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Analyze Skeleton-plugin suddenly stopped working!

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maringa

Analyze Skeleton-plugin suddenly stopped working!

Hi again,

My ImageJ programme is done, but now a really annoying error has occured! Whenever I use
the Analyze-skeleton plugin it shows an error message (looks like this: http://img200.imageshack.us/img200/8877/errorlma.jpg)

I've tried the following:
- update Fiji
- uninstall and reinstall fiji
- install ImageJ again

It has nothing to do with my macro, no matter how I use Analyze Skeleton I get the same error message. How can it suddenly be like this?
My macro really need to use analyse-skeleton so this is very annoying!

Thanks for your help :)

maringa

Re: Analyze Skeleton-plugin suddenly stopped working!

edit: I also tried to install ImageJ on another computer, install analyze_skeleton and then try it out and the SAME error occured...

Michael Doube

Re: Analyze Skeleton-plugin suddenly stopped working!

In reply to this post by maringa

To the Fiji folks and Ignacio:

What is the state of development of the AnalyzeSkeleton_ included in
Fiji? I did a bunch of work on the plugin recently but am not sure if
my changes were included in the official version.

Mike

maringa wrote:

> Hi again,
>
> My ImageJ programme is done, but now a really annoying error has occured!
> Whenever I use
> the Analyze-skeleton plugin it shows an error message (looks like this:
> http://img200.imageshack.us/img200/8877/errorlma.jpg)
>
> I've tried the following:
> - update Fiji
> - uninstall and reinstall fiji
> - install ImageJ again
>
> It has nothing to do with my macro, no matter how I use Analyze Skeleton I
> get the same error message. How can it suddenly be like this?
> My macro really need to use analyse-skeleton so this is very annoying!
>
> Thanks for your help :)
>
>

David Webster

Re: Analyze Skeleton-plugin suddenly stopped working!

In reply to this post by maringa

All,

I can run Analyze-skeleton with no problems as follows:

run("Blobs (25K)");
run("Make Binary");
run("Skeletonize (2D/3D)");
run("Analyze Skeleton (2D/3D)");

I am using ImageJ 1.43b and analyzeskeleton_.jar downloaded on 2/22/09. What
is your setup?

David Webster

On Sat, Jul 11, 2009 at 10:42 PM, maringa <[hidden email]>wrote:

karo03

Re: Analyze Skeleton-plugin suddenly stopped working!

Hi, Skeleton (and Java) experts,
I have another observation with this AnalyzeSkeleton_.jar:
Putting it in my plugin folder there is no Skeleton->Analyze
Skeleton(2d/3d) entry.
Putting it in a sub-directory of the plugin folder, say 3D, there is
also no entry.
However run("Analyze Skeleton (2D/3D)"); does work!

With Skeletonize_.jar everything is as described in the corresponding
wiki.

I am on a MacBook using ImageJ64.

Any explanation?

Regards
Karsten

Am 13.07.2009 um 19:15 schrieb David Webster:

> All,
>
> I can run Analyze-skeleton with no problems as follows:
>
> run("Blobs (25K)");
> run("Make Binary");
> run("Skeletonize (2D/3D)");
> run("Analyze Skeleton (2D/3D)");
>
> I am using ImageJ 1.43b and analyzeskeleton_.jar downloaded on
> 2/22/09. What
> is your setup?
>
> David Webster
>
> On Sat, Jul 11, 2009 at 10:42 PM, maringa <[hidden email]
> >wrote:
>
>> Hi again,
>>
>> My ImageJ programme is done, but now a really annoying error has
>> occured!
>> Whenever I use
>> the Analyze-skeleton plugin it shows an error message (looks like
>> this:
>> http://img200.imageshack.us/img200/8877/errorlma.jpg)
>>
>> I've tried the following:
>> - update Fiji
>> - uninstall and reinstall fiji
>> - install ImageJ again
>>
>> It has nothing to do with my macro, no matter how I use Analyze
>> Skeleton I
>> get the same error message. How can it suddenly be like this?
>> My macro really need to use analyse-skeleton so this is very
>> annoying!
>>
>> Thanks for your help :)
>>
>>
>> --
>> View this message in context:
>> http://n2.nabble.com/Analyze-Skeleton-plugin-suddenly-stopped-working%21-tp3244907p3244907.html
>> Sent from the ImageJ mailing list archive at Nabble.com.
>>

Karsten
[hidden email]

maringa

RE: Analyze Skeleton-plugin suddenly stopped working!

