Opening VSI files on Fiji

[Filipe DV]

Hi everyone,
I have had some trouble opening VSI files on FIJI. If I try to open them using Bioformats, here is the message that I get:
(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%)
 
java.lang.IllegalArgumentException: Invalid series: 0
        at loci.formats.FormatReader.seriesToCoreIndex(FormatReader.java:1198)
        at loci.formats.FormatReader.setSeries(FormatReader.java:927)
        at loci.formats.MetadataTools.populatePixels(MetadataTools.java:179)
        at loci.formats.MetadataTools.populatePixels(MetadataTools.java:97)
        at loci.formats.in.CellSensReader.initFile(CellSensReader.java:456)
        at loci.formats.FormatReader.setId(FormatReader.java:1317)
        at loci.formats.ImageReader.setId(ImageReader.java:753)
        at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:406)
        at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:388)
        at io.scif.AbstractParser.parse(AbstractParser.java:252)
        at io.scif.AbstractParser.parse(AbstractParser.java:335)
        at io.scif.AbstractParser.parse(AbstractParser.java:52)
        at io.scif.AbstractReader.setSource(AbstractReader.java:270)
        at io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:90)
        at io.scif.img.ImgOpener.createReader(ImgOpener.java:542)
        at io.scif.img.ImgOpener.openImgs(ImgOpener.java:144)
        at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:266)
        at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:250)
        at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:78)
        at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50)
        at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:134)
        at net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:327)
        at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:150)
        at ij.IJ.runPlugIn(IJ.java)
        at ij.Executer.runCommand(Executer.java:131)
        at ij.Executer.run(Executer.java:64)
        at java.lang.Thread.run(Thread.java:695)

If I try to open it using BIOP plugin, I also get a "macro error" message:
Relative Path, adding Path to Fiji
Full path to BIOPLib :/Applications/Fiji.app/plugins/BIOP/BIOPLib.ijm
Empty Library. Adding BIOPLib Library.
java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        at loci.plugins.macro.MacroFunctions.handleExtension(MacroFunctions.java:83)
        at ij.macro.ExtensionDescriptor.dispatch(ExtensionDescriptor.java:288)
        at ij.macro.Functions.doExt(Functions.java:4261)
        at ij.macro.Functions.getStringFunction(Functions.java:267)
        at ij.macro.Interpreter.getStringTerm(Interpreter.java:1283)
        at ij.macro.Interpreter.getString(Interpreter.java:1262)
        at ij.macro.Interpreter.doStatement(Interpreter.java:277)
        at ij.macro.Interpreter.doBlock(Interpreter.java:598)
        at ij.macro.Interpreter.runUserFunction(Interpreter.java:307)
        at ij.macro.Interpreter.doUserFunctionAssignment(Interpreter.java:877)
        at ij.macro.Interpreter.doAssignment(Interpreter.java:717)
        at ij.macro.Interpreter.doStatement(Interpreter.java:241)
        at ij.macro.Interpreter.doStatements(Interpreter.java:214)
        at ij.macro.Interpreter.run(Interpreter.java:111)
        at ij.macro.Interpreter.run(Interpreter.java:81)
        at ij.macro.MacroRunner.run(MacroRunner.java:139)
        at java.lang.Thread.run(Thread.java:695)
Caused by: java.lang.IllegalArgumentException: Invalid series: 0
        at loci.formats.FormatReader.seriesToCoreIndex(FormatReader.java:1198)
        at loci.formats.FormatReader.setSeries(FormatReader.java:927)
        at loci.formats.MetadataTools.populatePixels(MetadataTools.java:179)
        at loci.formats.MetadataTools.populatePixels(MetadataTools.java:97)
        at loci.formats.in.CellSensReader.initFile(CellSensReader.java:456)
        at loci.formats.FormatReader.setId(FormatReader.java:1317)
        at loci.formats.ImageReader.setId(ImageReader.java:753)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569)
        at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569)
        at loci.plugins.macro.LociFunctions.setId(LociFunctions.java:402)
        ... 21 more

I have ticked the updates from both Bioformats and BIOP and my software is up to date. I really don't know what is going on. I tried to go through every solution I have found on this forum, but none has worked.
Your help will be very much appreciated.
Thanks a lot,
Filipe

[Olivier Burri]

Dear Filipe,

As far as I can see, the error seems to come because he cannot see the number of series.

VSI files usually have a folder associated with them with the same name as the .VSI.

Eg you would have "Image01.vsi" and a folder in the same place called "_Image01_"

If this folder is missing there could be some issues.

We just tried opening some VSI files with and without the associated folder but were unable to replicate the "Invalid Series: 0" error. The best would be to send the dataset to Bioformats and see if they can help. Otherwise (If it's not too massive) you would post a link here and we can have a look.

Also please make sure bioformats is up to date. Take both update sites :
Bioformats and LOCI

All the best and good luck

Olivier Burri
Image Processing Specialist
EPFL BioImaging & Optics Platform
EPFL SV PTECH BIOP

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[Filipe DV]

Dear Olivier,
Thanks a lot for your quick answer. Here is the procedure I use with Metasystems:
When the scanning is done, I stitch each file to a local disc that we have. This gives me a folder called "Image01~A" that contains the following files: "Image01~A.vsi", "Image01~A.vsa", "Image01~A.vsr" but no other folder. I tried to take all the other files and put them in an _Image01~A_ folder in the same location as the VSI file, but I still get the same error.
Do you think the problem may come from that?

[Filipe DV]

By the way, the data set can be accessed here:
http://dl.free.fr/gNluLSgVz
Hope this is enough, thanks for your help!

[ctrueden]

Hi Filipe,

> java.lang.IllegalArgumentException: Invalid series: 0
>         at loci.formats.FormatReader.seriesToCoreIndex(
FormatReader.java:1198)

Looks like an issue with Bio-Formats. For instructions on reporting bugs to
the Bio-Formats team, see:


http://openmicroscopy.org/site/support/bio-formats/about/bug-reporting.html

Regards,
Curtis

On Mon, Nov 17, 2014 at 9:57 AM, Filipe DV <[hidden email]>
wrote:

> By the way, the data set can be accessed here:
> http://dl.free.fr/gNluLSgVz
> Hope this is enough, thanks for your help!
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Opening-VSI-files-on-Fiji-tp5010477p5010485.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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