There are multiple ways of tracing a soma. If one uses multiple paths to trace it and performs Sholl on the traced structure, SNT will consider such paths as independent objects, which is unexpected. A way around it is to select all paths, then deselect manually the paths one is not interested before generating the Sholl profile. This may not be practical for large reconstructions. The issue is discussed in the forum and fiji/Simple_Neurite_Tracer#5.
This PR does the following:
Adds a new option in prompt to exclude paths tagged by SWC types, so that one can perform Sholl only on "Axons", "Dendrites", "Both but not the soma", etc... This requires paths to be previously tagged using the SWC Type menu. This means one can also obtain profiles from cherry picked structures (such as branch points), which was not possible before.
Puts SNT and the tferr/ASA plugin on the same page. SNT did not use the conventions in http://imagej.net/Sholl, and that was always a source of confusion for users[1]
While at it, we corrected typos and some minor issues.
I've tried to split the changes into commits. Hopefully it will be easy to review. SNT is not macro recordable, and the above changes affect only the GUI for Sholl Analysis, so it should not affect any projects depending on SNT.
@ctrueden, I guess a new SNT version should be released once this merged? I could upload the jar from Jenkins to the Java8 update site, but I cannot create a new GitHub release on this repo directly.
[1] BTW, the proper way to ensure this sort of disparities would be to pass all the calculations to tferr/ASA, which is now quite mature. In retrospect, I should have worked on this long ago. I will try to find the time to work on it later on.
There are multiple ways of tracing a soma. If one uses multiple paths to trace it and performs Sholl on the traced structure, SNT will consider such paths as independent objects, which is unexpected. A way around it is to select all paths, then deselect manually the paths one is not interested before generating the Sholl profile. This may not be practical for large reconstructions. The issue is discussed in the forum and fiji/Simple_Neurite_Tracer#5.
This PR does the following:
I've tried to split the changes into commits. Hopefully it will be easy to review. SNT is not macro recordable, and the above changes affect only the GUI for Sholl Analysis, so it should not affect any projects depending on SNT.
@ctrueden, I guess a new SNT version should be released once this merged? I could upload the jar from Jenkins to the Java8 update site, but I cannot create a new GitHub release on this repo directly.
[1] BTW, the proper way to ensure this sort of disparities would be to pass all the calculations to tferr/ASA, which is now quite mature. In retrospect, I should have worked on this long ago. I will try to find the time to work on it later on.