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qupath / qupath-bioformats-extension

Extension to add Bio-Formats image support - **QuPath v0.1.2 only**
GNU General Public License v3.0
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Error Opening .CZI Files with Latest Extension #8

Closed LewisSwansea closed 4 years ago

LewisSwansea commented 6 years ago

This QuPath bioformats extension prevents me from opening some .czi files by returning the error messages below.

Any suggestion as to why this is the case would be extremely helpful as I am new to using QuPath and the current extensions to allow me to open these types of files.

Thanks.

Lewis

INFO: Refreshing extensions in C:\Users\QuPath\extensions INFO: Added extension: C:\Users\QuPath\extensions\bioformats_package (5).jar INFO: Added extension: C:\Users\QuPath\extensions\qupath-extension-bioformats (4).jar INFO: Bio-Formats version 5.9.0 INFO: Selected style: Modena Light INFO: Performing update check... INFO: Starting QuPath with parameters: [] INFO: Project set to Project: Project Test WARN: Unable to open F:\Slide Scanning\2018_08_023365.czi with OpenSlide: F:\Slide Scanning\2018_08_023365.czi: Not a file that OpenSlide can recognize WARN: Error opening F:\Slide Scanning\2018_08_023365.czi with ImageJ: Could not open F:\Slide Scanning\2018_08_023365.czi with ImageJ WARN: Unable to open F:\Slide Scanning\2018_08_023365.czi with OpenSlide: F:\Slide Scanning\2018_08_023365.czi: Not a file that OpenSlide can recognize WARN: Error opening F:\Slide Scanning\2018_08_023365.czi with ImageJ: Could not open F:\Slide Scanning\2018_08_023365.czi with ImageJ INFO: Returning server: Bio-Formats for F:\Slide Scanning\2018_08_023365.czi ERROR: java.lang.UnsatisfiedLinkError: ome.jxrlib.JXRJNI.new_DecodeContext()J ERROR: QuPath exception at ome.jxrlib.JXRJNI.new_DecodeContext(Native Method) at ome.jxrlib.DecodeContext.(DecodeContext.java:43) at ome.jxrlib.AbstractDecode.decodeFirstFrame(AbstractDecode.java:101) at ome.jxrlib.Decode.decodeFirstFrame(Decode.java:51) at loci.formats.services.JPEGXRServiceImpl.decompress(JPEGXRServiceImpl.java:53) at loci.formats.codec.JPEGXRCodec.decompress(JPEGXRCodec.java:84) at loci.formats.in.ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:3712) at loci.formats.in.ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:3669) at loci.formats.in.ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:3664) at loci.formats.in.ZeissCZIReader.openBytes(ZeissCZIReader.java:394) at loci.formats.FormatReader.openBytes(FormatReader.java:886) at loci.formats.ImageReader.openBytes(ImageReader.java:444) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:86) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:683) at qupath.lib.images.servers.BioFormatsImageServer.readBufferedImage(BioFormatsImageServer.java:95) at qupath.lib.images.stores.AbstractImageRegionStore.getThumbnail(AbstractImageRegionStore.java:354) at qupath.lib.gui.QuPathGUI.createNewImageData(QuPathGUI.java:2269) at qupath.lib.gui.QuPathGUI.createNewImageData(QuPathGUI.java:2258) at qupath.lib.gui.QuPathGUI.openImage(QuPathGUI.java:2236) at qupath.lib.gui.QuPathGUI.openImage(QuPathGUI.java:2152) at qupath.lib.gui.QuPathGUI.openImageEntry(QuPathGUI.java:2115) at qupath.lib.gui.panels.ProjectBrowser.lambda$new$1(ProjectBrowser.java:145) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$ClickGenerator.postProcess(Scene.java:3470) at javafx.scene.Scene$ClickGenerator.access$8100(Scene.java:3398) at javafx.scene.Scene$MouseHandler.process(Scene.java:3766) at javafx.scene.Scene$MouseHandler.access$1500(Scene.java:3485) at javafx.scene.Scene.impl_processMouseEvent(Scene.java:1762) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2494) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:380) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:294) at java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$354(GlassViewEventHandler.java:416) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:389) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:415) at com.sun.glass.ui.View.handleMouseEvent(View.java:555) at com.sun.glass.ui.View.notifyMouse(View.java:937) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$null$148(WinApplication.java:191) at java.lang.Thread.run(Thread.java:745) INFO: Returning server: Bio-Formats for F:\Slide Scanning\2018_08_023365.czi

petebankhead commented 6 years ago

It looks like it's related to JPEG-XR compression - you may need to install the Visual Studio 2015 C++ Redistributable, see https://github.com/qupath/qupath/wiki/Supported-image-formats#zeiss-czi

LewisSwansea commented 6 years ago

Thanks Pete!

That sorted out the problem!!