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Re: AnalyzeSkeleton, problem solved

Posted by David Webster on Jul 16, 2009; 5:35am
URL: http://imagej.273.s1.nabble.com/AnalyzeSkeleton-problem-solved-tp3691788p3691791.html

Ignacio,

As it turns out, the problem was caused by closing the "Tagged Skeleton"
image before the Results table was displayed. There is quite a delay between
image and results display, which is also why I didn't think it was being
displayed.

So, al problems solved.

David

On Wed, Jul 15, 2009 at 7:28 PM, Ignacio Arganda
<[hidden email]>wrote:

> Hey David,
>
> You need to skeletonize first the image. As you sent it, it can still be
> morphologically reduced. Otherwise the plugin is not going to work.
>
> And concerning inverting the image, you need to invert the LUT but not the
> values. Otherwise, again, it won't work.
>
> Hope i was useful!
>
> ignacio
>
> On Wed, Jul 15, 2009 at 9:56 PM, David Webster <[hidden email]
> >wrote:
>
> > Ignacio,
> >
> > I am still having 2 funny problems when running on the large example
> image
> > included in a previous email.
> >
> > Problem I ,When I run:
> >
> > selectWindow("tujiskeleton.jpg");
> > run("Analyze Skeleton (2D/3D)");
> > close();
> > I get the exception below when I close the output image of "Analyze
> > Skeleton
> > (2D/3D)"
> >
> > java.lang.NullPointerException
> >  at AnalyzeSkeleton_.getPixel(AnalyzeSkeleton_.java:646)
> >  at AnalyzeSkeleton_.getNeighborhood(AnalyzeSkeleton_.java:611)
> >  at AnalyzeSkeleton_.calculateTriplePoints(AnalyzeSkeleton_.java:385)
> >  at AnalyzeSkeleton_.run(AnalyzeSkeleton_.java:158)
> >  at
> >
> >
> ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:245)
> >  at
> ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:102)
> >  at ij.IJ.runUserPlugIn(IJ.java:177)
> >  at ij.IJ.runPlugIn(IJ.java:142)
> >  at ij.Executer.runCommand(Executer.java:121)
> >  at ij.Executer.run(Executer.java:55)
> >  at java.lang.Thread.run(Thread.java:619)
> >
> > Problem 2 occurs when I invert the input image and run "Analyze Skeleton
> > (2D/3D)" as below. After I close the output, I can't run a second time as
> > the input image is now locked.
> >
> > run("Invert");
> > run("Analyze Skeleton (2D/3D)");
> > close();
> > run("Analyze Skeleton (2D/3D)");
> > //Input is now locked
> > close();
> >
> > Note I don't get either problem with blobs.jpg so I assume it is
> something
> > to do with image size or number of skeletons.
> >
> > David
> >
> >
> >
> >
> > On Wed, Jul 15, 2009 at 12:32 PM, Ignacio Arganda <
> > [hidden email]
> > > wrote:
> >
> > > Dear all,
> > >
> > > I just updated the ImageJ-wiki site with a proper link to the JAR file:
> > >
> > >
> > >
> >
> http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:analyzeskeleton:start#download
> > >
> > > It should work now.
> > >
> > > If anyone wrote me an e-mail in last 4 days, I'm sorry but my account
> got
> > > broken and I didn't get it.
> > >
> > > Wayne and Johannes, thank you very much for making me know this was
> > > happening.
> > >
> > > Cheers!
> > >
> > > ignacio
> > >
> > > --
> > > Ignacio Arganda-Carreras, Ph.D.
> > > Institute of Neuroinformatics
> > > Uni/ETH Zurich
> > > Winterthurerstrasse 190
> > > Bau 55
> > > Zurich 8057
> > > +41 44 63 53 031
> > >
> > > Website: http://arantxa.ii.uam.es/~iarganda/index_EN.html<
> http://arantxa.ii.uam.es/%7Eiarganda/index_EN.html<http://arantxa.ii.uam.es/~iarganda/index_EN.html>
> >
> > >
> >
>
>
>
> --
>  Ignacio Arganda-Carreras, Ph.D.
> Institute of Neuroinformatics
> Uni/ETH Zurich
> Winterthurerstrasse 190
> Bau 55
> Zurich 8057
> +41 44 63 53 031
>
> Website: http://arantxa.ii.uam.es/~iarganda/index_EN.html
>