428346718162991<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ucar.unidata.io.RandomAccessFile.readFully(RandomAccessFile.java:852)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ucar.unidata.io.RandomAccessFile.readFully(RandomAccessFile.java:831)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ucar.unidata.io.RandomAccessFile.readString(RandomAccessFile.java:1522)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ucar.nc2.iosp.hdf5.FractalHeap.readIndirectBlock(FractalHeap.java:441)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ucar.nc2.iosp.hdf5.FractalHeap.readIndirectBlock(FractalHeap.java:498)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ucar.nc2.iosp.hdf5.FractalHeap.<init>(FractalHeap.java:182)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ucar.nc2.iosp.hdf5.H5header$DataObject.processAttributeInfoMessage(H5header.java:2477)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ucar.nc2.iosp.hdf5.H5header$DataObject.<init>(H5header.java:2463)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ucar.nc2.iosp.hdf5.H5header$DataObject.<init>(H5header.java:2294)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ucar.nc2.iosp.hdf5.H5header.getDataObject(H5header.java:2129)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ucar.nc2.iosp.hdf5.H5header.access$500(H5header.java:72)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ucar.nc2.iosp.hdf5.H5header$DataObjectFacade.<init>(H5header.java:2175)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ucar.nc2.iosp.hdf5.H5header.readGroupNew(H5header.java:4192)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ucar.nc2.iosp.hdf5.H5header.access$1000(H5header.java:72)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ucar.nc2.iosp.hdf5.H5header$H5Group.<init>(H5header.java:2262)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ucar.nc2.iosp.hdf5.H5header$H5Group.<init>(H5header.java:2220)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ucar.nc2.iosp.hdf5.H5header.makeNetcdfGroup(H5header.java:494)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ucar.nc2.iosp.hdf5.H5header.read(H5header.java:219)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ucar.nc2.iosp.hdf5.H5iosp.open(H5iosp.java:130)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ucar.nc2.NetcdfFile.<init>(NetcdfFile.java:1560)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ucar.nc2.NetcdfFile.open(NetcdfFile.java:835)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> at ucar.nc2.NetcdfFile.open(NetcdfFile.java:424)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> ... 34 more<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">James<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><b><span style="color:#1C2674">James Wainwright<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="color:#1C2674">Global Applications Specialist - Microscopy Systems<br>
<br>
<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="color:#1C2674">Tel: </span></b><span style="color:#1C2674">+44 (0) 2890 237 126 ext. 2130<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="color:#1C2674">Skype: </span></b><span style="color:#1C2674">andor.j.wainwright
<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="color:#1C2674">Mob: </span></b><span style="color:#1C2674">+44 (0) 7834 710 834<br>
<b>Web:</b> <a href="https://www.andor.com/microscopy-systems">https://www.andor.com/microscopy-systems</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:#1F497D"><br>
</span><span style="font-family:"Times New Roman",serif;color:#1F497D"><img border="0" width="128" height="38" style="width:1.3333in;height:.3958in" id="Picture_x0020_1" src="cid:image001.jpg@01D427F8.740E3D90" alt="logo"></span><o:p></o:p></p>
</div>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span lang="EN-US"> David Gault (Staff) <d.gault@dundee.ac.uk>
<br>
<b>Sent:</b> 27 July 2018 10:39<br>
<b>To:</b> WAINWRIGHT James <J.Wainwright@andor.com><br>
<b>Cc:</b> OME User Support List <ome-users@lists.openmicroscopy.org.uk>; WILDE Geraint <g.wilde@andor.com>; row_microscopy_support <row_microscopy_support@andor.com><br>
<b>Subject:</b> Re: -|EXT|- Re: [ome-users] Ticket ID: 001-00-019862__Issue importing large Multi-point scans into Fiji___Doesn't occur on smaller datasets<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks James, <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">That particular error looks to be due to not having the Netcdf upgrade, the important thing is that it has identified the file as Imaris HDF and is attempting to use the correct image reader.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Can you run the below ImageJ macro, selecting the file from the dialog box when prompted, and provide the output log:<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<div>
