Integrate-and-fire model with passive dendrite

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marakips
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Joined: Thu Apr 04, 2019 6:31 am

Integrate-and-fire model with passive dendrite

Post by marakips » Fri Apr 05, 2019 9:37 am

Dear all,

I would like to implement a very simple two-compartmental integrate-and-fire neuron with a passive dendrite.
Any advice would be much appreciated.

Thank you in advance for your time.

ted
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Re: Integrate-and-fire model with passive dendrite

Post by ted » Sat Apr 06, 2019 12:07 am

Use the CellBuilder to make a model cell with two sections called soma and dendrite. On the Geometry page, specify the L and diam of these sections, but leave each section's nseg == 1. Use the Biophysics page to insert pas and set appropriate values for Ra, cm, g_pas, and e_pas. If you've never used the CellBuilder before, work through the CellBuilder tutoral first (find the link on the Documentation page of www.neuron.edu). Remember to save your configured CellBuilder to a session file--don't just export hoc code from the CellBuilder and then discard the CellBuilder.

For the "spike" mechanism, get spikeout.mod from the NEURON code in ModelDB entry 83319--it's in here:
https://senselab.med.yale.edu/ModelDB/s ... ba/#tabs-2
Put spikeout.mod in the same directory as the hoc code that you exported from the CellBuilder, and compile it. The next time you start NEURON in that directory, it will have a new point process class called SpikeOut. Attach an instance of SpikeOut to the soma of your model cell. It will monitor somatic membrane potential for positive-going threshold crossings (threshold is specified by SpikeOut's thresh parameter, default value == 1 mV). When such a threshold crossing happens, SpikeOut will generate an event that can be delivered by NetCons to artificial spiking cells or event-driven synaptic mechanisms like ExpSyn and Exp2Syn. SpikeOut will also activate a conductance (magnitude specified by the grefrac parameter, default value 100 microsiemens) associated with reversal potential vrefrac (default value 0 mV) that persists for a fixed duration (specified by the refrac parameter, default value 5 ms). The purpose of this conductance change is to pull v back to the cell's resting potential, and to emulate a post-spike refractory period during which the cell is unresponsive to synaptic currents. You'll want to make sure that grefrac is big enough to quickly pull v back to resting potential and keep it there during the refractory interval; bigger values are generally better.

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