www.neuron.yale.edu

Hello,

I am working with a complicated 3d model in NEURON, and I'd like to basically get an adjacency matrix of the neuron. Is there a function which does this?

I know, for instance, that the topology() function has all of the information I want, I was just wondering if there was an easy way to output it in a format that is useful to me (adjacency). I suppose one problem is that NEURON keeps track of sections, and not nodes (I think at least). Then, equivalently, is there a function which gives all of the connected section of a particular section?

Thanks in advance.

Adam

With the SectionRef class you can discover the parent and children of any section.
With the SectionList class you can discover all root sections, and given any root section, you can use it to create a SectionList whose members are all sections that belong to that particular cell. Combine that with the SectionRef class and you can generate your own map of what is connected to what.
You may also find the forall and forsec iterators to be helpful in your application.

thanks! just what i needed.