problem with Trackmate

[David Michonneau]

Dear all,

I'm trying to do cell tracking using the plugin "Trackmate" in Fiji. It
was used to work but since two days, I always have this error message
when launching Trackmate :
(Fiji Is Just) ImageJ 1.48b; Java 1.6.0_51 [64-bit]; Mac OS X 10.8.4;
1035MB of 5991MB (17%)

java.lang.NoClassDefFoundError: net/imglib2/meta/Metadata
     at
fiji.plugin.trackmate.TrackMatePlugIn_.createTrackMate(TrackMatePlugIn_.java:54)
     at fiji.plugin.trackmate.TrackMatePlugIn_.run(TrackMatePlugIn_.java:22)
     at ij.IJ.runUserPlugIn(IJ.java:196)
     at ij.IJ.runPlugIn(IJ.java:160)
     at ij.Executer.runCommand(Executer.java:131)
     at ij.Executer.run(Executer.java:64)
     at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.ClassNotFoundException: net.imglib2.meta.Metadata
     at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
     at java.security.AccessController.doPrivileged(Native Method)
     at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
     at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
     at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
     ... 7 more

Does anyone have an idea about the origin of the problem ? Thank you
very much,

David

--
David Michonneau

Unité Dynamique des Réponses Immunes
Département d'Immunologie
Institut Pasteur
25 rue du Docteur Roux
75015 Paris
FRANCE

Phone: [phone]
Fax: + 33 1 40 61 32 00
Email: [hidden email]
www.pasteur.fr/recherche/unites/dri


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[dscho]

Hi David,

On Thu, 12 Sep 2013, David Michonneau wrote:

> I'm trying to do cell tracking using the plugin "Trackmate" in Fiji. It
> was used to work but since two days, I always have this error message
> when launching Trackmate :
> (Fiji Is Just) ImageJ 1.48b; Java 1.6.0_51 [64-bit]; Mac OS X 10.8.4; 1035MB
> of 5991MB (17%)
>
> java.lang.NoClassDefFoundError: net/imglib2/meta/Metadata

Sorry, my mistake. We fixed this last week in the source code, but I
simply forgot to upload a new version to the update site. After an update
with Help>Update Fiji, it should work now!

Ciao,
Johannes

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[David Michonneau]

Le 12/09/13 17:59, Johannes Schindelin a écrit :

> Hi David,
>
> On Thu, 12 Sep 2013, David Michonneau wrote:
>
>> I'm trying to do cell tracking using the plugin "Trackmate" in Fiji. It
>> was used to work but since two days, I always have this error message
>> when launching Trackmate :
>> (Fiji Is Just) ImageJ 1.48b; Java 1.6.0_51 [64-bit]; Mac OS X 10.8.4; 1035MB
>> of 5991MB (17%)
>>
>> java.lang.NoClassDefFoundError: net/imglib2/meta/Metadata
> Sorry, my mistake. We fixed this last week in the source code, but I
> simply forgot to upload a new version to the update site. After an update
> with Help>Update Fiji, it should work now!
>
> Ciao,
> Johannes

Hi Johannes,

Thank you for your response. With the update, there is no more trouble
to launch Trackmate. However, there is still some problem to track
cells. I'm trying to track cells in a film with multiple z stacks. When
I use trackmate with these films, it doesn't detect any spot (i have
tried with different value of blobs diameter and threshold but it didn't
change anything). Then, I have tried to make a z project before
analysis. With a z project, Trackmate detects a lot of spots, but it
doesn't track any of them (the final result is a null track speed and
each spot is tracked as a motionless cells during the whole film). Do
you know how I could solve this problem ? Thank you,

David

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[fabrice senger-2]

Hi there,

I unfortunatly experience the same kind of problem. In my case I have a
time lapse in wich I track a single spot, it's my test stack and previously
this was always workinf fine.
By know I can launch trackmate but could find no way to find and track this
"easy" feature.
So there must be another problem.

For the time being is ther a simple way to go back o the previous version
of FIJI ?

Thank youvery much for your efforts,

Fabrice.


