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NullPointerExceptions in Spot Segmentation - 3D Image Suite

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Feriel P
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NullPointerExceptions in Spot Segmentation - 3D Image Suite

Feriel P
Hi all!

I am a new ImageJ user trying to count punctate ROIs in a z-stack, and
after experimenting with different plugins have found that 3D Image Suite's
Spot Segmentation tool works extremely well. However, NullPointerExceptions
(pasted below) seem to consistently be thrown just after the 3D ROI Manager
is opened. This occurs whether I open and run 3D Spot Segmentation from the
Plugins menu, or use run("3D Spot Segmentation", ...) in a macro. Just to
make sure that this was not due to any quirks in the way in which our
images were taken, I tried this on the example stack 'Confocal Series',
using the spots in the red channel to generate the seeds and determine
ROIs. The exception exists for z-stacks of 8-bit and 16-bit formats.
Despite that, the segmented stack generated, as well as the final count in
the ROI Manager both seem correct, and the exception does not interrupt the
loop in our macro, so should I be worried about it at all? Any advice or
suggestions would be greatly appreciated!

Best,

Feriel Presswalla
Kellogg Eye Center
University of Michigan

---

*Parameters used in the 3D spot segmentation plugin:*
run("3D Spot Segmentation", "seeds_threshold=8000 local_background=0
radius_0=2 radius_1=4 radius_2=6 weigth=0.50 radius_max=3 sd_value=1
local_threshold=[Gaussian fit] seg_spot=Maximum watershed volume_min=1
volume_max=1000000 seeds=3D_MaximumLocal spots=raw radius_for_seeds=2
output=Both 32-bits");

*Console window readout:*

Reading header
Finding image offsets
Reading header
Finding image offsets
Getting universes
Universes opened 1
Universe ij3d.Image3DUniverse@4c963c
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
 at
javax.swing.plaf.basic.BasicListUI.updateLayoutState(BasicListUI.java:1351)
 at
javax.swing.plaf.basic.BasicListUI.maybeUpdateLayoutState(BasicListUI.java:1294)
 at javax.swing.plaf.basic.BasicListUI.paintImpl(BasicListUI.java:246)
 at javax.swing.plaf.basic.BasicListUI.paint(BasicListUI.java:222)
 at javax.swing.plaf.ComponentUI.update(ComponentUI.java:143)
 at javax.swing.JComponent.paintComponent(JComponent.java:752)
 at javax.swing.JComponent.paint(JComponent.java:1029)
 at javax.swing.JComponent.paintToOffscreen(JComponent.java:5124)
 at
javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1479)
 at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1410)
 at javax.swing.RepaintManager.paint(RepaintManager.java:1224)
 at javax.swing.JComponent._paintImmediately(JComponent.java:5072)
 at javax.swing.JComponent.paintImmediately(JComponent.java:4882)
 at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:785)
 at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:713)
 at javax.swing.RepaintManager.seqPaintDirtyRegions(RepaintManager.java:693)
 at
javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(SystemEventQueueUtilities.java:125)
 at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
 at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:642)
 at java.awt.EventQueue.access$000(EventQueue.java:85)
 at java.awt.EventQueue$1.run(EventQueue.java:603)
 at java.awt.EventQueue$1.run(EventQueue.java:601)
 at java.security.AccessController.doPrivileged(Native Method)
 at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
 at java.awt.EventQueue.dispatchEvent(EventQueue.java:612)
 at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
 at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
 at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
 at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
 at
javax.swing.plaf.basic.BasicListUI.updateLayoutState(BasicListUI.java:1314)
 at
javax.swing.plaf.basic.BasicListUI.maybeUpdateLayoutState(BasicListUI.java:1294)
 at javax.swing.plaf.basic.BasicListUI.paintImpl(BasicListUI.java:246)
 at javax.swing.plaf.basic.BasicListUI.paint(BasicListUI.java:222)
 at javax.swing.plaf.ComponentUI.update(ComponentUI.java:143)
 at javax.swing.JComponent.paintComponent(JComponent.java:752)
 at javax.swing.JComponent.paint(JComponent.java:1029)
 at javax.swing.JComponent.paintToOffscreen(JComponent.java:5124)
 at
javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1479)
 at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1410)
 at javax.swing.RepaintManager.paint(RepaintManager.java:1224)
 at javax.swing.JComponent._paintImmediately(JComponent.java:5072)
 at javax.swing.JComponent.paintImmediately(JComponent.java:4882)
 at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:785)
 at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:713)
 at javax.swing.RepaintManager.seqPaintDirtyRegions(RepaintManager.java:693)
 at
javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(SystemEventQueueUtilities.java:125)
 at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
 at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:642)
 at java.awt.EventQueue.access$000(EventQueue.java:85)
 at java.awt.EventQueue$1.run(EventQueue.java:603)
 at java.awt.EventQueue$1.run(EventQueue.java:601)
 at java.security.AccessController.doPrivileged(Native Method)
 at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
 at java.awt.EventQueue.dispatchEvent(EventQueue.java:612)
 at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
 at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
 at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
 at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
 at
javax.swing.plaf.basic.BasicListUI.updateLayoutState(BasicListUI.java:1351)
 at
javax.swing.plaf.basic.BasicListUI.maybeUpdateLayoutState(BasicListUI.java:1294)
 at javax.swing.plaf.basic.BasicListUI.paintImpl(BasicListUI.java:246)
 at javax.swing.plaf.basic.BasicListUI.paint(BasicListUI.java:222)
 at javax.swing.plaf.ComponentUI.update(ComponentUI.java:143)
 at javax.swing.JComponent.paintComponent(JComponent.java:752)
 at javax.swing.JComponent.paint(JComponent.java:1029)
 at javax.swing.JComponent.paintToOffscreen(JComponent.java:5124)
 at
javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1479)
 at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1410)
 at javax.swing.RepaintManager.paint(RepaintManager.java:1224)
 at javax.swing.JComponent._paintImmediately(JComponent.java:5072)
 at javax.swing.JComponent.paintImmediately(JComponent.java:4882)
 at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:785)
 at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:713)
 at javax.swing.RepaintManager.seqPaintDirtyRegions(RepaintManager.java:693)
 at
javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(SystemEventQueueUtilities.java:125)
 at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
 at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:642)
 at java.awt.EventQueue.access$000(EventQueue.java:85)
 at java.awt.EventQueue$1.run(EventQueue.java:603)
 at java.awt.EventQueue$1.run(EventQueue.java:601)
 at java.security.AccessController.doPrivileged(Native Method)
 at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
 at java.awt.EventQueue.dispatchEvent(EventQueue.java:612)
 at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
 at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
 at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
 at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

