I have been running the Sholl analysis plugin on .traces files from simple neurite tracer (Analysis ▷ Sholl ▷ Sholl Analysis (Tracings)…). I have a macro set up to batch this process so I really need this plugin to work. This worked for quite a while and then I began getting this exception:
(Fiji Is Just) ImageJ 2.0.0-rc-59/1.51k; Java 1.8.0_66 [64-bit]; Mac OS X 10.11.6; 27MB of 2831MB (<1%) java.lang.NullPointerException at java.util.Arrays.sort(Arrays.java:1246) at tracing.ShollAnalysisPlugin.guessInitialPaths(ShollAnalysisPlugin.java:398) at tracing.ShollAnalysisPlugin.showDialog(ShollAnalysisPlugin.java:254) at tracing.ShollAnalysisPlugin.run(ShollAnalysisPlugin.java:104) at ij.IJ.runUserPlugIn(IJ.java:217) at ij.IJ.runPlugIn(IJ.java:181) at ij.Executer.runCommand(Executer.java:137) at ij.Executer.run(Executer.java:66) at java.lang.Thread.run(Thread.java:745)
I’ve tried updating fiji, reinstalling fiji, reinstalling java 8, installing an older version of fiji, using older version of the sholl analysis and simple neurite tracer plugins. Sometimes I can get it to work again for a while on a different computer but inevitably eventually I get the same exception and can’t overcome it. Any help would be greatly appreciated!