Blank image window BigDataViewer/BigSticher/Multiview Reconstruction

Usage & Issues
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#1

Hi All,
I ahve recently moved over to use Ubuntu for light sheet data analysis and processing. Most frustratingly I am getting no display when using BigDataViewer in Fiji (ImageJ 2.0.0-rc-69/152i; java 1.8.0_172[64-bit]) on my Ubuntu machine and cannot work out why as it is working on a different Ubuntu machine 16.04.5 LTS and in Windows 10 where the Multiview dataset was defined.

My system is:
Ubuntu 18.04.1 LTS 64-bit
RAM: 188.8 GiB
Intel® Xeon® CPU E5-2620 v4 @ 2.10GHz × 32
GeForce GTX 1080/PCIe/SSE2
The ImageJ console gives me the following exception:

Exception in thread "PainterThread" java.lang.NoClassDefFoundError: net/imglib2/util/StopWatch
	at net.imglib2.cache.iotiming.IoStatistics.<init>(IoStatistics.java:21)
	at net.imglib2.cache.iotiming.CacheIoTiming.getIoStatistics(CacheIoTiming.java:30)
	at net.imglib2.cache.iotiming.CacheIoTiming.getIoStatistics(CacheIoTiming.java:17)
	at net.imglib2.cache.iotiming.CacheIoTiming.getIoTimeBudget(CacheIoTiming.java:40)
	at bdv.viewer.render.MultiResolutionRenderer.createProjector(MultiResolutionRenderer.java:658)
	at bdv.viewer.render.MultiResolutionRenderer.paint(MultiResolutionRenderer.java:496)
	at bdv.viewer.ViewerPanel.paint(ViewerPanel.java:485)
	at net.imglib2.ui.PainterThread.run(PainterThread.java:86)
Caused by: java.lang.ClassNotFoundException: net.imglib2.util.StopWatch
	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)
	... 8 more
Exception in thread "PainterThread" java.lang.NoClassDefFoundError: net/imglib2/util/StopWatch
	at net.imglib2.cache.iotiming.IoStatistics.<init>(IoStatistics.java:21)
	at net.imglib2.cache.iotiming.CacheIoTiming.getIoStatistics(CacheIoTiming.java:30)
	at net.imglib2.cache.iotiming.CacheIoTiming.getIoStatistics(CacheIoTiming.java:17)
	at net.imglib2.cache.iotiming.CacheIoTiming.getIoTimeBudget(CacheIoTiming.java:40)
	at bdv.viewer.render.MultiResolutionRenderer.createProjector(MultiResolutionRenderer.java:658)
	at bdv.viewer.render.MultiResolutionRenderer.paint(MultiResolutionRenderer.java:496)
	at bdv.viewer.ViewerPanel.paint(ViewerPanel.java:485)
	at net.imglib2.ui.PainterThread.run(PainterThread.java:86)

I attach a screenshot of the view I see in BigDataViewer below. It is clearly seeing that I have a fused image with 5 views.

Screenshot%20from%202019-02-08%2013-53-29
Screenshot%20from%202019-02-08%2013-53-291136×1268 411 KB

The same thing happens if I define a new dataset in Multiview Reconstruction or BigStitcher.

Can anyone help?
I don’t want to be forced back to Win 10 because of this.
Thanks,
Ben

#2

Hi Ben, @mnqslbs2

Try updating Fiji if you havn’t recently - I recall running into something similar recently and it was just a funny state in-between updates.

Let us know if that doesn’t fix it,
John

#3

Hi John, @bogovicj

When I first installed Fiji did and Update… and installed all at once:
BigStitcher
ClearVolume
clij
SIMcheck
SciView

So what I have now done is delete and reinstall a fresh download of Fiji.
This allows me to open an xml dataset in BigDataViewer (BDV).
I then added each update via the Update… command in turn:
BigStitcher --> BDV still works.
ClearVolume --> BDV still works.
clij --> BDV still works.
SIMcheck --> BDV still works.
SciView --> BDV no longer works, so my conclusion is that it is something to do with SciView.

Removing SciView via the Update… command fixes the issue.

It would be great if SciView and BDV were compatible in the same Fiji install, I guess for the time being I can use SciView in a different install of Fiji.

Thanks,

Ben

1 Like
#4

Nice find - thanks for doing this digging.

Agreed, though it may not be easy. @kephale would know.

John

#5

Upps, I missed this before, but have noticed now. We’re tracking this here: https://github.com/scenerygraphics/sciview/issues/173

The reason this is happening is because you will soon get working BDV volumes in SciView. We’ll smooth out the compatibility issues as soon as possible.

2 Likes
#6

Hi there! Sorry for the issue – I just checked our update site, and it looks and imglib2 JAR ended up there unfortunately, and that is what’s causing @mnqslbs2’s problems. It has (at the moment) nothing to do with our coming integration with BDV, because that is not yet included in the version on the update site. We’ll have an update up today or tomorrow that’ll solve that problem.

Sorry again!

#7

Please check the latest SciView release. This issue should now be resolved

3 Likes