IntSeg_3D freezing and locking FIJI

3d
segmentation
Tags: #<Tag:0x00007fd53ff63940> #<Tag:0x00007fd53ff63800>

#1

Hi, I’ve been using IntSeg_3d, which is an extremely useful plugin for me, but I’m having problems with it freezing and locking FIJI so that I have to close the program to get it to release. I’m working with 512x512x512 volumes on a standalone graphics computer; the memory is not the limiting factor. The error occurs when I’m getting to the edges of the volume and/or when trying to close holes. I’ve checked my Java and FIJI versions and am up to date. The exception isn’t always exactly the same, but an example follows. I would be very grateful if anyone can help with this - this plugin is key to finally getting to some information in these volumes that has been very elusive.

Exception in thread "AWT-EventQueue-0" java.lang.RuntimeException: Not a closed border: i = 4
	at segment3d.Growing_Surface.getIndependantBorders(Growing_Surface.java:257)
	at segment3d.Growing_Surface.closeHolesWithLessThanNEdges(Growing_Surface.java:286)
	at segment3d.Growing_Surface_Plugin.closeHoles(Growing_Surface_Plugin.java:90)
	at segment3d.Growing_Surface_Plugin$2.actionPerformed(Growing_Surface_Plugin.java:178)
	at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
	at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
	at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
	at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
	at javax.swing.AbstractButton.doClick(AbstractButton.java:357)
	at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809)
	at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850)
	at java.awt.Component.processMouseEvent(Component.java:6289)
	at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
	at java.awt.Component.processEvent(Component.java:6054)
	at java.awt.Container.processEvent(Container.java:2041)
	at java.awt.Component.dispatchEventImpl(Component.java:4652)
	at java.awt.Container.dispatchEventImpl(Container.java:2099)
	at java.awt.Component.dispatchEvent(Component.java:4482)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577)
	at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)
	at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
	at java.awt.Container.dispatchEventImpl(Container.java:2085)
	at java.awt.Component.dispatchEvent(Component.java:4482)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:644)
	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.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
	at java.awt.EventQueue$2.run(EventQueue.java:617)
	at java.awt.EventQueue$2.run(EventQueue.java:615)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:614)
	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)

#2

Maybe the author @bene.schmid has some comments on this? Recently, there was also an issue with IntSeg_3d mentioned on gitter: