petebankhead
commented
6 years ago Hi Tobias,
Orbit appears to use a different reader for .ndpi provided by Hamamastu - http://www.orbit.bio/2017/11/03/native-ndpis-reader/ - so that may explain the discrepancy.
If the images that fail in QuPath also don't work with Fiji/ImageJ + Bio-Formats then I suspect that may be where the problem lies, and it cannot be resolved within QuPath... although if you observe some of the QuPath failures being read successfully when using Bio-Formats elsewhere then I can investigate that.
I don't know if it's relevant here, but the image size 141568 x 107520 is rather large. The image size was also mentioned as a possible culprit for another issue here, and I'd be curious whether the images that work are smaller than those that don't.
TobiasMR
JohnKPan
sbesson
Hello Pete,
i´m using QuPath to analyze NDPIS files (fluorescence scans) from a Hamamatsu NanoZoomer scanner and with most of the files it works very well!
But now i stumbled on the following problem: some of the files can not be opended and i get an error notification (see below). It is kind of confusing because all files are from the same batch of scanning. In addition, they can be opened with the hamamatsu software called "NDP.view 2" and orbit (http://www.orbit.bio/) without any problems. Of note, i have trouble using ImageJ and Fiji (both with the bioformats extension), too.
Do you have any idea what is going on?
Thank you for your support, Tobias
INFO: Refreshing extensions in C:\Users\Redecket\QuPath\extensions INFO: Added extension: C:\Users\Redecket\QuPath\extensions\bioformats_package.jar INFO: Added extension: C:\Users\Redecket\QuPath\extensions\qupath-extension-bioformats.jar INFO: Bio-Formats version 5.9.2 INFO: Selected style: Modena Light INFO: Performing update check... INFO: Starting QuPath with parameters: [] WARN: Unable to open D:\2018_QuPath_Test_data\TRP1_08.ndpis with OpenSlide: D:\2018_QuPath_Test_data\TRP1_08.ndpis: Not a file that OpenSlide can recognize WARN: Error opening D:\2018_QuPath_Test_data\TRP1_08.ndpis with ImageJ: Could not open D:\2018_QuPath_Test_data\TRP1_08.ndpis with ImageJ INFO: NDPISReader initializing D:\2018_QuPath_Test_data\TRP1_08.ndpis INFO: Reading IFDs INFO: Populating metadata INFO: Populating OME metadata INFO: Generating memoization file D:\2018_QuPath_Test_data.TRP1_08.ndpis.bfmemo (17.70 MB) INFO: Returning server: Bio-Formats for D:\2018_QuPath_Test_data\TRP1_08.ndpis ERROR: Error reading image region D:\2018_QuPath_Test_data\TRP1_08.ndpis: x=0, y=0, w=141568, h=107520, z=0, t=0, downsample=141.57 for image size 4424 x 3360 at loci.formats.in.NDPIReader.openBytes(NDPIReader.java:175) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:198) at loci.formats.in.NDPISReader.openBytes(NDPISReader.java:117) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ImageReader.openBytes(ImageReader.java:444) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:86) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:730) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:95) at qupath.lib.images.stores.AbstractImageRegionStore$DefaultTileWorker$1.call(AbstractImageRegionStore.java:656) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) ERROR: Error reading image region D:\2018_QuPath_Test_data\TRP1_08.ndpis: x=0, y=0, w=141568, h=107520, z=0, t=0, downsample=141.57 for image size 4424 x 3360 at loci.formats.in.NDPIReader.openBytes(NDPIReader.java:175) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:198) at loci.formats.in.NDPISReader.openBytes(NDPISReader.java:117) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ImageReader.openBytes(ImageReader.java:444) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:86) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:730) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:95) at qupath.lib.images.stores.AbstractImageRegionStore$DefaultTileWorker$1.call(AbstractImageRegionStore.java:656) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) WARN: Strange 'bits per sample' of 0 INFO: Returning server: Bio-Formats for