Error using Irregular Watershed

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Error using Irregular Watershed

Pedro J CamelloDr Pedro J Camello
Hi all,

I´m getting the following error in the console while trying to apply the Irregular Watershed plugin to a binary image. I appreciate any help.

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Exception in thread "Irregular Watershed Preview" java.lang.NoClassDefFoundError: ij/blob/ManyBlobs
        at de.biomedical_imaging.ij.irregular_watershed.Watershed_Irregular_Features.run(Watershed_Irregular_Features.java:139)
        at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:266)
        at ij.plugin.filter.PlugInFilterRunner.runPreview(PlugInFilterRunner.java:513)
        at ij.plugin.filter.PlugInFilterRunner.run(PlugInFilterRunner.java:448)
        at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.ClassNotFoundException: ij.blob.ManyBlobs
        at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
        ... 5 more
Exception in thread "Irregular Watershed Preview" java.lang.NoClassDefFoundError: ij/blob/ManyBlobs
        at de.biomedical_imaging.ij.irregular_watershed.Watershed_Irregular_Features.run(Watershed_Irregular_Features.java:139)
        at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:266)
        at ij.plugin.filter.PlugInFilterRunner.runPreview(PlugInFilterRunner.java:513)
        at ij.plugin.filter.PlugInFilterRunner.run(PlugInFilterRunner.java:448)
        at java.lang.Thread.run(Thread.java:748)
Exception in thread "Watershed Irregular Features Preview" java.lang.NoClassDefFoundError: ij/blob/ManyBlobs
        at de.biovoxxel.toolbox.Watershed_Irregular_Features.run(Watershed_Irregular_Features.java:224)
        at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:266)
        at ij.plugin.filter.PlugInFilterRunner.runPreview(PlugInFilterRunner.java:513)
        at ij.plugin.filter.PlugInFilterRunner.run(PlugInFilterRunner.java:448)
        at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.ClassNotFoundException: ij.blob.ManyBlobs
        at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
        ... 5 more
Exception in thread "Irregular Watershed Preview" java.lang.NoClassDefFoundError: ij/blob/ManyBlobs
        at de.biomedical_imaging.ij.irregular_watershed.Watershed_Irregular_Features.run(Watershed_Irregular_Features.java:139)
        at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:266)
        at ij.plugin.filter.PlugInFilterRunner.runPreview(PlugInFilterRunner.java:513)
        at ij.plugin.filter.PlugInFilterRunner.run(PlugInFilterRunner.java:448)
        at java.lang.Thread.run(Thread.java:748)

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Re: Error using Irregular Watershed

Curtis Rueden-2
Hi Pedro,

When asking for help with third party plugins, it is very helpful to
explain:

1. What is this plugin / Where is the website.
2. Where you got the plugin / How you installed it (e.g. downloaded and
copied into ImageJ 1.x manually, or enabled an ImageJ update site in
ImageJ2/Fiji).
3. Steps for reproducing the failure you are seeing.

I assume you are talking about this plugin by Thorsten Wagner and Jan Funke:
  https://github.com/thorstenwagner/ij-irregular-watershed

Which I infer was forked from a function of Jan Brocher's BioVoxxel toolbox:

https://github.com/biovoxxel/BioVoxxel-Toolbox/blob/ebb8f9a66e12cab964c2b55e5e0e341174b6cafa/Biovoxxel_Plugins/src/main/java/de/biovoxxel/toolbox/Watershed_Irregular_Features.java

The ij-irregular-watershed plugin has a dependency on a library called
ij_blob:

https://github.com/thorstenwagner/ij-irregular-watershed/blob/123760d3fd759d52cd9bfabafc6aef3e963dac15/pom.xml

Your error message strongly suggests that the needed ij_blob dependency is
missing from your ImageJ installation.

- Did you build it yourself and install into ImageJ 1.x?
- Or maybe you turned on the ParticleSizer update site, which ships the
ij_irregular_watershed library, but seems to be lacking ij_blob?

You can find the ij_blob source code here:
https://github.com/thorstenwagner/ij-blob
And the IJ Blob wiki page at: https://imagej.net/IJ_Blob

I have CCed the author Thorsten Wagner.

Thorsten: should ParticleSizer ship ij_blob? What is the recommended
installation route for ij-irregular-watershed? I could not find any
documentation about it, nor any installation instructions on the IJ Blob
wiki page.

Thanks,
Curtis

--
Curtis Rueden
Software architect, LOCI/Eliceiri lab - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Have you tried the Image.sc Forum? https://forum.image.sc/



On Sun, Mar 8, 2020 at 7:05 AM Pedro J Camello <[hidden email]> wrote:

> Hi all,
>
> I´m getting the following error in the console while trying to apply the
> Irregular Watershed plugin to a binary image. I appreciate any help.
>
> cloooose
> cloooose
> cloooose
> cloooose
> cloooose
> cloooose
> Exception in thread "Irregular Watershed Preview"
> java.lang.NoClassDefFoundError: ij/blob/ManyBlobs
>         at
> de.biomedical_imaging.ij.irregular_watershed.Watershed_Irregular_Features.run(Watershed_Irregular_Features.java:139)
>         at
> ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:266)
>         at
> ij.plugin.filter.PlugInFilterRunner.runPreview(PlugInFilterRunner.java:513)
>         at
> ij.plugin.filter.PlugInFilterRunner.run(PlugInFilterRunner.java:448)
>         at java.lang.Thread.run(Thread.java:748)
> Caused by: java.lang.ClassNotFoundException: ij.blob.ManyBlobs
>         at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>         at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>         ... 5 more
> Exception in thread "Irregular Watershed Preview"
> java.lang.NoClassDefFoundError: ij/blob/ManyBlobs
>         at
> de.biomedical_imaging.ij.irregular_watershed.Watershed_Irregular_Features.run(Watershed_Irregular_Features.java:139)
>         at
> ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:266)
>         at
> ij.plugin.filter.PlugInFilterRunner.runPreview(PlugInFilterRunner.java:513)
>         at
> ij.plugin.filter.PlugInFilterRunner.run(PlugInFilterRunner.java:448)
>         at java.lang.Thread.run(Thread.java:748)
> Exception in thread "Watershed Irregular Features Preview"
> java.lang.NoClassDefFoundError: ij/blob/ManyBlobs
>         at
> de.biovoxxel.toolbox.Watershed_Irregular_Features.run(Watershed_Irregular_Features.java:224)
>         at
> ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:266)
>         at
> ij.plugin.filter.PlugInFilterRunner.runPreview(PlugInFilterRunner.java:513)
>         at
> ij.plugin.filter.PlugInFilterRunner.run(PlugInFilterRunner.java:448)
>         at java.lang.Thread.run(Thread.java:748)
> Caused by: java.lang.ClassNotFoundException: ij.blob.ManyBlobs
>         at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>         at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>         ... 5 more
> Exception in thread "Irregular Watershed Preview"
> java.lang.NoClassDefFoundError: ij/blob/ManyBlobs
>         at
> de.biomedical_imaging.ij.irregular_watershed.Watershed_Irregular_Features.run(Watershed_Irregular_Features.java:139)
>         at
> ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:266)
>         at
> ij.plugin.filter.PlugInFilterRunner.runPreview(PlugInFilterRunner.java:513)
>         at
> ij.plugin.filter.PlugInFilterRunner.run(PlugInFilterRunner.java:448)
>         at java.lang.Thread.run(Thread.java:748)
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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