Question about connectivity using pt3dadd

When Python is the interpreter, what is a good
design for the interface to the basic NEURON
concepts.

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maxwellphenderson
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Joined: Mon Mar 07, 2011 12:17 am

Question about connectivity using pt3dadd

Post by maxwellphenderson » Wed Jan 18, 2012 10:20 am

I had a question concerning the construction of neurons with complicated geometries using the pt3dadd command. I was curious about how the tool handles bifurcations, or what the best method of dealing with them would be. Basically, say I have a list of 3D coordinates and diameters for points outlining an axon; if I am just adding each point in line by line, will the 3D structure just keep connecting the current point entered to the previous point, or does it connect the new 3D point to the 3D point closest to it? Any input would be useful, thanks! :)

ted
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Re: Question about connectivity using pt3dadd

Post by ted » Wed Jan 18, 2012 10:41 am

A section is an unbranched cable, and represents an unbranched neurite.
pt3dadd statements add x,y,z,diam values at successive points along a section.
If you want branching, you need multiple sections and some connect statements.

Suggested reading that may help shed additional light:
{
chapter 5 and 6 of The NEURON Book
OR
"The NEURON simulation environment", available at
http://www.neuron.yale.edu/neuron/stati ... /nctoc.htm
}
AND
the Programmer's Reference entries on Geometry
http://www.neuron.yale.edu/neuron/stati ... l#Geometry
focussing particularly on the stuff that begins with the heading
3-D specification of geometry
and the documentation of pt3dadd itself

maxwellphenderson
Posts: 22
Joined: Mon Mar 07, 2011 12:17 am

Re: Question about connectivity using pt3dadd

Post by maxwellphenderson » Wed Jan 18, 2012 10:52 am

Thanks for the reply! Very helpful.

ted
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Re: Question about connectivity using pt3dadd

Post by ted » Fri Jan 20, 2012 11:04 am

In summary, pt3dadd isn't about connectivity (the branching topology of a model cell). It's about geometry (the shape of an individual section). I should have put this at the end of my previous post, but putting it here may make it more readily seen by future readers.

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