D:\2018_QuPath_Test_data\TRP1_08 - 2018-04-25 21.33.31-Cy3-Alexa555.ndpi ERROR: Error opening image 0 for region java.awt.Rectangle[x=0,y=0,width=4424,height=3360] at loci.formats.in.NDPIReader.openBytes(NDPIReader.java:175) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ImageReader.openBytes(ImageReader.java:444) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:86) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:683) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:95) at qupath.lib.images.servers.AbstractImageServer.getBufferedThumbnail(AbstractImageServer.java:70) at qupath.lib.gui.helpers.DisplayHelpers.estimateImageType(DisplayHelpers.java:117) at qupath.lib.gui.QuPathGUI.createNewImageData(QuPathGUI.java:2269) at qupath.lib.gui.QuPathGUI.createNewImageData(QuPathGUI.java:2258) at qupath.lib.gui.QuPathGUI.openImage(QuPathGUI.java:2236) at qupath.lib.gui.viewer.DragDropFileImportListener.handleFileDrop(DragDropFileImportListener.java:253) at qupath.lib.gui.viewer.DragDropFileImportListener.handle(DragDropFileImportListener.java:115) at qupath.lib.gui.viewer.DragDropFileImportListener.handle(DragDropFileImportListener.java:59) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) 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.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) 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.Scene$DnDGesture.fireEvent(Scene.java:2933) at javafx.scene.Scene$DnDGesture.processTargetDrop(Scene.java:3159) at javafx.scene.Scene$DnDGesture.access$6400(Scene.java:2909) at javafx.scene.Scene$DropTargetListener.drop(Scene.java:2873) at com.sun.javafx.tk.quantum.GlassSceneDnDEventHandler.lambda$handleDragDrop$309(GlassSceneDnDEventHandler.java:95) at java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassSceneDnDEventHandler.handleDragDrop(GlassSceneDnDEventHandler.java:92) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleDragDrop$363(GlassViewEventHandler.java:700) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:389) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleDragDrop(GlassViewEventHandler.java:699) at com.sun.glass.ui.View.handleDragDrop(View.java:712) at com.sun.glass.ui.View.notifyDragDrop(View.java:1037) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$null$148(WinApplication.java:191) at java.lang.Thread.run(Thread.java:745) ERROR: Error reading image region D:\2018_QuPath_Test_data\TRP1_08 - 2018-04-25 21.33.31-Cy3-Alexa555.ndpi: x=0, y=0, w=141568, h=107520, z=0, t=0, downsample=643.49 for image size 4424 x 3360 at qupath.lib.images.servers.BioFormatsImageServer.resize(BioFormatsImageServer.java:864) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:689) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:95) at qupath.lib.images.servers.AbstractImageServer.getBufferedThumbnail(AbstractImageServer.java:70) at qupath.lib.gui.helpers.DisplayHelpers.estimateImageType(DisplayHelpers.java:117) at qupath.lib.gui.QuPathGUI.createNewImageData(QuPathGUI.java:2269) at qupath.lib.gui.QuPathGUI.createNewImageData(QuPathGUI.java:2258) at qupath.lib.gui.QuPathGUI.openImage(QuPathGUI.java:2236) at qupath.lib.gui.viewer.DragDropFileImportListener.handleFileDrop(DragDropFileImportListener.java:253) at qupath.lib.gui.viewer.DragDropFileImportListener.handle(DragDropFileImportListener.java:115) at qupath.lib.gui.viewer.DragDropFileImportListener.handle(DragDropFileImportListener.java:59) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) 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.