IntSeg_3D freezing and locking FIJI

Tags: #<Tag:0x00007fd53ff63940> #<Tag:0x00007fd53ff63800>


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(
	at segment3d.Growing_Surface.closeHolesWithLessThanNEdges(
	at segment3d.Growing_Surface_Plugin.closeHoles(
	at segment3d.Growing_Surface_Plugin$2.actionPerformed(
	at javax.swing.AbstractButton.fireActionPerformed(
	at javax.swing.AbstractButton$Handler.actionPerformed(
	at javax.swing.DefaultButtonModel.fireActionPerformed(
	at javax.swing.DefaultButtonModel.setPressed(
	at javax.swing.AbstractButton.doClick(
	at javax.swing.plaf.basic.BasicMenuItemUI.doClick(
	at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(
	at java.awt.Component.processMouseEvent(
	at javax.swing.JComponent.processMouseEvent(
	at java.awt.Component.processEvent(
	at java.awt.Container.processEvent(
	at java.awt.Component.dispatchEventImpl(
	at java.awt.Container.dispatchEventImpl(
	at java.awt.Component.dispatchEvent(
	at java.awt.LightweightDispatcher.retargetMouseEvent(
	at java.awt.LightweightDispatcher.processMouseEvent(
	at java.awt.LightweightDispatcher.dispatchEvent(
	at java.awt.Container.dispatchEventImpl(
	at java.awt.Component.dispatchEvent(
	at java.awt.EventQueue.dispatchEventImpl(
	at java.awt.EventQueue.access$000(
	at java.awt.EventQueue$
	at java.awt.EventQueue$
	at Method)
	at java.awt.EventQueue$
	at java.awt.EventQueue$
	at Method)
	at java.awt.EventQueue.dispatchEvent(
	at java.awt.EventDispatchThread.pumpOneEventForFilters(
	at java.awt.EventDispatchThread.pumpEventsForFilter(
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(
	at java.awt.EventDispatchThread.pumpEvents(
	at java.awt.EventDispatchThread.pumpEvents(


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