Hi,

I would like to use Vaa3d for automated tracing of neurons to generate .swc files, and then analyse them quantitatively in NeuroM (as per recommendations in https://link.springer.com/article/10.100...). I would like to ask: after obtaining a good .swc from one of the neuron_tracing plugins (most likely will be using APP2), what are the steps required to prepare the .swc for NeuroM, and which are the plugins most suitable for those steps? 

For example, in my (very shallow) understanding, I guess that I need to:

1) Clean away detected segments that do not belong to the main neuron (eg if some background/noise near the neuron is detected)
-  I know I can manually remove these by using 'delete multiple neuron-segments by a stroke', but is it possible to select multiple segments (eg by drawing a selection box) and delete all of them at one go, as the segments detected from the background tend to be quite numerous? 
- Is there a plug-in that does this automatically? I tried the 'join all neuron segments (and remove all duplicated nodes)' function but this didn't seem to do anything obvious. I also tried NeuronToolbox/pruning_swc_simple but get 'no branch has been pruned' every time, even if I set the segment length to say 10000

2) Add/ extend segments that were not automatically detected
- I am doing this by: additionally trace a dendrite manually using the '1 right-stroke to define 3D curve' functions, save this together with the auto tracing (as an .eswc), and then convert this to .swc
- How do I ensure that the manually traced segments have the correct parent? 
- Will I have to run sort_neuron_swc whenever I add segments to the automatic tracing?

3) Will I need to annotate the segments as soma/ dendrite ('node type') for NeuroM to work on the .swc properly, and how can I do this?
- Is this what NeuronToolbox/subtree_labelling and /hierarchical_labelling are for?

4) If I do the tracing manually/ the traced segments belong to the same neuron but are not connected to each other, do I need to first connect them back up, or is it correct that NeuroM can handle this?
- I tried the NeuronToolbox/neuron_connector, but this did not seem to connect any floating branches (even under configuration to connect all, shortest distance) - is this not the right plugin for this?

More generally, is there a page with more description about what each of the plugins in NeuronToolbox are meant to be used for and how to use them? The toolbox looks like it would be super useful, but the description in the 'about' within vaa3d is very brief, so it is hard to know which plugin to use. I think it would be really helpful if there was a sort of flowchart describing when to use each plugin! 

Thank you very much for the great software, and support on the forum!