Re: AnalyzeSkeleton, problem solved

Posted by Ignacio Arganda-Carreras on Jul 16, 2009; 2:28am
URL: http://imagej.273.s1.nabble.com/AnalyzeSkeleton-problem-solved-tp3691788p3691790.html

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
> > [phone]
> >
> > Website: http://arantxa.ii.uam.es/~iarganda/index_EN.html<http://arantxa.ii.uam.es/%7Eiarganda/index_EN.html>
> >
>

--
Ignacio Arganda-Carreras, Ph.D.
Institute of Neuroinformatics
Uni/ETH Zurich
Winterthurerstrasse 190
Bau 55
Zurich 8057
[phone]

Website: http://arantxa.ii.uam.es/~iarganda/index_EN.html