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Thomas Boudier-4
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Re: NullPointerExceptions in Spot Segmentation - 3D Image Suite

Thomas Boudier-4
Dear Feriel,

Thanks for your email and glad to see our plugins are useful ;) . It
looks like the problem is only a problem for displaying the 3DManager, I
also sometimes have this kind of error, it is related to the way Java
displays graphical elements, maybe it will be corrected in future
version of Java. Meanwhile if you have questions or questions about the
spotSegmentation plugin, do not hesitate to contact me.

Best,

Thomas


On 14/11/2015 03:43, Feriel P wrote:

> Hi all!
>
> I am a new ImageJ user trying to count punctate ROIs in a z-stack, and
> after experimenting with different plugins have found that 3D Image Suite's
> Spot Segmentation tool works extremely well. However, NullPointerExceptions
> (pasted below) seem to consistently be thrown just after the 3D ROI Manager
> is opened. This occurs whether I open and run 3D Spot Segmentation from the
> Plugins menu, or use run("3D Spot Segmentation", ...) in a macro. Just to
> make sure that this was not due to any quirks in the way in which our
> images were taken, I tried this on the example stack 'Confocal Series',
> using the spots in the red channel to generate the seeds and determine
> ROIs. The exception exists for z-stacks of 8-bit and 16-bit formats.
> Despite that, the segmented stack generated, as well as the final count in
> the ROI Manager both seem correct, and the exception does not interrupt the
> loop in our macro, so should I be worried about it at all? Any advice or
> suggestions would be greatly appreciated!
>
> Best,
>
> Feriel Presswalla
> Kellogg Eye Center
> University of Michigan
>
> ---
>
> *Parameters used in the 3D spot segmentation plugin:*
> run("3D Spot Segmentation", "seeds_threshold=8000 local_background=0
> radius_0=2 radius_1=4 radius_2=6 weigth=0.50 radius_max=3 sd_value=1
> local_threshold=[Gaussian fit] seg_spot=Maximum watershed volume_min=1
> volume_max=1000000 seeds=3D_MaximumLocal spots=raw radius_for_seeds=2
> output=Both 32-bits");
>
> *Console window readout:*
>
> Reading header
> Finding image offsets
> Reading header
> Finding image offsets
> Getting universes
> Universes opened 1
> Universe ij3d.Image3DUniverse@4c963c
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
>   at
> javax.swing.plaf.basic.BasicListUI.updateLayoutState(BasicListUI.java:1351)
>   at
> javax.swing.plaf.basic.BasicListUI.maybeUpdateLayoutState(BasicListUI.java:1294)
>   at javax.swing.plaf.basic.BasicListUI.paintImpl(BasicListUI.java:246)
>   at javax.swing.plaf.basic.BasicListUI.paint(BasicListUI.java:222)
>   at javax.swing.plaf.ComponentUI.update(ComponentUI.java:143)
>   at javax.swing.JComponent.paintComponent(JComponent.java:752)
>   at javax.swing.JComponent.paint(JComponent.java:1029)
>   at javax.swing.JComponent.paintToOffscreen(JComponent.java:5124)
>   at
> javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1479)
>   at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1410)
>   at javax.swing.RepaintManager.paint(RepaintManager.java:1224)
>   at javax.swing.JComponent._paintImmediately(JComponent.java:5072)
>   at javax.swing.JComponent.paintImmediately(JComponent.java:4882)
>   at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:785)
>   at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:713)
>   at javax.swing.RepaintManager.seqPaintDirtyRegions(RepaintManager.java:693)
>   at
> javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(SystemEventQueueUtilities.java:125)
>   at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
>   at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:642)
>   at java.awt.EventQueue.access$000(EventQueue.java:85)
>   at java.awt.EventQueue$1.run(EventQueue.java:603)
>   at java.awt.EventQueue$1.run(EventQueue.java:601)
>   at java.security.AccessController.doPrivileged(Native Method)
>   at
> java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
>   at java.awt.EventQueue.dispatchEvent(EventQueue.java:612)
>   at
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
>   at
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
>   at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
>   at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
