<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Filipe,<div><br></div><div>Quick update on your issue with the .VSI format. The files you have sent us are in MetaSystems format which is currently not supported. I've CC'd you on the Task for supporting it: <a href="http://trac.openmicroscopy.org.uk/ome/ticket/12483">http://trac.openmicroscopy.org.uk/ome/ticket/12483</a><div apple-content-edited="true"><div><br></div>Cheers,
</div><div apple-content-edited="true">Emil</div><div apple-content-edited="true"><br></div>
<br><div><div>On 17 Nov 2014, at 21:02, Filipe De Vadder <<a href="mailto:filipe.devadder@gmail.com">filipe.devadder@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html charset=us-ascii"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div id="message5010477" class="message-text adbayes-content" style="cursor: text; overflow-x: auto;">Hello,</div><div id="message5010477" class="message-text adbayes-content" style="cursor: text; overflow-x: auto;">I have had some trouble opening VSI files on FIJI. If I try to open them using Bioformats on hyper stack (but the other options are not working either), here is the message that I get: <br class="">(Fiji Is Just) ImageJ 2.0.0-rc-15/1.49k; Java 1.6.0_65 [64-bit]; Mac OS X 10.10; 22MB of 1067MB (2%) <br class=""> <br class="">java.lang.IllegalArgumentException: Invalid series: 0 <br class=""> at loci.formats.FormatReader.seriesToCoreIndex(FormatReader.java:1198) <br class=""> at loci.formats.FormatReader.setSeries(FormatReader.java:927) <br class=""> at loci.formats.MetadataTools.populatePixels(MetadataTools.java:179) <br class=""> at loci.formats.MetadataTools.populatePixels(MetadataTools.java:97) <br class=""> at loci.formats.in.CellSensReader.initFile(CellSensReader.java:456) <br class=""> at loci.formats.FormatReader.setId(FormatReader.java:1317) <br class=""> at loci.formats.ImageReader.setId(ImageReader.java:753) <br class=""> at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:406) <br class=""> at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:388) <br class=""> at io.scif.AbstractParser.parse(AbstractParser.java:252) <br class=""> at io.scif.AbstractParser.parse(AbstractParser.java:335) <br class=""> at io.scif.AbstractParser.parse(AbstractParser.java:52) <br class=""> at io.scif.AbstractReader.setSource(AbstractReader.java:270) <br class=""> at io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:90) <br class=""> at io.scif.img.ImgOpener.createReader(ImgOpener.java:542) <br class=""> at io.scif.img.ImgOpener.openImgs(ImgOpener.java:144) <br class=""> at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:266) <br class=""> at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:250) <br class=""> at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:78) <br class=""> at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50) <br class=""> at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:134) <br class=""> at net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:327) <br class=""> at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:150) <br class=""> at ij.IJ.runPlugIn(IJ.java) <br class=""> at ij.Executer.runCommand(Executer.java:131) <br class=""> at ij.Executer.run(Executer.java:64) <br class=""> at java.lang.Thread.run(Thread.java:695) <br class=""><br class="">I have tried to open on Windows but still the same message.</div><div id="message5010477" class="message-text adbayes-content" style="cursor: text; overflow-x: auto;">If I try to open it using BIOP plugin, I also get a "macro error" message: <br class="">Relative Path, adding Path to Fiji <br class="">Full path to BIOPLib :/Applications/Fiji.app/plugins/BIOP/BIOPLib.ijm <br class="">Empty Library. Adding BIOPLib Library. <br class="">java.lang.reflect.InvocationTargetException <br class=""> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) <br class=""> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) <br class=""> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) <br class=""> at java.lang.reflect.Method.invoke(Method.java:597) <br class=""> at loci.plugins.macro.MacroFunctions.handleExtension(MacroFunctions.java:83) <br class=""> at ij.macro.ExtensionDescriptor.dispatch(ExtensionDescriptor.java:288) <br class=""> at ij.macro.Functions.doExt(Functions.java:4261) <br class=""> at ij.macro.Functions.getStringFunction(Functions.java:267) <br class=""> at ij.macro.Interpreter.getStringTerm(Interpreter.java:1283) <br class=""> at ij.macro.Interpreter.getString(Interpreter.java:1262) <br class=""> at ij.macro.Interpreter.doStatement(Interpreter.java:277) <br class=""> at ij.macro.Interpreter.doBlock(Interpreter.java:598) <br class=""> at ij.macro.Interpreter.runUserFunction(Interpreter.java:307) <br class=""> at ij.macro.Interpreter.doUserFunctionAssignment(Interpreter.java:877) <br class=""> at ij.macro.Interpreter.doAssignment(Interpreter.java:717) <br class=""> at ij.macro.Interpreter.doStatement(Interpreter.java:241) <br class=""> at ij.macro.Interpreter.doStatements(Interpreter.java:214) <br class=""> at ij.macro.Interpreter.run(Interpreter.java:111) <br class=""> at ij.macro.Interpreter.run(Interpreter.java:81) <br class=""> at ij.macro.MacroRunner.run(MacroRunner.java:139) <br class=""> at java.lang.Thread.run(Thread.java:695) <br class="">Caused by: java.lang.IllegalArgumentException: Invalid series: 0 <br class=""> at loci.formats.FormatReader.seriesToCoreIndex(FormatReader.java:1198) <br class=""> at loci.formats.FormatReader.setSeries(FormatReader.java:927) <br class=""> at loci.formats.MetadataTools.populatePixels(MetadataTools.java:179) <br class=""> at loci.formats.MetadataTools.populatePixels(MetadataTools.java:97) <br class=""> at loci.formats.in.CellSensReader.initFile(CellSensReader.java:456) <br class=""> at loci.formats.FormatReader.setId(FormatReader.java:1317) <br class=""> at loci.formats.ImageReader.setId(ImageReader.java:753) <br class=""> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) <br class=""> at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270) <br class=""> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) <br class=""> at loci.plugins.macro.LociFunctions.setId(LociFunctions.java:402) <br class=""> ... 21 more <br class=""><br class="">I have ticked the updates from both Bioformats, LOCI and BIOP and my software is up to date. I really don't know what is going on. My bioformats version is the latest release.</div><div id="message5010477" class="message-text adbayes-content" style="cursor: text; overflow-x: auto;">If you want, you can access the file I am trying to open (and all other files in the same folder) at: <a href="http://dl.free.fr/gNluLSgVz" class="">http://dl.free.fr/gNluLSgVz</a></div><div id="message5010477" class="message-text adbayes-content" style="cursor: text; overflow-x: auto;">I hope this is enough to know what is going on.<br class="">Your help will be very much appreciated. <br class="">Thanks a lot, <br class="">Filipe</div><div class=""><br class=""></div><div class=" ad" style="clear: both; margin: 2em 0px 1em; visibility: visible !important; height: auto !important; position: static !important; top: auto !important; left: auto !important; width: 675px !important;"><div class="div752938" style="font-family: Verdana, Geneva, Helvetica, Arial, sans-serif; font-size: 13px; width: 336px; float: left; clear: none;"></div><div class="div601350" style="font-family: Verdana, Geneva, Helvetica, Arial, sans-serif; font-size: 13px; width: 336px; float: left; clear: none;"></div></div></div>_______________________________________________<br>ome-users mailing list<br><a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br></blockquote></div><br></div></body></html>