Opening Olympus VSI Files from virtual Slide Scanner

[cxallan]

That implies you have a set of JAR mismatches Oli and is not a bug with the reader. Do you still have loci_tools.jar in your Fiji plugins folder?

[Oli]

Hi

That implies you have a set of JAR mismatches Oli and is not a bug with the reader. Do you still have loci_tools.jar in your Fiji plugins folder?

No there isn't any loci_tools.jar file in the plugins folder. Only loci_plugins-4.4-SNAPSHOT.jar

Best

Oli

[mlinkert]

Hi Oli,

Updating Fiji to use the latest version of Bio-Formats is unfortunately kind of a pain at the moment. If you haven't already, I would suggest first running the Fiji updater (to get back to a known state) by selecting "Help > Update Fiji". That should give you a fairly recent version of Bio-Formats, but not quite the very latest trunk build.

From there, to get the latest trunk build you will need to download all of the files in the "trunk build" column in the "Bio-Formats component builds" section of http://loci.wisc.edu/bio-formats/downloads. Then you will need to copy each of those files to the similarly-named file in Fiji's 'jars' or 'plugins' directory - be sure to overwrite the old file, so that you do not end up with e.g. a loci_plugins.jar and a loci_plugins-4.4-SNAPSHOT.jar.

You should only need to do that once - with recent trunk builds, "Plugins > LOCI > Update LOCI Plugins" is fixed to work with Fiji again.

If that all sounds like too much pain, then you can wait a few days for us to release the 4.4.4 version of Bio-Formats, which I have been promised will be included in Fiji's updater more or less right away. Then all you have to do is run the Fiji updater, and then use "Plugins > LOCI > Update LOCI Plugins" as usual in the future.

-Melissa

[Oli]

Dear Melissa,

Thank you for the suggestions. Unfortunately I still get the same error when opening .VSI files.

I'll wait for the latest trunk build but for now we're stuck unfortunately.

Thanks again!

Oli

[Oli]

Dear Melissa,

For now the solution that has worked is as follows.
1. Get a new Fiji and update to latest version of everything using the built-in updater.
a. This still generates the error I had sent on the first post
2. Use LOCI->Update LOCI Plugins->Stable Build (4.3)

Rename loci_plugins-4.4-SNAPSHOT.jar to some other extension
Use the old loci-tools.jar

So far using the latest build is troublesome and until I can know where this is coming from I cannot update the LOCI plugins for our machines.
Let me know if you managed to replicate this error. It happens with every VSI file for us.

Best

Oli

[mlinkert]

Hi Oli,

For now the solution that has worked is as follows.
1. Get a new Fiji and update to latest version of everything using the built-in updater.
a. This still generates the error I had sent on the first post
2. Use LOCI->Update LOCI Plugins->Stable Build (4.3)

Rename loci_plugins-4.4-SNAPSHOT.jar to some other extension
Use the old loci-tools.jar

So far using the latest build is troublesome and until I can know where this is coming from I cannot update the LOCI plugins for our machines.
Let me know if you managed to replicate this error. It happens with every VSI file for us.

Sorry, just so that I understand: Fiji is now in a state where it is giving you the error message here:

http://trac.openmicroscopy.org.uk/ome/ticket/9618

...correct? Or are you still seeing this error: viewtopic.php?f=13&t=1244#p5765?

If it's the error message from ticket #9618, I can definitely duplicate that error with the data that you uploaded, we just have not yet had a chance to fix it. You will receive an automated email when we close that ticket.

-Melissa

[Oli]

Hi Melissa,

The previous error was not causing problems until the 4.5 Release of Loci Bio Formats.

Now we have a new problem when opening .vsi files

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 ij.Command.runPlugIn(Command.java:146)
at ij.Command.runCommand(Command.java:95)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:662)
Caused by: java.lang.NoSuchMethodError: loci.common.Region.intersects(Lloci/common/Region;)Z
at loci.formats.in.CellSensReader.openBytes(CellSensReader.java:250)
at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:197)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:226)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:318)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:255)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:318)
at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:273)
at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:265)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:306)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:306)
at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:190)
at loci.plugins.in.ImagePlusReader.readProcessors(ImagePlusReader.java:416)
at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:380)
at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)
at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:114)
at loci.plugins.in.Importer.readPixels(Importer.java:150)
at loci.plugins.in.Importer.run(Importer.java:89)
at loci.plugins.LociImporter.run(LociImporter.java:81)
at ij.IJ.runUserPlugIn(IJ.java:184)
at ij.IJ.runPlugIn(IJ.java:151)
... 8 more

This from just trying to open a small series from a VSI file. The thumnails present in the VSI open fine, it's just the large ones.

Best

Oli

[jmoore]

Hi Olli,

filling in for Melissa during ASCB, would you mind walking me through what version of everything you have? I.e. where is fiji installed and what versions of Bio-Formats you have? Also, are any files currently listed in red by the Fiji updater? What you be up for listing all the jars in your fiji install?

Thanks,
~Josh

[crueden]

Hi Oli,

I agree with jmoore: the error message ("NoSuchMethodError") indicates something skewed in your Fiji installation. Please run Help > Update Fiji and double check that your Fiji is totally up to date, with no locally modified files, and no local-only files.

For local-only files such as loci-common.jar, you can use the "Uninstall" button to remove them.
For locally modified files, you can right-click and choose "Update it" to obtain the latest version from the Fiji update site.

Thanks,
Curtis

[Oli]

Hi Curtis & Josh & Melissa,

Happy New Year to the team!

Sorry for the late reply, holidays and all that.

I've reinstalled the machine entirely for reasons beyond my control and that error seems to have gone.

We've found a couple more troublesome datasets recently. On a series of acquisitions, some images open, others yield the following error.

I've added the files to the following location in a zip file if you'd like to test it.
https://documents.epfl.ch/users/o/ob/oburri/www/Troublesome%20Datasets/vsiTroubleopening.zip

As always, thank you very much for your time!

Oli

Code: Select all

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:4020)
   at ij.macro.Functions.getStringFunction(Functions.java:260)
   at ij.macro.Interpreter.getStringTerm(Interpreter.java:1209)
   at ij.macro.Interpreter.getString(Interpreter.java:1188)
   at ij.macro.Interpreter.doStatement(Interpreter.java:264)
   at ij.macro.Interpreter.doStatements(Interpreter.java:207)
   at ij.macro.Interpreter.run(Interpreter.java:104)
   at ij.macro.Interpreter.run(Interpreter.java:74)
   at ij.macro.MacroRunner.run(MacroRunner.java:130)
   at java.lang.Thread.run(Thread.java:662)
Caused by: loci.common.enumeration.EnumException: Unable to find TiffCompresssion with code: 34712
   at loci.formats.tiff.TiffCompression.get(TiffCompression.java:220)
   at loci.formats.tiff.IFD.getCompression(IFD.java:664)
   at loci.formats.tiff.IFD.getSamplesPerPixel(IFD.java:638)
   at loci.formats.in.CellSensReader.initFile(CellSensReader.java:435)
   at loci.formats.FormatReader.setId(FormatReader.java:1238)
   at loci.formats.ImageReader.setId(ImageReader.java:742)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:552)
   at loci.formats.DimensionSwapper.setId(DimensionSwapper.java:285)
   at loci.formats.FileStitcher.initFile(FileStitcher.java:839)
   at loci.formats.FileStitcher.setId(FileStitcher.java:803)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:552)
   at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:552)
   at loci.plugins.macro.LociFunctions.setId(LociFunctions.java:398)
   ... 16 more