Issues Running Sholl Analysis on Simple Neurite Tracer

simpleneuritetracer
segmentation
Tags: #<Tag:0x00007fd54682c120> #<Tag:0x00007fd54683be40>

#1

Hi, new to the Forum. After I complete a tracing of a neuron with Simple Neurite Tracer, I select the innermost soma segment and use Shift+Ctrl+A to try and set a specific point as my center for analysis, but every time I get an error report:

Exception in thread “AWT-EventQueue-0” java.lang.NoSuchMethodError: org.jfree.chart.renderer.xy.XYBarRenderer.setGradientPaintTransformer(Lorg/jfree/ui/GradientPaintTransformer;)V

Followed by about 27 lines of other exceptions.

How do I set a certain section of my tracing as the center for sholl analysis without getting a massive exception report?


Have to revert to version 3.0.2 to get a sholl analysis reading Simple Neurite Tracer
#2

I’ve been having a lot of trouble with the Simple Neurite Tracer Program. I posted about the same issue earlier, but now I have details. I have been following the ImageJ online guide in order to get sholl analysis output from tracings, but it seems that no matter what version I’ve been using, I always end up with this same error report.

image

I’ve gone through and tested versions 3.0.2, 3.03, 3.1.3, 3.1.4, and 3.1.5 to try and resolve the issue, and so far only version 3.0.2 has given me the sholl analysis menu, but it also showed the same error report. The rest of the analysis worked. I want to know if this is a bug of some sort or user error, because I haven’t been able to find anything on the website.


#3

I haven’t been able to reproduce your issue with an up-to-date Fiji installation:

  • Run Analyze > Sholl > Sholl Analysis
  • On the dialog “There are no images open”, click Analyze Sample Image
  • On the following dialog, click OK

I get the following output:

image

image


Do you have any non-default update sites enabled in your installation? Some of these might ship an outdated version of JFreeChart…


#4

The issue comes up when I use the Sholl Analysis function described in the online manual. When I try to use the Shift+Ctrl+A command to set a portion of my trace as the center of analysis, that’s when the error report occurs


#5

Welcome to the forum @David-K, and thanks for the Console snapshot. Really useful. The preview plot of the Sholl Command relies on the jfreechart library that was recently updated. That error is caused by a method on that library that no longer allows un-defined (null) inputs. Why did we missed it?: The change seems to be undocumented, and Simple Neurite Tracer does not have compilation tests to evaluate this kind of bugs. Interesting it does not happen in any of the computers I use, but my setup is likely different from yours. A fix for this should be appearing soon on the updater. You can follow the progress here:


Have to revert to version 3.0.2 to get a sholl analysis reading Simple Neurite Tracer