ImageJ crashing

[Weller Andrew Francis]

Dear all,

I've recently upgraded my PC running Ubuntu Linux (6.06 LTS). I've
correctly installed Sun's JDK etc, but ever since ImageJ keeps crashing
whenever I do *anything*, even Help -> About ImageJ?! My command line
launcher reads:

java -Dplugins.dir=/home/aweller/ImageJ -Xmx128m
-cp /opt/ImageJ/ij.jar:/usr/lib/jvm/java-1.5.0-sun/lib/tools.jar
ij.ImageJ

which is all correct. Any ideas or similar problems with workarounds?

Thanks, Andy

[ctrueden]

Hi Andy,

I am running an up-to-date Ubuntu Linux Dapper with Sun's JDK 1.5.0_06, and
have had no trouble with ImageJ v1.37l. Have you tested with different
versions of the JDK? What kind of crash is it?

-Curtis

On 7/25/06, Andy Weller <[hidden email]> wrote:

>
> Dear all,
>
> I've recently upgraded my PC running Ubuntu Linux (6.06 LTS). I've
> correctly installed Sun's JDK etc, but ever since ImageJ keeps crashing
> whenever I do *anything*, even Help -> About ImageJ?! My command line
> launcher reads:
>
> java -Dplugins.dir=/home/aweller/ImageJ -Xmx128m
> -cp /opt/ImageJ/ij.jar:/usr/lib/jvm/java-1.5.0-sun/lib/tools.jar
> ij.ImageJ
>
> which is all correct. Any ideas or similar problems with workarounds?
>
> Thanks, Andy
>

[Albert Cardona]

This is an Ubuntu "problem": by default the 'java'
 command runs GCJ, the GNU java. If you want your 'java' command to run Sun's
1.5.0 java, you have several options:

- set the full path in your 'run' script: for instance, this is mine:
/usr/local/jdk1.5.0_07/bin/java -Xmx600m -classpath
ij.jar:postgresql-8.1-405.jdbc3.jar:/usr/local/jdk1.5.0_07/lib/tools.jar
ij.ImageJ

- add the /usr/local/jdk1.5.0_07/bin to your classpath, before anything else, in
your .bashrc :

export PATH=/usr/local/jdk1.5.0_07/bin:$PATH

- make an alias in your bashrc for 'java' :

alias java='/usr/local/jdk1.5.0_07/bin/java'


Be sure also to set your JAVA_HOME to the proper folder in your .bashrc:

export JAVA_HOME=/usr/local/j2sdk1.4.2_12

In this case I have it pointing to the 1.4.2 so anything I compile will be
compatible with 1.4.2 and onward.

A final note: ImageJ runs faster and better with java 1.6.0 beta (as far as I
can tell).

Albert

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[Andreas Jahnen]

Dear Andy,

I have the same configuration on my machine, and it works without problem.
Do you use the UBUNTU LInux provided JDK or you have installed it
manually?

So long,
        Andreas

-----------------------------------------------------------------
Andreas Jahnen  -  Ingenieur de Recherche
[hidden email]
-----------------------------------------------------------------
CRP Henri Tudor  -  http://www.santec.lu
29, Avenue John F. Kennedy
L-1855 Luxembourg
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ImageJ Interest Group <[hidden email]> wrote on 25/07/2006 04:57:44
PM:

> Dear all,
>
> I've recently upgraded my PC running Ubuntu Linux (6.06 LTS). I've
> correctly installed Sun's JDK etc, but ever since ImageJ keeps crashing
> whenever I do *anything*, even Help -> About ImageJ?! My command line
> launcher reads:
>
> java -Dplugins.dir=/home/aweller/ImageJ -Xmx128m
> -cp /opt/ImageJ/ij.jar:/usr/lib/jvm/java-1.5.0-sun/lib/tools.jar
> ij.ImageJ
>
> which is all correct. Any ideas or similar problems with workarounds?
>
> Thanks, Andy
>

[Weller Andrew Francis]

Thanks Albert,

This seems to be the problem - I have now pointed my launcher to Sun's
Java instead of GCJ.

/usr/lib/jvm/java-1.5.0-sun/bin/java -Dplugins.dir=/home/aweller/ImageJ
-Xmx128m
-cp /opt/ImageJ/ij.jar:/usr/lib/jvm/java-1.5.0-sun/lib/tools.jar
ij.ImageJ

Andy

On Wed, 2006-07-26 at 07:46 +0200, Albert Cardona wrote:

> This is an Ubuntu "problem": by default the 'java'
>  command runs GCJ, the GNU java. If you want your 'java' command to run Sun's
> 1.5.0 java, you have several options:
>
> - set the full path in your 'run' script: for instance, this is mine:
> /usr/local/jdk1.5.0_07/bin/java -Xmx600m -classpath
> ij.jar:postgresql-8.1-405.jdbc3.jar:/usr/local/jdk1.5.0_07/lib/tools.jar
> ij.ImageJ
>
> - add the /usr/local/jdk1.5.0_07/bin to your classpath, before anything else, in
> your .bashrc :
>
> export PATH=/usr/local/jdk1.5.0_07/bin:$PATH
>
> - make an alias in your bashrc for 'java' :
>
> alias java='/usr/local/jdk1.5.0_07/bin/java'
>
>
> Be sure also to set your JAVA_HOME to the proper folder in your .bashrc:
>
> export JAVA_HOME=/usr/local/j2sdk1.4.2_12
>
> In this case I have it pointing to the 1.4.2 so anything I compile will be
> compatible with 1.4.2 and onward.
>
> A final note: ImageJ runs faster and better with java 1.6.0 beta (as far as I
> can tell).
>
> Albert

