Dear nest developer,
Is there a pre-implemented nest model allowing multiplicative aggregation of compartments/dendritic branches. I am looking for a model that will allow multiplicative aggregation of two dendritic branches at the soma.
I very much appreciate any support provided. Best regards, Benedikt
Dear Benedict,
NEST comes with a simple conductance-based three-compartment integrate and fire neuron model. Its name is iaf_cond_alpha_mc. The model has compartments for the soma, the distal dendrite and the proximal dendrite. An example of how to connect it can be found here:
https://nest-simulator.readthedocs.io/en/latest/guides/connection_management...
The source code of the model is here:
https://github.com/nest/nest-simulator/blob/master/models/iaf_cond_alpha_mc.... https://github.com/nest/nest-simulator/blob/master/models/iaf_cond_alpha_mc....
If you should need much more complex or realistic multi-compartment models, NEST might not be the right tool for you and you should have a look at Arbor:
https://github.com/arbor-sim/arbor
Best regards, Jochen!
On 17.12.19 12:52, benediktr@hotmail.de wrote:
Dear nest developer,
Is there a pre-implemented nest model allowing multiplicative aggregation of compartments/dendritic branches. I am looking for a model that will allow multiplicative aggregation of two dendritic branches at the soma.
I very much appreciate any support provided. Best regards, Benedikt _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
-- Dr. Jochen Martin Eppler Phone: +49(2461)61-96653 ---------------------------------- Simulation Laboratory Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation
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Hello Jochen, thank you for your support!
If I understand the connection topology correctly the distal compartment is connected to the proximal compartment which in turn is connected to the soma (d->p->s.) I am looking for a model with two separate dendritic compartments that are not interconnected yet both connect directly to the soma: branch1->soma<- branch2. Modelling the exact spatial relations, dimensions of compartments is not important to me.
Potentially NestML is an alternative here. I have read the NestML language documentation but am not sure whether there are limitations imposed on the model esp. the update block. There is mainly three things I need: 1) topology (b1->s<-b2) 2)passing membrane voltages from branches to soma 3)multiplicative aggregation at soma Soma is essentially only integrating membrane voltages from the compartments in a multiplicative manner, ie. concurrent spike arrival at both compartments evoke significantly higher depolarizations of the membrane potential at soma. The soma then fires when a certain threshold is reached. Can this be done with NestML?
Best, Benedikt
Dear Benedikt,
Yes, this should be possible in NESTML. Define two input ports for b1 and b2 (see the multisynapse example in the documentation for how to do this). The membrane potential (say, *V_m*) can be used to affect the synaptic currents, e.g.:
I_b1 = f(V_m) * convolve(I_shape, spikes_b1) I_b2 = g(V_m) * convolve(I_shape, spikes_b2)
for some functions *f* and *g*. Then simply enter the membrane potential dynamics as you want it to be, e.g. for multiplicative interaction
V_m' = const * I_b1 * I_b2
You could of course also define different membrane voltage for each individual compartment.
I would suggest to look at the multisynapse example (https://github.com/nest/nestml/blob/master/doc/nestml_language.md#synaptic-i...) and go from there. Please feel free to post updates and questions to this thread, or if you run into any errors or bugs to post an issue on https://github.com/nest/nestml/.
Kind regards, Charl
On Tue, Feb 18, 2020, at 22:20, Benedikt Rank wrote:
Hello Jochen, thank you for your support!
If I understand the connection topology correctly the distal compartment is connected to the proximal compartment which in turn is connected to the soma (d->p->s.) I am looking for a model with two separate dendritic compartments that are not interconnected yet both connect directly to the soma: branch1->soma<- branch2. Modelling the exact spatial relations, dimensions of compartments is not important to me.
Potentially NestML is an alternative here. I have read the NestML language documentation but am not sure whether there are limitations imposed on the model esp. the update block. There is mainly three things I need:
- topology (b1->s<-b2)
2)passing membrane voltages from branches to soma 3)multiplicative aggregation at soma Soma is essentially only integrating membrane voltages from the compartments in a multiplicative manner, ie. concurrent spike arrival at both compartments evoke significantly higher depolarizations of the membrane potential at soma. The soma then fires when a certain threshold is reached. Can this be done with NestML?
Best, Benedikt _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
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Benedikt Rank -
benediktr＠hotmail.de
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Charl Linssen -
Jochen Martin Eppler