Re: 3D Spot Segmentation

Posted by Thomas Boudier-4 on Jul 06, 2016; 1:46am
URL: http://imagej.273.s1.nabble.com/3D-Spot-Segmentation-tp5016817p5016819.html

Hi Feriel,

Sorry I updated the 3D ImageJ Suite yesterday, this new version is now
compatible with new developments of Fiji and uses the new 3D viewer, so
you need to install the package "3D" from the lsit of update sites in
the Fiji update. Hope it will solve your porblem.

Best,

Thomas


On 06/07/2016 01:52, Feriel P wrote:

> Hi guys,
>
> Has anyone else had any issues with the 3D Image Suite's 3D Spot
> Segmentation plugin? I have been trying to run it on many images through a
> macro to generate an object count, then use the extension
> Ext.Manager3D_Count(nb_obj); to get the count from the 3D ROI Manager and
> assign it to a variable. This line worked fine in the macro yesterday, but
> today it throws an error window that says "Unrecognized Ext function
> Ext.<Manager3D_Count>(nb_obj) in line...". I also tried to run the 3D Spot
> Segmentation plugin outside the macro but the 3D ROI Manager did not open
> and I got the Exception window message below. I am still a novice at
> ImageJ, so if anyone has any suggestions on what the issue is/what I can do
> to get this plugin and its functions running again I would greatly
> appreciate it!
>
> Thanks,
> -Feriel
>
> *Error Message:*
>
> (Fiji Is Just) ImageJ 2.0.0-rc-43/1.51e18; Java 1.6.0_24 [32-bit]; Windows
> 7 6.1; 239MB of 1211MB (19%)
>
> java.lang.NoClassDefFoundError: org/scijava/java3d/View
>   at java.lang.Class.getDeclaredMethods0(Native Method)
>   at java.lang.Class.privateGetDeclaredMethods(Class.java:2427)
>   at java.lang.Class.getDeclaredMethod(Class.java:1935)
>   at java.awt.Component.isCoalesceEventsOverriden(Component.java:5974)
>   at java.awt.Component.access$500(Component.java:170)
>   at java.awt.Component$3.run(Component.java:5928)
>   at java.awt.Component$3.run(Component.java:5926)
>   at java.security.AccessController.doPrivileged(Native Method)
>   at java.awt.Component.checkCoalescing(Component.java:5925)
>   at java.awt.Component.<init>(Component.java:5894)
>   at java.awt.Container.<init>(Container.java:251)
>   at java.awt.Window.<init>(Window.java:431)
>   at java.awt.Frame.<init>(Frame.java:403)
>   at java.awt.Frame.<init>(Frame.java:368)
>   at javax.swing.JFrame.<init>(JFrame.java:158)
>   at mcib_plugins.tools.RoiManager3D_2.<init>(RoiManager3D_2.java:113)
>   at mcib_plugins.SeedSpots_Plus.Segmentation(SeedSpots_Plus.java:266)
>   at mcib_plugins.SeedSpots_Plus.run(SeedSpots_Plus.java:198)
>   at ij.IJ.runUserPlugIn(IJ.java:217)
>   at ij.IJ.runPlugIn(IJ.java:181)
>   at ij.Executer.runCommand(Executer.java:137)
>   at ij.Executer.run(Executer.java:66)
>   at java.lang.Thread.run(Thread.java:662)
> Caused by: java.lang.ClassNotFoundException: org.scijava.java3d.View
>   at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
>   at java.security.AccessController.doPrivileged(Native Method)
>   at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
>   at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
>   at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
>   at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
>   ... 23 more
>
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>

--
   /***************************************************************/
      Thomas Boudier, Associate Professor, UPMC,
      Université Pierre et Marie Curie, Paris, France.
      BII (BioInformatics Institute)/UMI 2955 IPAL, Singapore.
/**************************************************************/


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