[ctrueden]

Hi,

There is a great article on switching Ubuntu over to the Sun JDK here:
http://www.docuverse.com/blog/donpark/EntryViewPage.aspx?guid=f171bafc-abce-4d2e-a18b-3aba4ad32c52

Doing is this way is nice because it keeps all your packaging dependencies
in place, with no need to throw anything into /usr/local.

-Curtis

On 7/26/06, Andy Weller <[hidden email]> wrote:

>
> Thanks Albert,
>
> This seems to be the problem - I have now pointed my launcher to Sun's
> Java instead of GCJ.
>
> /usr/lib/jvm/java-1.5.0-sun/bin/java -Dplugins.dir=/home/aweller/ImageJ
> -Xmx128m
> -cp /opt/ImageJ/ij.jar:/usr/lib/jvm/java-1.5.0-sun/lib/tools.jar
> ij.ImageJ
>
> Andy
>
> On Wed, 2006-07-26 at 07:46 +0200, Albert Cardona wrote:
> > This is an Ubuntu "problem": by default the 'java'
> >  command runs GCJ, the GNU java. If you want your 'java' command to run
> Sun's
> > 1.5.0 java, you have several options:
> >
> > - set the full path in your 'run' script: for instance, this is mine:
> > /usr/local/jdk1.5.0_07/bin/java -Xmx600m -classpath
> > ij.jar:postgresql-8.1-405.jdbc3.jar:/usr/local/jdk1.5.0_07/lib/tools.jar
> > ij.ImageJ
> >
> > - add the /usr/local/jdk1.5.0_07/bin to your classpath, before anything
> else, in
> > your .bashrc :
> >
> > export PATH=/usr/local/jdk1.5.0_07/bin:$PATH
> >
> > - make an alias in your bashrc for 'java' :
> >
> > alias java='/usr/local/jdk1.5.0_07/bin/java'
> >
> >
> > Be sure also to set your JAVA_HOME to the proper folder in your .bashrc:
> >
> > export JAVA_HOME=/usr/local/j2sdk1.4.2_12
> >
> > In this case I have it pointing to the 1.4.2 so anything I compile will
> be
> > compatible with 1.4.2 and onward.
> >
> > A final note: ImageJ runs faster and better with java 1.6.0 beta (as far
> as I
> > can tell).
> >
> > Albert
>

[Liu, Dongfang (NIH/NIAID) [F]]

Dear All,

I need to cut 300 frames time-series images using rectangle tool. Is
there a macro to do this? It is time consuming to do it manually. I did
it manually as following:
Step 1: open the time series images
Step 2: use the rectangle tool(13*13 pixels) to select AOI in time
series image, "Ctrl+C"  to copy the AOI,  
Step 3: Ctrl+N to open new image,---OK---- Ctrl+V to save the AOI,
Step 4: Save as tiff in a folder.
Is there a macro to do that?

Thanks
Best regards,
Don  

[Liu, Dongfang (NIH/NIAID) [F]]

Thank you for your reply,

When I save , I cannot save them as individual images. How to get "
File>Save>Image Sequence."? When I save, in the save window, there is no
choice for image sequence. Where to get the "image sequence"?
Another problem is the AOI objective is moving, you cannot get the right
position for the AOI.


-----Original Message-----
From: Joel Sheffield [mailto:[hidden email]]
Sent: Wednesday, July 26, 2006 3:30 PM
To: Liu, Dongfang (NIH/NIAID) [F]
Subject: Re: Maroc for cutting 300 frames 13*13 pixels AOI in
time-series image

You should be able to open the entire series as a stack.  If the
images are separate, use File>import>sequence.  Then you can draw the
rectangle once, and use Image>crop to crop the entire stack.  You can
then save the individual images if you like by using File>Save>Image
Sequence.

Good Luck,

> Dear All,
>
> I need to cut 300 frames time-series images using rectangle tool. Is
> there a macro to do this? It is time consuming to do it manually. I
> did it manually as following: Step 1: open the time series images Step
> 2: use the rectangle tool(13*13 pixels) to select AOI in time series
> image, "Ctrl+C"  to copy the AOI,   Step 3: Ctrl+N to open new
> image,---OK---- Ctrl+V to save the AOI, Step 4: Save as tiff in a
> folder. Is there a macro to do that?
>
> Thanks
> Best regards,
> Don  

Joel B. Sheffield, Ph.D.
Biology Department, Temple University
1900 North 12th Street
Philadelphia, PA 19122
[hidden email]  
[phone], fax [phone]
http://astro.temple.edu/~jbs