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) 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.Scene$DnDGesture.fireEvent(Scene.java:2933) at javafx.scene.Scene$DnDGesture.processTargetDrop(Scene.java:3159) at javafx.scene.Scene$DnDGesture.access$6400(Scene.java:2909) at javafx.scene.Scene$DropTargetListener.drop(Scene.java:2873) at com.sun.javafx.tk.quantum.GlassSceneDnDEventHandler.lambda$handleDragDrop$309(GlassSceneDnDEventHandler.java:95) at java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassSceneDnDEventHandler.handleDragDrop(GlassSceneDnDEventHandler.java:92) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleDragDrop$363(GlassViewEventHandler.java:700) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:389) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleDragDrop(GlassViewEventHandler.java:699) at com.sun.glass.ui.View.handleDragDrop(View.java:712) at com.sun.glass.ui.View.notifyDragDrop(View.java:1037) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$null$148(WinApplication.java:191) at java.lang.Thread.run(Thread.java:745) ERROR: Error opening image 0 for region java.awt.Rectangle[x=0,y=0,width=4424,height=3360] at loci.formats.in.NDPIReader.openBytes(NDPIReader.java:175) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ImageReader.openBytes(ImageReader.java:444) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:86) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:683) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:95) at qupath.lib.images.stores.AbstractImageRegionStore$DefaultTileWorker$1.call(AbstractImageRegionStore.java:656) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) ERROR: Error reading image region D:\2018_QuPath_Test_data\TRP1_08 - 2018-04-25 21.33.31-Cy3-Alexa555.ndpi: x=0, y=0, w=141568, h=107520, z=0, t=0, downsample=141.57 for image size 4424 x 3360 at qupath.lib.images.servers.BioFormatsImageServer.resize(BioFormatsImageServer.java:864) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:689) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:95) at qupath.lib.images.stores.AbstractImageRegionStore$DefaultTileWorker$1.call(AbstractImageRegionStore.java:656) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) WARN: Strange 'bits per sample' of 0 INFO: Returning server: Bio-Formats for D:\2018_QuPath_Test_data\TRP1_08 - 2018-04-25 21.33.31-FITC-Alexa488.ndpi ERROR: Error opening image 0 for region java.awt.Rectangle[x=0,y=0,width=4424,height=3360] at loci.formats.in.NDPIReader.openBytes(NDPIReader.java:175) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ImageReader.openBytes(ImageReader.java:444) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:86) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:683) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:95) at qupath.lib.images.servers.AbstractImageServer.getBufferedThumbnail(AbstractImageServer.java:70) at qupath.lib.gui.helpers.DisplayHelpers.estimateImageType(DisplayHelpers.java:117) at qupath.lib.gui.QuPathGUI.createNewImageData(QuPathGUI.java:2269) at qupath.lib.gui.QuPathGUI.createNewImageData(QuPathGUI.java:2258) at qupath.lib.gui.QuPathGUI.openImage(QuPathGUI.java:2236) at qupath.lib.gui.viewer.DragDropFileImportListener.handleFileDrop(DragDropFileImportListener.java:253) at qupath.lib.gui.viewer.DragDropFileImportListener.handle(DragDropFileImportListener.java:115) at qupath.lib.gui.viewer.DragDropFileImportListener.handle(DragDropFileImportListener.java:59) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) 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.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) 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.Scene$DnDGesture.fireEvent(Scene.java:2933) at javafx.scene.Scene$DnDGesture.processTargetDrop(Scene.java:3159) at javafx.scene.Scene$DnDGesture.access$6400(Scene.java:2909) at javafx.scene.Scene$DropTargetListener.drop(Scene.java:2873) at com.sun.javafx.tk.quantum.GlassSceneDnDEventHandler.lambda$handleDragDrop$309(GlassSceneDnDEventHandler.java:95) at java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassSceneDnDEventHandler.handleDragDrop(GlassSceneDnDEventHandler.java:92) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleDragDrop$363(GlassViewEventHandler.java:700) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:389) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleDragDrop(GlassViewEventHandler.java:699) at com.sun.glass.ui.View.handleDragDrop(View.java:712) at com.sun.glass.ui.View.notifyDragDrop(View.java:1037) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$null$148(WinApplication.java:191) at