Clean Install Problems with Mosaic Suite

Hi Everyone,
I recently installed Mosaic Suite and loved it. It would do everything I wanted except generate the R script. In my infinite wisdom I decided to do a clean install to see if I could fix that problem. Now it throws an exception and I get no data. The exception text is

(Fiji Is Just) ImageJ 2.0.0-rc-49/1.51d; Java 1.8.0_91 [64-bit]; Windows 8.1 6.3; 189MB of 12139MB (1%)
 
java.lang.NoClassDefFoundError: Skeletonize3D_/Skeletonize3D_
	at mosaic.bregman.segmentation.ObjectProperties.calculateLength(ObjectProperties.java:159)
	at mosaic.bregman.segmentation.ObjectProperties.run(ObjectProperties.java:58)
	at mosaic.bregman.segmentation.ImagePatches.processPatches(ImagePatches.java:172)
	at mosaic.bregman.segmentation.SquasshSegmentation.stepTwoSegmentation(SquasshSegmentation.java:118)
	at mosaic.bregman.segmentation.SquasshSegmentation.run(SquasshSegmentation.java:81)
	at mosaic.bregman.SquasshLauncher.segmentChannel(SquasshLauncher.java:416)
	at mosaic.bregman.SquasshLauncher.segmentFrame(SquasshLauncher.java:325)
	at mosaic.bregman.SquasshLauncher.<init>(SquasshLauncher.java:139)
	at mosaic.plugins.BregmanGLM_Batch.runLocally(BregmanGLM_Batch.java:177)
	at mosaic.plugins.BregmanGLM_Batch.setup(BregmanGLM_Batch.java:150)
	at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:48)
	at ij.IJ.runUserPlugIn(IJ.java:218)
	at ij.IJ.runPlugIn(IJ.java:180)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.ClassNotFoundException: Skeletonize3D_.Skeletonize3D_
	at java.net.URLClassLoader.findClass(Unknown Source)
	at java.lang.ClassLoader.loadClass(Unknown Source)
	at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
	at java.lang.ClassLoader.loadClass(Unknown Source)
	... 16 more

For good measure I tried to load ImageJ and get Mosaic Suite to work there. I get farther in that it will generate the images but throws an exception and won’t generate data. the text for that exception is:

ImageJ 1.51d; Java 1.8.0_77 [64-bit]; Windows 8.1 6.3; 149MB of 12205MB (1%)
 
org.dozer.MappingException: java.lang.ClassNotFoundException: org.dozer.util.DefaultClassLoader
	at org.dozer.util.MappingUtils.throwMappingException(MappingUtils.java:82)
	at org.dozer.util.DefaultClassLoader.loadClass(DefaultClassLoader.java:38)
	at org.dozer.DozerInitializer.loadBeanType(DozerInitializer.java:115)
	at org.dozer.DozerInitializer.initialize(DozerInitializer.java:97)
	at org.dozer.DozerInitializer.init(DozerInitializer.java:74)
	at org.dozer.DozerBeanMapper.init(DozerBeanMapper.java:173)
	at org.dozer.DozerBeanMapper.<init>(DozerBeanMapper.java:99)
	at org.dozer.DozerBeanMapper.<init>(DozerBeanMapper.java:94)
	at org.supercsv.io.dozer.CsvDozerBeanWriter.<init>(CsvDozerBeanWriter.java:65)
	at mosaic.utils.io.csv.CSV.writeData(CSV.java:391)
	at mosaic.utils.io.csv.CSV.Write(CSV.java:209)
	at mosaic.bregman.SquasshLauncher.writeImageDataCsv(SquasshLauncher.java:868)
	at mosaic.bregman.SquasshLauncher.<init>(SquasshLauncher.java:143)
	at mosaic.plugins.BregmanGLM_Batch.runLocally(BregmanGLM_Batch.java:177)
	at mosaic.plugins.BregmanGLM_Batch.setup(BregmanGLM_Batch.java:150)
	at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:48)
	at ij.IJ.runUserPlugIn(IJ.java:218)
	at ij.IJ.runPlugIn(IJ.java:180)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.ClassNotFoundException: org.dozer.util.DefaultClassLoader
	at java.net.URLClassLoader.findClass(Unknown Source)
	at java.lang.ClassLoader.loadClass(Unknown Source)
	at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
	at java.lang.ClassLoader.loadClass(Unknown Source)
	at java.lang.Class.forName0(Native Method)
	at java.lang.Class.forName(Unknown Source)
	at org.apache.commons.lang3.ClassUtils.getClass(ClassUtils.java:823)
	at org.apache.commons.lang3.ClassUtils.getClass(ClassUtils.java:889)
	at org.apache.commons.lang3.ClassUtils.getClass(ClassUtils.java:872)
	at org.dozer.util.DefaultClassLoader.loadClass(DefaultClassLoader.java:36)
	... 19 more

Any help would be greatly appreciated.

I couldn’t reproduce this with an up-to-date Fiji installation. Did you install the MOSAIC suite just by activating the MOSAIC ToolSuite update site? What were the steps that you took to get this exception?

So my clean install is not as clean as I think. What I did is delete all instances of Fiji and ImageJ on my computer and any preference files I could find (including hidden files). However my prior settings are being loaded into Fiji and Squassh so I must be missing something and maybe that is the problem. I did install Mosaic Suite from the update site and I opened a small image stack. I crop it for faster processing and then run Squassh. It runs through the initial processing and segmentation but then when it gets to the point where it usually generates the images it throws that exception.

First problem reported above is now solved. Second one is only reproducible in ImageJ1 and currently I have no idea what is wrong. Please use ImageJ2 or latest Fiji (and because of last changes Java8).