3D Spot Segmentation

[Feriel P]

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

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Thomas Boudier-4]

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
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html