java.lang.Thread.run(Thread.java:745) ERROR: Error reading image region D:\2018_QuPath_Test_data\TRP1_08 - 2018-04-25 21.33.31-FITC-Alexa488.ndpi: x=0, y=0, w=141568, h=107520, z=0, t=0, downsample=643.49 for image size 4424 x 3360 at qupath.lib.images.servers.BioFormatsImageServer.resize(BioFormatsImageServer.java:864) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:689) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:95) at qupath.lib.images.servers.AbstractImageServer.getBufferedThumbnail(AbstractImageServer.java:70) at qupath.lib.gui.helpers.DisplayHelpers.estimateImageType(DisplayHelpers.java:117) at qupath.lib.gui.QuPathGUI.createNewImageData(QuPathGUI.java:2269) at qupath.lib.gui.QuPathGUI.createNewImageData(QuPathGUI.java:2258) at qupath.lib.gui.QuPathGUI.openImage(QuPathGUI.java:2236) at qupath.lib.gui.viewer.DragDropFileImportListener.handleFileDrop(DragDropFileImportListener.java:253) at qupath.lib.gui.viewer.DragDropFileImportListener.handle(DragDropFileImportListener.java:115) at qupath.lib.gui.viewer.DragDropFileImportListener.handle(DragDropFileImportListener.java:59) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) 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.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) 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.Scene$DnDGesture.fireEvent(Scene.java:2933) at javafx.scene.Scene$DnDGesture.processTargetDrop(Scene.java:3159) at javafx.scene.Scene$DnDGesture.access$6400(Scene.java:2909) at javafx.scene.Scene$DropTargetListener.drop(Scene.java:2873) at com.sun.javafx.tk.quantum.GlassSceneDnDEventHandler.lambda$handleDragDrop$309(GlassSceneDnDEventHandler.java:95) at java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassSceneDnDEventHandler.handleDragDrop(GlassSceneDnDEventHandler.java:92) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleDragDrop$363(GlassViewEventHandler.java:700) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:389) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleDragDrop(GlassViewEventHandler.java:699) at com.sun.glass.ui.View.handleDragDrop(View.java:712) at com.sun.glass.ui.View.notifyDragDrop(View.java:1037) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$null$148(WinApplication.java:191) at java.lang.Thread.run(Thread.java:745) ERROR: Error opening image 0 for region java.awt.Rectangle[x=0,y=0,width=4424,height=3360] at loci.formats.in.NDPIReader.openBytes(NDPIReader.java:175) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ImageReader.openBytes(ImageReader.java:444) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:86) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:683) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:95) at qupath.lib.images.stores.AbstractImageRegionStore$DefaultTileWorker$1.call(AbstractImageRegionStore.java:656) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) ERROR: Error reading image region D:\2018_QuPath_Test_data\TRP1_08 - 2018-04-25 21.33.31-FITC-Alexa488.ndpi: x=0, y=0, w=141568, h=107520, z=0, t=0, downsample=141.57 for image size 4424 x 3360 at qupath.lib.images.servers.BioFormatsImageServer.resize(BioFormatsImageServer.java:864) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:689) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:95) at qupath.lib.images.stores.AbstractImageRegionStore$DefaultTileWorker$1.call(AbstractImageRegionStore.java:656) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) ERROR: QuPath exception at qupath.lib.gui.viewer.QuPathViewer.updateBufferedImage(QuPathViewer.java:1583) at qupath.lib.gui.viewer.QuPathViewer.updateBufferedImage(QuPathViewer.java:1559) at qupath.lib.gui.viewer.QuPathViewer.paintViewer(QuPathViewer.java:1382) at qupath.lib.gui.viewer.QuPathViewer.paintCanvas(QuPathViewer.java:371) at qupath.lib.gui.viewer.QuPathViewerPlus.paintCanvas(QuPathViewerPlus.java:277) at qupath.lib.gui.viewer.QuPathViewer.lambda$repaint$4(QuPathViewer.java:452) at com.sun.javafx.application.PlatformImpl.lambda$null$173(PlatformImpl.java:295) at