Joining traces on imagej - simple neurite tracer

segmentation
fiji
trackmate
Tags: #<Tag:0x00007fb87bc4efd8> #<Tag:0x00007fb87bc4ee20> #<Tag:0x00007fb87bc4ea60>

#1

Hi!
I’m using SNT to trace a photon stack of a very complicated interneurone. I need the neurone connections to be correct as I will use the data for analysis later. From one of my primary dendrites, I’ve started a path in the middle of it. The path is in the correct place, however it is not connected to the path before it so it becomes primary and I need it to show as a secondary path starting from the primary dendrite. I’ve done a lot of the tracing of this neurone and starting again will take me forever so if anyone knows a way of conjoining the paths, so that it starts from the correct point (and not the middle of a path) please let me know.

Thank you,
Mariam

(Images for extra detail)


#2

Hello @MimiB,

Why don’t you join the two paths by creating a very small branch between them? That would solve your problem, no?


#3

Hi @iarganda,
I tried that but it didn’t change it so that it would start on the right branch.


#4

I don’t understand, what happened when you join the paths then?

I tried this and it works for me.


#5

@MimiB, the step-by-step instructions use outdated screenshots but should definitely work. A couple of tips:

  • Zoom in as much as possible so that you can access end-points with ease
  • You may want to toggle the “snap-to-neurite”, shortcut: s
  • You may want to toggle “visibility of all paths”: 5

Unfortunately, the user interface to edit existing paths is quite limited. We really wanted to improve it, but it is hard to allocate time for it. That being said, creating a small connector path should have negligible effects, if any.