Re: Bio-Formats importer broken after latest Fiji update?

Posted by Aryeh Weiss on Mar 24, 2015; 11:22am
URL: http://imagej.273.s1.nabble.com/Bio-Formats-importer-broken-after-latest-Fiji-update-tp5012127p5012129.html

On 3/24/15 12:25 PM, Martin Höhne wrote:

> Dear All,
>
> Fiji just did it´s auto-update after startup, and it seems that the
> bioformats-importer is broken.
>
> Plugin > Bio-Formats > Bio-Formats Importer
>
> gives the error message pasted below. Is this a general problem or only my
> configuration (Latest Fiji on Win7)
>
> Thanks
> Martin
>
> ---------
> (Fiji Is Just) ImageJ 2.0.0-rc-26/1.49p; Java 1.6.0_24 [64-bit]; Windows 7
> 6.1; 23MB of 2975MB (<1%)
>  
> java.lang.NoClassDefFoundError: Could not initialize class
> loci.common.Location
> at loci.plugins.in.ImporterOptions.parseArg(ImporterOptions.java:171)
> at loci.plugins.in.Importer.parseOptions(Importer.java:112)
> at loci.plugins.in.Importer.run(Importer.java:69)
> at loci.plugins.LociImporter.run(LociImporter.java:78)
> at ij.IJ.runUserPlugIn(IJ.java:199)
> at ij.IJ.runPlugIn(IJ.java:163)
> at ij.Executer.runCommand(Executer.java:131)
> at ij.Executer.run(Executer.java:64)
> at java.lang.Thread.run(Thread.java:662)
>
>
>

I confirm this on OSX Yosemite. You can work around by deselecting the
Bioformats update site, so that you get Bioformats from the Fiji update
site. They are still at 5.0.7, and it works. However, if you read
complicated ND2 files, you will need the 5.0.2 version of the gpl jar file.

--aryeh

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

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