<p class="MsoNormal">run("Bio-Formats Macro Extensions");<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">id = File.openDialog("Choose a file");<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Ext.getFormat(id, format)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">print("ID is " + id);<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">print("File format is: " + format);<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Ext.setId(id);<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Ext.getSeriesCount(seriesCount);<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">for (s=0; s<seriesCount; s++) {<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> Ext.setSeries(s);<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> Ext.getSizeX(sizeX);<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> Ext.getSizeY(sizeY);<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> Ext.getSizeZ(sizeZ);<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> Ext.getSizeC(sizeC);<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> Ext.getSizeT(sizeT);<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> print("Series #" + s + ": image resolution is " + sizeX + " x " + sizeY);<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> print("Focal plane count = " + sizeZ);<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> print("Channel count = " + sizeC);<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> print("Time point count = " + sizeT);<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">}<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Ext.close();<o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">With Thanks,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">David Gault<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On 26 Jul 2018, at 12:47, WAINWRIGHT James <<a href="mailto:J.Wainwright@ANDOR.COM">J.Wainwright@ANDOR.COM</a>> wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">Hi David,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Here are the results:<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Checking file format [Bitplane Imaris 5.5 (HDF)]<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Initializing reader<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">ImarisHDFReader initializing 2018-07-25_08.45.37_Sample Prefix_Protocol.ims<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Exception in thread "main" java.io.IOException: java.lang.IllegalStateException:<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> should equal FHIB<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at ucar.nc2.NetcdfFile.open(NetcdfFile.java:425)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at ucar.nc2.NetcdfFile.open(NetcdfFile.java:392)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at ucar.nc2.NetcdfFile.open(NetcdfFile.java:379)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at ucar.nc2.NetcdfFile.open(NetcdfFile.java:367)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at loci.formats.services.NetCDFServiceImpl.init(NetCDFServiceImpl.java:310)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at loci.formats.services.NetCDFServiceImpl.setFile(NetCDFServiceImpl.java:103)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at loci.formats.in.ImarisHDFReader.initFile(ImarisHDFReader.java:246)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at loci.formats.FormatReader.setId(FormatReader.java:1397)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at loci.formats.ImageReader.setId(ImageReader.java:842)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:1034)<o:p></o:p></p>
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<div>
<p class="MsoNormal"> at loci.formats.tools.ImageInfo.main(ImageInfo.java:1120)<o:p></o:p></p>
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<div>
<p class="MsoNormal">Caused by: java.lang.IllegalStateException: should equal FHIB<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at ucar.nc2.iosp.hdf5.FractalHeap.readIndirectBlock(FractalHeap.java:401)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at ucar.nc2.iosp.hdf5.FractalHeap.readIndirectBlock(FractalHeap.java:456)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at ucar.nc2.iosp.hdf5.FractalHeap.<init>(FractalHeap.java:186)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at ucar.nc2.iosp.hdf5.H5header$DataObject.processAttributeInfoMessage(H5header.java:2344)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at ucar.nc2.iosp.hdf5.H5header$DataObject.<init>(H5header.java:2332)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at ucar.nc2.iosp.hdf5.H5header$DataObject.<init>(H5header.java:2180)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at ucar.nc2.iosp.hdf5.H5header.getDataObject(H5header.java:2027)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at ucar.nc2.iosp.hdf5.H5header.access$600(H5header.java:70)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at ucar.nc2.iosp.hdf5.H5header$DataObjectFacade.<init>(H5header.java:2073)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at ucar.nc2.iosp.hdf5.H5header.readGroupNew(H5header.java:3920)<o:p></o:p></p>
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<div>
<p class="MsoNormal"> at ucar.nc2.iosp.hdf5.H5header.access$900(H5header.java:70)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at ucar.nc2.iosp.hdf5.H5header$H5Group.<init>(H5header.java:2153)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at ucar.nc2.iosp.hdf5.H5header$H5Group.<init>(H5header.java:2118)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at ucar.nc2.iosp.hdf5.H5header.makeNetcdfGroup(H5header.java:472)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at ucar.nc2.iosp.hdf5.H5header.read(H5header.java:215)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at ucar.nc2.iosp.hdf5.H5iosp.open(H5iosp.java:128)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at ucar.nc2.NetcdfFile.<init>(NetcdfFile.java:1521)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> at ucar.nc2.NetcdfFile.open(NetcdfFile.java:813)<o:p></o:p></p>
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<div>
<p class="MsoNormal"> at ucar.nc2.NetcdfFile.open(NetcdfFile.java:422)<o:p></o:p></p>
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<div>
<p class="MsoNormal"> ... 11 more<o:p></o:p></p>
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<div>
<p class="MsoNormal"> <o:p></o:p></p>