2013/9/13 David Michonneau <[hidden email]>

> Le 12/09/13 17:59, Johannes Schindelin a écrit :
>
>  Hi David,
>>
>> On Thu, 12 Sep 2013, David Michonneau wrote:
>>
>>  I'm trying to do cell tracking using the plugin "Trackmate" in Fiji. It
>>> was used to work but since two days, I always have this error message
>>> when launching Trackmate :
>>> (Fiji Is Just) ImageJ 1.48b; Java 1.6.0_51 [64-bit]; Mac OS X 10.8.4;
>>> 1035MB
>>> of 5991MB (17%)
>>>
>>> java.lang.**NoClassDefFoundError: net/imglib2/meta/Metadata
>>>
>> Sorry, my mistake. We fixed this last week in the source code, but I
>> simply forgot to upload a new version to the update site. After an update
>> with Help>Update Fiji, it should work now!
>>
>> Ciao,
>> Johannes
>>
> Hi Johannes,
>
> Thank you for your response. With the update, there is no more trouble to
> launch Trackmate. However, there is still some problem to track cells. I'm
> trying to track cells in a film with multiple z stacks. When I use
> trackmate with these films, it doesn't detect any spot (i have tried with
> different value of blobs diameter and threshold but it didn't change
> anything). Then, I have tried to make a z project before analysis. With a z
> project, Trackmate detects a lot of spots, but it doesn't track any of them
> (the final result is a null track speed and each spot is tracked as a
> motionless cells during the whole film). Do you know how I could solve this
> problem ? Thank you,
>
> David
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>

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[ctrueden]

Hi Fabrice,


> In my case I have a time lapse in wich I track a single spot, it's my
> test stack and previously this was always workinf fine.

Jean-Yves or Johannes (TrackMate developers) will have to comment on this
part, but...

> For the time being is ther a simple way to go back o the previous
> version of FIJI ?

You can download the "Life-Line" version of Fiji from the Downloads page:
    http://fiji.sc/Downloads

This is a stable version of Fiji from July 15, 2013.

In the future we want to add the ability to Fiji & ImageJ2 to freely
upgrade/downgrade to any chosen version. With the way ImageJ update sites
work, this would be quite doable, but we have not yet implemented it yet.

Regards,
Curtis


On Fri, Sep 13, 2013 at 9:58 AM, Fabrice Senger <[hidden email]>wrote:

> Hi there,
>
> I unfortunatly experience the same kind of problem. In my case I have a
> time lapse in wich I track a single spot, it's my test stack and previously
> this was always workinf fine.
> By know I can launch trackmate but could find no way to find and track this
> "easy" feature.
> So there must be another problem.
>
> For the time being is ther a simple way to go back o the previous version
> of FIJI ?
>
> Thank youvery much for your efforts,
>
> Fabrice.
>
>
> 2013/9/13 David Michonneau <[hidden email]>
>
> > Le 12/09/13 17:59, Johannes Schindelin a écrit :
> >
> >  Hi David,
> >>
> >> On Thu, 12 Sep 2013, David Michonneau wrote:
> >>
> >>  I'm trying to do cell tracking using the plugin "Trackmate" in Fiji. It
> >>> was used to work but since two days, I always have this error message
> >>> when launching Trackmate :
> >>> (Fiji Is Just) ImageJ 1.48b; Java 1.6.0_51 [64-bit]; Mac OS X 10.8.4;
> >>> 1035MB
> >>> of 5991MB (17%)
> >>>
> >>> java.lang.**NoClassDefFoundError: net/imglib2/meta/Metadata
> >>>
> >> Sorry, my mistake. We fixed this last week in the source code, but I
> >> simply forgot to upload a new version to the update site. After an
> update
> >> with Help>Update Fiji, it should work now!
> >>
> >> Ciao,
> >> Johannes
> >>
> > Hi Johannes,
> >
> > Thank you for your response. With the update, there is no more trouble to
> > launch Trackmate. However, there is still some problem to track cells.
> I'm
> > trying to track cells in a film with multiple z stacks. When I use
> > trackmate with these films, it doesn't detect any spot (i have tried with
> > different value of blobs diameter and threshold but it didn't change
> > anything). Then, I have tried to make a z project before analysis. With
> a z
> > project, Trackmate detects a lot of spots, but it doesn't track any of
> them
> > (the final result is a null track speed and each spot is tracked as a
> > motionless cells during the whole film). Do you know how I could solve
> this
> > problem ? Thank you,
> >
> > David
> >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<
> http://imagej.nih.gov/ij/list.html>
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[chin]