java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.application.PlatformImpl.lambda$runLater$174(PlatformImpl.java:294) at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$null$148(WinApplication.java:191) at java.lang.Thread.run(Thread.java:745) ERROR: Error reading image region D:\2018_QuPath_Test_data\TRP1_08.ndpis: x=0, y=0, w=141568, h=107520, z=0, t=0, downsample=141.57 for image size 4424 x 3360 at loci.formats.in.NDPIReader.openBytes(NDPIReader.java:175) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:198) at loci.formats.in.NDPISReader.openBytes(NDPISReader.java:117) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ImageReader.openBytes(ImageReader.java:444) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:86) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:730) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:95) at qupath.lib.images.stores.AbstractImageRegionStore$DefaultTileWorker$1.call(AbstractImageRegionStore.java:656) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) ERROR: QuPath exception at qupath.lib.gui.viewer.QuPathViewer.updateBufferedImage(QuPathViewer.java:1583) at qupath.lib.gui.viewer.QuPathViewer.updateBufferedImage(QuPathViewer.java:1559) at qupath.lib.gui.viewer.QuPathViewer.paintViewer(QuPathViewer.java:1382) at qupath.lib.gui.viewer.QuPathViewer.paintCanvas(QuPathViewer.java:371) at qupath.lib.gui.viewer.QuPathViewerPlus.paintCanvas(QuPathViewerPlus.java:277) at qupath.lib.gui.viewer.QuPathViewer.lambda$repaint$4(QuPathViewer.java:452) at com.sun.javafx.application.PlatformImpl.lambda$null$173(PlatformImpl.java:295) at java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.application.PlatformImpl.lambda$runLater$174(PlatformImpl.java:294) at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$null$148(WinApplication.java:191) at java.lang.Thread.run(Thread.java:745) ERROR: Error reading image region D:\2018_QuPath_Test_data\TRP1_08.ndpis: x=0, y=0, w=141568, h=107520, z=0, t=0, downsample=141.57 for image size 4424 x 3360 at loci.formats.in.NDPIReader.openBytes(NDPIReader.java:175) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:198) at loci.formats.in.NDPISReader.openBytes(NDPISReader.java:117) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ImageReader.openBytes(ImageReader.java:444) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:86) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:730) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:95) at qupath.lib.images.stores.AbstractImageRegionStore$DefaultTileWorker$1.call(AbstractImageRegionStore.java:656) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) ERROR: QuPath exception at qupath.lib.gui.viewer.QuPathViewer.updateBufferedImage(QuPathViewer.java:1583) at qupath.lib.gui.viewer.QuPathViewer.updateBufferedImage(QuPathViewer.java:1559) at qupath.lib.gui.viewer.QuPathViewer.paintViewer(QuPathViewer.java:1382) at qupath.lib.gui.viewer.QuPathViewer.paintCanvas(QuPathViewer.java:371) at qupath.lib.gui.viewer.QuPathViewerPlus.paintCanvas(QuPathViewerPlus.java:277) at qupath.lib.gui.viewer.QuPathViewer.lambda$repaint$4(QuPathViewer.java:452) at com.sun.javafx.application.PlatformImpl.lambda$null$173(PlatformImpl.java:295) at java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.application.PlatformImpl.lambda$runLater$174(PlatformImpl.java:294) at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$null$148(WinApplication.java:191) at java.lang.Thread.run(Thread.java:745) ERROR: Error reading image region D:\2018_QuPath_Test_data\TRP1_08.ndpis: x=0, y=0, w=141568, h=107520, z=0, t=0, downsample=141.57 for image size 4424 x 3360 at loci.formats.in.NDPIReader.openBytes(NDPIReader.java:175) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:198) at loci.formats.in.NDPISReader.openBytes(NDPISReader.java:117) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ImageReader.openBytes(ImageReader.java:444) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:86) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:730) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:95) at