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<div>
<p class="MsoNormal">I don’t know how to check the first 8 bytes? (I considered opening the file in notepad, but I don’t fancy trying that on a 95GB file...)<o:p></o:p></p>
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<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">James<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
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<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<div>
<p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span class="apple-converted-space"><span lang="EN-US"> </span></span><span lang="EN-US">David Gault (Staff) <<a href="mailto:d.gault@dundee.ac.uk">d.gault@dundee.ac.uk</a>><span class="apple-converted-space"> </span><br>
<b>Sent:</b><span class="apple-converted-space"> </span>26 July 2018 11:19<br>
<b>To:</b><span class="apple-converted-space"> </span>WAINWRIGHT James <<a href="mailto:J.Wainwright@andor.com">J.Wainwright@andor.com</a>>; OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>>;
WILDE Geraint <<a href="mailto:g.wilde@andor.com">g.wilde@andor.com</a>>; row_microscopy_support <<a href="mailto:row_microscopy_support@andor.com">row_microscopy_support@andor.com</a>><br>
<b>Subject:</b><span class="apple-converted-space"> </span>Re: -|EXT|- Re: [ome-users] Ticket ID: 001-00-019862__Issue importing large Multi-point scans into Fiji___Doesn't occur on smaller datasets</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Hi James,<span class="apple-converted-space"> </span><o:p></o:p></p>
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<div>
<p class="MsoNormal"> <o:p></o:p></p>
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<div>
<div>
<p class="MsoNormal">If you download the command line tools from <a href="https://www.openmicroscopy.org/bio-formats/downloads/"><span style="color:purple">https://www.openmicroscopy.org/bio-formats/downloads/</span></a> can you reproduce the error using:<o:p></o:p></p>
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<div>
<div>
<p class="MsoNormal"><b>showinf -nopix path/to/file/sample.ims</b><o:p></o:p></p>
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<div>
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<p class="MsoNormal"> <o:p></o:p></p>
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<div>
<p class="MsoNormal">Also if you are able to check the first 8 bytes of the file that would allow us to confirm the expected signature.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<div>
<p class="MsoNormal">With Thanks,<o:p></o:p></p>
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<div>
<div>
<p class="MsoNormal">David Gault<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<p class="MsoNormal">On 25 Jul 2018, at 09:54, WAINWRIGHT James <<a href="mailto:J.Wainwright@ANDOR.COM"><span style="color:purple">J.Wainwright@ANDOR.COM</span></a>> wrote:<o:p></o:p></p>
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<div>
<p class="MsoNormal"> <o:p></o:p></p>
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<div>
<div>
<p class="MsoNormal">Hi David,<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<div>
<p class="MsoNormal">I have now repeated the problem, which is independent of using a Virtual Stack.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<div>
<p class="MsoNormal">The problem happens somewhere between 57GB and 95GB – for example, a 57GB file opens fine, but the 95GB file generates the following error message:<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<div>
<p class="MsoNormal"><image001.png><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<div>
<p class="MsoNormal">This is using the latest netCDF from<span class="apple-converted-space"> </span><a href="https://www.unidata.ucar.edu/downloads/netcdf/netcdf-java-4/index.jsp"><span style="color:purple">https://www.unidata.ucar.edu/downloads/netcdf/netcdf-java-4/index.jsp</span></a><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<div>
<p class="MsoNormal">How can I provide more information on how to troubleshoot this?<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<div>
<p class="MsoNormal">Many thanks!<o:p></o:p></p>
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<div>
<p class="MsoNormal"> <o:p></o:p></p>
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<div>
<p class="MsoNormal">James<o:p></o:p></p>
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<div>
<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><b><span style="color:#1C2674">James Wainwright</span></b><o:p></o:p></p>
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<div>
<p class="MsoNormal"><span style="color:#1C2674">Global Applications Specialist - Microscopy Systems<br>
<br>
<br>
<br>
</span><o:p></o:p></p>
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<div>
<p class="MsoNormal"><b><span style="color:#1C2674">Tel: <span class="apple-converted-space"> </span></span></b><span style="color:#1C2674">+44 (0) 2890 237 126 ext. 2130</span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="color:#1C2674">Skype: <span class="apple-converted-space"> </span></span></b><span style="color:#1C2674">andor.j.wainwright</span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="color:#1C2674">Mob: <span class="apple-converted-space"> </span></span></b><span style="color:#1C2674">+44 (0) 7834 710 834<br>
<b>Web:</b> <span class="apple-converted-space"> </span><a href="https://www.andor.com/microscopy-systems"><span style="color:purple">https://www.andor.com/microscopy-systems</span></a></span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:#1F497D"><br>