In reply to this post by David Webster

Hi David,

I e-mailed the author of the plugin, and he updated it but it's still not working.
I updated my fiji last week and I also updated ImageJ to 1.42q
running analyzeskeleton_.jar downloaded 07/13/09

Here is my input image: 8bit skeletonized neurite image: http://img27.imageshack.us/img27/9027/tujiskeleton.jpg

Martina

Från: David Webster (via Nabble) [ml-user+[hidden email]]
Skickat: den 13 juli 2009 23:16
Till: Martina A K Johansson
Ämne: Re: Analyze Skeleton-plugin suddenly stopped working!

View message @ http://n2.nabble.com/Analyze-Skeleton-plugin-suddenly-stopped-working%21-tp3244907p3251808.html
To unsubscribe from Analyze Skeleton-plugin suddenly stopped working!, click here.

Wayne Rasband

Re: Analyze Skeleton-plugin suddenly stopped working!

On Jul 15, 2009, at 5:27 AM, maringa wrote:

> Hi David,
>
> I e-mailed the author of the plugin, and he updated it but it's still
> not working.
> I updated my fiji last week and I also updated ImageJ to 1.42q
> running analyzeskeleton_.jar downloaded 07/13/09
>
> Here is my input image: 8bit skeletonized neurite image:
> http://img27.imageshack.us/img27/9027/tujiskeleton.jpg

The analyzeskeleton_.jar file is corrupted. It causes ImageJ to throw
this exception to the console on startup:

[LaunchRunner Error] ij.ImageJ.main(String[]) threw an exception:
java.lang.InternalError: jzentry == 0,
jzfile = 1480704,
total = 5,
name = /Users/wayne/ImageJ/plugins/Analyze/analyzeskeleton_.jar,
i = 3,
message = invalid LOC header (bad signature)
at java.util.zip.ZipFile$2.nextElement(ZipFile.java:322)
at ij.Menus.getConfigurationFile(Menus.java:744)
at ij.Menus.installJarPlugins(Menus.java:550)
at ij.Menus.installPlugins(Menus.java:475)
at ij.Menus.addMenuBar(Menus.java:226)
at ij.ImageJ.<init>(ImageJ.java:123)
at ij.ImageJ.main(ImageJ.java:553)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.jav
a:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)
at java.lang.reflect.Method.invoke(Method.java:324)
at apple.launcher.LaunchRunner.run(LaunchRunner.java:88)
at apple.launcher.LaunchRunner.callMain(LaunchRunner.java:50)Jul 15
12:55:28 Wayne-Rasbands-Computer kernel: arp:

You can work around this problem by rebuilding the jar file or by
extracting AnalyzeSkeleton_.java from the jar file and compiling and
running it using Plugins>Compile and Run.

-wayne

dscho

Re: Analyze Skeleton-plugin suddenly stopped working!

Hi,

On Wed, 15 Jul 2009, Wayne Rasband wrote:

> On Jul 15, 2009, at 5:27 AM, maringa wrote:
>
> >I e-mailed the author of the plugin, and he updated it but it's still
> >not working. I updated my fiji last week and I also updated ImageJ to
> >1.42q running analyzeskeleton_.jar downloaded 07/13/09
> >
> >Here is my input image: 8bit skeletonized neurite image:
> >http://img27.imageshack.us/img27/9027/tujiskeleton.jpg
>
> The analyzeskeleton_.jar file is corrupted.

Now I finally get it. Y'all are talking about the analyzeskeleton_.jar
from the ImageJ Docu Wiki (which is also referenced from the Fiji Wiki).
After downloading that, I can verify that yes, it is not a valid .jar
file.

However, I was always talking about the AnalyzeSkeleton_.jar you get via
Help>Update Fiji (you have to run Fiji for this, of course). This is not
corrupted.

Ignacio, care to upload a correct one to the ImageJ Docu Wiki?