qupath.lib.images.stores.AbstractImageRegionStore$DefaultTileWorker$1.call(AbstractImageRegionStore.java:656) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) ERROR: QuPath exception at qupath.lib.gui.viewer.QuPathViewer.updateBufferedImage(QuPathViewer.java:1583) at qupath.lib.gui.viewer.QuPathViewer.updateBufferedImage(QuPathViewer.java:1559) at qupath.lib.gui.viewer.QuPathViewer.paintViewer(QuPathViewer.java:1382) at qupath.lib.gui.viewer.QuPathViewer.paintCanvas(QuPathViewer.java:371) at qupath.lib.gui.viewer.QuPathViewerPlus.paintCanvas(QuPathViewerPlus.java:277) at qupath.lib.gui.viewer.QuPathViewer.lambda$repaint$4(QuPathViewer.java:452) at com.sun.javafx.application.PlatformImpl.lambda$null$173(PlatformImpl.java:295) at java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.application.PlatformImpl.lambda$runLater$174(PlatformImpl.java:294) at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$null$148(WinApplication.java:191) at java.lang.Thread.run(Thread.java:745) ERROR: Error reading image region D:\2018_QuPath_Test_data\TRP1_08.ndpis: x=0, y=0, w=141568, h=107520, z=0, t=0, downsample=141.57 for image size 4424 x 3360 at loci.formats.in.NDPIReader.openBytes(NDPIReader.java:175) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:198) at loci.formats.in.NDPISReader.openBytes(NDPISReader.java:117) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ImageReader.openBytes(ImageReader.java:444) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:86) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:730) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:95) at qupath.lib.images.stores.AbstractImageRegionStore$DefaultTileWorker$1.call(AbstractImageRegionStore.java:656) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) ERROR: QuPath exception at qupath.lib.gui.viewer.QuPathViewer.updateBufferedImage(QuPathViewer.java:1583) at qupath.lib.gui.viewer.QuPathViewer.updateBufferedImage(QuPathViewer.java:1559) at qupath.lib.gui.viewer.QuPathViewer.paintViewer(QuPathViewer.java:1382) at qupath.lib.gui.viewer.QuPathViewer.paintCanvas(QuPathViewer.java:371) at qupath.lib.gui.viewer.QuPathViewerPlus.paintCanvas(QuPathViewerPlus.java:277) at qupath.lib.gui.viewer.QuPathViewer.lambda$repaint$4(QuPathViewer.java:452) at com.sun.javafx.application.PlatformImpl.lambda$null$173(PlatformImpl.java:295) at java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.application.PlatformImpl.lambda$runLater$174(PlatformImpl.java:294) at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$null$148(WinApplication.java:191) at java.lang.Thread.run(Thread.java:745) ERROR: Error reading image region D:\2018_QuPath_Test_data\TRP1_08.ndpis: x=0, y=0, w=141568, h=107520, z=0, t=0, downsample=141.57 for image size 4424 x 3360 at loci.formats.in.NDPIReader.openBytes(NDPIReader.java:175) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:198) at loci.formats.in.NDPISReader.openBytes(NDPISReader.java:117) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ImageReader.openBytes(ImageReader.java:444) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:86) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:730) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:95) at qupath.lib.images.stores.AbstractImageRegionStore$DefaultTileWorker$1.call(AbstractImageRegionStore.java:656) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) ERROR: QuPath exception at qupath.lib.gui.viewer.QuPathViewer.updateBufferedImage(QuPathViewer.java:1583) at qupath.lib.gui.viewer.QuPathViewer.updateBufferedImage(QuPathViewer.java:1559) at qupath.lib.gui.viewer.QuPathViewer.paintViewer(QuPathViewer.java:1382) at qupath.lib.gui.viewer.QuPathViewer.paintCanvas(QuPathViewer.java:371) at qupath.lib.gui.viewer.QuPathViewerPlus.paintCanvas(QuPathViewerPlus.java:277) at qupath.lib.gui.viewer.QuPathViewer.lambda$repaint$4(QuPathViewer.java:452) at com.sun.javafx.application.PlatformImpl.lambda$null$173(PlatformImpl.java:295) at java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.application.PlatformImpl.lambda$runLater$174(PlatformImpl.java:294) at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$null$148(WinApplication.java:191) at