</span><span style="font-family:"Times New Roman",serif;color:#1F497D"><image002.jpg></span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
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<p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span class="apple-converted-space"><span lang="EN-US"> </span></span><span lang="EN-US">David Gault (Staff) [<a href="mailto:d.gault@dundee.ac.uk"><span style="color:purple">mailto:d.gault@dundee.ac.uk</span></a>]<span class="apple-converted-space"> </span><br>
<b>Sent:</b><span class="apple-converted-space"> </span>23 July 2018 18:54<br>
<b>To:</b><span class="apple-converted-space"> </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk"><span style="color:purple">ome-users@lists.openmicroscopy.org.uk</span></a>><br>
<b>Cc:</b><span class="apple-converted-space"> </span>row_microscopy_support <<a href="mailto:row_microscopy_support@andor.com"><span style="color:purple">row_microscopy_support@andor.com</span></a>>; WILDE Geraint <<a href="mailto:g.wilde@andor.com"><span style="color:purple">g.wilde@andor.com</span></a>>;
WAINWRIGHT James <<a href="mailto:J.Wainwright@andor.com"><span style="color:purple">J.Wainwright@andor.com</span></a>><br>
<b>Subject:</b><span class="apple-converted-space"> </span>-|EXT|- Re: [ome-users] Ticket ID: 001-00-019862__Issue importing large Multi-point scans into Fiji___Doesn't occur on smaller datasets</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Hi James,<span class="apple-converted-space"> </span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<div>
<p class="MsoNormal">In the Bio-Formats importer options there is a section labelled "Memory management”, from this if you select the option “Use Virtual Stack” then it will load each frame as required rather than reading the entire file at once.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">With Thanks,<o:p></o:p></p>
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<p class="MsoNormal">David Gault<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
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<div>
<p class="MsoNormal">On 23 Jul 2018, at 15:15, WAINWRIGHT James <<a href="mailto:J.Wainwright@ANDOR.COM"><span style="color:purple">J.Wainwright@ANDOR.COM</span></a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<div>
<p class="MsoNormal">Just to add that these are IMS files and that we have “patched” FIJI with the latest netCDF file with the jar from here:<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><a href="https://www.unidata.ucar.edu/downloads/netcdf/netcdf-java-4/index.jsp"><span style="color:#954F72">https://www.unidata.ucar.edu/downloads/netcdf/netcdf-java-4/index.jsp</span></a><o:p></o:p></p>
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<div>
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<p class="MsoNormal"> <o:p></o:p></p>
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<div>
<div>
<div>
<p class="MsoNormal">James<o:p></o:p></p>
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<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><b><span style="color:#1C2674">James Wainwright</span></b><o:p></o:p></p>
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<div>
<div>
<div>
<p class="MsoNormal"><span style="color:#1C2674">Global Applications Specialist - Microscopy Systems<br>
<br>
<br>
<br>
<br>
</span><o:p></o:p></p>
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</div>
<div>
<div>
<div>
<p class="MsoNormal"><b><span style="color:#1C2674">Tel: <span class="apple-converted-space"> </span></span></b><span style="color:#1C2674">+44 (0) 2890 237 126 ext. 2130</span><o:p></o:p></p>
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<div>
<div>
<p class="MsoNormal"><b><span style="color:#1C2674">Skype: <span class="apple-converted-space"> </span></span></b><span style="color:#1C2674">andor.j.wainwright</span><o:p></o:p></p>
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<div>
<div>
<p class="MsoNormal"><b><span style="color:#1C2674">Mob: <span class="apple-converted-space"> </span></span></b><span style="color:#1C2674">+44 (0) 7834 710 834<br>
<b>Web:</b> <span class="apple-converted-space"> </span><a href="https://www.andor.com/microscopy-systems"><span style="color:purple">https://www.andor.com/microscopy-systems</span></a></span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:#1F497D"><br>
</span><span style="font-family:"Times New Roman",serif;color:#1F497D"><image002.jpg></span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span class="apple-converted-space"><span lang="EN-US"> </span></span><span lang="EN-US">row_microscopy_support<span class="apple-converted-space"> </span><br>
<b>Sent:</b><span class="apple-converted-space"> </span>23 July 2018 15:05<br>
<b>To:</b><span class="apple-converted-space"> </span><a href="mailto:ome-users@lists.openmicroscopy.org.uk"><span style="color:#954F72">ome-users@lists.openmicroscopy.org.uk</span></a><br>
<b>Cc:</b><span class="apple-converted-space"> </span>row_microscopy_support <<a href="mailto:row_microscopy_support@andor.com"><span style="color:#954F72">row_microscopy_support@andor.com</span></a>>; WILDE Geraint <<a href="mailto:g.wilde@andor.com"><span style="color:#954F72">g.wilde@andor.com</span></a>>;
WAINWRIGHT James <<a href="mailto:J.Wainwright@andor.com"><span style="color:#954F72">J.Wainwright@andor.com</span></a>><br>
