www.neuron.yale.edu

Hi all,
I have just begin to learn to use NEURON and have a very primary question.
I am trying to apply the extracellular mechanism to a series of nerve cell. I want to simulate voltage-controlled extracellular stimulation, so I am giving to e_extracellular potentials values that correspond to field potentials I have calculated using a Finite Element model. I suppose I should employ both hh and extracellular mechanisms to each cell and the e_ extracellular is just the potential I have obtained with the finite element method.
Could you please let me know whether the approach I use is right or not?
Thank you in advance.

That will work. Default extracellular parameters are
xg = 1e9
xc = 0
xraxial = 1e9
so the nodes just outside the cell membrane are effectively connected directly to
e_extracellular, and isolated from each other.

Use the Vector class's play() method to drive e_extracellular. Note that there is no membrane
at the 0 or 1 ends, so e_extracelluar exists only at positions that correspond to internal
nodes, e.g. For the most general case, each e_extracellular will need its own pair of voltage and time
Vectors. If the extracellular field is generated by current sources applied to an ohmic
medium, it is possible to use a single Vector pair for each current source, and use
precomputed transfer resistances (between each current source and each e_extracellular)
to synthesize the e_extracellulars "on the fly" via linear superposition.

If you need to deal with real cellular morphologies (detailed anatomical reconstructions
of real cells), let me know.

Dear Ted,
My name is Lewis. I'm a new Neuron user and working with the 6.0.4 version of Neuron on Windows XP.
Now, I am doing some research work about spinal cord stimulation, i.e. using cuff electrodes in epidural space to stimulate the nerve in spinal cord for restoring given function. I have used Maxwell, which is a finite element software for calculation of static electric field, to calculate the electric field distribution in spinal cord, and want to employ such numerical results (potential values) to simulate the responds in nerve cells with NEURON.
I really need real cellular morphologies in spinal cord for more precise calculation. Do you have such material? If you have, could you please send a copy to me. My e-mail is luckychild76@gmail.com. Thank you so much for your very useful response and very kind help.

http://neuromorpho.org is a searchable collection of quantitative morphometry of many types
of neurons. Among other things, it contains many motoneurons, but I don't know if any of them
include axons, which could be quite important for extracellular stimulation. You may have
to make your own axon model and attach it to the soma.

Before using any morphometric data from any source, be sure to read the paper(s) that
describe how the data were obtained. Pay close attention to what kind of stain was
used, how completeness of fill was assessed, whether cells were rejected because of
amputation of branches, whether shrinkage was estimated and corrected, numerical
aperture of the objective lens, and optical resolution. If you can't find the paper that
provides such methodological details, or if no paper exists, don't try to use the data in a
computational model--you'll just be wasting your time.

Also read these two papers, which discuss common problems and pitfalls, and how to
detect them:

Kaspirzhny AV, Gogan P, Horcholle-Bossavit G, Tyc-Dumont S.
Neuronal morphology data bases: morphological noise and assesment
of data quality. Network: Computation in Neural Systems 13:357�380, 2002.

Scorcioni, R., Lazarewicz, M.T., and Ascoli, G.A. Quantitative morphometry
of hippocampal pyramidal cells: differences between anatomical classes and
reconstructing laboratories. Journal of Comparative Neurology 473:177-193, 2004.

Dear ted,
I have found the first paper you mentioned above. But it is not free. Could you please send me this paper? Thank you in advance.

I have found the first paper you mentioned above. But it is not free. Could you please send me this paper?

No. You might check the authors' web sites to see if they provide a pdf.

Their basic message was: examine the data for evidence of instrumental or operational
sources of error. The most important idea in the paper was to examine the diameter
measurements (e.g. by plotting a histogram with bins ~ 0.2 um wide), and ask these
questions:
What is the smallest diameter that was recorded? (for most cells, should be smaller than 1 um)
Does the histogram contain only a few, widely-spaced peaks? If so, and the peaks are evenly
spaced, then there may be an instrumentation problem. If the peaks are irregularly spaced,
there may be an operator problem ("favorite numbers").

You may find a pdf of the second paper--which is no less important than Kaspirzhny et al.--
at Ascoli's WWW site.

Thank you for your help. I will read this paper carefully.

Hi,

I am also interested in applying the results from a FEM model to a NEURON model as extracellular stimulation. You said that we should "Use the Vector class's play() method to drive e_extracellular." Can you point me towards any examples of how to do this?

Thanks.

This should get you started:
Extracellular stimulation and recording
https://www.neuron.yale.edu/phpBB2/viewtopic.php?t=167
in the Hot tips area of The NEURON Forum

thanks