Current diffusion to nearby sections ?

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camilhamdane
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Joined: Mon Aug 05, 2019 7:37 am

Current diffusion to nearby sections ?

Post by camilhamdane » Thu Aug 22, 2019 5:19 am

Hello there,

I am currently making my first simulation in NEURON using Python. I am trying to simulate a retina architecture, and especially the retinal ganglion cells with their axons. I used the available 3d specification to get a grid of 10 by 10 neurons which looks like this:

Image

Ultimately I'd like to have a current clamp in the center of the grid, which would stimulate a group of neurons in a circle.
1) Now, the question is whether it was possible to induce the diffusion of current from an axon for example, to the other overlapping axons ?
2) Would I have to have a current clamp for each one of the neurons I'd like to stimulate if the diffusion is not possible ?
The thing is, that I am not sure if the pt3dadd function is purely graphic, or if the biophysics work with it...

Here the code I used (simplified to 2 sections, soma & axons) to get each neuron of the grid:
Image

Thank you,
Camil

ted
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Re: Current diffusion to nearby sections ?

Post by ted » Thu Aug 22, 2019 8:57 pm

NEURON simulates neuronal membrane currents and membrane potentials. It does not contain the computational machinery necessary to simulate extracellular potentials produced by extracellular stimulation or by currents generated by neuronal activity. It is possible build models that include such interactions, but the user must add the equations that describe them. The task is not trivial, especially if the model's neurons have significant spatial extent, and there are many neurons.

NEURON's IClamp is a computational model of a single electrode current clamp. It can be used to inject current into a single cell at a single location.

camilhamdane
Posts: 7
Joined: Mon Aug 05, 2019 7:37 am

Re: Current diffusion to nearby sections ?

Post by camilhamdane » Mon Aug 26, 2019 10:17 am

Hey there ted, thank you for your response.

Following what you said, I chose to work with individual clamps for each cell, rather than having extracellular stimulation by a single electrode.

I had another thing in mind, for the similar project, and the grid of ganglion cells I have. I am currently integrating this grid of NEURON simulated cells in a retina architecture written in NEST, that is, the Bipolar, amacrine and horizontal cells are simulated using the NEST simulator.
I am not sure if you are familiar with this library for Python, but I figured I'd ask :
Is there an easy way to combine NEURON and NEST, that is, connecting a NEURON section to a NEST neuron ? I thought about injecting the incoming voltage from the NEST cell to the NEURON cell using a voltage clamp, but I fear this might not be the most resource-friendly idea...

Thank you for letting me know :)
Camil

ted
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Re: Current diffusion to nearby sections ?

Post by ted » Mon Aug 26, 2019 1:31 pm

I chose to work with individual clamps for each cell, rather than having extracellular stimulation by a single electrode.
In other words, using the "activation function" approach to implement stimulation. That won't work for ephaptic interactions between axons, but at least it is a way to stimulate cells.
I had another thing in mind, for the similar project, and the grid of ganglion cells I have. I am currently integrating this grid of NEURON simulated cells in a retina architecture written in NEST, that is, the Bipolar, amacrine and horizontal cells are simulated using the NEST simulator.
I am not sure if you are familiar with this library for Python, but I figured I'd ask :
Is there an easy way to combine NEURON and NEST, that is, connecting a NEURON section to a NEST neuron ? I thought about injecting the incoming voltage from the NEST cell to the NEURON cell using a voltage clamp, but I fear this might not be the most resource-friendly idea...
The scarcest resource is human time and expertise. Speaking of which, this part of your question lies outside of mine--I'll have to refer it to one of my collaborators.

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