<b>Subject:</b><span class="apple-converted-space"> </span>Ticket ID: 001-00-019862__Issue importing large Multi-point scans into Fiji___Doesn't occur on smaller datasets</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Hi,<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">We have a customer in Australia that is acquiring large Multi-point datasets. Can be upwards of 500GB data sets each time.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">They capture full Frame, no Binning (1024x1024 pixels), dual channel ( 2 simultaneous cameras acquiring) and 60-100 Z planes on multiple X/Y positions in an overnight (timelapse) protocol. These files can be upwards of 80Gb per XY position.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">The problem they have is when they try and import these large data sets to FIJI it fails, however if they perform a similar experiment, only smaller in size there is no issue.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">After asking the customer to perform a couple of tests for us, this is what they discovered:<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">“<b><i>Definitely looks to be a file size issue. Tried the smaller 1.5Gb files yesterday and it worked fine. Did a longer experiment (same experimental setup just with more z-slices and more time points so the file was around 60Gb and
these are failing. The only other difference was that the small files that worked had been captured using two channel sequential while the large files that don’t work were captured with dual channel simultaneous capture.”</i></b><o:p></o:p></p>
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<p class="MsoNormal">Any advice/workaround you can supply for handling these larger datasets would be appreciated.<o:p></o:p></p>
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<p class="MsoNormal">Best,<o:p></o:p></p>
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<p class="MsoNormal"><b>Phil Mullan</b><br>
Product Support Engineer (Microscopy Systems)<br>
Europe, Middle East & Africa<o:p></o:p></p>
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<p class="MsoNormal"><b>Tel:<span class="apple-converted-space"> </span></b>+44 (0) 28 9023 7126<span class="apple-converted-space"> </span><b>Ext.<span class="apple-converted-space"> </span></b>2732<br>
<b>Fax:<span class="apple-converted-space"> </span></b>+44 (0) 28 9031 0792<span class="apple-converted-space"> </span><br>
<b>Web:</b> <span class="apple-converted-space"> </span><a href="http://www.andor.com/" target="_blank"><span style="color:purple">andor.com/support</span></a><span class="apple-converted-space"> </span><br>
<br>
<image003.jpg><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">___________________________________________________________________________<br>
This e-mail is confidential and is for the addressee only. Please refer to<span class="apple-converted-space"> </span><br>
</span><a href="http://www.oxinst.com/email-statement"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:#954F72">www.oxinst.com/email-statement</span></a><span class="apple-converted-space"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif"> </span></span><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">for
regulatory information. _______________________________________________<br>
ome-users mailing list<br>
</span><a href="mailto:ome-users@lists.openmicroscopy.org.uk"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:#954F72">ome-users@lists.openmicroscopy.org.uk</span></a><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif"><br>
</span><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:#954F72">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</span></a><o:p></o:p></p>
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<p class="MsoNormal"><br>
<span style="font-size:10.0pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">___________________________________________________________________________<br>
This e-mail is confidential and is for the addressee only. Please refer to<span class="apple-converted-space"> </span><br>
</span><a href="http://www.oxinst.com/email-statement"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:purple">www.oxinst.com/email-statement</span></a><span class="apple-converted-space"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif"> </span></span><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">for
regulatory information.</span><o:p></o:p></p>
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</blockquote>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><br>
<span style="font-size:10.0pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">___________________________________________________________________________<br>
This e-mail is confidential and is for the addressee only. Please refer to<span class="apple-converted-space"> </span><br>
</span><a href="http://www.oxinst.com/email-statement"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:purple">www.oxinst.com/email-statement</span></a><span class="apple-converted-space"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif"> </span></span><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">for
regulatory information.</span><o:p></o:p></p>
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</blockquote>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><br>
<span style="font-size:10.0pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
<o:p></o:p></p>
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___________________________________________________________________________<br>
This e-mail is confidential and is for the addressee only. Please refer to <br>
<a href="http://www.oxinst.com/email-statement">www.oxinst.com/email-statement</a> for regulatory information.
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