Problems with Grid/Collection Stitching

[Michael Johnson]

I'm trying to stitch together 16 65536 voxel 8-bit images using the Grid/Collection stitching plugin and encounter the following error:

java.lang.NoClassDefFoundError: Could not initialize class loci.common.IniParser
        at loci.plugins.prefs.OptionsList.<init>(OptionsList.java:66)
        at loci.plugins.in.ImporterOptions.<init>(ImporterOptions.java:158)
        at mpicbg.stitching.ImageCollectionElement.open(ImageCollectionElement.java:90)
        at Stitching_Grid.getGridLayout(Stitching_Grid.java:990)
        at Stitching_Grid.run(Stitching_Grid.java:307)
        at ij.IJ.runUserPlugIn(IJ.java:196)
        at ij.IJ.runPlugIn(IJ.java:160)
        at ij.Executer.runCommand(Executer.java:128)
        at ij.Executer.run(Executer.java:64)
        at java.lang.Thread.run(Thread.java:662)

I have tried stitching the images as Imaris files and tiff files, but get the same error. Any suggestions?

Thanks,
Michael

[dscho]

Hi Michael,

On Tue, 7 Oct 2014, Michael Johnson wrote:

> I'm trying to stitch together 16 65536 voxel 8-bit images using the
> Grid/Collection stitching plugin and encounter the following error:
>
> java.lang.NoClassDefFoundError: Could not initialize class
> loci.common.IniParser

That has nothing to do with the data you try to stitch but with a class
that cannot be found. In my setup, the loci.common.IniParser can be found
in Fiji.app/jars/bio-formats/formats-common-5.0.5.jar. You could find out
where it is in your setup (if it is there at all) by calling
Plugins>Examples>Find Jar For Class.

Ciao,
Johannes

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[Michael Johnson]

Johannes,

Thank you for responding. I do not seem to have the loci.common.IniParser. I tried using the Find Jar for Class plug in, but don't have that either. I tried going through the same pathway as yours and can't seem to find any jar file by the name formats-common-5.0.5.jar. I also tried using a JAR search engine, but that didn't seem to help me either. Do you know of a way that I can get this class? Are these default plugins, should I uninstall and then reinstall ImageJ?

Thanks,
Michael

[ctrueden]

Hi Michael,

> I do not seem to have the loci.common.IniParser. I tried using the
> Find Jar for Class plug in, but don't have that either.

Are you using Fiji? Or the standalone download of Stitching for plain
ImageJ 1.x?

The Stitching plugin development team all uses Fiji, so it wouldn't
surprise me if none of us have tested it with ImageJ 1.x recently -- or if
Stephan hasn't updated the standalone bundle recently. I would encourage
you to use Fiji for maximum convenience: http://fiji.sc/Downloads

Regards,
Curtis

On Thu, Oct 9, 2014 at 2:21 PM, Michael Johnson <[hidden email]>
wrote:

> Johannes,
>
> Thank you for responding. I do not seem to have the loci.common.IniParser.
> I
> tried using the Find Jar for Class plug in, but don't have that either. I
> tried going through the same pathway as yours and can't seem to find any
> jar
> file by the name formats-common-5.0.5.jar. I also tried using a JAR search
> engine, but that didn't seem to help me either. Do you know of a way that I
> can get this class? Are these default plugins, should I uninstall and then
> reinstall ImageJ?
>
> Thanks,
> Michael
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Problems-with-Grid-Collection-Stitching-tp5009952p5009983.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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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Michael Johnson]

Hi Curtis,

 

Curtis Rueden wrote

Hi Michael,

> I do not seem to have the loci.common.IniParser. I tried using the
> Find Jar for Class plug in, but don't have that either.

Are you using Fiji? Or the standalone download of Stitching for plain
ImageJ 1.x?

I am using Fiji but it was an outdated version and for some reason had several duplicate commands. I've cleaned it up and updated the version and the Stitching plugin is now working great! Thanks for your help.

Michael