Error when importing .swc traces

imagej
neuroanatomy

#1

Hi,
I am currently unable to load traces in .swc format using the import function provided by Neuroanatomy. Below is the error message I get as soon as I select the command. Does anybody else experience this issue?

Thanks,
Giovanni

(Fiji Is Just) ImageJ 2.0.0-rc-65/1.51w; Java 1.8.0_66 [64-bit]; Windows 7 6.1; 3118MB of 24459MB (12%)
java.lang.NoSuchMethodError: tracing.SimpleNeuriteTracer: method <init>()V not found
at ipnat.ImportTracings.<init>(ImportTracings.java:130)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
at java.lang.Class.newInstance(Class.java:442)
at ij.IJ.runUserPlugIn(IJ.java:219)
at ij.IJ.runPlugIn(IJ.java:185)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:63)
at java.lang.Thread.run(Thread.java:745)

#2

Hi @gcardone

It is my fault. The SNT API changed a lot and I forgot to update those IJ1 plugins in the Neuroanatomy update site. Please give some time to look into it. If you need immediate help, I could probably post a scripting alternative, if you give us more details on what you are doing…

(BTW, The ImportTracings plugin will likely become legacy, because SNT can now import SWC files without having access to the initial traced image.)


#3

@gcardone, Just pushed an update with a temporary fix. Could you please cf it fixes the issue you were having?


#4

Hi @tferr, I checked the new version and it seems to work as intended (except for a abababab message in the log…). Thank you very much!
I am using ImportTracings from a custom script to load traces generated from SNT and perform some specialized analysis: in the future, will it be still possible to do it this way? Thanks again.


#5

Probably, What kind of specialized analysis are you trying to do?


#6

Combining manual traces of axons from SNT with information from other channels about nuclei, dendrites and transduction efficiency, derived with a separate script.