Input of morphologic data, creation of output files

[antonioc]

Gentle,
I'm a PhD student in physics and I have more than a question about NEURON. I'm a beginner with the use of Neuron, but I should prepare a complex simulation with neurons and I need some informations. They are about
1) I looked about Neuron morphologic data acquisition but I haven't understood if, and how, the program acquire the diameter data automatically, putting them in the correct field on the Cell Builder.
2) How can I see the temporal evolution of the potential in a well defined poit of the cell?
3) I need to export in an external file the complete spatio-temporal evolution of the potential and of the current inside each segment of the cell. Is there a simple way to create such file?

I thank you for the informations,

Antonio M. Cassarà

[ted]

1) I looked about Neuron morphologic data acquisition but I haven't understood if, and how, the program acquire the diameter data automatically, putting them in the correct field on the Cell Builder.

There are two ways to specify the geometry (lengths and diameters) of a model cell:
stylized and "3D" (also called pt3d)--see
http://www.neuron.yale.edu/neuron/stati ... metry.html
The CellBuilder allows you to manually enter the geometry using the stylized specification.
However, if a model already exists (the test: does topology() produce a list of sections?),
the CellBuilder can import its topology (branching pattern) and 3D geometry--see the
CellBuilder tutorial on the Documentation page
http://www.neuron.yale.edu/neuron/docs

You can specify 3D geometry by writing (or using an algorithm to generate) statements
described here
http://www.neuron.yale.edu/neuron/stati ... metry.html
There are also several programs that can translate morphometric data files into hoc
code, e.g. cvapp. The latest tool for converting morphometric data into a model is
NEURON's Import3D tool--see its tutorial on the Documentation page.

2) How can I see the temporal evolution of the potential in a well defined poit of the cell?

Plot it vs. time. Use the GUI to bring up a "voltage axis graph"--see the tutorial
Construction and Use of Models: Part 1. Elementary Tools
on the Documentation page. Then use that graph's "Plot what?" tool, which is discussed
in the FAQ list
http://www.neuron.yale.edu/neuron/faq/general-questions
under the item
How do I plot something other than membrane potential?

Alternatively, you can do it all in hoc--read about the Graph class's plot method
in the Programmer's Reference
http://www.neuron.yale.edu/neuron/stati ... graph.html

3) I need to export in an external file the complete spatio-temporal evolution of the potential and of the current inside each segment of the cell. Is there a simple way to create such file?

Everything is possible with programming.
Use the Vector class's record method to record whatever variables you want.
This will require iteration over all internal nodes
forall for (x,0) {
. . . statements that create a new Vector and set up Vector recording . . .
}
Then, at the end of the simulation, write the Vectors to one or more files.

and of the current

Which current do you have in mind? If you want transmembrane current, you'll need
to insert the extracellular mechanism--read about that in the Programmer's Reference.
Don't forget that distributed mechanisms report their currents in density units, i.e.
mA/cm2, but point process currents are in absolute units, i.e. nA.