Training Error

[abadgerw]

I got everything installed and downloaded. I created training annotations (foreground and background) and ran training for a cellpose model through the cellsparse extension but received the following error:

ERROR: QuPath exception: pos < flushedPos!
java.lang.IndexOutOfBoundsException: pos < flushedPos!
at java.desktop/javax.imageio.stream.ImageInputStreamImpl.seek(Unknown Source)
at java.desktop/com.sun.imageio.plugins.png.IDATOutputStream.finishChunk(Unknown Source)
at java.desktop/com.sun.imageio.plugins.png.IDATOutputStream.deflate(Unknown Source)
at java.desktop/com.sun.imageio.plugins.png.IDATOutputStream.finish(Unknown Source)
at java.desktop/com.sun.imageio.plugins.png.PNGImageWriter.write_IDAT(Unknown Source)
at java.desktop/com.sun.imageio.plugins.png.PNGImageWriter.write(Unknown Source)
at java.desktop/javax.imageio.ImageWriter.write(Unknown Source)
at java.desktop/javax.imageio.ImageIO.doWrite(Unknown Source)
at java.desktop/javax.imageio.ImageIO.write(Unknown Source)
at org.elephant.cellsparse.AbstractCellsparseCommands.base64Encode(AbstractCellsparseCommands.java:37)
at org.elephant.cellsparse.AbstractCellsparseCommands.CellsparseCommand(AbstractCellsparseCommands.java:83)
at org.elephant.cellsparse.CellsparseCellposeExtension$CellsparseCellposeCommands.lambda$new$0(CellsparseCellposeExtension.java:51)
at qupath.lib.gui.QuPathGUI.lambda$createImageDataAction$0(QuPathGUI.java:387)
at org.controlsfx.control.action.Action.handle(Action.java:423)
at org.controlsfx.control.action.Action.handle(Action.java:64)
at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234)
at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49)
at javafx.event.Event.fireEvent(Event.java:198)
at javafx.scene.control.MenuItem.fire(MenuItem.java:459)
at com.sun.javafx.scene.control.GlobalMenuAdapter.lambda$bindMenuItemProperties$2(GlobalMenuAdapter.java:153)
at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234)
at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
at javafx.event.Event.fireEvent(Event.java:198)
at javafx.scene.control.MenuItem.fire(MenuItem.java:459)
at com.sun.javafx.tk.quantum.GlassSystemMenu$1.action(GlassSystemMenu.java:234)

Do you happen to know where this is stemming from?

Thanks in advance for your help!

[abadgerw]

@ksugar I also tested with stardist via cellsparse and got the same error as above.

[ksugar]

Hi @abadgerw, thank you for reporting the issue. Could you provide me with some information to investigate it further?

• Size of the input image (Width x Height)
• Number of channels of the input image
• Number of annotations
  Thanks!