BigSticher : issues creating dataset & which strategy for prealigned tiles

Hi !
I would like to concatenate tiles that have been prealigned with SIFT algorithm, so I wondered if making an alignment on overlapping regions was really necessary. The coordinates of the tiles (tiff format) are known, as they have been generated on QuPath on prealigned whole slide images before being processed on imageJ. Now I would like to open the full processed image on QuPath but I failed to recontruct the mosaic with big Stitcher.
I tried Plugins > Big Stitcher > Big Sticher > Define a new dataset (automatic loader) > then default parameters in the dialog box as shown in the Neubias demo (@hoerldavid ?) but I really do not understand the error message I get (I’m not sure it’s a memory problem as I tried on a few tiles as well). I also checked the versions as in the post gui exception
The headless mode doesn’t work either. Is it due to the properties of the files ?

[ERROR] Module threw error
java.lang.NoClassDefFoundError: bdv/util/BehaviourTransformEventHandlerPlanar$BehaviourTransformEventHandlerPlanarFactory
	at net.preibisch.stitcher.gui.popup.BDVPopupStitching.createBDV(BDVPopupStitching.java:298)
	at net.preibisch.stitcher.gui.StitchingExplorerPanel.<init>(StitchingExplorerPanel.java:205)
	at net.preibisch.stitcher.gui.StitchingExplorer.<init>(StitchingExplorer.java:113)
	at net.preibisch.stitcher.plugin.BigStitcher.run(BigStitcher.java:80)
	at org.scijava.command.CommandModule.run(CommandModule.java:196)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
	at org.scijava.thread.DefaultThreadService.lambda$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:748)
Caused by: java.lang.ClassNotFoundException: bdv.util.BehaviourTransformEventHandlerPlanar$BehaviourTransformEventHandlerPlanarFactory
	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	... 13 more

and in the console when running headless mode :

Error while executing the main() method of class 'net.imagej.Main':
java.lang.IllegalArgumentException: Invalid service: sc.fiji.bdvpg.scijava.services.SourceAndConverterBdvDisplayService
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:278)
etc (quite long) 

Thank you in advance for your help ! I can provide further information if necessary

Hi @Egl!

It’s because BigStitcher and BigDataViewer-Playground are not compatible for the moment… BigDataViewer-Playground is using dependencies which do not have yet make their way into ImageJ.

Just remove the BigDataViewer Playground update site, and restart Fiji, this should fix BigStitcher.

Best,

Nicolas

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It works, thank you ! However, I still get error messages referring to BDV in the headless mode, I don’t know why …

Is it still the same error message ?

Invalid service: sc.fiji.bdvpg.scijava.services.SourceAndConverterBdvDisplayService

Because this service is only in BigDataViewer-Playground. So you should at least have a different error ? Do you have a different one ? If not, can you check with a ‘fresh Fiji’ ?

Sorry for delayed answer ! It seems to work when removing the jar files related to BDV from the plugin folder, thanks a lot !

Hi, the BigStitcher update site now contains BDV-10, so this should be working as well.

2 Likes