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[OBSOLETE] Whole Slide Image (WSI) Registration With ImageJ/Fiji, Elastix and QuPath
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oburri
Last Edited
Jan 9 2024, 15:39

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chiarutt created this document.Mar 25 2021, 10:19
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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 

请问如何注册小鼠脑图谱到对应的脑片图像并生成对应的ROI?

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oburri changed the title from Whole Slide Image Registration With ImageJ/Fiji and QuPath to Whole Slide Image (WSI) Registration With ImageJ/Fiji and QuPath.Apr 22 2021, 13:29
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chiarutt edited the content of this document. (Show Details)Apr 23 2021, 12:52
chiarutt edited the content of this document. (Show Details)Apr 24 2021, 23:27

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.

chiarutt added a subscriber: chiarutt.Nov 2 2021, 16:29

HI @manandhar.sandeep,

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

chiarutt edited the content of this document. (Show Details)Nov 2 2021, 16:33
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chiarutt changed the title from Whole Slide Image (WSI) Registration With ImageJ/Fiji and QuPath to Whole Slide Image (WSI) Registration With ImageJ/Fiji, Elastix and QuPath.
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chiarutt changed the title from Whole Slide Image (WSI) Registration With ImageJ/Fiji, Elastix and QuPath to Whole Slide Image (WSI) Registration With ImageJ/Fiji, Elastix and QuPath [Warpy].Nov 11 2021, 23:31
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chiarutt changed the title from Whole Slide Image (WSI) Registration With ImageJ/Fiji, Elastix and QuPath to Whole Slide Image (WSI) Registration With ImageJ/Fiji, Elastix and QuPath [Warpy].Nov 11 2021, 23:34
chiarutt published a new version of this document.Nov 11 2021, 23:37
chiarutt changed the title from Whole Slide Image (WSI) Registration With ImageJ/Fiji and QuPath to Whole Slide Image (WSI) Registration With ImageJ/Fiji, Elastix and QuPath [Warpy].Nov 11 2021, 23:39
chiarutt edited the content of this document. (Show Details)
chiarutt changed the title from Whole Slide Image (WSI) Registration With ImageJ/Fiji and QuPath to Whole Slide Image (WSI) Registration With ImageJ/Fiji, Elastix and QuPath [Warpy].
chiarutt edited the content of this document. (Show Details)
chiarutt changed the title from Whole Slide Image (WSI) Registration With ImageJ/Fiji and QuPath to Whole Slide Image (WSI) Registration With ImageJ/Fiji, Elastix and QuPath [Warpy].
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chiarutt changed the title from Whole Slide Image (WSI) Registration With ImageJ/Fiji and QuPath to Whole Slide Image (WSI) Registration With ImageJ/Fiji, Elastix and QuPath [Warpy].Nov 11 2021, 23:48
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chiarutt changed the title from Whole Slide Image (WSI) Registration With ImageJ/Fiji, Elastix and QuPath [Warpy] to Whole Slide Image (WSI) Registration With ImageJ/Fiji, Elastix and QuPath [OBSOLETE].Nov 17 2021, 20:50
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chiarutt changed the title from Whole Slide Image (WSI) Registration With ImageJ/Fiji, Elastix and QuPath [OBSOLETE] to [OBSOLETE] Whole Slide Image (WSI) Registration With ImageJ/Fiji, Elastix and QuPath.
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chiarutt edited the content of this document. (Show Details)Nov 17 2021, 20:53
chiarutt edited the content of this document. (Show Details)Nov 18 2021, 11:02

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!

chiarutt edited the content of this document. (Show Details)Nov 25 2021, 09:04

@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

chiarutt edited the content of this document. (Show Details)Jan 10 2022, 10:13
chiarutt edited the content of this document. (Show Details)
chiarutt edited the content of this document. (Show Details)Jan 7 2024, 12:23
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