>   at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
>   at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
>   at
> javax.swing.plaf.basic.BasicListUI.updateLayoutState(BasicListUI.java:1314)
>   at
> javax.swing.plaf.basic.BasicListUI.maybeUpdateLayoutState(BasicListUI.java:1294)
>   at javax.swing.plaf.basic.BasicListUI.paintImpl(BasicListUI.java:246)
>   at javax.swing.plaf.basic.BasicListUI.paint(BasicListUI.java:222)
>   at javax.swing.plaf.ComponentUI.update(ComponentUI.java:143)
>   at javax.swing.JComponent.paintComponent(JComponent.java:752)
>   at javax.swing.JComponent.paint(JComponent.java:1029)
>   at javax.swing.JComponent.paintToOffscreen(JComponent.java:5124)
>   at
> javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1479)
>   at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1410)
>   at javax.swing.RepaintManager.paint(RepaintManager.java:1224)
>   at javax.swing.JComponent._paintImmediately(JComponent.java:5072)
>   at javax.swing.JComponent.paintImmediately(JComponent.java:4882)
>   at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:785)
>   at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:713)
>   at javax.swing.RepaintManager.seqPaintDirtyRegions(RepaintManager.java:693)
>   at
> javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(SystemEventQueueUtilities.java:125)
>   at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
>   at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:642)
>   at java.awt.EventQueue.access$000(EventQueue.java:85)
>   at java.awt.EventQueue$1.run(EventQueue.java:603)
>   at java.awt.EventQueue$1.run(EventQueue.java:601)
>   at java.security.AccessController.doPrivileged(Native Method)
>   at
> java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
>   at java.awt.EventQueue.dispatchEvent(EventQueue.java:612)
>   at
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
>   at
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
>   at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
>   at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
>   at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
>   at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
>   at
> javax.swing.plaf.basic.BasicListUI.updateLayoutState(BasicListUI.java:1351)
>   at
> javax.swing.plaf.basic.BasicListUI.maybeUpdateLayoutState(BasicListUI.java:1294)
>   at javax.swing.plaf.basic.BasicListUI.paintImpl(BasicListUI.java:246)
>   at javax.swing.plaf.basic.BasicListUI.paint(BasicListUI.java:222)
>   at javax.swing.plaf.ComponentUI.update(ComponentUI.java:143)
>   at javax.swing.JComponent.paintComponent(JComponent.java:752)
>   at javax.swing.JComponent.paint(JComponent.java:1029)
>   at javax.swing.JComponent.paintToOffscreen(JComponent.java:5124)
>   at
> javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1479)
>   at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1410)
>   at javax.swing.RepaintManager.paint(RepaintManager.java:1224)
>   at javax.swing.JComponent._paintImmediately(JComponent.java:5072)
>   at javax.swing.JComponent.paintImmediately(JComponent.java:4882)
>   at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:785)
>   at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:713)
>   at javax.swing.RepaintManager.seqPaintDirtyRegions(RepaintManager.java:693)
>   at
> javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(SystemEventQueueUtilities.java:125)
>   at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
>   at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:642)
>   at java.awt.EventQueue.access$000(EventQueue.java:85)
>   at java.awt.EventQueue$1.run(EventQueue.java:603)
>   at java.awt.EventQueue$1.run(EventQueue.java:601)
>   at java.security.AccessController.doPrivileged(Native Method)
>   at
> java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
>   at java.awt.EventQueue.dispatchEvent(EventQueue.java:612)
>   at
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
>   at
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
>   at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
>   at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
>   at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
>   at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

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