java.lang.Thread.run(Thread.java:745) ERROR: Error reading image region D:\2018_QuPath_Test_data\TRP1_08.ndpis: x=0, y=0, w=141568, h=107520, z=0, t=0, downsample=141.57 for image size 4424 x 3360 at loci.formats.in.NDPIReader.openBytes(NDPIReader.java:175) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:198) at loci.formats.in.NDPISReader.openBytes(NDPISReader.java:117) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ImageReader.openBytes(ImageReader.java:444) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:86) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:730) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:95) at qupath.lib.images.stores.AbstractImageRegionStore$DefaultTileWorker$1.call(AbstractImageRegionStore.java:656) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) WARN: Unable to open D:\2018_QuPath_Test_data\TRP1_08 - 2018-04-25 21.33.31.ndpis with OpenSlide: D:\2018_QuPath_Test_data\TRP1_08 - 2018-04-25 21.33.31.ndpis: Not a file that OpenSlide can recognize WARN: Error opening D:\2018_QuPath_Test_data\TRP1_08 - 2018-04-25 21.33.31.ndpis with ImageJ: Could not open D:\2018_QuPath_Test_data\TRP1_08 - 2018-04-25 21.33.31.ndpis with ImageJ INFO: NDPISReader initializing D:\2018_QuPath_Test_data\TRP1_08 - 2018-04-25 21.33.31.ndpis INFO: Reading IFDs INFO: Populating metadata INFO: Populating OME metadata INFO: Generating memoization file D:\2018_QuPath_Test_data.TRP1_08 - 2018-04-25 21.33.31.ndpis.bfmemo (17.70 MB) INFO: Returning server: Bio-Formats for D:\2018_QuPath_Test_data\TRP1_08 - 2018-04-25 21.33.31.ndpis ERROR: Error reading image region D:\2018_QuPath_Test_data\TRP1_08 - 2018-04-25 21.33.31.ndpis: x=0, y=0, w=141568, h=107520, z=0, t=0, downsample=141.57 for image size 4424 x 3360 at loci.formats.in.NDPIReader.openBytes(NDPIReader.java:175) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:198) at loci.formats.in.NDPISReader.openBytes(NDPISReader.java:117) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ImageReader.openBytes(ImageReader.java:444) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:86) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:730) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:95) at qupath.lib.images.stores.AbstractImageRegionStore$DefaultTileWorker$1.call(AbstractImageRegionStore.java:656) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) ERROR: Error reading image region D:\2018_QuPath_Test_data\TRP1_08 - 2018-04-25 21.33.31.ndpis: x=0, y=0, w=141568, h=107520, z=0, t=0, downsample=141.57 for image size 4424 x 3360 at loci.formats.in.NDPIReader.openBytes(NDPIReader.java:175) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:198) at loci.formats.in.NDPISReader.openBytes(NDPISReader.java:117) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ImageReader.openBytes(ImageReader.java:444) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:86) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:730) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:95) at qupath.lib.images.stores.AbstractImageRegionStore$DefaultTileWorker$1.call(AbstractImageRegionStore.java:656) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) ERROR: QuPath exception at qupath.lib.gui.viewer.QuPathViewer.updateBufferedImage(QuPathViewer.java:1583) at qupath.lib.gui.viewer.QuPathViewer.updateBufferedImage(QuPathViewer.java:1559) at qupath.lib.gui.viewer.QuPathViewer.paintViewer(QuPathViewer.java:1382) at qupath.lib.gui.viewer.QuPathViewer.paintCanvas(QuPathViewer.java:371) at qupath.lib.gui.viewer.QuPathViewerPlus.paintCanvas(QuPathViewerPlus.java:277) at qupath.lib.gui.viewer.QuPathViewer.lambda$repaint$4(QuPathViewer.java:452) at com.sun.javafx.application.PlatformImpl.lambda$null$173(PlatformImpl.java:295) at java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.application.PlatformImpl.lambda$runLater$174(PlatformImpl.java:294) at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$null$148(WinApplication.java:191) at java.lang.Thread.run(Thread.java:745) ERROR: