Division of existing arealists?

trakem2

#1

Hi all,

I’m using trakem2 to segment dendrites and axons from EM images. I have segmented entire dendrites including spines and would now like to divide an existing arealist into smaller segments which represent the spines only.

Is there a way to do this to existing arealists? Ideally something that will let me select a portion of an existing area list and give it a new arealist.

I realise I can segment them manually and create new arealists myself, but this will be time consuming for new and existing dendrites. I’ve included screenshots of how I manually segmented the existing area.

Is there anything else that may be of help?


#2

Hi @gm25

Welcome to the forum!

As far as I know, TrakEM2 doesn’t have something built-in for that, but I don’t think it’ll hard to build a script that does it. I’ll try to find some time this week to look into it.

What I have in mind would make your workflow something like this:

  1. Make a new AreaList that is very rough (only taking care near the spine boundary, and making sure it covers the whole spine.
  2. Run some script that asks you for two AreaLists (A - “rough spine” and B - “your carefully segmented neuron”), and changes A so that it is the intersection of A and B.

Does that sound like it would help?

John


#3

Hi bogovicij

Yes that should work perfectly! I’ve little knowledge of coding but hopefully my fellow students can help implement this.

Thank you very much