Problem with BigWarp: Does not start

Hi all!

I am trying to align two channels from a lightsheet dataset and I wanted to use BigWarp (since I think would be the most straightforward option). I have convert my dataset to HDF5 as well (original were tif stacks), but I still get the following error:

(Fiji Is Just) ImageJ 2.0.0-rc-69/1.52p; Java 1.8.0_66 [64-bit]; Windows 10 10.0; 89061MB of 98146MB (90%)
 


java.lang.NoClassDefFoundError: net/imglib2/display/RealARGBColorConverter$Imp0
	at bigwarp.BigWarp.addWarpMagnitudeSource(BigWarp.java:1633)
	at bigwarp.BigWarp.<init>(BigWarp.java:328)
	at bigwarp.BigWarp.<init>(BigWarp.java:279)
	at bdv.ij.BigWarpImagePlusPlugIn.run(BigWarpImagePlusPlugIn.java:82)
	at ij.IJ.runUserPlugIn(IJ.java:230)
	at ij.IJ.runPlugIn(IJ.java:193)
	at ij.IJ.runPlugIn(IJ.java:182)
	at net.imagej.legacy.command.LegacyCommand.run(LegacyCommand.java:59)
	at org.scijava.command.CommandModule.run(CommandModule.java:199)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
	at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)

Does any one have any idea on how to solve it?

Also, if someone is familiar with registration and alignment of different channels and of the stacks of the same dataset, I would be very happy of hearing suggestions (I have tried with Line Stack alignment with SIFT and StackReg and the results are not really satisfactory).

Thank you all!

Cheers,

Carlos

2 Likes

Hi @Patinetilla (Carlos),

Welcome to the forum!

I’m aware of the issue and am fixing it now.
See also this thread:

Thanks for reporting,

John

1 Like

I think it’s working again, a temporary fix is available, see here:

1 Like

All good! It is working! I will let you know if it solves my issues, but that´s a different story!
Thanks for your code (and for such a fast debug):slight_smile:

Cheers,
Carlos

1 Like

In case you see weird stuff after transforming…