Hi Fabrice,

There is no problem on TrackMate. The previous Fiji (8/13 updated version) with TackMate v2.1.0 works correctly for spot tracking. While using the latest version of Fiji, the Trackmate will act oddly as you described.

chin

[fabrice senger-2]

Yes, i know,

unfortunatly I could not make the way back to 8/13 ...it's avery nice tool
hope the guys could fix it

Fabrice.


2013/9/17 chin <[hidden email]>

> Hi Fabrice,
>
> There is no problem on TrackMate. The previous Fiji (8/13 updated version)
> with TackMate v2.1.0 works correctly for spot tracking. While using the
> latest version of Fiji, the Trackmate will act oddly as you described.
>
> chin
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/problem-with-Trackmate-tp5004766p5004813.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Gby]

Dear all,

i've extended the Fiji-Plugin Trackmate for our biological department. Since almost two weeks the same exception as David Michonneau mentioned happend:

(Fiji Is Just) ImageJ 1.48c; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 28MB of 18405MB (<1%)
 
java.lang.NoClassDefFoundError: net/imglib2/meta/Metadata
        at fiji.plugin.trackmate.TrackMatePlugIn_.createTrackMate(TrackMatePlugIn_.java:54)
        at fiji.plugin.trackmate.TrackMatePlugIn_.run(TrackMatePlugIn_.java:22)
        at ij.IJ.runUserPlugIn(IJ.java:196)
        at ij.IJ.runPlugIn(IJ.java:160)
        at ij.Executer.runCommand(Executer.java:131)
        at ij.Executer.run(Executer.java:64)
        at java.lang.Thread.run(Thread.java:662)
Caused by: java.lang.ClassNotFoundException: net.imglib2.meta.Metadata
        at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
        ... 7 more

Unfortunately the latest update or the use of the latest version didn't solve the problem.
If I use the unmodified trackmate, it works, but if i add my own classes it crashes.
Can anyone help me or give me a hint, where to find the origin of this problem?

Gby

[dscho]

Hi Gby,

On Mon, 23 Sep 2013, Gby wrote:

> i've extended the Fiji-Plugin Trackmate for our biological department.
> Since almost two weeks the same exception as David Michonneau mentioned
> happend:
>
> (Fiji Is Just) ImageJ 1.48c; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 28MB of
> 18405MB (<1%)
>  
> java.lang.NoClassDefFoundError: net/imglib2/meta/Metadata
> at
> fiji.plugin.trackmate.TrackMatePlugIn_.createTrackMate(TrackMatePlugIn_.java:54)
> at fiji.plugin.trackmate.TrackMatePlugIn_.run(TrackMatePlugIn_.java:22)
> at ij.IJ.runUserPlugIn(IJ.java:196)
> at ij.IJ.runPlugIn(IJ.java:160)
> at ij.Executer.runCommand(Executer.java:131)
> at ij.Executer.run(Executer.java:64)
> at java.lang.Thread.run(Thread.java:662)
> Caused by: java.lang.ClassNotFoundException: net.imglib2.meta.Metadata
> at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
> at java.security.AccessController.doPrivileged(Native Method)
> at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
> ... 7 more
>
> Unfortunately the latest update or the use of the latest version didn't
> solve the problem.
> If I use the unmodified trackmate, it works, but if i add my own classes it
> crashes.
> Can anyone help me or give me a hint, where to find the origin of this
> problem?

Is there a public source code repository (preferably GitHub so it is easy
for me to provide the fixes)?

Ciao,
Johannes

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