bioformats

[Kenton Arkill]

Hi
I normally drag and drop lieca (.lif) files onto Fiji and it opens them. It
seems since my last update that bioformats is not working anyone else had
this? Is there a way of unupdating? I did update ImageJ and Fiji manually
(ie from the help menu not on start up.

Error message:
(Fiji Is Just) ImageJ 2.0.0-rc-28/1.49q; Java 1.6.0_24 [64-bit]; Windows 7
6.1; 38MB of 2927MB (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)

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Mark Hiner]

Hi Kenton,

> bioformats is not working anyone else had this?

I wasn't able to reproduce this error - I only tried using the importer
with and without the Bio-Formats update site enabled though.

You might want to use the Report a Bug[1] feature since it will include
additional information about your Fiji installation. My first assumption is
that there may be a conflict with an update site you have enabled - but
that's just speculation.

> Is there a way of unupdating?

Not yet, sadly.

Best,
Mark

[1] http://imagej.net/Report_a_Bug

On Thu, Apr 9, 2015 at 8:41 AM, Kenton Arkill <[hidden email]>
wrote:

> Hi
> I normally drag and drop lieca (.lif) files onto Fiji and it opens them. It
> seems since my last update that bioformats is not working anyone else had
> this? Is there a way of unupdating? I did update ImageJ and Fiji manually
> (ie from the help menu not on start up.
>
> Error message:
> (Fiji Is Just) ImageJ 2.0.0-rc-28/1.49q; Java 1.6.0_24 [64-bit]; Windows 7
> 6.1; 38MB of 2927MB (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)
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Kenton Arkill]

Thanks Mark

I tried a few things and in the end took bioformats-5 out of the updates
and  restarted and then added them in again (via Bioformats 4 first if it
made a difference). It seemed to work. Incidentally just removing the main
bioformats.jar and replacing it did not
Something must have got muddled...Shrug
Kenton

On 9 April 2015 at 16:01, Mark Hiner <[hidden email]> wrote:

> Hi Kenton,
>
> > bioformats is not working anyone else had this?
>
> I wasn't able to reproduce this error - I only tried using the importer
> with and without the Bio-Formats update site enabled though.
>
> You might want to use the Report a Bug[1] feature since it will include
> additional information about your Fiji installation. My first assumption is
> that there may be a conflict with an update site you have enabled - but
> that's just speculation.
>
> > Is there a way of unupdating?
>
> Not yet, sadly.
>
> Best,
> Mark
>
> [1] http://imagej.net/Report_a_Bug
>
> On Thu, Apr 9, 2015 at 8:41 AM, Kenton Arkill <[hidden email]>
> wrote:
>
> > Hi
> > I normally drag and drop lieca (.lif) files onto Fiji and it opens them.
> It
> > seems since my last update that bioformats is not working anyone else had
> > this? Is there a way of unupdating? I did update ImageJ and Fiji manually
> > (ie from the help menu not on start up.
> >
> > Error message:
> > (Fiji Is Just) ImageJ 2.0.0-rc-28/1.49q; Java 1.6.0_24 [64-bit]; Windows
> 7
> > 6.1; 38MB of 2927MB (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)
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html