QuPATH - Create Warpy Registration Error - Image Analysis

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Hi Everyone,

UPDATE: It seems like I was able to start the Warpy registration, however once I put in the landmarks (rectangles) I received error where Coarse Affine Registration was able to start, but then the program gets stuck here. I believe it should be followed by a landmark registration.

image 1920×1104 160 KB

Below is the error code

Keymap list file C:\Users\steve\AppData\Roaming\fiji\bigdataviewer\config\keymaps\keymaps.yaml not found. Using builtin styles.
[WARNING] 2 exceptions occurred during plugin discovery.
Appearance settings file C:\Users\steve\AppData\Roaming\fiji\bigdataviewer\config/appearance.yaml not found. Using defaults.
[WARNING] Ignoring unsupported output: p1 [net.imglib2.RealPoint]
[WARNING] Ignoring unsupported output: p2 [net.imglib2.RealPoint]
IN action listener
Add point -1.2051654445343618:-0.4872674722166416
Add point -1.2051654445343618:0.012732527783358427
Add point -1.2051654445343618:0.5127325277833584
Add point -0.7051654445343618:-0.4872674722166416
Add point -0.7051654445343618:0.012732527783358427
Add point -0.7051654445343618:0.5127325277833584
Add point -0.2051654445343618:-0.4872674722166416
Add point -0.2051654445343618:0.012732527783358427
Add point -0.2051654445343618:0.5127325277833584
Add point 0.2948345554656382:-0.4872674722166416
Add point 0.2948345554656382:0.012732527783358427
Add point 0.2948345554656382:0.5127325277833584
Add point 0.7948345554656382:-0.4872674722166416
Add point 0.7948345554656382:0.012732527783358427
Add point 0.7948345554656382:0.5127325277833584
[WARNING] Ignoring unsupported output: pts [net.imglib2.RealPoint]
[WARNING] Ignoring unsupported output: pts [net.imglib2.RealPoint]
[WARNING] Ignoring unsupported output: pts [net.imglib2.RealPoint]
[WARNING] Ignoring unsupported output: pts [net.imglib2.RealPoint]
[WARNING] Ignoring unsupported output: pts [net.imglib2.RealPoint]
[WARNING] Ignoring unsupported output: pts [net.imglib2.RealPoint]
[WARNING] Ignoring unsupported output: pts [net.imglib2.RealPoint]
[WARNING] Ignoring unsupported output: pts [net.imglib2.RealPoint]
[WARNING] Ignoring unsupported output: pts [net.imglib2.RealPoint]
[WARNING] Ignoring unsupported output: pts [net.imglib2.RealPoint]
[WARNING] Ignoring unsupported output: pts [net.imglib2.RealPoint]
[WARNING] Ignoring unsupported output: pts [net.imglib2.RealPoint]
[WARNING] Ignoring unsupported output: pts [net.imglib2.RealPoint]
[WARNING] Ignoring unsupported output: pts [net.imglib2.RealPoint]
[WARNING] Ignoring unsupported output: pts [net.imglib2.RealPoint]
----------- First registration - Coarse Affine
java.lang.UnsupportedOperationException
at itc.transforms.elastix.ElastixTransform.load(ElastixTransform.java:266)
at ch.epfl.biop.sourceandconverter.register.Elastix2DAffineRegister.run(Elastix2DAffineRegister.java:160)
at ch.epfl.biop.scijava.command.source.register.Elastix2DAffineRegisterCommand.run(Elastix2DAffineRegisterCommand.java:72)
at org.scijava.command.CommandModule.run(CommandModule.java:196)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:163)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
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:750)
[ERROR] Error during registration
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 ch.epfl.biop.scijava.command.source.register.Wizard2DWholeScanRegisterCommand.run(Wizard2DWholeScanRegisterCommand.java:297)
at org.scijava.command.CommandModule.run(CommandModule.java:196)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:163)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
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:750)
Caused by: java.lang.RuntimeException: Module threw exception
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
… 6 more
Caused by: java.lang.NullPointerException
at net.imglib2.realtransform.AffineTransform3D.set(AffineTransform3D.java:761)
at bdv.tools.transformation.TransformedSource.setFixedTransform(TransformedSource.java:176)
at sc.fiji.bdvpg.sourceandconverter.transform.SourceAffineTransformer.apply(SourceAffineTransformer.java:89)
at ch.epfl.biop.scijava.command.source.register.RegisterWholeSlideScans2DCommand.run(RegisterWholeSlideScans2DCommand.java:127)
at org.scijava.command.CommandModule.run(CommandModule.java:196)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:163)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
… 6 more
java.lang.NullPointerException
at net.imglib2.realtransform.AbstractRealTransformSequence.add(AbstractRealTransformSequence.java:84)
at ch.epfl.biop.scijava.command.source.register.WarpyRegisterCommand.run(WarpyRegisterCommand.java:129)
at org.scijava.command.CommandModule.run(CommandModule.java:196)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:163)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
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:750)

Any help is greatly appreciated, thank you!

Hi @sshen85 ,

Can you try to follow the instructions detailed here and report back ?

The script should help narrow down where the issue is.

Best,

Nicolas

Hey @NicoKiaru ,

Thanks for the reply! I tried the script and I believe it does work? (Since the last and the 2nd last image are both rotated).

Below are some images attached.

Thanks!

image 1844×1313 154 KB image 1069×499 107 KB image 1457×534 153 KB

Hey Nicolas,

I repeated the procedure again with “Millimeter” but still encountered the same error unfortunately. I left every other setting as default as well. Just kind of lost on where this problem originate from.

Best,
Steven

And post the content in this thread. Here’s my info for instance:

OS and Dependencies Info

OS Windows 10
ImageJ 2.9.0
IJ 1.53t
ABBA 0.5.3
BigWarp 7.0.7
Bdv 10.4.3
Bdv Vistools 1.0.0-beta-31
Bdv Biop Tools 0.5.12
Bdv Playground 0.6.6
Biop Image Loader 0.4.4
Biop Wrappers 0.7.11
Registration Server 0.1.4
(Legacy) Bdv BioFormats 0.4.4
Updates sites: ImageJ Fiji Java-8 FLIMJ PTBIOP