Ciao,
Dscho

David Webster

Re: Analyze Skeleton-plugin suddenly stopped working!

In reply to this post by Wayne Rasband

All,

In fact, winzip wont even read things out of the jar file.

David

On Wed, Jul 15, 2009 at 10:11 AM, Wayne Rasband <[hidden email]> wrote:

> On Jul 15, 2009, at 5:27 AM, maringa wrote:
>
> Hi David,
>>
>> I e-mailed the author of the plugin, and he updated it but it's still not
>> working.
>> I updated my fiji last week and I also updated ImageJ to 1.42q
>> running analyzeskeleton_.jar downloaded 07/13/09
>>
>> Here is my input image: 8bit skeletonized neurite image:
>> http://img27.imageshack.us/img27/9027/tujiskeleton.jpg
>>
>
> The analyzeskeleton_.jar file is corrupted. It causes ImageJ to throw this
> exception to the console on startup:
>
> [LaunchRunner Error] ij.ImageJ.main(String[]) threw an exception:
> java.lang.InternalError: jzentry == 0,
> jzfile = 1480704,
> total = 5,
> name = /Users/wayne/ImageJ/plugins/Analyze/analyzeskeleton_.jar,
> i = 3,
> message = invalid LOC header (bad signature)
> at java.util.zip.ZipFile$2.nextElement(ZipFile.java:322)
> at ij.Menus.getConfigurationFile(Menus.java:744)
> at ij.Menus.installJarPlugins(Menus.java:550)
> at ij.Menus.installPlugins(Menus.java:475)
> at ij.Menus.addMenuBar(Menus.java:226)
> at ij.ImageJ.<init>(ImageJ.java:123)
> at ij.ImageJ.main(ImageJ.java:553)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:324)
> at apple.launcher.LaunchRunner.run(LaunchRunner.java:88)
> at apple.launcher.LaunchRunner.callMain(LaunchRunner.java:50)Jul 15
> 12:55:28 Wayne-Rasbands-Computer kernel: arp:
>
> You can work around this problem by rebuilding the jar file or by
> extracting AnalyzeSkeleton_.java from the jar file and compiling and running
> it using Plugins>Compile and Run.
>
> -wayne
>

David Webster

Re: Analyze Skeleton-plugin suddenly stopped working!

In reply to this post by dscho

All,

I got the current (imageJ wiki version) AnalyzeSkeleton_.java "un-jar'ed"
from AnalyzeSkeleton_.jar and did the "Compile and Run". The first compile
gives me this funny error message. "error: error reading
C:\PROGRA~1\ImageJ\plugins\analyzeskeletonNEW.jar; null" Then I compiled it
again and got some warnings but the compile works.

I've also noticed that neither the old or new versions will return a results
table on Maringa's example image. But the do so on my example using
blobs.jpg.

The apparent confusion highlites my hesitancy to use FIJI as then
differences between it and imageJ aren't obvious to me.

David Webster

On Wed, Jul 15, 2009 at 10:44 AM, Johannes Schindelin <
[hidden email]> wrote:

> Hi,
>
> On Wed, 15 Jul 2009, Wayne Rasband wrote:
>
> > On Jul 15, 2009, at 5:27 AM, maringa wrote:
> >
> > >I e-mailed the author of the plugin, and he updated it but it's still
> > >not working. I updated my fiji last week and I also updated ImageJ to
> > >1.42q running analyzeskeleton_.jar downloaded 07/13/09
> > >
> > >Here is my input image: 8bit skeletonized neurite image:
> > >http://img27.imageshack.us/img27/9027/tujiskeleton.jpg
> >
> > The analyzeskeleton_.jar file is corrupted.
>
> Now I finally get it. Y'all are talking about the analyzeskeleton_.jar
> from the ImageJ Docu Wiki (which is also referenced from the Fiji Wiki).
> After downloading that, I can verify that yes, it is not a valid .jar
> file.
>
> However, I was always talking about the AnalyzeSkeleton_.jar you get via
> Help>Update Fiji (you have to run Fiji for this, of course). This is not
> corrupted.
>
> Ignacio, care to upload a correct one to the ImageJ Docu Wiki?
>
> Ciao,
> Dscho
>

Ignacio Arganda-Carreras

Re: Analyze Skeleton-plugin suddenly stopped working!

