IMAGEJ bundled with all plug ins request

[Gareth Howell]

Dear list

I understand that there is a web site I can download IJ bundled with all the plug ins. Is this true? Would someone be able to send me the URL?

Thanks in advance.

Gareth

[dscho]

Hi,

On Tue, 2 Jun 2009, Gareth Howell wrote:

> I understand that there is a web site I can download IJ bundled with all
> the plug ins. Is this true? Would someone be able to send me the URL?

Maybe you mean Fiji: http://pacific.mpi-cbg.de

It does not contain _all_ plugins, though.

Ciao,
Dscho

[Daniel James White]

On Jun 3, 2009, at 6:00 AM, IMAGEJ automatic digest system wrote:

>
> Date:    Tue, 2 Jun 2009 10:42:01 +0100
> From:    Gareth Howell <[hidden email]>
> Subject: IMAGEJ bundled with all plug ins request
>
> Dear list
>
> I understand that there is a web site I can download IJ bundled with  
> all th=
> e plug ins. Is this true? Would someone be able to send me the URL?
>
> Thanks in advance.
>
> Gareth

for microscopy there is a well maintained bundle at
http://www.macbiophotonics.ca/downloads.htm
thanks to Tony Collins.

In the Fiji project,
we are adding more and more plugins also.
http://pacific.mpi-cbg.de

you can get the plugins you want from MBF plugins collection .zip file
and add them to fiji plugins directory if you like.
The you get the benefits of Fiji,
and the plugins you want.

All plugins would be a big ask, as there are probably hundreds....

cheers

Dan



Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

[phone] (German Mobile)
+49  (0)351 210 2627 (Work phone at MPI-CBG)
+49  (0)351 210 1078 (Fax MPI-CBG LMF)

http://www.bioimagexd.net  BioImageXD
http://pacific.mpi-cbg.de Fiji Fiji is just ImageJ - Batteries Included
http://www.chalkie.org.uk
[hidden email]
( [hidden email] )

[Martin Höhne]

<quote author="Dan White">

you can get the plugins you want from MBF plugins collection .zip file
and add them to fiji plugins directory if you like.
The you get the benefits of Fiji,
and the plugins you want.

 
I tried this, but for me it doesn't work for all plugins. E.g. when trying to use the nucelus counter plugin (in MBF in: plugins>particle analysis>nucleus counter) I get the error message shown below from Fiji. Do I need to copy more that just the files from the plugin folder?

Thank you,
Martin
------------
here's the message:

java.lang.NoClassDefFoundError: Particle Analysis/Nucleus_Counter (wrong name: Nucleus_Counter)
        at java.lang.ClassLoader.defineClass1(Native Method)
        at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
        at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
        at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
        at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
        at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:140)
        at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:132)
        at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:127)
        at fiji.scripting.java.PlugInExecutor.tryRun(PlugInExecutor.java:122)
        at fiji.scripting.java.PlugInExecutor.tryRun(PlugInExecutor.java:102)
        at fiji.scripting.java.PlugInExecutor.run(PlugInExecutor.java:83)
        at fiji.scripting.java.PlugInExecutor.run(PlugInExecutor.java:77)
        at fiji.scripting.java.PlugInExecutor.run(PlugInExecutor.java:73)
        at fiji.scripting.java.Refresh_Javas.runPlugin(Refresh_Javas.java:339)
        at fiji.scripting.java.Refresh_Javas.compileAndRun(Refresh_Javas.java:126)
        at fiji.scripting.java.Refresh_Javas.runScript(Refresh_Javas.java:70)
        at common.RefreshScripts.run(RefreshScripts.java:266)
        at fiji.scripting.java.Refresh_Javas.run(Refresh_Javas.java:60)
        at ij.IJ.runUserPlugIn(IJ.java:183)
        at ij.IJ.runPlugIn(IJ.java:150)
        at ij.Executer.runCommand(Executer.java:124)
        at ij.Executer.run(Executer.java:61)
        at java.lang.Thread.run(Thread.java:619)