![]() ![]() ![]() : : Module threw exceptionĪt .report(FutureTask.java:122)Īt .get(FutureTask.java:192)Īt .(TextEditor.java:2932)Īt .$600(TextEditor.java:185)Īt .$9.execute(TextEditor.java:2421)Īt .$Executer$1.run(TextEditor.java:2049)Ĭaused by: : Module threw exceptionĪt .call(ModuleRunner.java:127)Īt .call(ModuleRunner.java:63)Īt .lambda$wrap$2(DefaultThreadService.java:225)Īt .run(FutureTask.java:266)Īt .runWorker(ThreadPoolExecutor.java:1149)Īt $n(ThreadPoolExecutor.java:624)Ĭaused by: Īt .(JavaEngineBindings.java:92)Īt .put(AbstractScriptEngine.java:97)Īt .run(ScriptModule.java:146)Īt .run(ModuleRunner.java:163)Īt .call(ModuleRunner.java:124) ![]() groovy extension to test Elastix functionality on Fiji: I have indicated the extension location for elastix and transformix within the executable location in Fiji and I have gotten this message: Transformix -> set :-) Elastix -> set :-)įollowing which, I encountered the following error message in the console window when I have tested to run the. Could you let me know how to solve this issue? : com/google/gson/RuntimeTypeAdapterFactoryĪt ch.RealTransformDeSerializer.getRealTransformAdapter(RealTransformDeSerializer.java:23)Īt ch.serialize(RealTransformDeSerializer.java:46)Īt ch.TransformHelper.getRealTransform(TransformHelper.java:320)Īt ch.ansferMatchingAnnotationsToImage(TransformHelper.java:189)Īt ch.TransformHelper$transferMatchingAnnotationsToImage.call(Unknown Source)Īt .(CallSiteArray.java:47)Īt .(AbstractCallSite.java:125)Īt .(AbstractCallSite.java:157)Īt (GroovyScriptEngineImpl.java:317)Īt (GroovyScriptEngineImpl.java:155)Īt .DefaultScriptEditor.executeScript(DefaultScriptEditor.java:982)Īt .DefaultScriptEditor.executeScript(DefaultScriptEditor.java:914)Īt .DefaultScriptEditor.executeScript(DefaultScriptEditor.java:829)Īt .DefaultScriptEditor$2.run(DefaultScriptEditor.java:1345)Īt java.base/$RunnableAdapter.call(Unknown Source)Īt java.base/.run(Unknown Source)Īt java.base/.runWorker(Unknown Source)Īt java.base/$n(Unknown Source)Īt java.base/(Unknown Source)Ĭaused by at java.base/(Unknown Source)Īt java.base/(Unknown Source) ![]() INFO: Found 1 candidate transforms for ĮRROR: com/google/gson/RuntimeTypeAdapterFactory Execute Plugins › BIOP › Set and Check Wrappers then indicate the proper location of executable files.Indicate elastix and transformix executable location in Fiji:.\elastix -help to check proper functioning as well Not tested on mac and linux, but you probably need to type either elastix -help or.Check that you got some useful help message and not errors. On windows launch a command console cmd.exe, go to the elastix folder, then type elastix.exe -help.Check, in a command line that elastix can run:.For windows users, you also need to install Visual C++ redistributable, you'll most probably need vc_redist.圆4.exe.This documentation has been tested for elastix 5.0.1. Download the latest release of elastix for your OS.To enable automated registrations capabilities, install elastix:.Enable the bigdataviewer-playground update site, then restart Fiji.In this documentation, a demo dataset is used where a fluorescent WSI image is registered to a RGB DAB image. Reasonably, if the sample is not too deformed, registration at the cellular level can be achieved on the whole slide area. This workflow allows to register slides with transformations which are more complex than affine transform. This page documents a way to register whole slide images in Fiji and analyze their result in QuPath. ![]()
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