Hello David,

Did you use the version I just uploaded?

ignacio

On Wed, Jul 15, 2009 at 3:14 PM, David Webster <[hidden email]>wrote:

> All,
>
> I got the current (imageJ wiki version) AnalyzeSkeleton_.java "un-jar'ed"
> from AnalyzeSkeleton_.jar and did the "Compile and Run". The first compile
> gives me this funny error message. "error: error reading
> C:\PROGRA~1\ImageJ\plugins\analyzeskeletonNEW.jar; null" Then I compiled it
> again and got some warnings but the compile works.
>
> I've also noticed that neither the old or new versions will return a
> results
> table on Maringa's example image. But the do so on my example using
> blobs.jpg.
>
> The apparent confusion highlites my hesitancy to use FIJI as then
> differences between it and imageJ aren't obvious to me.
>
> David Webster
>
>
> On Wed, Jul 15, 2009 at 10:44 AM, Johannes Schindelin <
> [hidden email]> wrote:
>
> > Hi,
> >
> > On Wed, 15 Jul 2009, Wayne Rasband wrote:
> >
> > > On Jul 15, 2009, at 5:27 AM, maringa wrote:
> > >
> > > >I e-mailed the author of the plugin, and he updated it but it's still
> > > >not working. I updated my fiji last week and I also updated ImageJ to
> > > >1.42q running analyzeskeleton_.jar downloaded 07/13/09
> > > >
> > > >Here is my input image: 8bit skeletonized neurite image:
> > > >http://img27.imageshack.us/img27/9027/tujiskeleton.jpg
> > >
> > > The analyzeskeleton_.jar file is corrupted.
> >
> > Now I finally get it. Y'all are talking about the analyzeskeleton_.jar
> > from the ImageJ Docu Wiki (which is also referenced from the Fiji Wiki).
> > After downloading that, I can verify that yes, it is not a valid .jar
> > file.
> >
> > However, I was always talking about the AnalyzeSkeleton_.jar you get via
> > Help>Update Fiji (you have to run Fiji for this, of course). This is not
> > corrupted.
> >
> > Ignacio, care to upload a correct one to the ImageJ Docu Wiki?
> >
> > Ciao,
> > Dscho
> >
>

--
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

David Webster

Re: Analyze Skeleton-plugin suddenly stopped working!

Ignacio,

Our emails crossed in the mail. Your new version works fine.

I am curious about the limitation to 255 skeletons/image. Is this imposed by
the results table?

David

On Wed, Jul 15, 2009 at 3:41 PM, Ignacio Arganda
<[hidden email]>wrote:

> Hello David,
>
> Did you use the version I just uploaded?
>
> ignacio
>
> On Wed, Jul 15, 2009 at 3:14 PM, David Webster <[hidden email]
> >wrote:
>
> > All,
> >
> > I got the current (imageJ wiki version) AnalyzeSkeleton_.java "un-jar'ed"
> > from AnalyzeSkeleton_.jar and did the "Compile and Run". The first
> compile
> > gives me this funny error message. "error: error reading
> > C:\PROGRA~1\ImageJ\plugins\analyzeskeletonNEW.jar; null" Then I compiled
> it
> > again and got some warnings but the compile works.
> >
> > I've also noticed that neither the old or new versions will return a
> > results
> > table on Maringa's example image. But the do so on my example using
> > blobs.jpg.
> >
> > The apparent confusion highlites my hesitancy to use FIJI as then
> > differences between it and imageJ aren't obvious to me.
> >
> > David Webster
> >
> >
> > On Wed, Jul 15, 2009 at 10:44 AM, Johannes Schindelin <
> > [hidden email]> wrote:
> >
> > > Hi,
> > >
> > > On Wed, 15 Jul 2009, Wayne Rasband wrote:
> > >
> > > > On Jul 15, 2009, at 5:27 AM, maringa wrote:
> > > >
> > > > >I e-mailed the author of the plugin, and he updated it but it's
> still
> > > > >not working. I updated my fiji last week and I also updated ImageJ
> to
> > > > >1.42q running analyzeskeleton_.jar downloaded 07/13/09
> > > > >
> > > > >Here is my input image: 8bit skeletonized neurite image:
> > > > >http://img27.imageshack.us/img27/9027/tujiskeleton.jpg
> > > >
> > > > The analyzeskeleton_.jar file is corrupted.
> > >
> > > Now I finally get it. Y'all are talking about the analyzeskeleton_.jar
> > > from the ImageJ Docu Wiki (which is also referenced from the Fiji
> Wiki).
> > > After downloading that, I can verify that yes, it is not a valid .jar
> > > file.
> > >
> > > However, I was always talking about the AnalyzeSkeleton_.jar you get
> via
> > > Help>Update Fiji (you have to run Fiji for this, of course). This is
> not
> > > corrupted.
> > >
> > > Ignacio, care to upload a correct one to the ImageJ Docu Wiki?
> > >
> > > Ciao,
> > > Dscho
> > >
> >
>
>
>
> --
> 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
>

