http://imagej.273.s1.nabble.com/NullPointerExceptions-in-Spot-Segmentation-3D-Image-Suite-tp5014948p5014955.html
Thanks for your email and glad to see our plugins are useful ;) . It
version of Java. Meanwhile if you have questions or questions about the
> 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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