[OBSOLETE] Whole Slide Image (WSI) Registration With ImageJ/Fiji, Elastix and QuPath
- Last Author
- oburri
- Last Edited
- Jan 9 2024, 15:39
Event Timeline
i was wondering how to register ＭＯＵＳＥ BRAIN ＡＴＬＡＳ INTO ＴＨＥ IHC ＢＲＡＩＮ SLIECE（４０ＵＭ） AND ＢＡＳＥＤ ON ＴＨＥ ＢＲＡＩＮ ＲＥＧＩＯＮ ＴＯ ＧＥＮＥＲＡＴＥ RELATED ＲＯＩ, THEN AUTO ＣＯＵＮＴ THE ＰＯＳＩＴＩＶＥ SIGNAL ＰＯＩＮＴＳ IN ＥＡＣＨ ROI
Hi,
I am getting this error upon running the transform_objects.groovy from QuPath:
INFO: Found 1 candidate transforms for xxxxxxxxxxxxxxx.ome.tif
ERROR: com/google/gson/RuntimeTypeAdapterFactory
java.lang.NoClassDefFoundError: com/google/gson/RuntimeTypeAdapterFactory
at ch.epfl.biop.qupath.transform.RealTransformDeSerializer.getRealTransformAdapter(RealTransformDeSerializer.java:23)
at ch.epfl.biop.qupath.transform.RealTransformDeSerializer.deserialize(RealTransformDeSerializer.java:46)
at ch.epfl.biop.qupath.transform.TransformHelper.getRealTransform(TransformHelper.java:320)
at ch.epfl.biop.qupath.transform.TransformHelper.transferMatchingAnnotationsToImage(TransformHelper.java:189)
at ch.epfl.biop.qupath.transform.TransformHelper$transferMatchingAnnotationsToImage.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:157)
at Script1.run(Script1.groovy:10)
at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl.eval(GroovyScriptEngineImpl.java:317)
at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl.eval(GroovyScriptEngineImpl.java:155)
at qupath.lib.gui.scripting.DefaultScriptEditor.executeScript(DefaultScriptEditor.java:982)
at qupath.lib.gui.scripting.DefaultScriptEditor.executeScript(DefaultScriptEditor.java:914)
at qupath.lib.gui.scripting.DefaultScriptEditor.executeScript(DefaultScriptEditor.java:829)
at qupath.lib.gui.scripting.DefaultScriptEditor$2.run(DefaultScriptEditor.java:1345)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)
Caused by com.google.gson.RuntimeTypeAdapterFactory at java.base/java.net.URLClassLoader.findClass(Unknown Source)
at java.base/java.lang.ClassLoader.loadClass(Unknown Source)
at java.base/java.lang.ClassLoader.loadClass(Unknown Source)
at ch.epfl.biop.qupath.transform.RealTransformDeSerializer.getRealTransformAdapter(RealTransformDeSerializer.java:23)
at ch.epfl.biop.qupath.transform.RealTransformDeSerializer.deserialize(RealTransformDeSerializer.java:46)
at ch.epfl.biop.qupath.transform.TransformHelper.getRealTransform(TransformHelper.java:320)
at ch.epfl.biop.qupath.transform.TransformHelper.transferMatchingAnnotationsToImage(TransformHelper.java:189)
at ch.epfl.biop.qupath.transform.TransformHelper$transferMatchingAnnotationsToImage.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:157)
at Script1.run(Script1.groovy:10)
at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl.eval(GroovyScriptEngineImpl.java:317)
at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl.eval(GroovyScriptEngineImpl.java:155)
at qupath.lib.gui.scripting.DefaultScriptEditor.executeScript(DefaultScriptEditor.java:982)
at qupath.lib.gui.scripting.DefaultScriptEditor.executeScript(DefaultScriptEditor.java:914)
at qupath.lib.gui.scripting.DefaultScriptEditor.executeScript(DefaultScriptEditor.java:829)
at qupath.lib.gui.scripting.DefaultScriptEditor$2.run(DefaultScriptEditor.java:1345)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)I am not versed in java at all. Could you let me know how to solve this issue?
Thanks.
It's much better to ask on forum.image.sc. THe main problem is that you are using QuPath 0.3.0. The workflow has not been updated yet
Hi,
I have indicated the extension location for elastix and transformix within the executable location in Fiji and I have gotten this message: [INFO] Transformix -> set :-) Elastix -> set :-)
Following which, I encountered the following error message in the console window when I have tested to run the .groovy extension to test Elastix functionality on Fiji:
[ERROR] java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at org.scijava.ui.swing.script.TextEditor.evalScript(TextEditor.java:2932)
at org.scijava.ui.swing.script.TextEditor.access$600(TextEditor.java:185)
at org.scijava.ui.swing.script.TextEditor$9.execute(TextEditor.java:2421)
at org.scijava.ui.swing.script.TextEditor$Executer$1.run(TextEditor.java:2049)
Caused by: java.lang.RuntimeException: Module threw exception
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.UnsupportedOperationException
at org.scijava.plugins.scripting.java.JavaEngineBindings.put(JavaEngineBindings.java:92)
at org.scijava.script.AbstractScriptEngine.put(AbstractScriptEngine.java:97)
at org.scijava.script.ScriptModule.run(ScriptModule.java:146)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:163)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
... 6 more
java.awt.dnd.InvalidDnDOperationException: No drop current
at sun.awt.dnd.SunDropTargetContextPeer.getTransferData(SunDropTargetContextPeer.java:245)
at sun.awt.datatransfer.TransferableProxy.getTransferData(TransferableProxy.java:73)
at java.awt.dnd.DropTargetContext$TransferableProxy.getTransferData(DropTargetContext.java:376)
at org.scijava.ui.swing.script.TextEditorTab$1.drop(TextEditorTab.java:109)
at java.awt.dnd.DropTarget.drop(DropTarget.java:455)
at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538)
at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852)
at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776)
at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48)
at java.awt.Component.dispatchEventImpl(Component.java:4744)
at java.awt.Container.dispatchEventImpl(Container.java:2297)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4609)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4471)
at java.awt.Container.dispatchEventImpl(Container.java:2283)
at java.awt.Window.dispatchEventImpl(Window.java:2746)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84)
at java.awt.EventQueue$4.run(EventQueue.java:733)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:730)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
[ERROR] java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at org.scijava.ui.swing.script.TextEditor.evalScript(TextEditor.java:2932)
at org.scijava.ui.swing.script.TextEditor.access$600(TextEditor.java:185)
at org.scijava.ui.swing.script.TextEditor$9.execute(TextEditor.java:2421)
at org.scijava.ui.swing.script.TextEditor$Executer$1.run(TextEditor.java:2049)
Caused by: java.lang.RuntimeException: Module threw exception
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.UnsupportedOperationException
at org.scijava.plugins.scripting.java.JavaEngineBindings.put(JavaEngineBindings.java:92)
at org.scijava.script.AbstractScriptEngine.put(AbstractScriptEngine.java:97)
at org.scijava.script.ScriptModule.run(ScriptModule.java:146)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:163)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
... 6 more
FYI, I'm not someone who is well versed with Java or any programming language. Can someone kindly assist me on this? Thank you so much!
@WeiJie please use forum.image.sc for issues about this workflow. However, here to be honest I don't see what's wrong at first glance. The error looks pretty weird because there's a drag and drop message error