David Webster

Re: Analyze Skeleton-plugin suddenly stopped working!

In reply to this post by maringa

Martina,

Did you get your questions answwered OK? I noticed that the Fiji version of
analyzeskeleton_.jar doesn't produce a results file that is broken down by
skeleton. Also, on your test image the it may take some time to produce the
results file (after display of the tagged skeleton image). Also, your test
image isn't binary, so you need to run it thru "Make Binary" and Skeletonize
before ruiing Analyze Skeleton.

David

On Wed, Jul 15, 2009 at 2:27 AM, maringa <[hidden email]>wrote:

> Hi David,
>
> I e-mailed the author of the plugin, and he updated it but it's still not
> working.
> I updated my fiji last week and I also updated ImageJ to 1.42q
> running analyzeskeleton_.jar downloaded 07/13/09
>
> Here is my input image: 8bit skeletonized neurite image:
> http://img27.imageshack.us/img27/9027/tujiskeleton.jpg
>
> Martina
> ________________________________
> Från: David Webster (via Nabble) [[hidden email]<ml-user%[hidden email]>
> ]
> Skickat: den 13 juli 2009 23:16
> Till: Martina A K Johansson
> Ämne: Re: Analyze Skeleton-plugin suddenly stopped working!
>
> All,
>
> I can run Analyze-skeleton with no problems as follows:
>
> run("Blobs (25K)");
> run("Make Binary");
> run("Skeletonize (2D/3D)");
> run("Analyze Skeleton (2D/3D)");
>
> I am using ImageJ 1.43b and analyzeskeleton_.jar downloaded on 2/22/09.
> What
> is your setup?
>
> David Webster
>
> On Sat, Jul 11, 2009 at 10:42 PM, maringa <martinaj@...<
> http://n2.nabble.com/user/SendEmail.jtp?type=node&node=3251808&i=0>>wrote:
>
> > Hi again,
> >
> > My ImageJ programme is done, but now a really annoying error has occured!
> > Whenever I use
> > the Analyze-skeleton plugin it shows an error message (looks like this:
> > http://img200.imageshack.us/img200/8877/errorlma.jpg)
> >
> > I've tried the following:
> > - update Fiji
> > - uninstall and reinstall fiji
> > - install ImageJ again
> >
> > It has nothing to do with my macro, no matter how I use Analyze Skeleton
> I
> > get the same error message. How can it suddenly be like this?
> > My macro really need to use analyse-skeleton so this is very annoying!
> >
> > Thanks for your help :)
> >
> >
> > --
> > View this message in context:
> >
> http://n2.nabble.com/Analyze-Skeleton-plugin-suddenly-stopped-working%21-tp3244907p3244907.html
> > Sent from the ImageJ mailing list archive at Nabble.com.
> >
>
>
> ________________________________
> View message @
> http://n2.nabble.com/Analyze-Skeleton-plugin-suddenly-stopped-working%21-tp3244907p3251808.html
> To unsubscribe from Analyze Skeleton-plugin suddenly stopped working!,
> click here< (link removed) >.
>
>
> --
> View this message in context:
> http://n2.nabble.com/Analyze-Skeleton-plugin-suddenly-stopped-working%21-tp3244907p3262004.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>