Error reading image region D:\2018_QuPath_Test_data\TRP1_08 - 2018-04-25 21.33.31.ndpis: x=0, y=0, w=141568, h=107520, z=0, t=0, downsample=141.57 for image size 4424 x 3360 at loci.formats.in.NDPIReader.openBytes(NDPIReader.java:175) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:198) at loci.formats.in.NDPISReader.openBytes(NDPISReader.java:117) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ImageReader.openBytes(ImageReader.java:444) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:86) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:730) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:95) at qupath.lib.images.stores.AbstractImageRegionStore$DefaultTileWorker$1.call(AbstractImageRegionStore.java:656) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) ERROR: QuPath exception at qupath.lib.gui.viewer.QuPathViewer.updateBufferedImage(QuPathViewer.java:1583) at qupath.lib.gui.viewer.QuPathViewer.updateBufferedImage(QuPathViewer.java:1559) at qupath.lib.gui.viewer.QuPathViewer.paintViewer(QuPathViewer.java:1382) at qupath.lib.gui.viewer.QuPathViewer.paintCanvas(QuPathViewer.java:371) at qupath.lib.gui.viewer.QuPathViewerPlus.paintCanvas(QuPathViewerPlus.java:277) at qupath.lib.gui.viewer.QuPathViewer.lambda$repaint$4(QuPathViewer.java:452) at com.sun.javafx.application.PlatformImpl.lambda$null$173(PlatformImpl.java:295) at java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.application.PlatformImpl.lambda$runLater$174(PlatformImpl.java:294) at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$null$148(WinApplication.java:191) at java.lang.Thread.run(Thread.java:745) ERROR: Error reading image region D:\2018_QuPath_Test_data\TRP1_08 - 2018-04-25 21.33.31.ndpis: x=0, y=0, w=141568, h=107520, z=0, t=0, downsample=141.57 for image size 4424 x 3360 at loci.formats.in.NDPIReader.openBytes(NDPIReader.java:175) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:198) at loci.formats.in.NDPISReader.openBytes(NDPISReader.java:117) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ImageReader.openBytes(ImageReader.java:444) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:86) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:730) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:95) at qupath.lib.images.stores.AbstractImageRegionStore$DefaultTileWorker$1.call(AbstractImageRegionStore.java:656) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) ERROR: QuPath exception at qupath.lib.gui.viewer.QuPathViewer.updateBufferedImage(QuPathViewer.java:1583) at qupath.lib.gui.viewer.QuPathViewer.updateBufferedImage(QuPathViewer.java:1559) at qupath.lib.gui.viewer.QuPathViewer.paintViewer(QuPathViewer.java:1382) at qupath.lib.gui.viewer.QuPathViewer.paintCanvas(QuPathViewer.java:371) at qupath.lib.gui.viewer.QuPathViewerPlus.paintCanvas(QuPathViewerPlus.java:277) at qupath.lib.gui.viewer.QuPathViewer.lambda$repaint$4(QuPathViewer.java:452) at com.sun.javafx.application.PlatformImpl.lambda$null$173(PlatformImpl.java:295) at java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.application.PlatformImpl.lambda$runLater$174(PlatformImpl.java:294) at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$null$148(WinApplication.java:191) at java.lang.Thread.run(Thread.java:745) ERROR: Error reading image region D:\2018_QuPath_Test_data\TRP1_08 - 2018-04-25 21.33.31.ndpis: x=0, y=0, w=141568, h=107520, z=0, t=0, downsample=141.57 for image size 4424 x 3360 at loci.formats.in.NDPIReader.openBytes(NDPIReader.java:175) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:198) at loci.formats.in.NDPISReader.openBytes(NDPISReader.java:117) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ImageReader.openBytes(ImageReader.java:444) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:86) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:730) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:95) at qupath.lib.images.stores.AbstractImageRegionStore$DefaultTileWorker$1.call(AbstractImageRegionStore.java:656) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745)