AnalyzeSkeleton, problem solved

[Ignacio Arganda-Carreras]

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

[David Webster]

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
>

[Ignacio Arganda-Carreras]

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

[David Webster]

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